PSIBLAST 2.2.27+


Reference: Stephen F. Altschul, Thomas L. Madden, Alejandro A.
Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J.
Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of
protein database search programs", Nucleic Acids Res. 25:3389-3402.


Reference for compositional score matrix adjustment: Stephen F.
Altschul, John C. Wootton, E. Michael Gertz, Richa Agarwala,
Aleksandr Morgulis, Alejandro A. Schaffer, and Yi-Kuo Yu (2005)
"Protein database searches using compositionally adjusted
substitution matrices", FEBS J. 272:5101-5109.


Reference for composition-based statistics starting in round 2:
Alejandro A. Schaffer, L. Aravind, Thomas L. Madden, Sergei
Shavirin, John L. Spouge, Yuri I. Wolf, Eugene V. Koonin, and
Stephen F. Altschul (2001), "Improving the accuracy of PSI-BLAST
protein database searches with composition-based statistics and
other refinements", Nucleic Acids Res. 29:2994-3005.



Database: uniprot_sprot.fasta
           563,082 sequences; 202,799,066 total letters

Results from round 1


Query= YP_009725301.1 3C-like proteinase [Severe acute respiratory syndrome
coronavirus 2]

Length=306
                                                                      Score     E
Sequences producing significant alignments:                          (Bits)  Value

  sp|P0DTC1|R1A_SARS2 Replicase polyprotein 1a OS=Severe acute re...   652    0.0   
  sp|P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab OS=Severe acute ...   649    0.0   
  sp|P0C6F5|R1A_BC279 Replicase polyprotein 1a OS=Bat coronavirus...   635    0.0   
  sp|P0C6U8|R1A_CVHSA Replicase polyprotein 1a OS=Human SARS coro...   634    0.0   
  sp|P0C6V9|R1AB_BC279 Replicase polyprotein 1ab OS=Bat coronavir...   632    0.0   
  sp|P0C6F8|R1A_BCHK3 Replicase polyprotein 1a OS=Bat coronavirus...   630    0.0   
  sp|P0C6T7|R1A_BCRP3 Replicase polyprotein 1a OS=Bat coronavirus...   630    0.0   
  sp|P0C6X7|R1AB_CVHSA Replicase polyprotein 1ab OS=Human SARS co...   631    0.0   
  sp|P0C6W6|R1AB_BCRP3 Replicase polyprotein 1ab OS=Bat coronavir...   628    0.0   
  sp|P0C6W2|R1AB_BCHK3 Replicase polyprotein 1ab OS=Bat coronavir...   628    0.0   
  sp|P0C6T6|R1A_BCHK9 Replicase polyprotein 1a OS=Bat coronavirus...   342    3e-104
  sp|P0C6W5|R1AB_BCHK9 Replicase polyprotein 1ab OS=Bat coronavir...   341    7e-104
  sp|K9N638|R1A_MERS1 Replicase polyprotein 1a OS=Middle East res...   322    2e-97 
  sp|K9N7C7|R1AB_MERS1 Replicase polyprotein 1ab OS=Middle East r...   320    7e-97 
  sp|P0C6T5|R1A_BCHK5 Replicase polyprotein 1a OS=Bat coronavirus...   311    8e-94 
  sp|P0C6W4|R1AB_BCHK5 Replicase polyprotein 1ab OS=Bat coronavir...   311    2e-93 
  sp|P0C6U9|R1A_CVM2 Replicase polyprotein 1a OS=Murine coronavir...   310    2e-93 
  sp|P0C6X8|R1AB_CVM2 Replicase polyprotein 1ab OS=Murine coronav...   310    3e-93 
  sp|P0C6T4|R1A_BCHK4 Replicase polyprotein 1a OS=Bat coronavirus...   308    8e-93 
  sp|P0C6F7|R1A_BC133 Replicase polyprotein 1a OS=Bat coronavirus...   308    2e-92 
  sp|P0C6W3|R1AB_BCHK4 Replicase polyprotein 1ab OS=Bat coronavir...   308    2e-92 
  sp|P0C6V1|R1A_CVMJH Replicase polyprotein 1a OS=Murine coronavi...   307    3e-92 
  sp|P0C6W1|R1AB_BC133 Replicase polyprotein 1ab OS=Bat coronavir...   307    4e-92 
  sp|P0C6Y0|R1AB_CVMJH Replicase polyprotein 1ab OS=Murine corona...   306    5e-92 
  sp|P0C6V0|R1A_CVMA5 Replicase polyprotein 1a OS=Murine coronavi...   305    1e-91 
  sp|P0C6X9|R1AB_CVMA5 Replicase polyprotein 1ab OS=Murine corona...   305    2e-91 
  sp|P0C6U7|R1A_CVHOC Replicase polyprotein 1a OS=Human coronavir...   304    3e-91 
  sp|P0C6U1|R1A_CVBQ Replicase polyprotein 1a OS=Bovine coronavir...   304    4e-91 
  sp|P0C6X0|R1AB_CVBQ Replicase polyprotein 1ab OS=Bovine coronav...   303    5e-91 
  sp|P0C6T8|R1A_CVBEN Replicase polyprotein 1a OS=Bovine coronavi...   303    6e-91 
  sp|P0C6T9|R1A_CVBLU Replicase polyprotein 1a OS=Bovine coronavi...   303    6e-91 
  sp|P0C6X6|R1AB_CVHOC Replicase polyprotein 1ab OS=Human coronav...   303    7e-91 
  sp|P0C6W7|R1AB_CVBEN Replicase polyprotein 1ab OS=Bovine corona...   303    1e-90 
  sp|P0C6W8|R1AB_CVBLU Replicase polyprotein 1ab OS=Bovine corona...   303    1e-90 
  sp|P0C6U5|R1A_CVHN5 Replicase polyprotein 1a OS=Human coronavir...   302    1e-90 
  sp|P0C6U3|R1A_CVHN1 Replicase polyprotein 1a OS=Human coronavir...   302    1e-90 
  sp|P0C6U4|R1A_CVHN2 Replicase polyprotein 1a OS=Human coronavir...   302    2e-90 
  sp|P0C6X4|R1AB_CVHN5 Replicase polyprotein 1ab OS=Human coronav...   302    2e-90 
  sp|P0C6X2|R1AB_CVHN1 Replicase polyprotein 1ab OS=Human coronav...   302    2e-90 
  sp|P0C6X3|R1AB_CVHN2 Replicase polyprotein 1ab OS=Human coronav...   301    2e-90 
  sp|P0C6U0|R1A_CVBM Replicase polyprotein 1a OS=Bovine coronavir...   298    5e-89 
  sp|P0C6W9|R1AB_CVBM Replicase polyprotein 1ab OS=Bovine coronav...   297    8e-89 
  sp|P0C6F6|R1A_BC512 Replicase polyprotein 1a OS=Bat coronavirus...   274    1e-80 
  sp|P0C6W0|R1AB_BC512 Replicase polyprotein 1ab OS=Bat coronavir...   273    1e-80 
  sp|P0C6V6|R1A_PEDV7 Replicase polyprotein 1a OS=Porcine epidemi...   264    2e-77 
  sp|P0C6Y4|R1AB_PEDV7 Replicase polyprotein 1ab OS=Porcine epide...   263    5e-77 
  sp|Q98VG9|R1AB_FIPV Replicase polyprotein 1ab OS=Feline coronav...   254    8e-74 
  sp|P0C6V2|R1A_CVPPU Replicase polyprotein 1a OS=Porcine transmi...   254    9e-74 
  sp|P0C6Y5|R1AB_CVPPU Replicase polyprotein 1ab OS=Porcine trans...   253    1e-73 
  sp|P0C6U6|R1A_CVHNL Replicase polyprotein 1a OS=Human coronavir...   250    1e-72 
  sp|P0C6X5|R1AB_CVHNL Replicase polyprotein 1ab OS=Human coronav...   250    1e-72 
  sp|P0C6U2|R1A_CVH22 Replicase polyprotein 1a OS=Human coronavir...   239    7e-69 
  sp|P0C6X1|R1AB_CVH22 Replicase polyprotein 1ab OS=Human coronav...   238    2e-68 
  sp|P0C6V4|R1A_IBVBC Replicase polyprotein 1a OS=Avian infectiou...   228    7e-65 
  sp|P0C6V3|R1A_IBVB Replicase polyprotein 1a OS=Avian infectious...   228    7e-65 
  sp|P0C6Y2|R1AB_IBVBC Replicase polyprotein 1ab OS=Avian infecti...   227    1e-64 
  sp|P0C6Y1|R1AB_IBVB Replicase polyprotein 1ab OS=Avian infectio...   227    1e-64 
  sp|P0C6V5|R1A_IBVM Replicase polyprotein 1a OS=Avian infectious...   225    5e-64 
  sp|P0C6Y3|R1AB_IBVM Replicase polyprotein 1ab OS=Avian infectio...   224    1e-63 
  sp|Q6AE15|HIS4_LEIXX 1-(5-phosphoribosyl)-5-[(5-phosphoribosyla...  33.1    2.6   


> sp|P0DTC1|R1A_SARS2 Replicase polyprotein 1a OS=Severe acute 
respiratory syndrome coronavirus 2 OX=2697049 PE=1 SV=1
Length=4405

 Score =  652 bits (1681),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 306/306 (100%), Positives = 306/306 (100%), Gaps = 0/306 (0%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR
Sbjct  3264  SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  3323

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
             KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG
Sbjct  3324  KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  3383

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
             SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN
Sbjct  3384  SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  3443

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE
Sbjct  3444  FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  3503

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
             PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
Sbjct  3504  PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  3563

Query  301   SGVTFQ  306
             SGVTFQ
Sbjct  3564  SGVTFQ  3569


> sp|P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab OS=Severe acute 
respiratory syndrome coronavirus 2 OX=2697049 GN=rep PE=1 
SV=1
Length=7096

 Score =  649 bits (1674),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 306/306 (100%), Positives = 306/306 (100%), Gaps = 0/306 (0%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR
Sbjct  3264  SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  3323

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
             KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG
Sbjct  3324  KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  3383

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
             SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN
Sbjct  3384  SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  3443

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE
Sbjct  3444  FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  3503

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
             PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
Sbjct  3504  PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  3563

Query  301   SGVTFQ  306
             SGVTFQ
Sbjct  3564  SGVTFQ  3569


> sp|P0C6F5|R1A_BC279 Replicase polyprotein 1a OS=Bat coronavirus 
279/2005 OX=389167 GN=1a PE=3 SV=1
Length=4388

 Score =  635 bits (1639),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 294/306 (96%), Positives = 303/306 (99%), Gaps = 0/306 (0%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDD VYCPRHVICT+EDMLNPNYEDLLIR
Sbjct  3247  SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLIR  3306

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
             KSNH+FLVQAGNVQLRVIGHSMQNC+L+LKVDT+NPKTPKYKFVRIQPGQTFSVLACYNG
Sbjct  3307  KSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNG  3366

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
             SPSGVYQCAMRPN+TIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEG 
Sbjct  3367  SPSGVYQCAMRPNYTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGK  3426

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGPFVDRQTAQAAGTDTTIT+NVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE
Sbjct  3427  FYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  3486

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
             PLTQDHVDILGPLSAQTGIAVLDMCA+LKELLQNGMNGRTILGS +LEDEFTPFDVVRQC
Sbjct  3487  PLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQC  3546

Query  301   SGVTFQ  306
             SGVTFQ
Sbjct  3547  SGVTFQ  3552


> sp|P0C6U8|R1A_CVHSA Replicase polyprotein 1a OS=Human SARS coronavirus 
OX=694009 GN=1a PE=1 SV=1
Length=4382

 Score =  634 bits (1634),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 294/306 (96%), Positives = 302/306 (99%), Gaps = 0/306 (0%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDD VYCPRHVICT+EDMLNPNYEDLLIR
Sbjct  3241  SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLIR  3300

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
             KSNH+FLVQAGNVQLRVIGHSMQNC+L+LKVDT+NPKTPKYKFVRIQPGQTFSVLACYNG
Sbjct  3301  KSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNG  3360

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
             SPSGVYQCAMRPN TIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEG 
Sbjct  3361  SPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGK  3420

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGPFVDRQTAQAAGTDTTIT+NVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE
Sbjct  3421  FYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  3480

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
             PLTQDHVDILGPLSAQTGIAVLDMCA+LKELLQNGMNGRTILGS +LEDEFTPFDVVRQC
Sbjct  3481  PLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQC  3540

Query  301   SGVTFQ  306
             SGVTFQ
Sbjct  3541  SGVTFQ  3546


> sp|P0C6V9|R1AB_BC279 Replicase polyprotein 1ab OS=Bat coronavirus 
279/2005 OX=389167 GN=rep PE=3 SV=1
Length=7079

 Score =  632 bits (1631),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 294/306 (96%), Positives = 303/306 (99%), Gaps = 0/306 (0%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDD VYCPRHVICT+EDMLNPNYEDLLIR
Sbjct  3247  SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLIR  3306

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
             KSNH+FLVQAGNVQLRVIGHSMQNC+L+LKVDT+NPKTPKYKFVRIQPGQTFSVLACYNG
Sbjct  3307  KSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNG  3366

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
             SPSGVYQCAMRPN+TIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEG 
Sbjct  3367  SPSGVYQCAMRPNYTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGK  3426

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGPFVDRQTAQAAGTDTTIT+NVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE
Sbjct  3427  FYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  3486

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
             PLTQDHVDILGPLSAQTGIAVLDMCA+LKELLQNGMNGRTILGS +LEDEFTPFDVVRQC
Sbjct  3487  PLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQC  3546

Query  301   SGVTFQ  306
             SGVTFQ
Sbjct  3547  SGVTFQ  3552


> sp|P0C6F8|R1A_BCHK3 Replicase polyprotein 1a OS=Bat coronavirus 
HKU3 OX=442736 GN=1a PE=3 SV=1
Length=4376

 Score =  630 bits (1626),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 292/306 (95%), Positives = 302/306 (99%), Gaps = 0/306 (0%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDD VYCPRHV+CT+EDMLNPNY+DLLIR
Sbjct  3235  SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVVCTAEDMLNPNYDDLLIR  3294

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
             KSNH+FLVQAGNVQLRVIGHSMQNC+L+LKVDT+NPKTPKYKFVRIQPGQTFSVLACYNG
Sbjct  3295  KSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNG  3354

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
             SPSGVYQCAMRPN TIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEG 
Sbjct  3355  SPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGK  3414

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGPFVDRQTAQAAGTDTTIT+NVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE
Sbjct  3415  FYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  3474

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
             PLTQDHVDILGPLSAQTGIAVLDMCA+LKELLQNGMNGRTILGS +LEDEFTPFDVVRQC
Sbjct  3475  PLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQC  3534

Query  301   SGVTFQ  306
             SGVTFQ
Sbjct  3535  SGVTFQ  3540


> sp|P0C6T7|R1A_BCRP3 Replicase polyprotein 1a OS=Bat coronavirus 
Rp3/2004 OX=349344 GN=1a PE=3 SV=1
Length=4380

 Score =  630 bits (1626),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 293/306 (96%), Positives = 301/306 (98%), Gaps = 0/306 (0%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDD VYCPRHVICT+EDMLNPNYEDLLIR
Sbjct  3239  SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLIR  3298

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
             KSNH+FLVQAGNVQLRVIGHSMQNC+L+LKVDT+NPKTPKYKFVRIQPGQTFSVLACYNG
Sbjct  3299  KSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNG  3358

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
             SPSGVYQCAMRPN TIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPT VHAGTDLEG 
Sbjct  3359  SPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTEVHAGTDLEGK  3418

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGPFVDRQTAQAAGTDTTIT+NVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE
Sbjct  3419  FYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  3478

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
             PLTQDHVDILGPLSAQTGIAVLDMCA+LKELLQNGMNGRTILGS +LEDEFTPFDVVRQC
Sbjct  3479  PLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQC  3538

Query  301   SGVTFQ  306
             SGVTFQ
Sbjct  3539  SGVTFQ  3544


> sp|P0C6X7|R1AB_CVHSA Replicase polyprotein 1ab OS=Human SARS 
coronavirus OX=694009 GN=rep PE=1 SV=1
Length=7073

 Score =  631 bits (1628),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 294/306 (96%), Positives = 302/306 (99%), Gaps = 0/306 (0%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDD VYCPRHVICT+EDMLNPNYEDLLIR
Sbjct  3241  SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLIR  3300

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
             KSNH+FLVQAGNVQLRVIGHSMQNC+L+LKVDT+NPKTPKYKFVRIQPGQTFSVLACYNG
Sbjct  3301  KSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNG  3360

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
             SPSGVYQCAMRPN TIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEG 
Sbjct  3361  SPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGK  3420

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGPFVDRQTAQAAGTDTTIT+NVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE
Sbjct  3421  FYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  3480

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
             PLTQDHVDILGPLSAQTGIAVLDMCA+LKELLQNGMNGRTILGS +LEDEFTPFDVVRQC
Sbjct  3481  PLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQC  3540

Query  301   SGVTFQ  306
             SGVTFQ
Sbjct  3541  SGVTFQ  3546


> sp|P0C6W6|R1AB_BCRP3 Replicase polyprotein 1ab OS=Bat coronavirus 
Rp3/2004 OX=349344 GN=rep PE=3 SV=1
Length=7071

 Score =  628 bits (1620),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 293/306 (96%), Positives = 301/306 (98%), Gaps = 0/306 (0%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDD VYCPRHVICT+EDMLNPNYEDLLIR
Sbjct  3239  SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLIR  3298

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
             KSNH+FLVQAGNVQLRVIGHSMQNC+L+LKVDT+NPKTPKYKFVRIQPGQTFSVLACYNG
Sbjct  3299  KSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNG  3358

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
             SPSGVYQCAMRPN TIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPT VHAGTDLEG 
Sbjct  3359  SPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTEVHAGTDLEGK  3418

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGPFVDRQTAQAAGTDTTIT+NVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE
Sbjct  3419  FYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  3478

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
             PLTQDHVDILGPLSAQTGIAVLDMCA+LKELLQNGMNGRTILGS +LEDEFTPFDVVRQC
Sbjct  3479  PLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQC  3538

Query  301   SGVTFQ  306
             SGVTFQ
Sbjct  3539  SGVTFQ  3544


> sp|P0C6W2|R1AB_BCHK3 Replicase polyprotein 1ab OS=Bat coronavirus 
HKU3 OX=442736 GN=rep PE=3 SV=1
Length=7067

 Score =  628 bits (1620),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 292/306 (95%), Positives = 302/306 (99%), Gaps = 0/306 (0%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDD VYCPRHV+CT+EDMLNPNY+DLLIR
Sbjct  3235  SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVVCTAEDMLNPNYDDLLIR  3294

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
             KSNH+FLVQAGNVQLRVIGHSMQNC+L+LKVDT+NPKTPKYKFVRIQPGQTFSVLACYNG
Sbjct  3295  KSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNG  3354

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
             SPSGVYQCAMRPN TIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEG 
Sbjct  3355  SPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGK  3414

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGPFVDRQTAQAAGTDTTIT+NVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE
Sbjct  3415  FYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  3474

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
             PLTQDHVDILGPLSAQTGIAVLDMCA+LKELLQNGMNGRTILGS +LEDEFTPFDVVRQC
Sbjct  3475  PLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQC  3534

Query  301   SGVTFQ  306
             SGVTFQ
Sbjct  3535  SGVTFQ  3540


> sp|P0C6T6|R1A_BCHK9 Replicase polyprotein 1a OS=Bat coronavirus 
HKU9 OX=694006 GN=1a PE=3 SV=1
Length=4248

 Score =  342 bits (876),  Expect = 3e-104, Method: Compositional matrix adjust.
 Identities = 159/306 (52%), Positives = 214/306 (70%), Gaps = 0/306 (0%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             +G  +MA PSG VE C+V+V  G+ TLNG+WLD+ V CPRHV+C+ +++ NP+Y  L +R
Sbjct  3104  AGLTRMAHPSGLVEPCLVKVNYGSMTLNGIWLDNFVICPRHVMCSRDELANPDYPRLSMR  3163

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              +N++F V      +RVIGH+M+  +LKL VD  NPKTP Y F+R+  GQ  S+LACY+G
Sbjct  3164  AANYDFHVSQNGHNIRVIGHTMEGSLLKLTVDVNNPKTPAYSFIRVSTGQAMSLLACYDG  3223

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P+GVY C +R N T++ SFL GSCGS GF ++   V FCY+H +ELP G H GTD  G 
Sbjct  3224  LPTGVYTCTLRSNGTMRASFLCGSCGSPGFVMNGKEVQFCYLHQLELPNGTHTGTDFSGV  3283

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGPF D+Q  Q A  D TITVNVLAWLYAAV++G+ WFL + + +  +FN  A+KY  +
Sbjct  3284  FYGPFEDKQVPQLAAPDCTITVNVLAWLYAAVLSGENWFLTKSSISPAEFNNCAVKYMCQ  3343

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +T + + +L PL+A+TGI+V  M ++LK LL  G  GRTI+GS  LEDE TP+D+ RQ 
Sbjct  3344  SVTSESLQVLQPLAAKTGISVERMLSALKVLLSAGFCGRTIMGSCSLEDEHTPYDIGRQM  3403

Query  301   SGVTFQ  306
              GV  Q
Sbjct  3404  LGVKLQ  3409


> sp|P0C6W5|R1AB_BCHK9 Replicase polyprotein 1ab OS=Bat coronavirus 
HKU9 OX=694006 GN=rep PE=1 SV=1
Length=6930

 Score =  341 bits (874),  Expect = 7e-104, Method: Compositional matrix adjust.
 Identities = 159/306 (52%), Positives = 214/306 (70%), Gaps = 0/306 (0%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             +G  +MA PSG VE C+V+V  G+ TLNG+WLD+ V CPRHV+C+ +++ NP+Y  L +R
Sbjct  3104  AGLTRMAHPSGLVEPCLVKVNYGSMTLNGIWLDNFVICPRHVMCSRDELANPDYPRLSMR  3163

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              +N++F V      +RVIGH+M+  +LKL VD  NPKTP Y F+R+  GQ  S+LACY+G
Sbjct  3164  AANYDFHVSQNGHNIRVIGHTMEGSLLKLTVDVNNPKTPAYSFIRVSTGQAMSLLACYDG  3223

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P+GVY C +R N T++ SFL GSCGS GF ++   V FCY+H +ELP G H GTD  G 
Sbjct  3224  LPTGVYTCTLRSNGTMRASFLCGSCGSPGFVMNGKEVQFCYLHQLELPNGTHTGTDFSGV  3283

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGPF D+Q  Q A  D TITVNVLAWLYAAV++G+ WFL + + +  +FN  A+KY  +
Sbjct  3284  FYGPFEDKQVPQLAAPDCTITVNVLAWLYAAVLSGENWFLTKSSISPAEFNNCAVKYMCQ  3343

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +T + + +L PL+A+TGI+V  M ++LK LL  G  GRTI+GS  LEDE TP+D+ RQ 
Sbjct  3344  SVTSESLQVLQPLAAKTGISVERMLSALKVLLSAGFCGRTIMGSCSLEDEHTPYDIGRQM  3403

Query  301   SGVTFQ  306
              GV  Q
Sbjct  3404  LGVKLQ  3409


> sp|K9N638|R1A_MERS1 Replicase polyprotein 1a OS=Middle East respiratory 
syndrome-related coronavirus (isolate United Kingdom/H123990006/2012) 
OX=1263720 GN=1a PE=1 SV=1
Length=4391

 Score =  322 bits (824),  Expect = 2e-97, Method: Compositional matrix adjust.
 Identities = 157/310 (51%), Positives = 207/310 (67%), Gaps = 8/310 (3%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM+ PSG VE CMVQVTCG+ TLNGLWLD+ V+CPRHV+C ++ + +PNY+ LLI 
Sbjct  3248  SGLVKMSHPSGDVEACMVQVTCGSMTLNGLWLDNTVWCPRHVMCPADQLSDPNYDALLIS  3307

Query  61    KSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLAC  117
              +NH+F VQ        LRV+GH+MQ  +LKL VD ANP TP Y F  ++PG  FSVLAC
Sbjct  3308  MTNHSFSVQKHIGAPANLRVVGHAMQGTLLKLTVDVANPSTPAYTFTTVKPGAAFSVLAC  3367

Query  118   YNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDL  177
             YNG P+G +   MRPN+TIKGSFL GSCGSVG+  +   ++FCYMH MEL  G H G+  
Sbjct  3368  YNGRPTGTFTVVMRPNYTIKGSFLCGSCGSVGYTKEGSVINFCYMHQMELANGTHTGSAF  3427

Query  178   EGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKY  237
             +G  YG F+D+Q  Q   TD   +VNV+AWLYAA++NG  WF+    T++  FN  A+  
Sbjct  3428  DGTMYGAFMDKQVHQVQLTDKYCSVNVVAWLYAAILNGCAWFVKPNRTSVVSFNEWALAN  3487

Query  238   NY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDV  296
              + E +    VD+   L+ +TG+A+  +  ++++L   G  G+ ILGS +LEDEFTP DV
Sbjct  3488  QFTEFVGTQSVDM---LAVKTGVAIEQLLYAIQQLY-TGFQGKQILGSTMLEDEFTPEDV  3543

Query  297   VRQCSGVTFQ  306
               Q  GV  Q
Sbjct  3544  NMQIMGVVMQ  3553


> sp|K9N7C7|R1AB_MERS1 Replicase polyprotein 1ab OS=Middle East 
respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012) 
OX=1263720 GN=rep PE=1 SV=1
Length=7078

 Score =  320 bits (821),  Expect = 7e-97, Method: Compositional matrix adjust.
 Identities = 157/310 (51%), Positives = 207/310 (67%), Gaps = 8/310 (3%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM+ PSG VE CMVQVTCG+ TLNGLWLD+ V+CPRHV+C ++ + +PNY+ LLI 
Sbjct  3248  SGLVKMSHPSGDVEACMVQVTCGSMTLNGLWLDNTVWCPRHVMCPADQLSDPNYDALLIS  3307

Query  61    KSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLAC  117
              +NH+F VQ        LRV+GH+MQ  +LKL VD ANP TP Y F  ++PG  FSVLAC
Sbjct  3308  MTNHSFSVQKHIGAPANLRVVGHAMQGTLLKLTVDVANPSTPAYTFTTVKPGAAFSVLAC  3367

Query  118   YNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDL  177
             YNG P+G +   MRPN+TIKGSFL GSCGSVG+  +   ++FCYMH MEL  G H G+  
Sbjct  3368  YNGRPTGTFTVVMRPNYTIKGSFLCGSCGSVGYTKEGSVINFCYMHQMELANGTHTGSAF  3427

Query  178   EGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKY  237
             +G  YG F+D+Q  Q   TD   +VNV+AWLYAA++NG  WF+    T++  FN  A+  
Sbjct  3428  DGTMYGAFMDKQVHQVQLTDKYCSVNVVAWLYAAILNGCAWFVKPNRTSVVSFNEWALAN  3487

Query  238   NY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDV  296
              + E +    VD+   L+ +TG+A+  +  ++++L   G  G+ ILGS +LEDEFTP DV
Sbjct  3488  QFTEFVGTQSVDM---LAVKTGVAIEQLLYAIQQLY-TGFQGKQILGSTMLEDEFTPEDV  3543

Query  297   VRQCSGVTFQ  306
               Q  GV  Q
Sbjct  3544  NMQIMGVVMQ  3553


> sp|P0C6T5|R1A_BCHK5 Replicase polyprotein 1a OS=Bat coronavirus 
HKU5 OX=694008 GN=1a PE=3 SV=1
Length=4481

 Score =  311 bits (798),  Expect = 8e-94, Method: Compositional matrix adjust.
 Identities = 155/310 (50%), Positives = 208/310 (67%), Gaps = 8/310 (3%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KMA PSG VE CMVQVTCG+ TLNGLWLD+ V+CPRHV+C ++ + +PNY+ LL+ 
Sbjct  3339  SGLVKMAAPSGVVENCMVQVTCGSMTLNGLWLDNYVWCPRHVMCPADQLSDPNYDALLVS  3398

Query  61    KSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLAC  117
             K+N +F+VQ        LRV+GH+M   +LKL V++ANP+TP Y F  ++PG +FSVLAC
Sbjct  3399  KTNLSFIVQKNVGAPANLRVVGHTMVGTLLKLTVESANPQTPAYTFTTVKPGASFSVLAC  3458

Query  118   YNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDL  177
             YNG P+GV+   MR N TIKGSFL GSCGSVG+  + + ++FCYMH MEL  G H G   
Sbjct  3459  YNGRPTGVFMVNMRQNSTIKGSFLCGSCGSVGYTQEGNVINFCYMHQMELSNGTHTGCAF  3518

Query  178   EGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKY  237
             +G  YG F DRQ  Q   +D   T+N++AWLYAA++NG  WF+    T +  FN  AM  
Sbjct  3519  DGVMYGAFEDRQVHQVQLSDKYCTINIVAWLYAAILNGCNWFVKPNKTGIATFNEWAMSN  3578

Query  238   NY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDV  296
              + E +    VD+   L+ +TG++V  +  ++ + L  G  G+TILG+++LEDEFTP DV
Sbjct  3579  QFTEFIGTQSVDM---LAHKTGVSVEQLLYAI-QTLHKGFQGKTILGNSMLEDEFTPDDV  3634

Query  297   VRQCSGVTFQ  306
               Q  GV  Q
Sbjct  3635  NMQVMGVVMQ  3644


> sp|P0C6W4|R1AB_BCHK5 Replicase polyprotein 1ab OS=Bat coronavirus 
HKU5 OX=694008 GN=rep PE=3 SV=1
Length=7182

 Score =  311 bits (796),  Expect = 2e-93, Method: Compositional matrix adjust.
 Identities = 155/310 (50%), Positives = 208/310 (67%), Gaps = 8/310 (3%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KMA PSG VE CMVQVTCG+ TLNGLWLD+ V+CPRHV+C ++ + +PNY+ LL+ 
Sbjct  3339  SGLVKMAAPSGVVENCMVQVTCGSMTLNGLWLDNYVWCPRHVMCPADQLSDPNYDALLVS  3398

Query  61    KSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLAC  117
             K+N +F+VQ        LRV+GH+M   +LKL V++ANP+TP Y F  ++PG +FSVLAC
Sbjct  3399  KTNLSFIVQKNVGAPANLRVVGHTMVGTLLKLTVESANPQTPAYTFTTVKPGASFSVLAC  3458

Query  118   YNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDL  177
             YNG P+GV+   MR N TIKGSFL GSCGSVG+  + + ++FCYMH MEL  G H G   
Sbjct  3459  YNGRPTGVFMVNMRQNSTIKGSFLCGSCGSVGYTQEGNVINFCYMHQMELSNGTHTGCAF  3518

Query  178   EGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKY  237
             +G  YG F DRQ  Q   +D   T+N++AWLYAA++NG  WF+    T +  FN  AM  
Sbjct  3519  DGVMYGAFEDRQVHQVQLSDKYCTINIVAWLYAAILNGCNWFVKPNKTGIATFNEWAMSN  3578

Query  238   NY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDV  296
              + E +    VD+   L+ +TG++V  +  ++ + L  G  G+TILG+++LEDEFTP DV
Sbjct  3579  QFTEFIGTQSVDM---LAHKTGVSVEQLLYAI-QTLHKGFQGKTILGNSMLEDEFTPDDV  3634

Query  297   VRQCSGVTFQ  306
               Q  GV  Q
Sbjct  3635  NMQVMGVVMQ  3644


> sp|P0C6U9|R1A_CVM2 Replicase polyprotein 1a OS=Murine coronavirus 
(strain 2) OX=76344 GN=1a PE=3 SV=1
Length=4416

 Score =  310 bits (795),  Expect = 2e-93, Method: Compositional matrix adjust.
 Identities = 155/306 (51%), Positives = 200/306 (65%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM FP+ KVE C+V VT G  TLNGLWLDD VYCPRHVIC+S DM +P+Y +LL R
Sbjct  3280  SGIVKMVFPTSKVEPCVVSVTYGNMTLNGLWLDDKVYCPRHVICSSADMTDPDYSNLLCR  3339

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
               + +F V +G + L V+ + MQ  +L L V   NP TPKY F  ++PG+TF+VLA YNG
Sbjct  3340  VISSDFCVMSGRMSLTVMSYQMQGSLLVLTVTLQNPNTPKYSFGVVKPGETFTVLAAYNG  3399

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
                G +   MR ++TIKGSFL GSCGSVG+ +  D V F YMH +EL TG H GTD  GN
Sbjct  3400  KSQGAFHVTMRSSYTIKGSFLCGSCGSVGYVLTGDSVRFVYMHQLELSTGCHTGTDFSGN  3459

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D T TVNV+AWLYAA++N   WF+   + +L +FN+ AM   + 
Sbjct  3460  FYGPYRDAQVVQLPVQDYTQTVNVVAWLYAAILNRCNWFVQSDSCSLEEFNVWAMTNGFS  3519

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  L  L++ TG+ V  + A++K L  +G  G+ ILGS +LEDE TP DV +Q 
Sbjct  3520  SIKADLV--LDALASMTGVTVEQILAAIKRLY-SGFQGKQILGSCVLEDELTPSDVYQQL  3576

Query  301   SGVTFQ  306
             +GV  Q
Sbjct  3577  AGVKLQ  3582


> sp|P0C6X8|R1AB_CVM2 Replicase polyprotein 1ab OS=Murine coronavirus 
(strain 2) OX=76344 GN=rep PE=3 SV=1
Length=7124

 Score =  310 bits (794),  Expect = 3e-93, Method: Compositional matrix adjust.
 Identities = 155/306 (51%), Positives = 200/306 (65%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM FP+ KVE C+V VT G  TLNGLWLDD VYCPRHVIC+S DM +P+Y +LL R
Sbjct  3280  SGIVKMVFPTSKVEPCVVSVTYGNMTLNGLWLDDKVYCPRHVICSSADMTDPDYSNLLCR  3339

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
               + +F V +G + L V+ + MQ  +L L V   NP TPKY F  ++PG+TF+VLA YNG
Sbjct  3340  VISSDFCVMSGRMSLTVMSYQMQGSLLVLTVTLQNPNTPKYSFGVVKPGETFTVLAAYNG  3399

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
                G +   MR ++TIKGSFL GSCGSVG+ +  D V F YMH +EL TG H GTD  GN
Sbjct  3400  KSQGAFHVTMRSSYTIKGSFLCGSCGSVGYVLTGDSVRFVYMHQLELSTGCHTGTDFSGN  3459

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D T TVNV+AWLYAA++N   WF+   + +L +FN+ AM   + 
Sbjct  3460  FYGPYRDAQVVQLPVQDYTQTVNVVAWLYAAILNRCNWFVQSDSCSLEEFNVWAMTNGFS  3519

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  L  L++ TG+ V  + A++K L  +G  G+ ILGS +LEDE TP DV +Q 
Sbjct  3520  SIKADLV--LDALASMTGVTVEQILAAIKRLY-SGFQGKQILGSCVLEDELTPSDVYQQL  3576

Query  301   SGVTFQ  306
             +GV  Q
Sbjct  3577  AGVKLQ  3582


> sp|P0C6T4|R1A_BCHK4 Replicase polyprotein 1a OS=Bat coronavirus 
HKU4 OX=694007 GN=1a PE=1 SV=1
Length=4434

 Score =  308 bits (790),  Expect = 8e-93, Method: Compositional matrix adjust.
 Identities = 154/310 (50%), Positives = 205/310 (66%), Gaps = 8/310 (3%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM+ PSG VE C+VQVTCG+ TLNGLWLD+ V+CPRH++C ++ + +PNY+ LLI 
Sbjct  3292  SGLVKMSAPSGAVENCIVQVTCGSMTLNGLWLDNTVWCPRHIMCPADQLTDPNYDALLIS  3351

Query  61    KSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLAC  117
             K+NH+F+VQ        LRV+ HSM   +LKL VD ANP TP Y F  ++PG +FSVLAC
Sbjct  3352  KTNHSFIVQKHIGAQANLRVVAHSMVGVLLKLTVDVANPSTPAYTFSTVKPGASFSVLAC  3411

Query  118   YNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDL  177
             YNG P+GV+   +R N TIKGSFL GSCGSVG+  +   ++F YMH MEL  G H G+  
Sbjct  3412  YNGKPTGVFTVNLRHNSTIKGSFLCGSCGSVGYTENGGVINFVYMHQMELSNGTHTGSSF  3471

Query  178   EGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKY  237
             +G  YG F D+QT Q   TD   T+NV+AWLYAAV+NG +WF+      +  +N  A+  
Sbjct  3472  DGVMYGAFEDKQTHQLQLTDKYCTINVVAWLYAAVLNGCKWFVKPTRVGIVTYNEWALSN  3531

Query  238   NY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDV  296
              + E +    +D+   L+ +TG++V  M A+++  L  G  G+TILG + LEDEFTP DV
Sbjct  3532  QFTEFVGTQSIDM---LAHRTGVSVEQMLAAIQS-LHAGFQGKTILGQSTLEDEFTPDDV  3587

Query  297   VRQCSGVTFQ  306
               Q  GV  Q
Sbjct  3588  NMQVMGVVMQ  3597


> sp|P0C6F7|R1A_BC133 Replicase polyprotein 1a OS=Bat coronavirus 
133/2005 OX=389230 GN=1a PE=3 SV=1
Length=4441

 Score =  308 bits (788),  Expect = 2e-92, Method: Compositional matrix adjust.
 Identities = 154/310 (50%), Positives = 205/310 (66%), Gaps = 8/310 (3%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM+ PSG VE C+VQVTCG+ TLNGLWLD+ V+CPRH++C ++ + +PNY+ LLI 
Sbjct  3299  SGLVKMSAPSGAVENCIVQVTCGSMTLNGLWLDNTVWCPRHIMCPADQLTDPNYDALLIS  3358

Query  61    KSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLAC  117
             K+NH+F+VQ        LRV+ HSM   +LKL VD ANP TP Y F  ++PG +FSVLAC
Sbjct  3359  KTNHSFIVQKHIGAQANLRVVAHSMVGVLLKLTVDVANPSTPAYTFSTVKPGASFSVLAC  3418

Query  118   YNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDL  177
             YNG P+GV+   +R N TIKGSFL GSCGSVG+  +   ++F YMH MEL  G H G+  
Sbjct  3419  YNGKPTGVFTVNLRHNSTIKGSFLCGSCGSVGYTENGGVLNFVYMHQMELSNGTHTGSSF  3478

Query  178   EGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKY  237
             +G  YG F D+QT Q   TD   T+NV+AWLYAAV+NG +WF+      +  +N  A+  
Sbjct  3479  DGVMYGAFEDKQTHQLQLTDKYCTINVVAWLYAAVLNGCKWFVKPTRVGIVTYNEWALSN  3538

Query  238   NY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDV  296
              + E +    +D+   L+ +TG++V  M A+++  L  G  G+TILG + LEDEFTP DV
Sbjct  3539  QFTEFVGTQSIDM---LAHRTGVSVEQMLAAIQS-LHAGFQGKTILGQSTLEDEFTPDDV  3594

Query  297   VRQCSGVTFQ  306
               Q  GV  Q
Sbjct  3595  NMQVMGVVMQ  3604


> sp|P0C6W3|R1AB_BCHK4 Replicase polyprotein 1ab OS=Bat coronavirus 
HKU4 OX=694007 GN=rep PE=1 SV=1
Length=7119

 Score =  308 bits (788),  Expect = 2e-92, Method: Compositional matrix adjust.
 Identities = 154/310 (50%), Positives = 205/310 (66%), Gaps = 8/310 (3%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM+ PSG VE C+VQVTCG+ TLNGLWLD+ V+CPRH++C ++ + +PNY+ LLI 
Sbjct  3292  SGLVKMSAPSGAVENCIVQVTCGSMTLNGLWLDNTVWCPRHIMCPADQLTDPNYDALLIS  3351

Query  61    KSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLAC  117
             K+NH+F+VQ        LRV+ HSM   +LKL VD ANP TP Y F  ++PG +FSVLAC
Sbjct  3352  KTNHSFIVQKHIGAQANLRVVAHSMVGVLLKLTVDVANPSTPAYTFSTVKPGASFSVLAC  3411

Query  118   YNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDL  177
             YNG P+GV+   +R N TIKGSFL GSCGSVG+  +   ++F YMH MEL  G H G+  
Sbjct  3412  YNGKPTGVFTVNLRHNSTIKGSFLCGSCGSVGYTENGGVINFVYMHQMELSNGTHTGSSF  3471

Query  178   EGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKY  237
             +G  YG F D+QT Q   TD   T+NV+AWLYAAV+NG +WF+      +  +N  A+  
Sbjct  3472  DGVMYGAFEDKQTHQLQLTDKYCTINVVAWLYAAVLNGCKWFVKPTRVGIVTYNEWALSN  3531

Query  238   NY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDV  296
              + E +    +D+   L+ +TG++V  M A+++  L  G  G+TILG + LEDEFTP DV
Sbjct  3532  QFTEFVGTQSIDM---LAHRTGVSVEQMLAAIQS-LHAGFQGKTILGQSTLEDEFTPDDV  3587

Query  297   VRQCSGVTFQ  306
               Q  GV  Q
Sbjct  3588  NMQVMGVVMQ  3597


> sp|P0C6V1|R1A_CVMJH Replicase polyprotein 1a OS=Murine coronavirus 
(strain JHM) OX=11144 GN=1a PE=1 SV=1
Length=4474

 Score =  307 bits (786),  Expect = 3e-92, Method: Compositional matrix adjust.
 Identities = 154/306 (50%), Positives = 199/306 (65%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ KVE C+V VT G  TLNGLWLDD VYCPRHVIC+S DM +P+Y +LL R
Sbjct  3337  SGIVKMVSPTSKVEPCVVSVTYGNMTLNGLWLDDKVYCPRHVICSSADMTDPDYPNLLCR  3396

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              ++ +F V +  + L V+ + MQ  +L L V   NP TPKY F  ++PG+TF+VLA YNG
Sbjct  3397  VTSSDFCVMSDRMSLTVMSYQMQGSLLVLTVTLQNPNTPKYSFGVVKPGETFTVLAAYNG  3456

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   MR + TIKGSFL GSCGSVG+ +  D V F YMH +EL TG H GTD  GN
Sbjct  3457  RPQGAFHVVMRSSHTIKGSFLCGSCGSVGYVLTGDSVRFVYMHQLELSTGCHTGTDFSGN  3516

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D T TVNV+AWLYAA++N   WF+   + +L +FN+ AM   + 
Sbjct  3517  FYGPYRDAQVVQLPVQDYTQTVNVVAWLYAAILNRCNWFVQSDSCSLEEFNVWAMTNGFS  3576

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  L  L++ TG+ V  + A++K  L +G  G+ ILGS +LEDE TP DV +Q 
Sbjct  3577  SIKADLV--LDALASMTGVTVEQVLAAIKR-LHSGFQGKQILGSCVLEDELTPSDVYQQL  3633

Query  301   SGVTFQ  306
             +GV  Q
Sbjct  3634  AGVKLQ  3639


> sp|P0C6W1|R1AB_BC133 Replicase polyprotein 1ab OS=Bat coronavirus 
133/2005 OX=389230 GN=rep PE=3 SV=1
Length=7126

 Score =  307 bits (786),  Expect = 4e-92, Method: Compositional matrix adjust.
 Identities = 154/310 (50%), Positives = 205/310 (66%), Gaps = 8/310 (3%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM+ PSG VE C+VQVTCG+ TLNGLWLD+ V+CPRH++C ++ + +PNY+ LLI 
Sbjct  3299  SGLVKMSAPSGAVENCIVQVTCGSMTLNGLWLDNTVWCPRHIMCPADQLTDPNYDALLIS  3358

Query  61    KSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLAC  117
             K+NH+F+VQ        LRV+ HSM   +LKL VD ANP TP Y F  ++PG +FSVLAC
Sbjct  3359  KTNHSFIVQKHIGAQANLRVVAHSMVGVLLKLTVDVANPSTPAYTFSTVKPGASFSVLAC  3418

Query  118   YNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDL  177
             YNG P+GV+   +R N TIKGSFL GSCGSVG+  +   ++F YMH MEL  G H G+  
Sbjct  3419  YNGKPTGVFTVNLRHNSTIKGSFLCGSCGSVGYTENGGVLNFVYMHQMELSNGTHTGSSF  3478

Query  178   EGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKY  237
             +G  YG F D+QT Q   TD   T+NV+AWLYAAV+NG +WF+      +  +N  A+  
Sbjct  3479  DGVMYGAFEDKQTHQLQLTDKYCTINVVAWLYAAVLNGCKWFVKPTRVGIVTYNEWALSN  3538

Query  238   NY-EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDV  296
              + E +    +D+   L+ +TG++V  M A+++  L  G  G+TILG + LEDEFTP DV
Sbjct  3539  QFTEFVGTQSIDM---LAHRTGVSVEQMLAAIQS-LHAGFQGKTILGQSTLEDEFTPDDV  3594

Query  297   VRQCSGVTFQ  306
               Q  GV  Q
Sbjct  3595  NMQVMGVVMQ  3604


> sp|P0C6Y0|R1AB_CVMJH Replicase polyprotein 1ab OS=Murine coronavirus 
(strain JHM) OX=11144 GN=rep PE=1 SV=1
Length=7180

 Score =  306 bits (785),  Expect = 5e-92, Method: Compositional matrix adjust.
 Identities = 154/306 (50%), Positives = 199/306 (65%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ KVE C+V VT G  TLNGLWLDD VYCPRHVIC+S DM +P+Y +LL R
Sbjct  3337  SGIVKMVSPTSKVEPCVVSVTYGNMTLNGLWLDDKVYCPRHVICSSADMTDPDYPNLLCR  3396

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              ++ +F V +  + L V+ + MQ  +L L V   NP TPKY F  ++PG+TF+VLA YNG
Sbjct  3397  VTSSDFCVMSDRMSLTVMSYQMQGSLLVLTVTLQNPNTPKYSFGVVKPGETFTVLAAYNG  3456

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   MR + TIKGSFL GSCGSVG+ +  D V F YMH +EL TG H GTD  GN
Sbjct  3457  RPQGAFHVVMRSSHTIKGSFLCGSCGSVGYVLTGDSVRFVYMHQLELSTGCHTGTDFSGN  3516

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D T TVNV+AWLYAA++N   WF+   + +L +FN+ AM   + 
Sbjct  3517  FYGPYRDAQVVQLPVQDYTQTVNVVAWLYAAILNRCNWFVQSDSCSLEEFNVWAMTNGFS  3576

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  L  L++ TG+ V  + A++K  L +G  G+ ILGS +LEDE TP DV +Q 
Sbjct  3577  SIKADLV--LDALASMTGVTVEQVLAAIKR-LHSGFQGKQILGSCVLEDELTPSDVYQQL  3633

Query  301   SGVTFQ  306
             +GV  Q
Sbjct  3634  AGVKLQ  3639


> sp|P0C6V0|R1A_CVMA5 Replicase polyprotein 1a OS=Murine coronavirus 
(strain A59) OX=11142 GN=1a PE=1 SV=1
Length=4468

 Score =  305 bits (782),  Expect = 1e-91, Method: Compositional matrix adjust.
 Identities = 155/306 (51%), Positives = 199/306 (65%), Gaps = 4/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ KVE C+V VT G  TLNGLWLDD VYCPRHVIC+S DM +P+Y +LL R
Sbjct  3334  SGIVKMVSPTSKVEPCIVSVTYGNMTLNGLWLDDKVYCPRHVICSSADMTDPDYPNLLCR  3393

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              ++ +F V +G + L V+ + MQ C L L V   NP TPKY F  ++PG+TF+VLA YNG
Sbjct  3394  VTSSDFCVMSGRMSLTVMSYQMQGCQLVLTVTLQNPNTPKYSFGVVKPGETFTVLAAYNG  3453

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   +R + TIKGSFL GSCGSVG+ +  D V F YMH +EL TG H GTD  GN
Sbjct  3454  RPQGAFHVTLRSSHTIKGSFLCGSCGSVGYVLTGDSVRFVYMHQLELSTGCHTGTDFSGN  3513

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D T TVNV+AWLYAA+ N   WF+   + +L +FN+ AM   + 
Sbjct  3514  FYGPYRDAQVVQLPVQDYTQTVNVVAWLYAAIFNRCNWFVQSDSCSLEEFNVWAMTNGFS  3573

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  L  L++ TG+ V  + A++K  L +G  G+ ILGS +LEDE TP DV +Q 
Sbjct  3574  SIKADLV--LDALASMTGVTVEQVLAAIKR-LHSGFQGKQILGSCVLEDE-TPSDVYQQL  3629

Query  301   SGVTFQ  306
             +GV  Q
Sbjct  3630  AGVKLQ  3635


> sp|P0C6X9|R1AB_CVMA5 Replicase polyprotein 1ab OS=Murine coronavirus 
(strain A59) OX=11142 GN=rep PE=1 SV=1
Length=7176

 Score =  305 bits (781),  Expect = 2e-91, Method: Compositional matrix adjust.
 Identities = 155/306 (51%), Positives = 199/306 (65%), Gaps = 4/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ KVE C+V VT G  TLNGLWLDD VYCPRHVIC+S DM +P+Y +LL R
Sbjct  3334  SGIVKMVSPTSKVEPCIVSVTYGNMTLNGLWLDDKVYCPRHVICSSADMTDPDYPNLLCR  3393

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              ++ +F V +G + L V+ + MQ C L L V   NP TPKY F  ++PG+TF+VLA YNG
Sbjct  3394  VTSSDFCVMSGRMSLTVMSYQMQGCQLVLTVTLQNPNTPKYSFGVVKPGETFTVLAAYNG  3453

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   +R + TIKGSFL GSCGSVG+ +  D V F YMH +EL TG H GTD  GN
Sbjct  3454  RPQGAFHVTLRSSHTIKGSFLCGSCGSVGYVLTGDSVRFVYMHQLELSTGCHTGTDFSGN  3513

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D T TVNV+AWLYAA+ N   WF+   + +L +FN+ AM   + 
Sbjct  3514  FYGPYRDAQVVQLPVQDYTQTVNVVAWLYAAIFNRCNWFVQSDSCSLEEFNVWAMTNGFS  3573

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  L  L++ TG+ V  + A++K  L +G  G+ ILGS +LEDE TP DV +Q 
Sbjct  3574  SIKADLV--LDALASMTGVTVEQVLAAIKR-LHSGFQGKQILGSCVLEDE-TPSDVYQQL  3629

Query  301   SGVTFQ  306
             +GV  Q
Sbjct  3630  AGVKLQ  3635


> sp|P0C6U7|R1A_CVHOC Replicase polyprotein 1a OS=Human coronavirus 
OC43 OX=31631 GN=1a PE=3 SV=1
Length=4383

 Score =  304 bits (778),  Expect = 3e-91, Method: Compositional matrix adjust.
 Identities = 148/306 (48%), Positives = 198/306 (65%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ KVE C+V VT G  TLNGLWLDD VYCPRHVIC++ DM NP+Y +LL R
Sbjct  3247  SGIVKMVNPTSKVEPCVVSVTYGNMTLNGLWLDDKVYCPRHVICSASDMTNPDYTNLLCR  3306

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              ++ +F V    + L V+ + M+ C+L L V   N +TPKY F  ++PG+TF+VLA YNG
Sbjct  3307  VTSSDFTVLFDRLSLTVMSYQMRGCMLVLTVTLQNSRTPKYTFGVVKPGETFTVLAAYNG  3366

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   MR ++TIKGSFL GSCGSVG+ I  DCV F YMH +EL TG H GTD  G+
Sbjct  3367  KPQGAFHVTMRSSYTIKGSFLCGSCGSVGYVIMGDCVKFVYMHQLELSTGCHTGTDFNGD  3426

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D   +VN LAWLYAA++N   WF+     ++ DFN+ A+   + 
Sbjct  3427  FYGPYKDAQVVQLPIQDYIQSVNFLAWLYAAILNNCNWFIQSDKCSVEDFNVWALSNGFS  3486

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  +  L++ TG+++  + A++K  L+NG  GR I+GS   EDE TP DV +Q 
Sbjct  3487  QVKSDLV--IDALASMTGVSLETLLAAIKR-LKNGFQGRQIMGSCSFEDELTPSDVYQQL  3543

Query  301   SGVTFQ  306
             +G+  Q
Sbjct  3544  AGIKLQ  3549


> sp|P0C6U1|R1A_CVBQ Replicase polyprotein 1a OS=Bovine coronavirus 
(strain Quebec) OX=11133 GN=1a PE=3 SV=1
Length=4383

 Score =  304 bits (778),  Expect = 4e-91, Method: Compositional matrix adjust.
 Identities = 148/306 (48%), Positives = 198/306 (65%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ KVE C+V VT G  TLNGLWLDD VYCPRHVIC++ DM NP+Y +LL R
Sbjct  3247  SGIVKMVNPTSKVEPCIVSVTYGNMTLNGLWLDDKVYCPRHVICSASDMTNPDYTNLLCR  3306

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              ++ +F V    + L V+ + MQ C+L L V   N +TPKY F  ++PG+TF+VLA YNG
Sbjct  3307  VTSSDFTVLFDRLSLTVMSYQMQGCMLVLTVTLQNSRTPKYTFGVVKPGETFTVLAAYNG  3366

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   MR ++TIKGSFL GSCGSVG+ I  DCV F YMH +EL TG H GTD  G+
Sbjct  3367  KPQGAFHVTMRSSYTIKGSFLCGSCGSVGYVIMGDCVKFVYMHQLELSTGCHTGTDFNGD  3426

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D   +VN +AWLYAA++N   WF+     ++ DFN+ A+   + 
Sbjct  3427  FYGPYKDAQVVQLPVQDYIQSVNFVAWLYAAILNNCNWFVQSDKCSVEDFNVWALSNGFS  3486

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  +  L++ TG+++  + A++K  L+NG  GR I+GS   EDE TP DV +Q 
Sbjct  3487  QVKSDLV--IDALASMTGVSLETLLAAIKR-LKNGFQGRQIMGSCSFEDELTPSDVYQQL  3543

Query  301   SGVTFQ  306
             +G+  Q
Sbjct  3544  AGIKLQ  3549


> sp|P0C6X0|R1AB_CVBQ Replicase polyprotein 1ab OS=Bovine coronavirus 
(strain Quebec) OX=11133 GN=rep PE=3 SV=1
Length=7059

 Score =  303 bits (777),  Expect = 5e-91, Method: Compositional matrix adjust.
 Identities = 148/306 (48%), Positives = 198/306 (65%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ KVE C+V VT G  TLNGLWLDD VYCPRHVIC++ DM NP+Y +LL R
Sbjct  3247  SGIVKMVNPTSKVEPCIVSVTYGNMTLNGLWLDDKVYCPRHVICSASDMTNPDYTNLLCR  3306

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              ++ +F V    + L V+ + MQ C+L L V   N +TPKY F  ++PG+TF+VLA YNG
Sbjct  3307  VTSSDFTVLFDRLSLTVMSYQMQGCMLVLTVTLQNSRTPKYTFGVVKPGETFTVLAAYNG  3366

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   MR ++TIKGSFL GSCGSVG+ I  DCV F YMH +EL TG H GTD  G+
Sbjct  3367  KPQGAFHVTMRSSYTIKGSFLCGSCGSVGYVIMGDCVKFVYMHQLELSTGCHTGTDFNGD  3426

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D   +VN +AWLYAA++N   WF+     ++ DFN+ A+   + 
Sbjct  3427  FYGPYKDAQVVQLPVQDYIQSVNFVAWLYAAILNNCNWFVQSDKCSVEDFNVWALSNGFS  3486

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  +  L++ TG+++  + A++K  L+NG  GR I+GS   EDE TP DV +Q 
Sbjct  3487  QVKSDLV--IDALASMTGVSLETLLAAIKR-LKNGFQGRQIMGSCSFEDELTPSDVYQQL  3543

Query  301   SGVTFQ  306
             +G+  Q
Sbjct  3544  AGIKLQ  3549


> sp|P0C6T8|R1A_CVBEN Replicase polyprotein 1a OS=Bovine coronavirus 
(strain 98TXSF-110-ENT) OX=233262 GN=1a PE=3 SV=1
Length=4383

 Score =  303 bits (777),  Expect = 6e-91, Method: Compositional matrix adjust.
 Identities = 147/306 (48%), Positives = 198/306 (65%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ KVE C+V VT G  TLNGLWLDD VYCPRHVIC++ DM NP+Y +LL R
Sbjct  3247  SGIVKMVNPTSKVEPCIVSVTYGNMTLNGLWLDDKVYCPRHVICSASDMTNPDYTNLLCR  3306

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              ++ +F V    + L V+ + MQ C+L L V   N +TPKY F  ++PG+TF+VLA YNG
Sbjct  3307  VTSSDFTVLFDRLSLTVMSYQMQGCMLVLTVTLQNSRTPKYTFGVVKPGETFTVLAAYNG  3366

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   MR ++TIKGSFL GSCGSVG+ +  DCV F YMH +EL TG H GTD  G+
Sbjct  3367  KPQGAFHVTMRSSYTIKGSFLCGSCGSVGYVLMGDCVKFVYMHQLELSTGCHTGTDFNGD  3426

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D   +VN +AWLYAA++N   WF+     ++ DFN+ A+   + 
Sbjct  3427  FYGPYKDAQVVQLPVQDYIQSVNFVAWLYAAILNNCNWFVQSDKCSVEDFNVWALSNGFS  3486

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  +  L++ TG+++  + A++K  L+NG  GR I+GS   EDE TP DV +Q 
Sbjct  3487  QVKSDLV--IDALASMTGVSLETLLAAIKR-LKNGFQGRQIMGSCSFEDELTPSDVYQQL  3543

Query  301   SGVTFQ  306
             +G+  Q
Sbjct  3544  AGIKLQ  3549


> sp|P0C6T9|R1A_CVBLU Replicase polyprotein 1a OS=Bovine coronavirus 
(strain 98TXSF-110-LUN) OX=233264 GN=1a PE=3 SV=1
Length=4383

 Score =  303 bits (776),  Expect = 6e-91, Method: Compositional matrix adjust.
 Identities = 147/306 (48%), Positives = 198/306 (65%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ KVE C+V VT G  TLNGLWLDD VYCPRHVIC++ DM NP+Y +LL R
Sbjct  3247  SGIVKMVNPTSKVEPCIVSVTYGNMTLNGLWLDDKVYCPRHVICSASDMTNPDYTNLLCR  3306

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              ++ +F V    + L V+ + MQ C+L L V   N +TPKY F  ++PG+TF+VLA YNG
Sbjct  3307  VTSSDFTVLFDRLSLTVMSYQMQGCMLVLTVTLQNSRTPKYTFGVVKPGETFTVLAAYNG  3366

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   MR ++TIKGSFL GSCGSVG+ +  DCV F YMH +EL TG H GTD  G+
Sbjct  3367  KPQGAFHVTMRSSYTIKGSFLCGSCGSVGYVLMGDCVKFVYMHQLELSTGCHTGTDFNGD  3426

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D   +VN +AWLYAA++N   WF+     ++ DFN+ A+   + 
Sbjct  3427  FYGPYKDAQVVQLPVQDYIQSVNFVAWLYAAILNNCNWFVQSDKCSVEDFNVWALSNGFS  3486

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  +  L++ TG+++  + A++K  L+NG  GR I+GS   EDE TP DV +Q 
Sbjct  3487  QVKSDLV--IDALASMTGVSLETLLAAIKR-LKNGFQGRQIMGSCSFEDELTPSDVYQQL  3543

Query  301   SGVTFQ  306
             +G+  Q
Sbjct  3544  AGIKLQ  3549


> sp|P0C6X6|R1AB_CVHOC Replicase polyprotein 1ab OS=Human coronavirus 
OC43 OX=31631 GN=rep PE=3 SV=1
Length=7095

 Score =  303 bits (777),  Expect = 7e-91, Method: Compositional matrix adjust.
 Identities = 148/306 (48%), Positives = 198/306 (65%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ KVE C+V VT G  TLNGLWLDD VYCPRHVIC++ DM NP+Y +LL R
Sbjct  3247  SGIVKMVNPTSKVEPCVVSVTYGNMTLNGLWLDDKVYCPRHVICSASDMTNPDYTNLLCR  3306

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              ++ +F V    + L V+ + M+ C+L L V   N +TPKY F  ++PG+TF+VLA YNG
Sbjct  3307  VTSSDFTVLFDRLSLTVMSYQMRGCMLVLTVTLQNSRTPKYTFGVVKPGETFTVLAAYNG  3366

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   MR ++TIKGSFL GSCGSVG+ I  DCV F YMH +EL TG H GTD  G+
Sbjct  3367  KPQGAFHVTMRSSYTIKGSFLCGSCGSVGYVIMGDCVKFVYMHQLELSTGCHTGTDFNGD  3426

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D   +VN LAWLYAA++N   WF+     ++ DFN+ A+   + 
Sbjct  3427  FYGPYKDAQVVQLPIQDYIQSVNFLAWLYAAILNNCNWFIQSDKCSVEDFNVWALSNGFS  3486

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  +  L++ TG+++  + A++K  L+NG  GR I+GS   EDE TP DV +Q 
Sbjct  3487  QVKSDLV--IDALASMTGVSLETLLAAIKR-LKNGFQGRQIMGSCSFEDELTPSDVYQQL  3543

Query  301   SGVTFQ  306
             +G+  Q
Sbjct  3544  AGIKLQ  3549


> sp|P0C6W7|R1AB_CVBEN Replicase polyprotein 1ab OS=Bovine coronavirus 
(strain 98TXSF-110-ENT) OX=233262 GN=rep PE=3 SV=1
Length=7094

 Score =  303 bits (775),  Expect = 1e-90, Method: Compositional matrix adjust.
 Identities = 147/306 (48%), Positives = 198/306 (65%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ KVE C+V VT G  TLNGLWLDD VYCPRHVIC++ DM NP+Y +LL R
Sbjct  3247  SGIVKMVNPTSKVEPCIVSVTYGNMTLNGLWLDDKVYCPRHVICSASDMTNPDYTNLLCR  3306

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              ++ +F V    + L V+ + MQ C+L L V   N +TPKY F  ++PG+TF+VLA YNG
Sbjct  3307  VTSSDFTVLFDRLSLTVMSYQMQGCMLVLTVTLQNSRTPKYTFGVVKPGETFTVLAAYNG  3366

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   MR ++TIKGSFL GSCGSVG+ +  DCV F YMH +EL TG H GTD  G+
Sbjct  3367  KPQGAFHVTMRSSYTIKGSFLCGSCGSVGYVLMGDCVKFVYMHQLELSTGCHTGTDFNGD  3426

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D   +VN +AWLYAA++N   WF+     ++ DFN+ A+   + 
Sbjct  3427  FYGPYKDAQVVQLPVQDYIQSVNFVAWLYAAILNNCNWFVQSDKCSVEDFNVWALSNGFS  3486

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  +  L++ TG+++  + A++K  L+NG  GR I+GS   EDE TP DV +Q 
Sbjct  3487  QVKSDLV--IDALASMTGVSLETLLAAIKR-LKNGFQGRQIMGSCSFEDELTPSDVYQQL  3543

Query  301   SGVTFQ  306
             +G+  Q
Sbjct  3544  AGIKLQ  3549


> sp|P0C6W8|R1AB_CVBLU Replicase polyprotein 1ab OS=Bovine coronavirus 
(strain 98TXSF-110-LUN) OX=233264 GN=rep PE=3 SV=1
Length=7094

 Score =  303 bits (775),  Expect = 1e-90, Method: Compositional matrix adjust.
 Identities = 147/306 (48%), Positives = 198/306 (65%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ KVE C+V VT G  TLNGLWLDD VYCPRHVIC++ DM NP+Y +LL R
Sbjct  3247  SGIVKMVNPTSKVEPCIVSVTYGNMTLNGLWLDDKVYCPRHVICSASDMTNPDYTNLLCR  3306

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              ++ +F V    + L V+ + MQ C+L L V   N +TPKY F  ++PG+TF+VLA YNG
Sbjct  3307  VTSSDFTVLFDRLSLTVMSYQMQGCMLVLTVTLQNSRTPKYTFGVVKPGETFTVLAAYNG  3366

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   MR ++TIKGSFL GSCGSVG+ +  DCV F YMH +EL TG H GTD  G+
Sbjct  3367  KPQGAFHVTMRSSYTIKGSFLCGSCGSVGYVLMGDCVKFVYMHQLELSTGCHTGTDFNGD  3426

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D   +VN +AWLYAA++N   WF+     ++ DFN+ A+   + 
Sbjct  3427  FYGPYKDAQVVQLPVQDYIQSVNFVAWLYAAILNNCNWFVQSDKCSVEDFNVWALSNGFS  3486

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  +  L++ TG+++  + A++K  L+NG  GR I+GS   EDE TP DV +Q 
Sbjct  3487  QVKSDLV--IDALASMTGVSLETLLAAIKR-LKNGFQGRQIMGSCSFEDELTPSDVYQQL  3543

Query  301   SGVTFQ  306
             +G+  Q
Sbjct  3544  AGIKLQ  3549


> sp|P0C6U5|R1A_CVHN5 Replicase polyprotein 1a OS=Human coronavirus 
HKU1 (isolate N5) OX=443241 GN=1a PE=3 SV=1
Length=4421

 Score =  302 bits (774),  Expect = 1e-90, Method: Compositional matrix adjust.
 Identities = 150/306 (49%), Positives = 193/306 (63%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ K+E C+V VT G+ TLNGLWLDD VYCPRHVIC S +M  P+Y  LL R
Sbjct  3285  SGIVKMVSPTSKIEPCLVSVTYGSMTLNGLWLDDKVYCPRHVICLSSNMNEPDYSALLCR  3344

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              +  +F + +G + L V+ + MQ C L L V   NP TPKY F  ++PG+TF+VLA YNG
Sbjct  3345  VTLGDFTIMSGRMSLTVVSYQMQGCQLVLTVSLQNPYTPKYTFGVVKPGETFTVLAAYNG  3404

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   MR ++TIKGSFL GSCGSVG+ +  D V F YMH +EL TG H GTD  GN
Sbjct  3405  RPQGAFHVTMRSSYTIKGSFLCGSCGSVGYVLTGDSVKFVYMHQLELSTGCHTGTDFNGN  3464

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D   TVNV+AWLYAA++N   WF+     ++ DFN+ AM   + 
Sbjct  3465  FYGPYRDAQVVQLPVKDYVQTVNVIAWLYAAILNNCAWFVQNDVCSIEDFNVWAMTNGFS  3524

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  L  L++ TG+++  + A++K L   G  GR ILGS   EDE  P DV +Q 
Sbjct  3525  QVKADLV--LDALASMTGVSIETLLAAIKRLYM-GFQGRQILGSCTFEDELAPSDVYQQL  3581

Query  301   SGVTFQ  306
             +GV  Q
Sbjct  3582  AGVKLQ  3587


> sp|P0C6U3|R1A_CVHN1 Replicase polyprotein 1a OS=Human coronavirus 
HKU1 (isolate N1) OX=443239 GN=1a PE=1 SV=1
Length=4471

 Score =  302 bits (774),  Expect = 1e-90, Method: Compositional matrix adjust.
 Identities = 150/306 (49%), Positives = 193/306 (63%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ K+E C+V VT G+ TLNGLWLDD VYCPRHVIC+S +M  P+Y  LL R
Sbjct  3335  SGIVKMVSPTSKIEPCIVSVTYGSMTLNGLWLDDKVYCPRHVICSSSNMNEPDYSALLCR  3394

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              +  +F + +G + L V+ + MQ C L L V   NP TPKY F  ++PG+TF+VLA YNG
Sbjct  3395  VTLGDFTIMSGRMSLTVVSYQMQGCQLVLTVSLQNPYTPKYTFGNVKPGETFTVLAAYNG  3454

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   MR ++TIKGSFL GSCGSVG+ +  D V F YMH +EL TG H GTD  GN
Sbjct  3455  RPQGAFHVTMRSSYTIKGSFLCGSCGSVGYVLTGDSVKFVYMHQLELSTGCHTGTDFTGN  3514

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D   TVNV+AWLYAA++N   WF+     +  DFN+ AM   + 
Sbjct  3515  FYGPYRDAQVVQLPVKDYVQTVNVIAWLYAAILNNCAWFVQNDVCSTEDFNVWAMANGFS  3574

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  L  L++ TG+++  + A++K L   G  GR ILGS   EDE  P DV +Q 
Sbjct  3575  QVKADLV--LDALASMTGVSIETLLAAIKRLYM-GFQGRQILGSCTFEDELAPSDVYQQL  3631

Query  301   SGVTFQ  306
             +GV  Q
Sbjct  3632  AGVKLQ  3637


> sp|P0C6U4|R1A_CVHN2 Replicase polyprotein 1a OS=Human coronavirus 
HKU1 (isolate N2) OX=443240 GN=1a PE=3 SV=1
Length=4441

 Score =  302 bits (773),  Expect = 2e-90, Method: Compositional matrix adjust.
 Identities = 150/306 (49%), Positives = 193/306 (63%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ K+E C+V VT G+ TLNGLWLDD VYCPRHVIC S +M  P+Y  LL R
Sbjct  3305  SGIVKMVSPTSKIEPCIVSVTYGSMTLNGLWLDDKVYCPRHVICLSSNMNEPDYSALLCR  3364

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              +  +F + +G + L V+ + MQ C L L V   NP TPKY F  ++PG+TF+VLA YNG
Sbjct  3365  VTLGDFTIMSGRMSLTVVSYQMQGCQLVLTVSLQNPYTPKYTFGVVKPGETFTVLAAYNG  3424

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   MR ++TIKGSFL GSCGSVG+ +  D V F YMH +EL TG H GTD  GN
Sbjct  3425  RPQGAFHVTMRSSYTIKGSFLCGSCGSVGYVLTGDSVKFVYMHQLELSTGCHTGTDFTGN  3484

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D   TVNV+AWLYAA++N   WF+     ++ DFN+ AM   + 
Sbjct  3485  FYGPYRDAQVVQLPVKDYVQTVNVIAWLYAAILNNCAWFVQNDVCSIEDFNVWAMTNGFS  3544

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  L  L++ TG+++  + A++K L   G  GR ILGS   EDE  P DV +Q 
Sbjct  3545  QVKADLV--LDALASMTGVSIETLLAAIKRLYM-GFQGRQILGSCTFEDELAPSDVYQQL  3601

Query  301   SGVTFQ  306
             +GV  Q
Sbjct  3602  AGVKLQ  3607


> sp|P0C6X4|R1AB_CVHN5 Replicase polyprotein 1ab OS=Human coronavirus 
HKU1 (isolate N5) OX=443241 GN=rep PE=3 SV=1
Length=7132

 Score =  302 bits (773),  Expect = 2e-90, Method: Compositional matrix adjust.
 Identities = 150/306 (49%), Positives = 193/306 (63%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ K+E C+V VT G+ TLNGLWLDD VYCPRHVIC S +M  P+Y  LL R
Sbjct  3285  SGIVKMVSPTSKIEPCLVSVTYGSMTLNGLWLDDKVYCPRHVICLSSNMNEPDYSALLCR  3344

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              +  +F + +G + L V+ + MQ C L L V   NP TPKY F  ++PG+TF+VLA YNG
Sbjct  3345  VTLGDFTIMSGRMSLTVVSYQMQGCQLVLTVSLQNPYTPKYTFGVVKPGETFTVLAAYNG  3404

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   MR ++TIKGSFL GSCGSVG+ +  D V F YMH +EL TG H GTD  GN
Sbjct  3405  RPQGAFHVTMRSSYTIKGSFLCGSCGSVGYVLTGDSVKFVYMHQLELSTGCHTGTDFNGN  3464

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D   TVNV+AWLYAA++N   WF+     ++ DFN+ AM   + 
Sbjct  3465  FYGPYRDAQVVQLPVKDYVQTVNVIAWLYAAILNNCAWFVQNDVCSIEDFNVWAMTNGFS  3524

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  L  L++ TG+++  + A++K L   G  GR ILGS   EDE  P DV +Q 
Sbjct  3525  QVKADLV--LDALASMTGVSIETLLAAIKRLYM-GFQGRQILGSCTFEDELAPSDVYQQL  3581

Query  301   SGVTFQ  306
             +GV  Q
Sbjct  3582  AGVKLQ  3587


> sp|P0C6X2|R1AB_CVHN1 Replicase polyprotein 1ab OS=Human coronavirus 
HKU1 (isolate N1) OX=443239 GN=rep PE=3 SV=1
Length=7182

 Score =  302 bits (773),  Expect = 2e-90, Method: Compositional matrix adjust.
 Identities = 150/306 (49%), Positives = 193/306 (63%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ K+E C+V VT G+ TLNGLWLDD VYCPRHVIC+S +M  P+Y  LL R
Sbjct  3335  SGIVKMVSPTSKIEPCIVSVTYGSMTLNGLWLDDKVYCPRHVICSSSNMNEPDYSALLCR  3394

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              +  +F + +G + L V+ + MQ C L L V   NP TPKY F  ++PG+TF+VLA YNG
Sbjct  3395  VTLGDFTIMSGRMSLTVVSYQMQGCQLVLTVSLQNPYTPKYTFGNVKPGETFTVLAAYNG  3454

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   MR ++TIKGSFL GSCGSVG+ +  D V F YMH +EL TG H GTD  GN
Sbjct  3455  RPQGAFHVTMRSSYTIKGSFLCGSCGSVGYVLTGDSVKFVYMHQLELSTGCHTGTDFTGN  3514

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D   TVNV+AWLYAA++N   WF+     +  DFN+ AM   + 
Sbjct  3515  FYGPYRDAQVVQLPVKDYVQTVNVIAWLYAAILNNCAWFVQNDVCSTEDFNVWAMANGFS  3574

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  L  L++ TG+++  + A++K L   G  GR ILGS   EDE  P DV +Q 
Sbjct  3575  QVKADLV--LDALASMTGVSIETLLAAIKRLYM-GFQGRQILGSCTFEDELAPSDVYQQL  3631

Query  301   SGVTFQ  306
             +GV  Q
Sbjct  3632  AGVKLQ  3637


> sp|P0C6X3|R1AB_CVHN2 Replicase polyprotein 1ab OS=Human coronavirus 
HKU1 (isolate N2) OX=443240 GN=rep PE=3 SV=1
Length=7152

 Score =  301 bits (772),  Expect = 2e-90, Method: Compositional matrix adjust.
 Identities = 150/306 (49%), Positives = 193/306 (63%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ K+E C+V VT G+ TLNGLWLDD VYCPRHVIC S +M  P+Y  LL R
Sbjct  3305  SGIVKMVSPTSKIEPCIVSVTYGSMTLNGLWLDDKVYCPRHVICLSSNMNEPDYSALLCR  3364

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              +  +F + +G + L V+ + MQ C L L V   NP TPKY F  ++PG+TF+VLA YNG
Sbjct  3365  VTLGDFTIMSGRMSLTVVSYQMQGCQLVLTVSLQNPYTPKYTFGVVKPGETFTVLAAYNG  3424

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   MR ++TIKGSFL GSCGSVG+ +  D V F YMH +EL TG H GTD  GN
Sbjct  3425  RPQGAFHVTMRSSYTIKGSFLCGSCGSVGYVLTGDSVKFVYMHQLELSTGCHTGTDFTGN  3484

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D   TVNV+AWLYAA++N   WF+     ++ DFN+ AM   + 
Sbjct  3485  FYGPYRDAQVVQLPVKDYVQTVNVIAWLYAAILNNCAWFVQNDVCSIEDFNVWAMTNGFS  3544

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  L  L++ TG+++  + A++K L   G  GR ILGS   EDE  P DV +Q 
Sbjct  3545  QVKADLV--LDALASMTGVSIETLLAAIKRLYM-GFQGRQILGSCTFEDELAPSDVYQQL  3601

Query  301   SGVTFQ  306
             +GV  Q
Sbjct  3602  AGVKLQ  3607


> sp|P0C6U0|R1A_CVBM Replicase polyprotein 1a OS=Bovine coronavirus 
(strain Mebus) OX=11132 GN=1a PE=3 SV=1
Length=4383

 Score =  298 bits (762),  Expect = 5e-89, Method: Compositional matrix adjust.
 Identities = 146/306 (48%), Positives = 196/306 (64%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ KVE C+V VT G  TLNGLWL D VYCPRHVIC++ DM NP+Y +LL R
Sbjct  3247  SGIVKMVNPTSKVEPCIVSVTYGNMTLNGLWLGDKVYCPRHVICSASDMTNPDYTNLLCR  3306

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              ++ +F V    + L V+ + MQ C+L L V   N +TPKY F  ++PG+TF+VLA YNG
Sbjct  3307  VTSSDFTVLFDRLSLTVMSYQMQGCMLVLTVTLQNSRTPKYTFGVVKPGETFTVLAAYNG  3366

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   MR ++TIKGSFL GSCGSV + I  DCV F YMH +EL TG H GTD  G+
Sbjct  3367  KPQGAFHVTMRSSYTIKGSFLCGSCGSVVYVIMGDCVKFVYMHQLELSTGCHTGTDFNGD  3426

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D   +VN +AWLYAA++N   WF+     ++ DFN+ A+   + 
Sbjct  3427  FYGPYKDAQVVQLPVQDYIQSVNFVAWLYAAILNNCNWFVQSDKCSVEDFNVWALSNGFS  3486

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  +  L++ TG+++  + A++K  L+NG  GR I+GS   EDE TP DV +Q 
Sbjct  3487  QVKSDLV--IDALASMTGVSLETLLAAIKH-LKNGFQGRQIMGSCSFEDELTPSDVYQQL  3543

Query  301   SGVTFQ  306
             +G+  Q
Sbjct  3544  AGIKLQ  3549


> sp|P0C6W9|R1AB_CVBM Replicase polyprotein 1ab OS=Bovine coronavirus 
(strain Mebus) OX=11132 GN=rep PE=3 SV=1
Length=7094

 Score =  297 bits (761),  Expect = 8e-89, Method: Compositional matrix adjust.
 Identities = 146/306 (48%), Positives = 196/306 (64%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ KVE C+V VT G  TLNGLWL D VYCPRHVIC++ DM NP+Y +LL R
Sbjct  3247  SGIVKMVNPTSKVEPCIVSVTYGNMTLNGLWLGDKVYCPRHVICSASDMTNPDYTNLLCR  3306

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              ++ +F V    + L V+ + MQ C+L L V   N +TPKY F  ++PG+TF+VLA YNG
Sbjct  3307  VTSSDFTVLFDRLSLTVMSYQMQGCMLVLTVTLQNSRTPKYTFGVVKPGETFTVLAAYNG  3366

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   MR ++TIKGSFL GSCGSV + I  DCV F YMH +EL TG H GTD  G+
Sbjct  3367  KPQGAFHVTMRSSYTIKGSFLCGSCGSVVYVIMGDCVKFVYMHQLELSTGCHTGTDFNGD  3426

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D   +VN +AWLYAA++N   WF+     ++ DFN+ A+   + 
Sbjct  3427  FYGPYKDAQVVQLPVQDYIQSVNFVAWLYAAILNNCNWFVQSDKCSVEDFNVWALSNGFS  3486

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  +  L++ TG+++  + A++K  L+NG  GR I+GS   EDE TP DV +Q 
Sbjct  3487  QVKSDLV--IDALASMTGVSLETLLAAIKH-LKNGFQGRQIMGSCSFEDELTPSDVYQQL  3543

Query  301   SGVTFQ  306
             +G+  Q
Sbjct  3544  AGIKLQ  3549


> sp|P0C6F6|R1A_BC512 Replicase polyprotein 1a OS=Bat coronavirus 
512/2005 OX=693999 GN=1a PE=3 SV=1
Length=4128

 Score =  274 bits (700),  Expect = 1e-80, Method: Compositional matrix adjust.
 Identities = 140/307 (46%), Positives = 205/307 (67%), Gaps = 6/307 (2%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICT-SEDMLNPNYEDLLI  59
             +G RKMA PSG VEGC+V+V+ G  TLNGLWL D V CPRHVI + + ++++ ++   L+
Sbjct  3013  AGLRKMAQPSGIVEGCIVRVSYGNLTLNGLWLGDTVICPRHVIASNTTNVIDYDHAMSLV  3072

Query  60    RKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYN  119
             R   HNF + +GN+ L VI  SM+  +L +KV+ +N  TP Y +  ++PG +F++LACY+
Sbjct  3073  RL--HNFSISSGNMFLGVISASMRGTLLHIKVNQSNVNTPNYTYKVLKPGDSFNILACYD  3130

Query  120   GSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEG  179
             GS +GVY   MR N+TI+GSF++G+CGS G+NI+   V FCYMHH+EL +G H G+D++G
Sbjct  3131  GSAAGVYGVNMRTNYTIRGSFISGACGSPGYNINNGVVEFCYMHHLELGSGCHVGSDMDG  3190

Query  180   NFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNY  239
               YG + D+ T Q  G    +T NV +WLY A+INGDRW+L+  +  ++ +N  A++   
Sbjct  3191  TMYGKYEDQPTLQIEGASNLVTENVCSWLYGALINGDRWWLSSVSVGVDTYNEWALRNGM  3250

Query  240   EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQ  299
               L   +VD    L A+TG+ V  + AS+++L  N   G++ILG   L DEFT  +VV+Q
Sbjct  3251  TAL--KNVDCFSLLVAKTGVDVGRLLASIQKLHGN-FGGKSILGCTSLCDEFTLSEVVKQ  3307

Query  300   CSGVTFQ  306
               GVT Q
Sbjct  3308  MYGVTLQ  3314


> sp|P0C6W0|R1AB_BC512 Replicase polyprotein 1ab OS=Bat coronavirus 
512/2005 OX=693999 GN=rep PE=3 SV=1
Length=6793

 Score =  273 bits (699),  Expect = 1e-80, Method: Compositional matrix adjust.
 Identities = 140/307 (46%), Positives = 205/307 (67%), Gaps = 6/307 (2%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICT-SEDMLNPNYEDLLI  59
             +G RKMA PSG VEGC+V+V+ G  TLNGLWL D V CPRHVI + + ++++ ++   L+
Sbjct  3013  AGLRKMAQPSGIVEGCIVRVSYGNLTLNGLWLGDTVICPRHVIASNTTNVIDYDHAMSLV  3072

Query  60    RKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYN  119
             R   HNF + +GN+ L VI  SM+  +L +KV+ +N  TP Y +  ++PG +F++LACY+
Sbjct  3073  RL--HNFSISSGNMFLGVISASMRGTLLHIKVNQSNVNTPNYTYKVLKPGDSFNILACYD  3130

Query  120   GSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEG  179
             GS +GVY   MR N+TI+GSF++G+CGS G+NI+   V FCYMHH+EL +G H G+D++G
Sbjct  3131  GSAAGVYGVNMRTNYTIRGSFISGACGSPGYNINNGVVEFCYMHHLELGSGCHVGSDMDG  3190

Query  180   NFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNY  239
               YG + D+ T Q  G    +T NV +WLY A+INGDRW+L+  +  ++ +N  A++   
Sbjct  3191  TMYGKYEDQPTLQIEGASNLVTENVCSWLYGALINGDRWWLSSVSVGVDTYNEWALRNGM  3250

Query  240   EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQ  299
               L   +VD    L A+TG+ V  + AS+++L  N   G++ILG   L DEFT  +VV+Q
Sbjct  3251  TAL--KNVDCFSLLVAKTGVDVGRLLASIQKLHGN-FGGKSILGCTSLCDEFTLSEVVKQ  3307

Query  300   CSGVTFQ  306
               GVT Q
Sbjct  3308  MYGVTLQ  3314


> sp|P0C6V6|R1A_PEDV7 Replicase polyprotein 1a OS=Porcine epidemic 
diarrhea virus (strain CV777) OX=229032 GN=1a PE=1 SV=1
Length=4117

 Score =  264 bits (675),  Expect = 2e-77, Method: Compositional matrix adjust.
 Identities = 138/307 (45%), Positives = 198/307 (64%), Gaps = 6/307 (2%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSE-DMLNPNYEDLLI  59
             +G RKMA PSG VE C+V+V  G   LNGLWL D+V CPRHVI +S    ++ +Y   ++
Sbjct  2998  AGLRKMAQPSGVVEKCIVRVCYGNMALNGLWLGDIVMCPRHVIASSTTSTIDYDYALSVL  3057

Query  60    RKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYN  119
             R   HNF + +GNV L V+  +M+  +L++KV+  N  TPKY +  ++PG++F++LACY+
Sbjct  3058  RL--HNFSISSGNVFLGVVSATMRGALLQIKVNQNNVHTPKYTYRTVRPGESFNILACYD  3115

Query  120   GSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEG  179
             G+ +GVY   MR N+TI+GSF+NG+CGS G+NI+   V FCY+H +EL +G H G+DL+G
Sbjct  3116  GAAAGVYGVNMRSNYTIRGSFINGACGSPGYNINNGTVEFCYLHQLELGSGCHVGSDLDG  3175

Query  180   NFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNY  239
               YG + D+ T Q  G  +  T NVLA+LYAA+ING  W+L+     ++ FN  A+    
Sbjct  3176  VMYGGYEDQPTLQVEGASSLFTENVLAFLYAALINGSTWWLSSSRIAVDRFNEWAVHNGM  3235

Query  240   EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQ  299
                T  + D    L+A+TG+ V  + AS++ L +N   G+ ILG   L DEFT  +VVRQ
Sbjct  3236  T--TVGNTDCFSILAAKTGVDVQRLLASIQSLHKN-FGGKQILGHTSLTDEFTTGEVVRQ  3292

Query  300   CSGVTFQ  306
               GV  Q
Sbjct  3293  MYGVNLQ  3299


> sp|P0C6Y4|R1AB_PEDV7 Replicase polyprotein 1ab OS=Porcine epidemic 
diarrhea virus (strain CV777) OX=229032 GN=rep PE=1 SV=1
Length=6781

 Score =  263 bits (672),  Expect = 5e-77, Method: Compositional matrix adjust.
 Identities = 138/307 (45%), Positives = 198/307 (64%), Gaps = 6/307 (2%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSE-DMLNPNYEDLLI  59
             +G RKMA PSG VE C+V+V  G   LNGLWL D+V CPRHVI +S    ++ +Y   ++
Sbjct  2998  AGLRKMAQPSGVVEKCIVRVCYGNMALNGLWLGDIVMCPRHVIASSTTSTIDYDYALSVL  3057

Query  60    RKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYN  119
             R   HNF + +GNV L V+  +M+  +L++KV+  N  TPKY +  ++PG++F++LACY+
Sbjct  3058  RL--HNFSISSGNVFLGVVSATMRGALLQIKVNQNNVHTPKYTYRTVRPGESFNILACYD  3115

Query  120   GSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEG  179
             G+ +GVY   MR N+TI+GSF+NG+CGS G+NI+   V FCY+H +EL +G H G+DL+G
Sbjct  3116  GAAAGVYGVNMRSNYTIRGSFINGACGSPGYNINNGTVEFCYLHQLELGSGCHVGSDLDG  3175

Query  180   NFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNY  239
               YG + D+ T Q  G  +  T NVLA+LYAA+ING  W+L+     ++ FN  A+    
Sbjct  3176  VMYGGYEDQPTLQVEGASSLFTENVLAFLYAALINGSTWWLSSSRIAVDRFNEWAVHNGM  3235

Query  240   EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQ  299
                T  + D    L+A+TG+ V  + AS++ L +N   G+ ILG   L DEFT  +VVRQ
Sbjct  3236  T--TVGNTDCFSILAAKTGVDVQRLLASIQSLHKN-FGGKQILGHTSLTDEFTTGEVVRQ  3292

Query  300   CSGVTFQ  306
               GV  Q
Sbjct  3293  MYGVNLQ  3299


> sp|Q98VG9|R1AB_FIPV Replicase polyprotein 1ab OS=Feline coronavirus 
(strain FIPV WSU-79/1146) OX=33734 GN=rep PE=1 SV=2
Length=6709

 Score =  254 bits (648),  Expect = 8e-74, Method: Compositional matrix adjust.
 Identities = 135/306 (44%), Positives = 183/306 (60%), Gaps = 4/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG RKMA PSG VE C+V+V  G   LNGLWL D V CPRHVI +    +  NYE+ L  
Sbjct  2904  SGLRKMAQPSGVVEPCIVRVAYGNNVLNGLWLGDEVICPRHVIASDTSRV-INYENELSS  2962

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
                HNF +   N  L V+    +   L LKV+  NP TP++KF  ++PG++F++LACY G
Sbjct  2963  VRLHNFSIAKNNAFLGVVSAKYKGVNLVLKVNQVNPNTPEHKFKSVRPGESFNILACYEG  3022

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P  VY   MR   TIKGSF+ G+CGSVG+ ++   + F YMHH+EL  G H G++LEG 
Sbjct  3023  CPGSVYGVNMRSQGTIKGSFIAGTCGSVGYVLENGTLYFVYMHHLELGNGSHVGSNLEGE  3082

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
              YG + D+ + Q  GT+   + NV+A+LYAA+ING+RWF+   + TL  +N  A   ++ 
Sbjct  3083  MYGGYEDQPSMQLEGTNVMSSDNVVAFLYAALINGERWFVTNTSMTLESYNAWAKTNSFT  3142

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +     D    L+A+TG +V  +   +   L  G  GRTIL    L DEFTP +V+RQ 
Sbjct  3143  EIVS--TDAFNMLAAKTGYSVEKLLECIVR-LNKGFGGRTILSYGSLCDEFTPTEVIRQM  3199

Query  301   SGVTFQ  306
              GV  Q
Sbjct  3200  YGVNLQ  3205


> sp|P0C6V2|R1A_CVPPU Replicase polyprotein 1a OS=Porcine transmissible 
gastroenteritis coronavirus (strain Purdue) OX=11151 
GN=1a PE=1 SV=1
Length=4017

 Score =  254 bits (648),  Expect = 9e-74, Method: Compositional matrix adjust.
 Identities = 137/306 (45%), Positives = 185/306 (60%), Gaps = 4/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG RKMA PSG VE C+V+V+ G   LNGLWL D V CPRHVI  S+     NYE+ +  
Sbjct  2879  SGLRKMAQPSGLVEPCIVRVSYGNNVLNGLWLGDEVICPRHVI-ASDTTRVINYENEMSS  2937

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
                HNF V   NV L V+    +   L LKV+  NP TP++KF  I+ G++F++LACY G
Sbjct  2938  VRLHNFSVSKNNVFLGVVSARYKGVNLVLKVNQVNPNTPEHKFKSIKAGESFNILACYEG  2997

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P  VY   MR   TIKGSF+ G+CGSVG+ ++   + F YMHH+EL  G H G++ EG 
Sbjct  2998  CPGSVYGVNMRSQGTIKGSFIAGTCGSVGYVLENGILYFVYMHHLELGNGSHVGSNFEGE  3057

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
              YG + D+ + Q  GT+   + NV+A+LYAA+ING+RWF+   + +L  +N  A   ++ 
Sbjct  3058  MYGGYEDQPSMQLEGTNVMSSDNVVAFLYAALINGERWFVTNTSMSLESYNTWAKTNSFT  3117

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              L+    D    L+A+TG +V  +  S+   L  G  GRTIL    L DEFTP +V+RQ 
Sbjct  3118  ELSS--TDAFSMLAAKTGQSVEKLLDSIVR-LNKGFGGRTILSYGSLCDEFTPTEVIRQM  3174

Query  301   SGVTFQ  306
              GV  Q
Sbjct  3175  YGVNLQ  3180


> sp|P0C6Y5|R1AB_CVPPU Replicase polyprotein 1ab OS=Porcine transmissible 
gastroenteritis coronavirus (strain Purdue) OX=11151 
GN=rep PE=1 SV=1
Length=6684

 Score =  253 bits (647),  Expect = 1e-73, Method: Compositional matrix adjust.
 Identities = 137/306 (45%), Positives = 185/306 (60%), Gaps = 4/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG RKMA PSG VE C+V+V+ G   LNGLWL D V CPRHVI  S+     NYE+ +  
Sbjct  2879  SGLRKMAQPSGLVEPCIVRVSYGNNVLNGLWLGDEVICPRHVI-ASDTTRVINYENEMSS  2937

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
                HNF V   NV L V+    +   L LKV+  NP TP++KF  I+ G++F++LACY G
Sbjct  2938  VRLHNFSVSKNNVFLGVVSARYKGVNLVLKVNQVNPNTPEHKFKSIKAGESFNILACYEG  2997

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P  VY   MR   TIKGSF+ G+CGSVG+ ++   + F YMHH+EL  G H G++ EG 
Sbjct  2998  CPGSVYGVNMRSQGTIKGSFIAGTCGSVGYVLENGILYFVYMHHLELGNGSHVGSNFEGE  3057

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
              YG + D+ + Q  GT+   + NV+A+LYAA+ING+RWF+   + +L  +N  A   ++ 
Sbjct  3058  MYGGYEDQPSMQLEGTNVMSSDNVVAFLYAALINGERWFVTNTSMSLESYNTWAKTNSFT  3117

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              L+    D    L+A+TG +V  +  S+   L  G  GRTIL    L DEFTP +V+RQ 
Sbjct  3118  ELSS--TDAFSMLAAKTGQSVEKLLDSIVR-LNKGFGGRTILSYGSLCDEFTPTEVIRQM  3174

Query  301   SGVTFQ  306
              GV  Q
Sbjct  3175  YGVNLQ  3180


> sp|P0C6U6|R1A_CVHNL Replicase polyprotein 1a OS=Human coronavirus 
NL63 OX=277944 GN=1a PE=1 SV=1
Length=4060

 Score =  250 bits (639),  Expect = 1e-72, Method: Compositional matrix adjust.
 Identities = 136/307 (44%), Positives = 192/307 (63%), Gaps = 5/307 (2%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG +KMA PSG VE C+V+V  G+T LNG+WL D V CPRHVI  S  +L  +Y+     
Sbjct  2940  SGLKKMAQPSGCVERCVVRVCYGSTVLNGVWLGDTVTCPRHVIAPSTTVL-IDYDHAYST  2998

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
                HNF V    V L V+G +M   VL++KV  +N  TPK+ F  ++PG +F++LACY G
Sbjct  2999  MRLHNFSVSHNGVFLGVVGVTMHGSVLRIKVSQSNVHTPKHVFKTLKPGDSFNILACYEG  3058

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYD-CVSFCYMHHMELPTGVHAGTDLEG  179
               SGV+   +R NFTIKGSF+NG+CGS G+N+  D  V FCY+H +EL +G H G+D  G
Sbjct  3059  IASGVFGVNLRTNFTIKGSFINGACGSPGYNVRNDGTVEFCYLHQIELGSGAHVGSDFTG  3118

Query  180   NFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNY  239
             + YG F D+ + Q    +  ++ NV+A+LYAA++NG RW+L      ++ FN  AM   Y
Sbjct  3119  SVYGNFDDQPSLQVESANLMLSDNVVAFLYAALLNGCRWWLCSTRVNVDGFNEWAMANGY  3178

Query  240   EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQ  299
               ++   V+    L+A+TG++V  + AS++  L  G  G+ ILG + L DEFT  +VV+Q
Sbjct  3179  TSVSS--VECYSILAAKTGVSVEQLLASIQH-LHEGFGGKNILGYSSLCDEFTLAEVVKQ  3235

Query  300   CSGVTFQ  306
               GV  Q
Sbjct  3236  MYGVNLQ  3242


> sp|P0C6X5|R1AB_CVHNL Replicase polyprotein 1ab OS=Human coronavirus 
NL63 OX=277944 GN=rep PE=1 SV=1
Length=6729

 Score =  250 bits (639),  Expect = 1e-72, Method: Compositional matrix adjust.
 Identities = 136/307 (44%), Positives = 192/307 (63%), Gaps = 5/307 (2%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG +KMA PSG VE C+V+V  G+T LNG+WL D V CPRHVI  S  +L  +Y+     
Sbjct  2940  SGLKKMAQPSGCVERCVVRVCYGSTVLNGVWLGDTVTCPRHVIAPSTTVL-IDYDHAYST  2998

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
                HNF V    V L V+G +M   VL++KV  +N  TPK+ F  ++PG +F++LACY G
Sbjct  2999  MRLHNFSVSHNGVFLGVVGVTMHGSVLRIKVSQSNVHTPKHVFKTLKPGDSFNILACYEG  3058

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYD-CVSFCYMHHMELPTGVHAGTDLEG  179
               SGV+   +R NFTIKGSF+NG+CGS G+N+  D  V FCY+H +EL +G H G+D  G
Sbjct  3059  IASGVFGVNLRTNFTIKGSFINGACGSPGYNVRNDGTVEFCYLHQIELGSGAHVGSDFTG  3118

Query  180   NFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNY  239
             + YG F D+ + Q    +  ++ NV+A+LYAA++NG RW+L      ++ FN  AM   Y
Sbjct  3119  SVYGNFDDQPSLQVESANLMLSDNVVAFLYAALLNGCRWWLCSTRVNVDGFNEWAMANGY  3178

Query  240   EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQ  299
               ++   V+    L+A+TG++V  + AS++  L  G  G+ ILG + L DEFT  +VV+Q
Sbjct  3179  TSVSS--VECYSILAAKTGVSVEQLLASIQH-LHEGFGGKNILGYSSLCDEFTLAEVVKQ  3235

Query  300   CSGVTFQ  306
               GV  Q
Sbjct  3236  MYGVNLQ  3242


> sp|P0C6U2|R1A_CVH22 Replicase polyprotein 1a OS=Human coronavirus 
229E OX=11137 GN=1a PE=1 SV=1
Length=4085

 Score =  239 bits (611),  Expect = 7e-69, Method: Compositional matrix adjust.
 Identities = 126/307 (41%), Positives = 188/307 (61%), Gaps = 6/307 (2%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICT-SEDMLNPNYEDLLI  59
             +G RKMA PSG VE C+V+V  G T LNGLWL D+VYCPRHVI + +   ++ ++E  ++
Sbjct  2966  AGLRKMAQPSGFVEKCVVRVCYGNTVLNGLWLGDIVYCPRHVIASNTTSAIDYDHEYSIM  3025

Query  60    RKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYN  119
             R   HNF + +G   L V+G +M    LK+KV   N  TP++ F  ++ G+ F++LACY+
Sbjct  3026  RL--HNFSIISGTAFLGVVGATMHGVTLKIKVSQTNMHTPRHSFRTLKSGEGFNILACYD  3083

Query  120   GSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEG  179
             G   GV+   MR N+TI+GSF+NG+CGS G+N+    V F YMH +EL +G H G+  +G
Sbjct  3084  GCAQGVFGVNMRTNWTIRGSFINGACGSPGYNLKNGEVEFVYMHQIELGSGSHVGSSFDG  3143

Query  180   NFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNY  239
               YG F D+   Q    +  +TVNV+A+LYAA++NG  W+L      +  +N  A    +
Sbjct  3144  VMYGGFEDQPNLQVESANQMLTVNVVAFLYAAILNGCTWWLKGEKLFVEHYNEWAQANGF  3203

Query  240   EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQ  299
               +  +  D    L+A+TG+ V  +  ++ ++L NG  G+ ILG + L DEF+  +VV+Q
Sbjct  3204  TAMNGE--DAFSILAAKTGVCVERLLHAI-QVLNNGFGGKQILGYSSLNDEFSINEVVKQ  3260

Query  300   CSGVTFQ  306
               GV  Q
Sbjct  3261  MFGVNLQ  3267


> sp|P0C6X1|R1AB_CVH22 Replicase polyprotein 1ab OS=Human coronavirus 
229E OX=11137 GN=rep PE=1 SV=1
Length=6758

 Score =  238 bits (608),  Expect = 2e-68, Method: Compositional matrix adjust.
 Identities = 126/307 (41%), Positives = 188/307 (61%), Gaps = 6/307 (2%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICT-SEDMLNPNYEDLLI  59
             +G RKMA PSG VE C+V+V  G T LNGLWL D+VYCPRHVI + +   ++ ++E  ++
Sbjct  2966  AGLRKMAQPSGFVEKCVVRVCYGNTVLNGLWLGDIVYCPRHVIASNTTSAIDYDHEYSIM  3025

Query  60    RKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYN  119
             R   HNF + +G   L V+G +M    LK+KV   N  TP++ F  ++ G+ F++LACY+
Sbjct  3026  RL--HNFSIISGTAFLGVVGATMHGVTLKIKVSQTNMHTPRHSFRTLKSGEGFNILACYD  3083

Query  120   GSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEG  179
             G   GV+   MR N+TI+GSF+NG+CGS G+N+    V F YMH +EL +G H G+  +G
Sbjct  3084  GCAQGVFGVNMRTNWTIRGSFINGACGSPGYNLKNGEVEFVYMHQIELGSGSHVGSSFDG  3143

Query  180   NFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNY  239
               YG F D+   Q    +  +TVNV+A+LYAA++NG  W+L      +  +N  A    +
Sbjct  3144  VMYGGFEDQPNLQVESANQMLTVNVVAFLYAAILNGCTWWLKGEKLFVEHYNEWAQANGF  3203

Query  240   EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQ  299
               +  +  D    L+A+TG+ V  +  ++ ++L NG  G+ ILG + L DEF+  +VV+Q
Sbjct  3204  TAMNGE--DAFSILAAKTGVCVERLLHAI-QVLNNGFGGKQILGYSSLNDEFSINEVVKQ  3260

Query  300   CSGVTFQ  306
               GV  Q
Sbjct  3261  MFGVNLQ  3267


> sp|P0C6V4|R1A_IBVBC Replicase polyprotein 1a OS=Avian infectious 
bronchitis virus (strain Beaudette CK) OX=160235 GN=1a PE=3 
SV=1
Length=3951

 Score =  228 bits (581),  Expect = 7e-65, Method: Compositional matrix adjust.
 Identities = 131/317 (41%), Positives = 179/317 (56%), Gaps = 21/317 (7%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICT-SEDMLNPNYEDLLI  59
             SGF+K+  PS  VE C+V V+     LNGLWL D +YCPRHV+   S D  N    D+L 
Sbjct  2780  SGFKKLVSPSSAVEKCIVSVSYRGNNLNGLWLGDTIYCPRHVLGKFSGDQWN----DVLN  2835

Query  60    RKSNHNFLVQAGN-VQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACY  118
               +NH F V   + V L V+   ++  VL L+   AN +TPKYKF++   G +F++   Y
Sbjct  2836  LANNHEFEVTTQHGVTLNVVSRRLKGAVLILQTAVANAETPKYKFIKANCGDSFTIACAY  2895

Query  119   NGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLE  178
              G+  G+Y   MR N TI+ SFL G+CGSVGFNI+   V+F YMHH+ELP  +H GTDL 
Sbjct  2896  GGTVVGLYPVTMRSNGTIRASFLAGACGSVGFNIEKGVVNFFYMHHLELPNALHTGTDLM  2955

Query  179   GNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGD-------RWFLNRFTTTLNDFN  231
             G FYG +VD + AQ    D  +T N++AWLYAA+I+         +W L   T +++D+N
Sbjct  2956  GEFYGGYVDEEVAQRVPPDNLVTNNIVAWLYAAIISVKESSFSLPKW-LESTTVSVDDYN  3014

Query  232   LVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELL--QNGMNGRTILGSALLED  289
               A    + P +      +  LSA TG+   D+C  L+ ++   +   G  ILG    ED
Sbjct  3015  KWAGDNGFTPFSTSTA--ITKLSAITGV---DVCKLLRTIMVKNSQWGGDPILGQYNFED  3069

Query  290   EFTPFDVVRQCSGVTFQ  306
             E TP  V  Q  GV  Q
Sbjct  3070  ELTPESVFNQIGGVRLQ  3086


> sp|P0C6V3|R1A_IBVB Replicase polyprotein 1a OS=Avian infectious 
bronchitis virus (strain Beaudette) OX=11122 GN=1a PE=1 SV=1
Length=3951

 Score =  228 bits (581),  Expect = 7e-65, Method: Compositional matrix adjust.
 Identities = 131/317 (41%), Positives = 179/317 (56%), Gaps = 21/317 (7%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICT-SEDMLNPNYEDLLI  59
             SGF+K+  PS  VE C+V V+     LNGLWL D +YCPRHV+   S D  N    D+L 
Sbjct  2780  SGFKKLVSPSSAVEKCIVSVSYRGNNLNGLWLGDTIYCPRHVLGKFSGDQWN----DVLN  2835

Query  60    RKSNHNFLVQAGN-VQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACY  118
               +NH F V   + V L V+   ++  VL L+   AN +TPKYKF++   G +F++   Y
Sbjct  2836  LANNHEFEVTTQHGVTLNVVSRRLKGAVLILQTAVANAETPKYKFIKANCGDSFTIACAY  2895

Query  119   NGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLE  178
              G+  G+Y   MR N TI+ SFL G+CGSVGFNI+   V+F YMHH+ELP  +H GTDL 
Sbjct  2896  GGTVVGLYPVTMRSNGTIRASFLAGACGSVGFNIEKGVVNFFYMHHLELPNALHTGTDLM  2955

Query  179   GNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGD-------RWFLNRFTTTLNDFN  231
             G FYG +VD + AQ    D  +T N++AWLYAA+I+         +W L   T +++D+N
Sbjct  2956  GEFYGGYVDEEVAQRVPPDNLVTNNIVAWLYAAIISVKESSFSLPKW-LESTTVSVDDYN  3014

Query  232   LVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELL--QNGMNGRTILGSALLED  289
               A    + P +      +  LSA TG+   D+C  L+ ++   +   G  ILG    ED
Sbjct  3015  KWAGDNGFTPFSTSTA--ITKLSAITGV---DVCKLLRTIMVKNSQWGGDPILGQYNFED  3069

Query  290   EFTPFDVVRQCSGVTFQ  306
             E TP  V  Q  GV  Q
Sbjct  3070  ELTPESVFNQIGGVRLQ  3086


> sp|P0C6Y2|R1AB_IBVBC Replicase polyprotein 1ab OS=Avian infectious 
bronchitis virus (strain Beaudette CK) OX=160235 GN=rep 
PE=3 SV=1
Length=6629

 Score =  227 bits (579),  Expect = 1e-64, Method: Compositional matrix adjust.
 Identities = 131/317 (41%), Positives = 179/317 (56%), Gaps = 21/317 (7%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICT-SEDMLNPNYEDLLI  59
             SGF+K+  PS  VE C+V V+     LNGLWL D +YCPRHV+   S D  N    D+L 
Sbjct  2780  SGFKKLVSPSSAVEKCIVSVSYRGNNLNGLWLGDTIYCPRHVLGKFSGDQWN----DVLN  2835

Query  60    RKSNHNFLVQAGN-VQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACY  118
               +NH F V   + V L V+   ++  VL L+   AN +TPKYKF++   G +F++   Y
Sbjct  2836  LANNHEFEVTTQHGVTLNVVSRRLKGAVLILQTAVANAETPKYKFIKANCGDSFTIACAY  2895

Query  119   NGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLE  178
              G+  G+Y   MR N TI+ SFL G+CGSVGFNI+   V+F YMHH+ELP  +H GTDL 
Sbjct  2896  GGTVVGLYPVTMRSNGTIRASFLAGACGSVGFNIEKGVVNFFYMHHLELPNALHTGTDLM  2955

Query  179   GNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGD-------RWFLNRFTTTLNDFN  231
             G FYG +VD + AQ    D  +T N++AWLYAA+I+         +W L   T +++D+N
Sbjct  2956  GEFYGGYVDEEVAQRVPPDNLVTNNIVAWLYAAIISVKESSFSLPKW-LESTTVSVDDYN  3014

Query  232   LVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELL--QNGMNGRTILGSALLED  289
               A    + P +      +  LSA TG+   D+C  L+ ++   +   G  ILG    ED
Sbjct  3015  KWAGDNGFTPFSTSTA--ITKLSAITGV---DVCKLLRTIMVKNSQWGGDPILGQYNFED  3069

Query  290   EFTPFDVVRQCSGVTFQ  306
             E TP  V  Q  GV  Q
Sbjct  3070  ELTPESVFNQIGGVRLQ  3086


> sp|P0C6Y1|R1AB_IBVB Replicase polyprotein 1ab OS=Avian infectious 
bronchitis virus (strain Beaudette) OX=11122 GN=rep PE=1 
SV=1
Length=6629

 Score =  227 bits (579),  Expect = 1e-64, Method: Compositional matrix adjust.
 Identities = 131/317 (41%), Positives = 179/317 (56%), Gaps = 21/317 (7%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICT-SEDMLNPNYEDLLI  59
             SGF+K+  PS  VE C+V V+     LNGLWL D +YCPRHV+   S D  N    D+L 
Sbjct  2780  SGFKKLVSPSSAVEKCIVSVSYRGNNLNGLWLGDTIYCPRHVLGKFSGDQWN----DVLN  2835

Query  60    RKSNHNFLVQAGN-VQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACY  118
               +NH F V   + V L V+   ++  VL L+   AN +TPKYKF++   G +F++   Y
Sbjct  2836  LANNHEFEVTTQHGVTLNVVSRRLKGAVLILQTAVANAETPKYKFIKANCGDSFTIACAY  2895

Query  119   NGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLE  178
              G+  G+Y   MR N TI+ SFL G+CGSVGFNI+   V+F YMHH+ELP  +H GTDL 
Sbjct  2896  GGTVVGLYPVTMRSNGTIRASFLAGACGSVGFNIEKGVVNFFYMHHLELPNALHTGTDLM  2955

Query  179   GNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGD-------RWFLNRFTTTLNDFN  231
             G FYG +VD + AQ    D  +T N++AWLYAA+I+         +W L   T +++D+N
Sbjct  2956  GEFYGGYVDEEVAQRVPPDNLVTNNIVAWLYAAIISVKESSFSLPKW-LESTTVSVDDYN  3014

Query  232   LVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELL--QNGMNGRTILGSALLED  289
               A    + P +      +  LSA TG+   D+C  L+ ++   +   G  ILG    ED
Sbjct  3015  KWAGDNGFTPFSTSTA--ITKLSAITGV---DVCKLLRTIMVKNSQWGGDPILGQYNFED  3069

Query  290   EFTPFDVVRQCSGVTFQ  306
             E TP  V  Q  GV  Q
Sbjct  3070  ELTPESVFNQIGGVRLQ  3086


> sp|P0C6V5|R1A_IBVM Replicase polyprotein 1a OS=Avian infectious 
bronchitis virus (strain M41) OX=11127 GN=1a PE=1 SV=1
Length=3953

 Score =  225 bits (574),  Expect = 5e-64, Method: Compositional matrix adjust.
 Identities = 128/316 (41%), Positives = 175/316 (55%), Gaps = 19/316 (6%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             +GF+K+  PS  VE C+V V+     LNGLWL D +YCPRHV+          + D+L  
Sbjct  2782  AGFKKLVSPSSAVEKCIVSVSYRGNNLNGLWLGDSIYCPRHVL---GKFSGDQWGDVLNL  2838

Query  61    KSNHNFLVQAGN-VQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYN  119
              +NH F V   N V L V+   ++  VL L+   AN +TPKYKFV+   G +F++   Y 
Sbjct  2839  ANNHEFEVVTQNGVTLNVVSRRLKGAVLILQTAVANAETPKYKFVKANCGDSFTIACSYG  2898

Query  120   GSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEG  179
             G+  G+Y   MR N TI+ SFL G+CGSVGFNI+   V+F YMHH+ELP  +H GTDL G
Sbjct  2899  GTVIGLYPVTMRSNGTIRASFLAGACGSVGFNIEKGVVNFFYMHHLELPNALHTGTDLMG  2958

Query  180   NFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGD-------RWFLNRFTTTLNDFNL  232
              FYG +VD + AQ    D  +T N++AWLYAA+I+         +W L   T ++ D+N 
Sbjct  2959  EFYGGYVDEEVAQRVPPDNLVTNNIVAWLYAAIISVKESSFSQPKW-LESTTVSIEDYNR  3017

Query  233   VAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRT--ILGSALLEDE  290
              A    + P +      +  LSA TG+   D+C  L+ ++       +  ILG    EDE
Sbjct  3018  WASDNGFTPFSTSTA--ITKLSAITGV---DVCKLLRTIMVKSAQWGSDPILGQYNFEDE  3072

Query  291   FTPFDVVRQCSGVTFQ  306
              TP  V  Q  GV  Q
Sbjct  3073  LTPESVFNQVGGVRLQ  3088


> sp|P0C6Y3|R1AB_IBVM Replicase polyprotein 1ab OS=Avian infectious 
bronchitis virus (strain M41) OX=11127 GN=rep PE=1 SV=1
Length=6631

 Score =  224 bits (572),  Expect = 1e-63, Method: Compositional matrix adjust.
 Identities = 128/316 (41%), Positives = 174/316 (55%), Gaps = 19/316 (6%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             +GF+K+  PS  VE C+V V+     LNGLWL D +YCPRHV+          + D+L  
Sbjct  2782  AGFKKLVSPSSAVEKCIVSVSYRGNNLNGLWLGDSIYCPRHVL---GKFSGDQWGDVLNL  2838

Query  61    KSNHNFLVQAGN-VQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYN  119
              +NH F V   N V L V+   ++  VL L+   AN +TPKYKFV+   G +F++   Y 
Sbjct  2839  ANNHEFEVVTQNGVTLNVVSRRLKGAVLILQTAVANAETPKYKFVKANCGDSFTIACSYG  2898

Query  120   GSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEG  179
             G+  G+Y   MR N TI+ SFL G+CGSVGFNI+   V+F YMHH+ELP  +H GTDL G
Sbjct  2899  GTVIGLYPVTMRSNGTIRASFLAGACGSVGFNIEKGVVNFFYMHHLELPNALHTGTDLMG  2958

Query  180   NFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVI-------NGDRWFLNRFTTTLNDFNL  232
              FYG +VD + AQ    D  +T N++AWLYAA+I       +  +W L   T ++ D+N 
Sbjct  2959  EFYGGYVDEEVAQRVPPDNLVTNNIVAWLYAAIISVKESSFSQPKW-LESTTVSIEDYNR  3017

Query  233   VAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMN--GRTILGSALLEDE  290
              A    + P +      +  LSA TG+   D+C  L+ ++          ILG    EDE
Sbjct  3018  WASDNGFTPFSTSTA--ITKLSAITGV---DVCKLLRTIMVKSAQWGSDPILGQYNFEDE  3072

Query  291   FTPFDVVRQCSGVTFQ  306
              TP  V  Q  GV  Q
Sbjct  3073  LTPESVFNQVGGVRLQ  3088


> sp|Q6AE15|HIS4_LEIXX 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] 
imidazole-4-carboxamide isomerase OS=Leifsonia 
xyli subsp. xyli (strain CTCB07) OX=281090 GN=hisA 
PE=3 SV=1
Length=248

 Score = 33.1 bits (74),  Expect = 2.6, Method: Compositional matrix adjust.
 Identities = 19/41 (46%), Positives = 25/41 (61%), Gaps = 1/41 (2%)

Query  252  PLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFT  292
            P+ A  GIA LD  A+L+EL+  G+ G  I+G AL    FT
Sbjct  199  PVVASGGIASLDDIAALRELVSLGVEG-AIVGKALYSGAFT  238



Lambda      K        H        a         alpha
   0.323    0.138    0.433    0.792     4.96 

Gapped
Lambda      K        H        a         alpha    sigma
   0.267   0.0410    0.140     1.90     42.6     43.6 

Effective search space used: 25877591208
Results from round 2


Query= YP_009725301.1 3C-like proteinase [Severe acute respiratory syndrome
coronavirus 2]

Length=306
                                                                      Score     E
Sequences producing significant alignments:                          (Bits)  Value
Sequences used in model and found again:

  sp|P0C6V9|R1AB_BC279 Replicase polyprotein 1ab OS=Bat coronavir...   485    3e-154
  sp|P0C6F5|R1A_BC279 Replicase polyprotein 1a OS=Bat coronavirus...   485    3e-154
  sp|P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab OS=Severe acute ...   485    5e-154
  sp|P0DTC1|R1A_SARS2 Replicase polyprotein 1a OS=Severe acute re...   484    7e-154
  sp|P0C6X7|R1AB_CVHSA Replicase polyprotein 1ab OS=Human SARS co...   484    1e-153
  sp|P0C6U8|R1A_CVHSA Replicase polyprotein 1a OS=Human SARS coro...   483    2e-153
  sp|P0C6W2|R1AB_BCHK3 Replicase polyprotein 1ab OS=Bat coronavir...   482    5e-153
  sp|P0C6F8|R1A_BCHK3 Replicase polyprotein 1a OS=Bat coronavirus...   481    8e-153
  sp|P0C6W6|R1AB_BCRP3 Replicase polyprotein 1ab OS=Bat coronavir...   480    2e-152
  sp|P0C6T7|R1A_BCRP3 Replicase polyprotein 1a OS=Bat coronavirus...   480    2e-152
  sp|P0C6X8|R1AB_CVM2 Replicase polyprotein 1ab OS=Murine coronav...   470    5e-149
  sp|P0C6Y0|R1AB_CVMJH Replicase polyprotein 1ab OS=Murine corona...   470    7e-149
  sp|P0C6U9|R1A_CVM2 Replicase polyprotein 1a OS=Murine coronavir...   470    8e-149
  sp|P0C6V1|R1A_CVMJH Replicase polyprotein 1a OS=Murine coronavi...   469    1e-148
  sp|P0C6T8|R1A_CVBEN Replicase polyprotein 1a OS=Bovine coronavi...   469    2e-148
  sp|P0C6X0|R1AB_CVBQ Replicase polyprotein 1ab OS=Bovine coronav...   469    2e-148
  sp|P0C6T9|R1A_CVBLU Replicase polyprotein 1a OS=Bovine coronavi...   469    2e-148
  sp|P0C6U1|R1A_CVBQ Replicase polyprotein 1a OS=Bovine coronavir...   469    2e-148
  sp|P0C6W8|R1AB_CVBLU Replicase polyprotein 1ab OS=Bovine corona...   469    2e-148
  sp|P0C6W7|R1AB_CVBEN Replicase polyprotein 1ab OS=Bovine corona...   469    2e-148
  sp|P0C6U7|R1A_CVHOC Replicase polyprotein 1a OS=Human coronavir...   467    4e-148
  sp|P0C6X6|R1AB_CVHOC Replicase polyprotein 1ab OS=Human coronav...   468    5e-148
  sp|K9N638|R1A_MERS1 Replicase polyprotein 1a OS=Middle East res...   465    2e-147
  sp|K9N7C7|R1AB_MERS1 Replicase polyprotein 1ab OS=Middle East r...   465    3e-147
  sp|P0C6X9|R1AB_CVMA5 Replicase polyprotein 1ab OS=Murine corona...   465    4e-147
  sp|P0C6V0|R1A_CVMA5 Replicase polyprotein 1a OS=Murine coronavi...   464    7e-147
  sp|P0C6W9|R1AB_CVBM Replicase polyprotein 1ab OS=Bovine coronav...   464    8e-147
  sp|P0C6U0|R1A_CVBM Replicase polyprotein 1a OS=Bovine coronavir...   464    8e-147
  sp|P0C6W3|R1AB_BCHK4 Replicase polyprotein 1ab OS=Bat coronavir...   464    1e-146
  sp|P0C6W4|R1AB_BCHK5 Replicase polyprotein 1ab OS=Bat coronavir...   464    1e-146
  sp|P0C6X3|R1AB_CVHN2 Replicase polyprotein 1ab OS=Human coronav...   464    1e-146
  sp|P0C6X4|R1AB_CVHN5 Replicase polyprotein 1ab OS=Human coronav...   464    1e-146
  sp|P0C6U4|R1A_CVHN2 Replicase polyprotein 1a OS=Human coronavir...   463    1e-146
  sp|P0C6T4|R1A_BCHK4 Replicase polyprotein 1a OS=Bat coronavirus...   463    1e-146
  sp|P0C6U5|R1A_CVHN5 Replicase polyprotein 1a OS=Human coronavir...   463    1e-146
  sp|P0C6W1|R1AB_BC133 Replicase polyprotein 1ab OS=Bat coronavir...   463    2e-146
  sp|P0C6T5|R1A_BCHK5 Replicase polyprotein 1a OS=Bat coronavirus...   463    2e-146
  sp|P0C6X2|R1AB_CVHN1 Replicase polyprotein 1ab OS=Human coronav...   463    2e-146
  sp|P0C6U3|R1A_CVHN1 Replicase polyprotein 1a OS=Human coronavir...   462    2e-146
  sp|P0C6F7|R1A_BC133 Replicase polyprotein 1a OS=Bat coronavirus...   462    3e-146
  sp|P0C6Y4|R1AB_PEDV7 Replicase polyprotein 1ab OS=Porcine epide...   456    5e-144
  sp|P0C6V6|R1A_PEDV7 Replicase polyprotein 1a OS=Porcine epidemi...   455    6e-144
  sp|P0C6T6|R1A_BCHK9 Replicase polyprotein 1a OS=Bat coronavirus...   455    7e-144
  sp|P0C6F6|R1A_BC512 Replicase polyprotein 1a OS=Bat coronavirus...   455    9e-144
  sp|P0C6W5|R1AB_BCHK9 Replicase polyprotein 1ab OS=Bat coronavir...   455    1e-143
  sp|P0C6V2|R1A_CVPPU Replicase polyprotein 1a OS=Porcine transmi...   454    2e-143
  sp|P0C6W0|R1AB_BC512 Replicase polyprotein 1ab OS=Bat coronavir...   455    2e-143
  sp|P0C6Y5|R1AB_CVPPU Replicase polyprotein 1ab OS=Porcine trans...   454    2e-143
  sp|Q98VG9|R1AB_FIPV Replicase polyprotein 1ab OS=Feline coronav...   452    9e-143
  sp|P0C6U2|R1A_CVH22 Replicase polyprotein 1a OS=Human coronavir...   448    3e-141
  sp|P0C6X1|R1AB_CVH22 Replicase polyprotein 1ab OS=Human coronav...   447    6e-141
  sp|P0C6X5|R1AB_CVHNL Replicase polyprotein 1ab OS=Human coronav...   443    2e-139
  sp|P0C6U6|R1A_CVHNL Replicase polyprotein 1a OS=Human coronavir...   442    2e-139
  sp|P0C6V4|R1A_IBVBC Replicase polyprotein 1a OS=Avian infectiou...   398    5e-124
  sp|P0C6V3|R1A_IBVB Replicase polyprotein 1a OS=Avian infectious...   398    5e-124
  sp|P0C6Y2|R1AB_IBVBC Replicase polyprotein 1ab OS=Avian infecti...   397    2e-123
  sp|P0C6Y1|R1AB_IBVB Replicase polyprotein 1ab OS=Avian infectio...   396    2e-123
  sp|P0C6V5|R1A_IBVM Replicase polyprotein 1a OS=Avian infectious...   393    3e-122
  sp|P0C6Y3|R1AB_IBVM Replicase polyprotein 1ab OS=Avian infectio...   392    1e-121

Sequences not found previously or not previously below threshold:



> sp|P0C6V9|R1AB_BC279 Replicase polyprotein 1ab OS=Bat coronavirus 
279/2005 OX=389167 GN=rep PE=3 SV=1
Length=7079

 Score =  485 bits (1250),  Expect = 3e-154, Method: Composition-based stats.
 Identities = 294/306 (96%), Positives = 303/306 (99%), Gaps = 0/306 (0%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDD VYCPRHVICT+EDMLNPNYEDLLIR
Sbjct  3247  SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLIR  3306

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
             KSNH+FLVQAGNVQLRVIGHSMQNC+L+LKVDT+NPKTPKYKFVRIQPGQTFSVLACYNG
Sbjct  3307  KSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNG  3366

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
             SPSGVYQCAMRPN+TIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEG 
Sbjct  3367  SPSGVYQCAMRPNYTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGK  3426

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGPFVDRQTAQAAGTDTTIT+NVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE
Sbjct  3427  FYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  3486

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
             PLTQDHVDILGPLSAQTGIAVLDMCA+LKELLQNGMNGRTILGS +LEDEFTPFDVVRQC
Sbjct  3487  PLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQC  3546

Query  301   SGVTFQ  306
             SGVTFQ
Sbjct  3547  SGVTFQ  3552


> sp|P0C6F5|R1A_BC279 Replicase polyprotein 1a OS=Bat coronavirus 
279/2005 OX=389167 GN=1a PE=3 SV=1
Length=4388

 Score =  485 bits (1249),  Expect = 3e-154, Method: Composition-based stats.
 Identities = 294/306 (96%), Positives = 303/306 (99%), Gaps = 0/306 (0%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDD VYCPRHVICT+EDMLNPNYEDLLIR
Sbjct  3247  SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLIR  3306

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
             KSNH+FLVQAGNVQLRVIGHSMQNC+L+LKVDT+NPKTPKYKFVRIQPGQTFSVLACYNG
Sbjct  3307  KSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNG  3366

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
             SPSGVYQCAMRPN+TIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEG 
Sbjct  3367  SPSGVYQCAMRPNYTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGK  3426

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGPFVDRQTAQAAGTDTTIT+NVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE
Sbjct  3427  FYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  3486

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
             PLTQDHVDILGPLSAQTGIAVLDMCA+LKELLQNGMNGRTILGS +LEDEFTPFDVVRQC
Sbjct  3487  PLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQC  3546

Query  301   SGVTFQ  306
             SGVTFQ
Sbjct  3547  SGVTFQ  3552


> sp|P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab OS=Severe acute 
respiratory syndrome coronavirus 2 OX=2697049 GN=rep PE=1 
SV=1
Length=7096

 Score =  485 bits (1249),  Expect = 5e-154, Method: Composition-based stats.
 Identities = 306/306 (100%), Positives = 306/306 (100%), Gaps = 0/306 (0%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR
Sbjct  3264  SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  3323

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
             KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG
Sbjct  3324  KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  3383

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
             SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN
Sbjct  3384  SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  3443

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE
Sbjct  3444  FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  3503

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
             PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
Sbjct  3504  PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  3563

Query  301   SGVTFQ  306
             SGVTFQ
Sbjct  3564  SGVTFQ  3569


> sp|P0DTC1|R1A_SARS2 Replicase polyprotein 1a OS=Severe acute 
respiratory syndrome coronavirus 2 OX=2697049 PE=1 SV=1
Length=4405

 Score =  484 bits (1247),  Expect = 7e-154, Method: Composition-based stats.
 Identities = 306/306 (100%), Positives = 306/306 (100%), Gaps = 0/306 (0%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR
Sbjct  3264  SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  3323

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
             KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG
Sbjct  3324  KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  3383

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
             SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN
Sbjct  3384  SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  3443

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE
Sbjct  3444  FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  3503

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
             PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
Sbjct  3504  PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  3563

Query  301   SGVTFQ  306
             SGVTFQ
Sbjct  3564  SGVTFQ  3569


> sp|P0C6X7|R1AB_CVHSA Replicase polyprotein 1ab OS=Human SARS 
coronavirus OX=694009 GN=rep PE=1 SV=1
Length=7073

 Score =  484 bits (1245),  Expect = 1e-153, Method: Composition-based stats.
 Identities = 294/306 (96%), Positives = 302/306 (99%), Gaps = 0/306 (0%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDD VYCPRHVICT+EDMLNPNYEDLLIR
Sbjct  3241  SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLIR  3300

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
             KSNH+FLVQAGNVQLRVIGHSMQNC+L+LKVDT+NPKTPKYKFVRIQPGQTFSVLACYNG
Sbjct  3301  KSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNG  3360

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
             SPSGVYQCAMRPN TIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEG 
Sbjct  3361  SPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGK  3420

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGPFVDRQTAQAAGTDTTIT+NVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE
Sbjct  3421  FYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  3480

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
             PLTQDHVDILGPLSAQTGIAVLDMCA+LKELLQNGMNGRTILGS +LEDEFTPFDVVRQC
Sbjct  3481  PLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQC  3540

Query  301   SGVTFQ  306
             SGVTFQ
Sbjct  3541  SGVTFQ  3546


> sp|P0C6U8|R1A_CVHSA Replicase polyprotein 1a OS=Human SARS coronavirus 
OX=694009 GN=1a PE=1 SV=1
Length=4382

 Score =  483 bits (1243),  Expect = 2e-153, Method: Composition-based stats.
 Identities = 294/306 (96%), Positives = 302/306 (99%), Gaps = 0/306 (0%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDD VYCPRHVICT+EDMLNPNYEDLLIR
Sbjct  3241  SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLIR  3300

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
             KSNH+FLVQAGNVQLRVIGHSMQNC+L+LKVDT+NPKTPKYKFVRIQPGQTFSVLACYNG
Sbjct  3301  KSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNG  3360

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
             SPSGVYQCAMRPN TIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEG 
Sbjct  3361  SPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGK  3420

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGPFVDRQTAQAAGTDTTIT+NVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE
Sbjct  3421  FYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  3480

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
             PLTQDHVDILGPLSAQTGIAVLDMCA+LKELLQNGMNGRTILGS +LEDEFTPFDVVRQC
Sbjct  3481  PLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQC  3540

Query  301   SGVTFQ  306
             SGVTFQ
Sbjct  3541  SGVTFQ  3546


> sp|P0C6W2|R1AB_BCHK3 Replicase polyprotein 1ab OS=Bat coronavirus 
HKU3 OX=442736 GN=rep PE=3 SV=1
Length=7067

 Score =  482 bits (1241),  Expect = 5e-153, Method: Composition-based stats.
 Identities = 292/306 (95%), Positives = 302/306 (99%), Gaps = 0/306 (0%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDD VYCPRHV+CT+EDMLNPNY+DLLIR
Sbjct  3235  SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVVCTAEDMLNPNYDDLLIR  3294

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
             KSNH+FLVQAGNVQLRVIGHSMQNC+L+LKVDT+NPKTPKYKFVRIQPGQTFSVLACYNG
Sbjct  3295  KSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNG  3354

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
             SPSGVYQCAMRPN TIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEG 
Sbjct  3355  SPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGK  3414

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGPFVDRQTAQAAGTDTTIT+NVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE
Sbjct  3415  FYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  3474

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
             PLTQDHVDILGPLSAQTGIAVLDMCA+LKELLQNGMNGRTILGS +LEDEFTPFDVVRQC
Sbjct  3475  PLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQC  3534

Query  301   SGVTFQ  306
             SGVTFQ
Sbjct  3535  SGVTFQ  3540


> sp|P0C6F8|R1A_BCHK3 Replicase polyprotein 1a OS=Bat coronavirus 
HKU3 OX=442736 GN=1a PE=3 SV=1
Length=4376

 Score =  481 bits (1238),  Expect = 8e-153, Method: Composition-based stats.
 Identities = 292/306 (95%), Positives = 302/306 (99%), Gaps = 0/306 (0%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDD VYCPRHV+CT+EDMLNPNY+DLLIR
Sbjct  3235  SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVVCTAEDMLNPNYDDLLIR  3294

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
             KSNH+FLVQAGNVQLRVIGHSMQNC+L+LKVDT+NPKTPKYKFVRIQPGQTFSVLACYNG
Sbjct  3295  KSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNG  3354

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
             SPSGVYQCAMRPN TIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEG 
Sbjct  3355  SPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGK  3414

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGPFVDRQTAQAAGTDTTIT+NVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE
Sbjct  3415  FYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  3474

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
             PLTQDHVDILGPLSAQTGIAVLDMCA+LKELLQNGMNGRTILGS +LEDEFTPFDVVRQC
Sbjct  3475  PLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQC  3534

Query  301   SGVTFQ  306
             SGVTFQ
Sbjct  3535  SGVTFQ  3540


> sp|P0C6W6|R1AB_BCRP3 Replicase polyprotein 1ab OS=Bat coronavirus 
Rp3/2004 OX=349344 GN=rep PE=3 SV=1
Length=7071

 Score =  480 bits (1237),  Expect = 2e-152, Method: Composition-based stats.
 Identities = 293/306 (96%), Positives = 301/306 (98%), Gaps = 0/306 (0%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDD VYCPRHVICT+EDMLNPNYEDLLIR
Sbjct  3239  SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLIR  3298

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
             KSNH+FLVQAGNVQLRVIGHSMQNC+L+LKVDT+NPKTPKYKFVRIQPGQTFSVLACYNG
Sbjct  3299  KSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNG  3358

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
             SPSGVYQCAMRPN TIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPT VHAGTDLEG 
Sbjct  3359  SPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTEVHAGTDLEGK  3418

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGPFVDRQTAQAAGTDTTIT+NVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE
Sbjct  3419  FYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  3478

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
             PLTQDHVDILGPLSAQTGIAVLDMCA+LKELLQNGMNGRTILGS +LEDEFTPFDVVRQC
Sbjct  3479  PLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQC  3538

Query  301   SGVTFQ  306
             SGVTFQ
Sbjct  3539  SGVTFQ  3544


> sp|P0C6T7|R1A_BCRP3 Replicase polyprotein 1a OS=Bat coronavirus 
Rp3/2004 OX=349344 GN=1a PE=3 SV=1
Length=4380

 Score =  480 bits (1236),  Expect = 2e-152, Method: Composition-based stats.
 Identities = 293/306 (96%), Positives = 301/306 (98%), Gaps = 0/306 (0%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDD VYCPRHVICT+EDMLNPNYEDLLIR
Sbjct  3239  SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLIR  3298

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
             KSNH+FLVQAGNVQLRVIGHSMQNC+L+LKVDT+NPKTPKYKFVRIQPGQTFSVLACYNG
Sbjct  3299  KSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNG  3358

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
             SPSGVYQCAMRPN TIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPT VHAGTDLEG 
Sbjct  3359  SPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTEVHAGTDLEGK  3418

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGPFVDRQTAQAAGTDTTIT+NVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE
Sbjct  3419  FYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  3478

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
             PLTQDHVDILGPLSAQTGIAVLDMCA+LKELLQNGMNGRTILGS +LEDEFTPFDVVRQC
Sbjct  3479  PLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQC  3538

Query  301   SGVTFQ  306
             SGVTFQ
Sbjct  3539  SGVTFQ  3544


> sp|P0C6X8|R1AB_CVM2 Replicase polyprotein 1ab OS=Murine coronavirus 
(strain 2) OX=76344 GN=rep PE=3 SV=1
Length=7124

 Score =  470 bits (1211),  Expect = 5e-149, Method: Composition-based stats.
 Identities = 155/306 (51%), Positives = 200/306 (65%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM FP+ KVE C+V VT G  TLNGLWLDD VYCPRHVIC+S DM +P+Y +LL R
Sbjct  3280  SGIVKMVFPTSKVEPCVVSVTYGNMTLNGLWLDDKVYCPRHVICSSADMTDPDYSNLLCR  3339

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
               + +F V +G + L V+ + MQ  +L L V   NP TPKY F  ++PG+TF+VLA YNG
Sbjct  3340  VISSDFCVMSGRMSLTVMSYQMQGSLLVLTVTLQNPNTPKYSFGVVKPGETFTVLAAYNG  3399

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
                G +   MR ++TIKGSFL GSCGSVG+ +  D V F YMH +EL TG H GTD  GN
Sbjct  3400  KSQGAFHVTMRSSYTIKGSFLCGSCGSVGYVLTGDSVRFVYMHQLELSTGCHTGTDFSGN  3459

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D T TVNV+AWLYAA++N   WF+   + +L +FN+ AM   + 
Sbjct  3460  FYGPYRDAQVVQLPVQDYTQTVNVVAWLYAAILNRCNWFVQSDSCSLEEFNVWAMTNGFS  3519

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  L  L++ TG+ V  + A++K L  +G  G+ ILGS +LEDE TP DV +Q 
Sbjct  3520  SIKADLV--LDALASMTGVTVEQILAAIKRLY-SGFQGKQILGSCVLEDELTPSDVYQQL  3576

Query  301   SGVTFQ  306
             +GV  Q
Sbjct  3577  AGVKLQ  3582


> sp|P0C6Y0|R1AB_CVMJH Replicase polyprotein 1ab OS=Murine coronavirus 
(strain JHM) OX=11144 GN=rep PE=1 SV=1
Length=7180

 Score =  470 bits (1210),  Expect = 7e-149, Method: Composition-based stats.
 Identities = 154/306 (50%), Positives = 199/306 (65%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ KVE C+V VT G  TLNGLWLDD VYCPRHVIC+S DM +P+Y +LL R
Sbjct  3337  SGIVKMVSPTSKVEPCVVSVTYGNMTLNGLWLDDKVYCPRHVICSSADMTDPDYPNLLCR  3396

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              ++ +F V +  + L V+ + MQ  +L L V   NP TPKY F  ++PG+TF+VLA YNG
Sbjct  3397  VTSSDFCVMSDRMSLTVMSYQMQGSLLVLTVTLQNPNTPKYSFGVVKPGETFTVLAAYNG  3456

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   MR + TIKGSFL GSCGSVG+ +  D V F YMH +EL TG H GTD  GN
Sbjct  3457  RPQGAFHVVMRSSHTIKGSFLCGSCGSVGYVLTGDSVRFVYMHQLELSTGCHTGTDFSGN  3516

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D T TVNV+AWLYAA++N   WF+   + +L +FN+ AM   + 
Sbjct  3517  FYGPYRDAQVVQLPVQDYTQTVNVVAWLYAAILNRCNWFVQSDSCSLEEFNVWAMTNGFS  3576

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  L  L++ TG+ V  + A++K  L +G  G+ ILGS +LEDE TP DV +Q 
Sbjct  3577  SIKADLV--LDALASMTGVTVEQVLAAIKR-LHSGFQGKQILGSCVLEDELTPSDVYQQL  3633

Query  301   SGVTFQ  306
             +GV  Q
Sbjct  3634  AGVKLQ  3639


> sp|P0C6U9|R1A_CVM2 Replicase polyprotein 1a OS=Murine coronavirus 
(strain 2) OX=76344 GN=1a PE=3 SV=1
Length=4416

 Score =  470 bits (1209),  Expect = 8e-149, Method: Composition-based stats.
 Identities = 155/306 (51%), Positives = 200/306 (65%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM FP+ KVE C+V VT G  TLNGLWLDD VYCPRHVIC+S DM +P+Y +LL R
Sbjct  3280  SGIVKMVFPTSKVEPCVVSVTYGNMTLNGLWLDDKVYCPRHVICSSADMTDPDYSNLLCR  3339

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
               + +F V +G + L V+ + MQ  +L L V   NP TPKY F  ++PG+TF+VLA YNG
Sbjct  3340  VISSDFCVMSGRMSLTVMSYQMQGSLLVLTVTLQNPNTPKYSFGVVKPGETFTVLAAYNG  3399

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
                G +   MR ++TIKGSFL GSCGSVG+ +  D V F YMH +EL TG H GTD  GN
Sbjct  3400  KSQGAFHVTMRSSYTIKGSFLCGSCGSVGYVLTGDSVRFVYMHQLELSTGCHTGTDFSGN  3459

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D T TVNV+AWLYAA++N   WF+   + +L +FN+ AM   + 
Sbjct  3460  FYGPYRDAQVVQLPVQDYTQTVNVVAWLYAAILNRCNWFVQSDSCSLEEFNVWAMTNGFS  3519

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  L  L++ TG+ V  + A++K L  +G  G+ ILGS +LEDE TP DV +Q 
Sbjct  3520  SIKADLV--LDALASMTGVTVEQILAAIKRLY-SGFQGKQILGSCVLEDELTPSDVYQQL  3576

Query  301   SGVTFQ  306
             +GV  Q
Sbjct  3577  AGVKLQ  3582


> sp|P0C6V1|R1A_CVMJH Replicase polyprotein 1a OS=Murine coronavirus 
(strain JHM) OX=11144 GN=1a PE=1 SV=1
Length=4474

 Score =  469 bits (1208),  Expect = 1e-148, Method: Composition-based stats.
 Identities = 154/306 (50%), Positives = 199/306 (65%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ KVE C+V VT G  TLNGLWLDD VYCPRHVIC+S DM +P+Y +LL R
Sbjct  3337  SGIVKMVSPTSKVEPCVVSVTYGNMTLNGLWLDDKVYCPRHVICSSADMTDPDYPNLLCR  3396

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              ++ +F V +  + L V+ + MQ  +L L V   NP TPKY F  ++PG+TF+VLA YNG
Sbjct  3397  VTSSDFCVMSDRMSLTVMSYQMQGSLLVLTVTLQNPNTPKYSFGVVKPGETFTVLAAYNG  3456

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   MR + TIKGSFL GSCGSVG+ +  D V F YMH +EL TG H GTD  GN
Sbjct  3457  RPQGAFHVVMRSSHTIKGSFLCGSCGSVGYVLTGDSVRFVYMHQLELSTGCHTGTDFSGN  3516

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D T TVNV+AWLYAA++N   WF+   + +L +FN+ AM   + 
Sbjct  3517  FYGPYRDAQVVQLPVQDYTQTVNVVAWLYAAILNRCNWFVQSDSCSLEEFNVWAMTNGFS  3576

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  L  L++ TG+ V  + A++K  L +G  G+ ILGS +LEDE TP DV +Q 
Sbjct  3577  SIKADLV--LDALASMTGVTVEQVLAAIKR-LHSGFQGKQILGSCVLEDELTPSDVYQQL  3633

Query  301   SGVTFQ  306
             +GV  Q
Sbjct  3634  AGVKLQ  3639


> sp|P0C6T8|R1A_CVBEN Replicase polyprotein 1a OS=Bovine coronavirus 
(strain 98TXSF-110-ENT) OX=233262 GN=1a PE=3 SV=1
Length=4383

 Score =  469 bits (1206),  Expect = 2e-148, Method: Composition-based stats.
 Identities = 147/306 (48%), Positives = 198/306 (65%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ KVE C+V VT G  TLNGLWLDD VYCPRHVIC++ DM NP+Y +LL R
Sbjct  3247  SGIVKMVNPTSKVEPCIVSVTYGNMTLNGLWLDDKVYCPRHVICSASDMTNPDYTNLLCR  3306

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              ++ +F V    + L V+ + MQ C+L L V   N +TPKY F  ++PG+TF+VLA YNG
Sbjct  3307  VTSSDFTVLFDRLSLTVMSYQMQGCMLVLTVTLQNSRTPKYTFGVVKPGETFTVLAAYNG  3366

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   MR ++TIKGSFL GSCGSVG+ +  DCV F YMH +EL TG H GTD  G+
Sbjct  3367  KPQGAFHVTMRSSYTIKGSFLCGSCGSVGYVLMGDCVKFVYMHQLELSTGCHTGTDFNGD  3426

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D   +VN +AWLYAA++N   WF+     ++ DFN+ A+   + 
Sbjct  3427  FYGPYKDAQVVQLPVQDYIQSVNFVAWLYAAILNNCNWFVQSDKCSVEDFNVWALSNGFS  3486

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  +  L++ TG+++  + A++K  L+NG  GR I+GS   EDE TP DV +Q 
Sbjct  3487  QVKSDLV--IDALASMTGVSLETLLAAIKR-LKNGFQGRQIMGSCSFEDELTPSDVYQQL  3543

Query  301   SGVTFQ  306
             +G+  Q
Sbjct  3544  AGIKLQ  3549


> sp|P0C6X0|R1AB_CVBQ Replicase polyprotein 1ab OS=Bovine coronavirus 
(strain Quebec) OX=11133 GN=rep PE=3 SV=1
Length=7059

 Score =  469 bits (1207),  Expect = 2e-148, Method: Composition-based stats.
 Identities = 148/306 (48%), Positives = 198/306 (65%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ KVE C+V VT G  TLNGLWLDD VYCPRHVIC++ DM NP+Y +LL R
Sbjct  3247  SGIVKMVNPTSKVEPCIVSVTYGNMTLNGLWLDDKVYCPRHVICSASDMTNPDYTNLLCR  3306

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              ++ +F V    + L V+ + MQ C+L L V   N +TPKY F  ++PG+TF+VLA YNG
Sbjct  3307  VTSSDFTVLFDRLSLTVMSYQMQGCMLVLTVTLQNSRTPKYTFGVVKPGETFTVLAAYNG  3366

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   MR ++TIKGSFL GSCGSVG+ I  DCV F YMH +EL TG H GTD  G+
Sbjct  3367  KPQGAFHVTMRSSYTIKGSFLCGSCGSVGYVIMGDCVKFVYMHQLELSTGCHTGTDFNGD  3426

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D   +VN +AWLYAA++N   WF+     ++ DFN+ A+   + 
Sbjct  3427  FYGPYKDAQVVQLPVQDYIQSVNFVAWLYAAILNNCNWFVQSDKCSVEDFNVWALSNGFS  3486

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  +  L++ TG+++  + A++K  L+NG  GR I+GS   EDE TP DV +Q 
Sbjct  3487  QVKSDLV--IDALASMTGVSLETLLAAIKR-LKNGFQGRQIMGSCSFEDELTPSDVYQQL  3543

Query  301   SGVTFQ  306
             +G+  Q
Sbjct  3544  AGIKLQ  3549


> sp|P0C6T9|R1A_CVBLU Replicase polyprotein 1a OS=Bovine coronavirus 
(strain 98TXSF-110-LUN) OX=233264 GN=1a PE=3 SV=1
Length=4383

 Score =  469 bits (1206),  Expect = 2e-148, Method: Composition-based stats.
 Identities = 147/306 (48%), Positives = 198/306 (65%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ KVE C+V VT G  TLNGLWLDD VYCPRHVIC++ DM NP+Y +LL R
Sbjct  3247  SGIVKMVNPTSKVEPCIVSVTYGNMTLNGLWLDDKVYCPRHVICSASDMTNPDYTNLLCR  3306

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              ++ +F V    + L V+ + MQ C+L L V   N +TPKY F  ++PG+TF+VLA YNG
Sbjct  3307  VTSSDFTVLFDRLSLTVMSYQMQGCMLVLTVTLQNSRTPKYTFGVVKPGETFTVLAAYNG  3366

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   MR ++TIKGSFL GSCGSVG+ +  DCV F YMH +EL TG H GTD  G+
Sbjct  3367  KPQGAFHVTMRSSYTIKGSFLCGSCGSVGYVLMGDCVKFVYMHQLELSTGCHTGTDFNGD  3426

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D   +VN +AWLYAA++N   WF+     ++ DFN+ A+   + 
Sbjct  3427  FYGPYKDAQVVQLPVQDYIQSVNFVAWLYAAILNNCNWFVQSDKCSVEDFNVWALSNGFS  3486

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  +  L++ TG+++  + A++K  L+NG  GR I+GS   EDE TP DV +Q 
Sbjct  3487  QVKSDLV--IDALASMTGVSLETLLAAIKR-LKNGFQGRQIMGSCSFEDELTPSDVYQQL  3543

Query  301   SGVTFQ  306
             +G+  Q
Sbjct  3544  AGIKLQ  3549


> sp|P0C6U1|R1A_CVBQ Replicase polyprotein 1a OS=Bovine coronavirus 
(strain Quebec) OX=11133 GN=1a PE=3 SV=1
Length=4383

 Score =  469 bits (1206),  Expect = 2e-148, Method: Composition-based stats.
 Identities = 148/306 (48%), Positives = 198/306 (65%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ KVE C+V VT G  TLNGLWLDD VYCPRHVIC++ DM NP+Y +LL R
Sbjct  3247  SGIVKMVNPTSKVEPCIVSVTYGNMTLNGLWLDDKVYCPRHVICSASDMTNPDYTNLLCR  3306

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              ++ +F V    + L V+ + MQ C+L L V   N +TPKY F  ++PG+TF+VLA YNG
Sbjct  3307  VTSSDFTVLFDRLSLTVMSYQMQGCMLVLTVTLQNSRTPKYTFGVVKPGETFTVLAAYNG  3366

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   MR ++TIKGSFL GSCGSVG+ I  DCV F YMH +EL TG H GTD  G+
Sbjct  3367  KPQGAFHVTMRSSYTIKGSFLCGSCGSVGYVIMGDCVKFVYMHQLELSTGCHTGTDFNGD  3426

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D   +VN +AWLYAA++N   WF+     ++ DFN+ A+   + 
Sbjct  3427  FYGPYKDAQVVQLPVQDYIQSVNFVAWLYAAILNNCNWFVQSDKCSVEDFNVWALSNGFS  3486

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  +  L++ TG+++  + A++K  L+NG  GR I+GS   EDE TP DV +Q 
Sbjct  3487  QVKSDLV--IDALASMTGVSLETLLAAIKR-LKNGFQGRQIMGSCSFEDELTPSDVYQQL  3543

Query  301   SGVTFQ  306
             +G+  Q
Sbjct  3544  AGIKLQ  3549


> sp|P0C6W8|R1AB_CVBLU Replicase polyprotein 1ab OS=Bovine coronavirus 
(strain 98TXSF-110-LUN) OX=233264 GN=rep PE=3 SV=1
Length=7094

 Score =  469 bits (1207),  Expect = 2e-148, Method: Composition-based stats.
 Identities = 147/306 (48%), Positives = 198/306 (65%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ KVE C+V VT G  TLNGLWLDD VYCPRHVIC++ DM NP+Y +LL R
Sbjct  3247  SGIVKMVNPTSKVEPCIVSVTYGNMTLNGLWLDDKVYCPRHVICSASDMTNPDYTNLLCR  3306

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              ++ +F V    + L V+ + MQ C+L L V   N +TPKY F  ++PG+TF+VLA YNG
Sbjct  3307  VTSSDFTVLFDRLSLTVMSYQMQGCMLVLTVTLQNSRTPKYTFGVVKPGETFTVLAAYNG  3366

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   MR ++TIKGSFL GSCGSVG+ +  DCV F YMH +EL TG H GTD  G+
Sbjct  3367  KPQGAFHVTMRSSYTIKGSFLCGSCGSVGYVLMGDCVKFVYMHQLELSTGCHTGTDFNGD  3426

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D   +VN +AWLYAA++N   WF+     ++ DFN+ A+   + 
Sbjct  3427  FYGPYKDAQVVQLPVQDYIQSVNFVAWLYAAILNNCNWFVQSDKCSVEDFNVWALSNGFS  3486

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  +  L++ TG+++  + A++K  L+NG  GR I+GS   EDE TP DV +Q 
Sbjct  3487  QVKSDLV--IDALASMTGVSLETLLAAIKR-LKNGFQGRQIMGSCSFEDELTPSDVYQQL  3543

Query  301   SGVTFQ  306
             +G+  Q
Sbjct  3544  AGIKLQ  3549


> sp|P0C6W7|R1AB_CVBEN Replicase polyprotein 1ab OS=Bovine coronavirus 
(strain 98TXSF-110-ENT) OX=233262 GN=rep PE=3 SV=1
Length=7094

 Score =  469 bits (1207),  Expect = 2e-148, Method: Composition-based stats.
 Identities = 147/306 (48%), Positives = 198/306 (65%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ KVE C+V VT G  TLNGLWLDD VYCPRHVIC++ DM NP+Y +LL R
Sbjct  3247  SGIVKMVNPTSKVEPCIVSVTYGNMTLNGLWLDDKVYCPRHVICSASDMTNPDYTNLLCR  3306

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              ++ +F V    + L V+ + MQ C+L L V   N +TPKY F  ++PG+TF+VLA YNG
Sbjct  3307  VTSSDFTVLFDRLSLTVMSYQMQGCMLVLTVTLQNSRTPKYTFGVVKPGETFTVLAAYNG  3366

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   MR ++TIKGSFL GSCGSVG+ +  DCV F YMH +EL TG H GTD  G+
Sbjct  3367  KPQGAFHVTMRSSYTIKGSFLCGSCGSVGYVLMGDCVKFVYMHQLELSTGCHTGTDFNGD  3426

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D   +VN +AWLYAA++N   WF+     ++ DFN+ A+   + 
Sbjct  3427  FYGPYKDAQVVQLPVQDYIQSVNFVAWLYAAILNNCNWFVQSDKCSVEDFNVWALSNGFS  3486

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  +  L++ TG+++  + A++K  L+NG  GR I+GS   EDE TP DV +Q 
Sbjct  3487  QVKSDLV--IDALASMTGVSLETLLAAIKR-LKNGFQGRQIMGSCSFEDELTPSDVYQQL  3543

Query  301   SGVTFQ  306
             +G+  Q
Sbjct  3544  AGIKLQ  3549


> sp|P0C6U7|R1A_CVHOC Replicase polyprotein 1a OS=Human coronavirus 
OC43 OX=31631 GN=1a PE=3 SV=1
Length=4383

 Score =  467 bits (1203),  Expect = 4e-148, Method: Composition-based stats.
 Identities = 148/306 (48%), Positives = 198/306 (65%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ KVE C+V VT G  TLNGLWLDD VYCPRHVIC++ DM NP+Y +LL R
Sbjct  3247  SGIVKMVNPTSKVEPCVVSVTYGNMTLNGLWLDDKVYCPRHVICSASDMTNPDYTNLLCR  3306

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              ++ +F V    + L V+ + M+ C+L L V   N +TPKY F  ++PG+TF+VLA YNG
Sbjct  3307  VTSSDFTVLFDRLSLTVMSYQMRGCMLVLTVTLQNSRTPKYTFGVVKPGETFTVLAAYNG  3366

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   MR ++TIKGSFL GSCGSVG+ I  DCV F YMH +EL TG H GTD  G+
Sbjct  3367  KPQGAFHVTMRSSYTIKGSFLCGSCGSVGYVIMGDCVKFVYMHQLELSTGCHTGTDFNGD  3426

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D   +VN LAWLYAA++N   WF+     ++ DFN+ A+   + 
Sbjct  3427  FYGPYKDAQVVQLPIQDYIQSVNFLAWLYAAILNNCNWFIQSDKCSVEDFNVWALSNGFS  3486

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  +  L++ TG+++  + A++K  L+NG  GR I+GS   EDE TP DV +Q 
Sbjct  3487  QVKSDLV--IDALASMTGVSLETLLAAIKR-LKNGFQGRQIMGSCSFEDELTPSDVYQQL  3543

Query  301   SGVTFQ  306
             +G+  Q
Sbjct  3544  AGIKLQ  3549


> sp|P0C6X6|R1AB_CVHOC Replicase polyprotein 1ab OS=Human coronavirus 
OC43 OX=31631 GN=rep PE=3 SV=1
Length=7095

 Score =  468 bits (1204),  Expect = 5e-148, Method: Composition-based stats.
 Identities = 148/306 (48%), Positives = 198/306 (65%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ KVE C+V VT G  TLNGLWLDD VYCPRHVIC++ DM NP+Y +LL R
Sbjct  3247  SGIVKMVNPTSKVEPCVVSVTYGNMTLNGLWLDDKVYCPRHVICSASDMTNPDYTNLLCR  3306

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              ++ +F V    + L V+ + M+ C+L L V   N +TPKY F  ++PG+TF+VLA YNG
Sbjct  3307  VTSSDFTVLFDRLSLTVMSYQMRGCMLVLTVTLQNSRTPKYTFGVVKPGETFTVLAAYNG  3366

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   MR ++TIKGSFL GSCGSVG+ I  DCV F YMH +EL TG H GTD  G+
Sbjct  3367  KPQGAFHVTMRSSYTIKGSFLCGSCGSVGYVIMGDCVKFVYMHQLELSTGCHTGTDFNGD  3426

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D   +VN LAWLYAA++N   WF+     ++ DFN+ A+   + 
Sbjct  3427  FYGPYKDAQVVQLPIQDYIQSVNFLAWLYAAILNNCNWFIQSDKCSVEDFNVWALSNGFS  3486

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  +  L++ TG+++  + A++K  L+NG  GR I+GS   EDE TP DV +Q 
Sbjct  3487  QVKSDLV--IDALASMTGVSLETLLAAIKR-LKNGFQGRQIMGSCSFEDELTPSDVYQQL  3543

Query  301   SGVTFQ  306
             +G+  Q
Sbjct  3544  AGIKLQ  3549


> sp|K9N638|R1A_MERS1 Replicase polyprotein 1a OS=Middle East respiratory 
syndrome-related coronavirus (isolate United Kingdom/H123990006/2012) 
OX=1263720 GN=1a PE=1 SV=1
Length=4391

 Score =  465 bits (1198),  Expect = 2e-147, Method: Composition-based stats.
 Identities = 156/310 (50%), Positives = 206/310 (66%), Gaps = 8/310 (3%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM+ PSG VE CMVQVTCG+ TLNGLWLD+ V+CPRHV+C ++ + +PNY+ LLI 
Sbjct  3248  SGLVKMSHPSGDVEACMVQVTCGSMTLNGLWLDNTVWCPRHVMCPADQLSDPNYDALLIS  3307

Query  61    KSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLAC  117
              +NH+F VQ        LRV+GH+MQ  +LKL VD ANP TP Y F  ++PG  FSVLAC
Sbjct  3308  MTNHSFSVQKHIGAPANLRVVGHAMQGTLLKLTVDVANPSTPAYTFTTVKPGAAFSVLAC  3367

Query  118   YNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDL  177
             YNG P+G +   MRPN+TIKGSFL GSCGSVG+  +   ++FCYMH MEL  G H G+  
Sbjct  3368  YNGRPTGTFTVVMRPNYTIKGSFLCGSCGSVGYTKEGSVINFCYMHQMELANGTHTGSAF  3427

Query  178   EGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKY  237
             +G  YG F+D+Q  Q   TD   +VNV+AWLYAA++NG  WF+    T++  FN  A+  
Sbjct  3428  DGTMYGAFMDKQVHQVQLTDKYCSVNVVAWLYAAILNGCAWFVKPNRTSVVSFNEWALAN  3487

Query  238   NYE-PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDV  296
              +   +    VD+   L+ +TG+A+  +  ++++L   G  G+ ILGS +LEDEFTP DV
Sbjct  3488  QFTEFVGTQSVDM---LAVKTGVAIEQLLYAIQQLY-TGFQGKQILGSTMLEDEFTPEDV  3543

Query  297   VRQCSGVTFQ  306
               Q  GV  Q
Sbjct  3544  NMQIMGVVMQ  3553


> sp|K9N7C7|R1AB_MERS1 Replicase polyprotein 1ab OS=Middle East 
respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012) 
OX=1263720 GN=rep PE=1 SV=1
Length=7078

 Score =  465 bits (1198),  Expect = 3e-147, Method: Composition-based stats.
 Identities = 156/310 (50%), Positives = 206/310 (66%), Gaps = 8/310 (3%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM+ PSG VE CMVQVTCG+ TLNGLWLD+ V+CPRHV+C ++ + +PNY+ LLI 
Sbjct  3248  SGLVKMSHPSGDVEACMVQVTCGSMTLNGLWLDNTVWCPRHVMCPADQLSDPNYDALLIS  3307

Query  61    KSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLAC  117
              +NH+F VQ        LRV+GH+MQ  +LKL VD ANP TP Y F  ++PG  FSVLAC
Sbjct  3308  MTNHSFSVQKHIGAPANLRVVGHAMQGTLLKLTVDVANPSTPAYTFTTVKPGAAFSVLAC  3367

Query  118   YNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDL  177
             YNG P+G +   MRPN+TIKGSFL GSCGSVG+  +   ++FCYMH MEL  G H G+  
Sbjct  3368  YNGRPTGTFTVVMRPNYTIKGSFLCGSCGSVGYTKEGSVINFCYMHQMELANGTHTGSAF  3427

Query  178   EGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKY  237
             +G  YG F+D+Q  Q   TD   +VNV+AWLYAA++NG  WF+    T++  FN  A+  
Sbjct  3428  DGTMYGAFMDKQVHQVQLTDKYCSVNVVAWLYAAILNGCAWFVKPNRTSVVSFNEWALAN  3487

Query  238   NYE-PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDV  296
              +   +    VD+   L+ +TG+A+  +  ++++L   G  G+ ILGS +LEDEFTP DV
Sbjct  3488  QFTEFVGTQSVDM---LAVKTGVAIEQLLYAIQQLY-TGFQGKQILGSTMLEDEFTPEDV  3543

Query  297   VRQCSGVTFQ  306
               Q  GV  Q
Sbjct  3544  NMQIMGVVMQ  3553


> sp|P0C6X9|R1AB_CVMA5 Replicase polyprotein 1ab OS=Murine coronavirus 
(strain A59) OX=11142 GN=rep PE=1 SV=1
Length=7176

 Score =  465 bits (1197),  Expect = 4e-147, Method: Composition-based stats.
 Identities = 155/306 (51%), Positives = 199/306 (65%), Gaps = 4/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ KVE C+V VT G  TLNGLWLDD VYCPRHVIC+S DM +P+Y +LL R
Sbjct  3334  SGIVKMVSPTSKVEPCIVSVTYGNMTLNGLWLDDKVYCPRHVICSSADMTDPDYPNLLCR  3393

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              ++ +F V +G + L V+ + MQ C L L V   NP TPKY F  ++PG+TF+VLA YNG
Sbjct  3394  VTSSDFCVMSGRMSLTVMSYQMQGCQLVLTVTLQNPNTPKYSFGVVKPGETFTVLAAYNG  3453

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   +R + TIKGSFL GSCGSVG+ +  D V F YMH +EL TG H GTD  GN
Sbjct  3454  RPQGAFHVTLRSSHTIKGSFLCGSCGSVGYVLTGDSVRFVYMHQLELSTGCHTGTDFSGN  3513

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D T TVNV+AWLYAA+ N   WF+   + +L +FN+ AM   + 
Sbjct  3514  FYGPYRDAQVVQLPVQDYTQTVNVVAWLYAAIFNRCNWFVQSDSCSLEEFNVWAMTNGFS  3573

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  L  L++ TG+ V  + A++K  L +G  G+ ILGS +LEDE TP DV +Q 
Sbjct  3574  SIKADLV--LDALASMTGVTVEQVLAAIKR-LHSGFQGKQILGSCVLEDE-TPSDVYQQL  3629

Query  301   SGVTFQ  306
             +GV  Q
Sbjct  3630  AGVKLQ  3635


> sp|P0C6V0|R1A_CVMA5 Replicase polyprotein 1a OS=Murine coronavirus 
(strain A59) OX=11142 GN=1a PE=1 SV=1
Length=4468

 Score =  464 bits (1194),  Expect = 7e-147, Method: Composition-based stats.
 Identities = 155/306 (51%), Positives = 199/306 (65%), Gaps = 4/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ KVE C+V VT G  TLNGLWLDD VYCPRHVIC+S DM +P+Y +LL R
Sbjct  3334  SGIVKMVSPTSKVEPCIVSVTYGNMTLNGLWLDDKVYCPRHVICSSADMTDPDYPNLLCR  3393

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              ++ +F V +G + L V+ + MQ C L L V   NP TPKY F  ++PG+TF+VLA YNG
Sbjct  3394  VTSSDFCVMSGRMSLTVMSYQMQGCQLVLTVTLQNPNTPKYSFGVVKPGETFTVLAAYNG  3453

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   +R + TIKGSFL GSCGSVG+ +  D V F YMH +EL TG H GTD  GN
Sbjct  3454  RPQGAFHVTLRSSHTIKGSFLCGSCGSVGYVLTGDSVRFVYMHQLELSTGCHTGTDFSGN  3513

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D T TVNV+AWLYAA+ N   WF+   + +L +FN+ AM   + 
Sbjct  3514  FYGPYRDAQVVQLPVQDYTQTVNVVAWLYAAIFNRCNWFVQSDSCSLEEFNVWAMTNGFS  3573

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  L  L++ TG+ V  + A++K  L +G  G+ ILGS +LEDE TP DV +Q 
Sbjct  3574  SIKADLV--LDALASMTGVTVEQVLAAIKR-LHSGFQGKQILGSCVLEDE-TPSDVYQQL  3629

Query  301   SGVTFQ  306
             +GV  Q
Sbjct  3630  AGVKLQ  3635


> sp|P0C6W9|R1AB_CVBM Replicase polyprotein 1ab OS=Bovine coronavirus 
(strain Mebus) OX=11132 GN=rep PE=3 SV=1
Length=7094

 Score =  464 bits (1195),  Expect = 8e-147, Method: Composition-based stats.
 Identities = 146/306 (48%), Positives = 196/306 (64%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ KVE C+V VT G  TLNGLWL D VYCPRHVIC++ DM NP+Y +LL R
Sbjct  3247  SGIVKMVNPTSKVEPCIVSVTYGNMTLNGLWLGDKVYCPRHVICSASDMTNPDYTNLLCR  3306

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              ++ +F V    + L V+ + MQ C+L L V   N +TPKY F  ++PG+TF+VLA YNG
Sbjct  3307  VTSSDFTVLFDRLSLTVMSYQMQGCMLVLTVTLQNSRTPKYTFGVVKPGETFTVLAAYNG  3366

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   MR ++TIKGSFL GSCGSV + I  DCV F YMH +EL TG H GTD  G+
Sbjct  3367  KPQGAFHVTMRSSYTIKGSFLCGSCGSVVYVIMGDCVKFVYMHQLELSTGCHTGTDFNGD  3426

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D   +VN +AWLYAA++N   WF+     ++ DFN+ A+   + 
Sbjct  3427  FYGPYKDAQVVQLPVQDYIQSVNFVAWLYAAILNNCNWFVQSDKCSVEDFNVWALSNGFS  3486

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  +  L++ TG+++  + A++K  L+NG  GR I+GS   EDE TP DV +Q 
Sbjct  3487  QVKSDLV--IDALASMTGVSLETLLAAIKH-LKNGFQGRQIMGSCSFEDELTPSDVYQQL  3543

Query  301   SGVTFQ  306
             +G+  Q
Sbjct  3544  AGIKLQ  3549


> sp|P0C6U0|R1A_CVBM Replicase polyprotein 1a OS=Bovine coronavirus 
(strain Mebus) OX=11132 GN=1a PE=3 SV=1
Length=4383

 Score =  464 bits (1194),  Expect = 8e-147, Method: Composition-based stats.
 Identities = 146/306 (48%), Positives = 196/306 (64%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ KVE C+V VT G  TLNGLWL D VYCPRHVIC++ DM NP+Y +LL R
Sbjct  3247  SGIVKMVNPTSKVEPCIVSVTYGNMTLNGLWLGDKVYCPRHVICSASDMTNPDYTNLLCR  3306

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              ++ +F V    + L V+ + MQ C+L L V   N +TPKY F  ++PG+TF+VLA YNG
Sbjct  3307  VTSSDFTVLFDRLSLTVMSYQMQGCMLVLTVTLQNSRTPKYTFGVVKPGETFTVLAAYNG  3366

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   MR ++TIKGSFL GSCGSV + I  DCV F YMH +EL TG H GTD  G+
Sbjct  3367  KPQGAFHVTMRSSYTIKGSFLCGSCGSVVYVIMGDCVKFVYMHQLELSTGCHTGTDFNGD  3426

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D   +VN +AWLYAA++N   WF+     ++ DFN+ A+   + 
Sbjct  3427  FYGPYKDAQVVQLPVQDYIQSVNFVAWLYAAILNNCNWFVQSDKCSVEDFNVWALSNGFS  3486

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  +  L++ TG+++  + A++K  L+NG  GR I+GS   EDE TP DV +Q 
Sbjct  3487  QVKSDLV--IDALASMTGVSLETLLAAIKH-LKNGFQGRQIMGSCSFEDELTPSDVYQQL  3543

Query  301   SGVTFQ  306
             +G+  Q
Sbjct  3544  AGIKLQ  3549


> sp|P0C6W3|R1AB_BCHK4 Replicase polyprotein 1ab OS=Bat coronavirus 
HKU4 OX=694007 GN=rep PE=1 SV=1
Length=7119

 Score =  464 bits (1194),  Expect = 1e-146, Method: Composition-based stats.
 Identities = 152/309 (49%), Positives = 201/309 (65%), Gaps = 6/309 (2%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM+ PSG VE C+VQVTCG+ TLNGLWLD+ V+CPRH++C ++ + +PNY+ LLI 
Sbjct  3292  SGLVKMSAPSGAVENCIVQVTCGSMTLNGLWLDNTVWCPRHIMCPADQLTDPNYDALLIS  3351

Query  61    KSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLAC  117
             K+NH+F+VQ        LRV+ HSM   +LKL VD ANP TP Y F  ++PG +FSVLAC
Sbjct  3352  KTNHSFIVQKHIGAQANLRVVAHSMVGVLLKLTVDVANPSTPAYTFSTVKPGASFSVLAC  3411

Query  118   YNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDL  177
             YNG P+GV+   +R N TIKGSFL GSCGSVG+  +   ++F YMH MEL  G H G+  
Sbjct  3412  YNGKPTGVFTVNLRHNSTIKGSFLCGSCGSVGYTENGGVINFVYMHQMELSNGTHTGSSF  3471

Query  178   EGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKY  237
             +G  YG F D+QT Q   TD   T+NV+AWLYAAV+NG +WF+      +  +N  A+  
Sbjct  3472  DGVMYGAFEDKQTHQLQLTDKYCTINVVAWLYAAVLNGCKWFVKPTRVGIVTYNEWALSN  3531

Query  238   NYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVV  297
              +          +  L+ +TG++V  M A+++  L  G  G+TILG + LEDEFTP DV 
Sbjct  3532  QFTEFVG--TQSIDMLAHRTGVSVEQMLAAIQS-LHAGFQGKTILGQSTLEDEFTPDDVN  3588

Query  298   RQCSGVTFQ  306
              Q  GV  Q
Sbjct  3589  MQVMGVVMQ  3597


> sp|P0C6W4|R1AB_BCHK5 Replicase polyprotein 1ab OS=Bat coronavirus 
HKU5 OX=694008 GN=rep PE=3 SV=1
Length=7182

 Score =  464 bits (1194),  Expect = 1e-146, Method: Composition-based stats.
 Identities = 154/310 (50%), Positives = 207/310 (67%), Gaps = 8/310 (3%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KMA PSG VE CMVQVTCG+ TLNGLWLD+ V+CPRHV+C ++ + +PNY+ LL+ 
Sbjct  3339  SGLVKMAAPSGVVENCMVQVTCGSMTLNGLWLDNYVWCPRHVMCPADQLSDPNYDALLVS  3398

Query  61    KSNHNFLVQAG---NVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLAC  117
             K+N +F+VQ        LRV+GH+M   +LKL V++ANP+TP Y F  ++PG +FSVLAC
Sbjct  3399  KTNLSFIVQKNVGAPANLRVVGHTMVGTLLKLTVESANPQTPAYTFTTVKPGASFSVLAC  3458

Query  118   YNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDL  177
             YNG P+GV+   MR N TIKGSFL GSCGSVG+  + + ++FCYMH MEL  G H G   
Sbjct  3459  YNGRPTGVFMVNMRQNSTIKGSFLCGSCGSVGYTQEGNVINFCYMHQMELSNGTHTGCAF  3518

Query  178   EGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKY  237
             +G  YG F DRQ  Q   +D   T+N++AWLYAA++NG  WF+    T +  FN  AM  
Sbjct  3519  DGVMYGAFEDRQVHQVQLSDKYCTINIVAWLYAAILNGCNWFVKPNKTGIATFNEWAMSN  3578

Query  238   NYE-PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDV  296
              +   +    VD+   L+ +TG++V  +  +++  L  G  G+TILG+++LEDEFTP DV
Sbjct  3579  QFTEFIGTQSVDM---LAHKTGVSVEQLLYAIQT-LHKGFQGKTILGNSMLEDEFTPDDV  3634

Query  297   VRQCSGVTFQ  306
               Q  GV  Q
Sbjct  3635  NMQVMGVVMQ  3644


> sp|P0C6X3|R1AB_CVHN2 Replicase polyprotein 1ab OS=Human coronavirus 
HKU1 (isolate N2) OX=443240 GN=rep PE=3 SV=1
Length=7152

 Score =  464 bits (1194),  Expect = 1e-146, Method: Composition-based stats.
 Identities = 150/306 (49%), Positives = 193/306 (63%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ K+E C+V VT G+ TLNGLWLDD VYCPRHVIC S +M  P+Y  LL R
Sbjct  3305  SGIVKMVSPTSKIEPCIVSVTYGSMTLNGLWLDDKVYCPRHVICLSSNMNEPDYSALLCR  3364

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              +  +F + +G + L V+ + MQ C L L V   NP TPKY F  ++PG+TF+VLA YNG
Sbjct  3365  VTLGDFTIMSGRMSLTVVSYQMQGCQLVLTVSLQNPYTPKYTFGVVKPGETFTVLAAYNG  3424

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   MR ++TIKGSFL GSCGSVG+ +  D V F YMH +EL TG H GTD  GN
Sbjct  3425  RPQGAFHVTMRSSYTIKGSFLCGSCGSVGYVLTGDSVKFVYMHQLELSTGCHTGTDFTGN  3484

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D   TVNV+AWLYAA++N   WF+     ++ DFN+ AM   + 
Sbjct  3485  FYGPYRDAQVVQLPVKDYVQTVNVIAWLYAAILNNCAWFVQNDVCSIEDFNVWAMTNGFS  3544

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  L  L++ TG+++  + A++K L   G  GR ILGS   EDE  P DV +Q 
Sbjct  3545  QVKADLV--LDALASMTGVSIETLLAAIKRLYM-GFQGRQILGSCTFEDELAPSDVYQQL  3601

Query  301   SGVTFQ  306
             +GV  Q
Sbjct  3602  AGVKLQ  3607


> sp|P0C6X4|R1AB_CVHN5 Replicase polyprotein 1ab OS=Human coronavirus 
HKU1 (isolate N5) OX=443241 GN=rep PE=3 SV=1
Length=7132

 Score =  464 bits (1194),  Expect = 1e-146, Method: Composition-based stats.
 Identities = 150/306 (49%), Positives = 193/306 (63%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ K+E C+V VT G+ TLNGLWLDD VYCPRHVIC S +M  P+Y  LL R
Sbjct  3285  SGIVKMVSPTSKIEPCLVSVTYGSMTLNGLWLDDKVYCPRHVICLSSNMNEPDYSALLCR  3344

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              +  +F + +G + L V+ + MQ C L L V   NP TPKY F  ++PG+TF+VLA YNG
Sbjct  3345  VTLGDFTIMSGRMSLTVVSYQMQGCQLVLTVSLQNPYTPKYTFGVVKPGETFTVLAAYNG  3404

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   MR ++TIKGSFL GSCGSVG+ +  D V F YMH +EL TG H GTD  GN
Sbjct  3405  RPQGAFHVTMRSSYTIKGSFLCGSCGSVGYVLTGDSVKFVYMHQLELSTGCHTGTDFNGN  3464

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D   TVNV+AWLYAA++N   WF+     ++ DFN+ AM   + 
Sbjct  3465  FYGPYRDAQVVQLPVKDYVQTVNVIAWLYAAILNNCAWFVQNDVCSIEDFNVWAMTNGFS  3524

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  L  L++ TG+++  + A++K L   G  GR ILGS   EDE  P DV +Q 
Sbjct  3525  QVKADLV--LDALASMTGVSIETLLAAIKRLYM-GFQGRQILGSCTFEDELAPSDVYQQL  3581

Query  301   SGVTFQ  306
             +GV  Q
Sbjct  3582  AGVKLQ  3587


> sp|P0C6U4|R1A_CVHN2 Replicase polyprotein 1a OS=Human coronavirus 
HKU1 (isolate N2) OX=443240 GN=1a PE=3 SV=1
Length=4441

 Score =  463 bits (1192),  Expect = 1e-146, Method: Composition-based stats.
 Identities = 150/306 (49%), Positives = 193/306 (63%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ K+E C+V VT G+ TLNGLWLDD VYCPRHVIC S +M  P+Y  LL R
Sbjct  3305  SGIVKMVSPTSKIEPCIVSVTYGSMTLNGLWLDDKVYCPRHVICLSSNMNEPDYSALLCR  3364

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              +  +F + +G + L V+ + MQ C L L V   NP TPKY F  ++PG+TF+VLA YNG
Sbjct  3365  VTLGDFTIMSGRMSLTVVSYQMQGCQLVLTVSLQNPYTPKYTFGVVKPGETFTVLAAYNG  3424

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   MR ++TIKGSFL GSCGSVG+ +  D V F YMH +EL TG H GTD  GN
Sbjct  3425  RPQGAFHVTMRSSYTIKGSFLCGSCGSVGYVLTGDSVKFVYMHQLELSTGCHTGTDFTGN  3484

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D   TVNV+AWLYAA++N   WF+     ++ DFN+ AM   + 
Sbjct  3485  FYGPYRDAQVVQLPVKDYVQTVNVIAWLYAAILNNCAWFVQNDVCSIEDFNVWAMTNGFS  3544

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  L  L++ TG+++  + A++K L   G  GR ILGS   EDE  P DV +Q 
Sbjct  3545  QVKADLV--LDALASMTGVSIETLLAAIKRLYM-GFQGRQILGSCTFEDELAPSDVYQQL  3601

Query  301   SGVTFQ  306
             +GV  Q
Sbjct  3602  AGVKLQ  3607


> sp|P0C6T4|R1A_BCHK4 Replicase polyprotein 1a OS=Bat coronavirus 
HKU4 OX=694007 GN=1a PE=1 SV=1
Length=4434

 Score =  463 bits (1192),  Expect = 1e-146, Method: Composition-based stats.
 Identities = 152/309 (49%), Positives = 201/309 (65%), Gaps = 6/309 (2%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM+ PSG VE C+VQVTCG+ TLNGLWLD+ V+CPRH++C ++ + +PNY+ LLI 
Sbjct  3292  SGLVKMSAPSGAVENCIVQVTCGSMTLNGLWLDNTVWCPRHIMCPADQLTDPNYDALLIS  3351

Query  61    KSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLAC  117
             K+NH+F+VQ        LRV+ HSM   +LKL VD ANP TP Y F  ++PG +FSVLAC
Sbjct  3352  KTNHSFIVQKHIGAQANLRVVAHSMVGVLLKLTVDVANPSTPAYTFSTVKPGASFSVLAC  3411

Query  118   YNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDL  177
             YNG P+GV+   +R N TIKGSFL GSCGSVG+  +   ++F YMH MEL  G H G+  
Sbjct  3412  YNGKPTGVFTVNLRHNSTIKGSFLCGSCGSVGYTENGGVINFVYMHQMELSNGTHTGSSF  3471

Query  178   EGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKY  237
             +G  YG F D+QT Q   TD   T+NV+AWLYAAV+NG +WF+      +  +N  A+  
Sbjct  3472  DGVMYGAFEDKQTHQLQLTDKYCTINVVAWLYAAVLNGCKWFVKPTRVGIVTYNEWALSN  3531

Query  238   NYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVV  297
              +          +  L+ +TG++V  M A+++  L  G  G+TILG + LEDEFTP DV 
Sbjct  3532  QFTEFVG--TQSIDMLAHRTGVSVEQMLAAIQS-LHAGFQGKTILGQSTLEDEFTPDDVN  3588

Query  298   RQCSGVTFQ  306
              Q  GV  Q
Sbjct  3589  MQVMGVVMQ  3597


> sp|P0C6U5|R1A_CVHN5 Replicase polyprotein 1a OS=Human coronavirus 
HKU1 (isolate N5) OX=443241 GN=1a PE=3 SV=1
Length=4421

 Score =  463 bits (1192),  Expect = 1e-146, Method: Composition-based stats.
 Identities = 150/306 (49%), Positives = 193/306 (63%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ K+E C+V VT G+ TLNGLWLDD VYCPRHVIC S +M  P+Y  LL R
Sbjct  3285  SGIVKMVSPTSKIEPCLVSVTYGSMTLNGLWLDDKVYCPRHVICLSSNMNEPDYSALLCR  3344

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              +  +F + +G + L V+ + MQ C L L V   NP TPKY F  ++PG+TF+VLA YNG
Sbjct  3345  VTLGDFTIMSGRMSLTVVSYQMQGCQLVLTVSLQNPYTPKYTFGVVKPGETFTVLAAYNG  3404

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   MR ++TIKGSFL GSCGSVG+ +  D V F YMH +EL TG H GTD  GN
Sbjct  3405  RPQGAFHVTMRSSYTIKGSFLCGSCGSVGYVLTGDSVKFVYMHQLELSTGCHTGTDFNGN  3464

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D   TVNV+AWLYAA++N   WF+     ++ DFN+ AM   + 
Sbjct  3465  FYGPYRDAQVVQLPVKDYVQTVNVIAWLYAAILNNCAWFVQNDVCSIEDFNVWAMTNGFS  3524

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  L  L++ TG+++  + A++K L   G  GR ILGS   EDE  P DV +Q 
Sbjct  3525  QVKADLV--LDALASMTGVSIETLLAAIKRLYM-GFQGRQILGSCTFEDELAPSDVYQQL  3581

Query  301   SGVTFQ  306
             +GV  Q
Sbjct  3582  AGVKLQ  3587


> sp|P0C6W1|R1AB_BC133 Replicase polyprotein 1ab OS=Bat coronavirus 
133/2005 OX=389230 GN=rep PE=3 SV=1
Length=7126

 Score =  463 bits (1192),  Expect = 2e-146, Method: Composition-based stats.
 Identities = 152/309 (49%), Positives = 201/309 (65%), Gaps = 6/309 (2%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM+ PSG VE C+VQVTCG+ TLNGLWLD+ V+CPRH++C ++ + +PNY+ LLI 
Sbjct  3299  SGLVKMSAPSGAVENCIVQVTCGSMTLNGLWLDNTVWCPRHIMCPADQLTDPNYDALLIS  3358

Query  61    KSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLAC  117
             K+NH+F+VQ        LRV+ HSM   +LKL VD ANP TP Y F  ++PG +FSVLAC
Sbjct  3359  KTNHSFIVQKHIGAQANLRVVAHSMVGVLLKLTVDVANPSTPAYTFSTVKPGASFSVLAC  3418

Query  118   YNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDL  177
             YNG P+GV+   +R N TIKGSFL GSCGSVG+  +   ++F YMH MEL  G H G+  
Sbjct  3419  YNGKPTGVFTVNLRHNSTIKGSFLCGSCGSVGYTENGGVLNFVYMHQMELSNGTHTGSSF  3478

Query  178   EGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKY  237
             +G  YG F D+QT Q   TD   T+NV+AWLYAAV+NG +WF+      +  +N  A+  
Sbjct  3479  DGVMYGAFEDKQTHQLQLTDKYCTINVVAWLYAAVLNGCKWFVKPTRVGIVTYNEWALSN  3538

Query  238   NYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVV  297
              +          +  L+ +TG++V  M A+++  L  G  G+TILG + LEDEFTP DV 
Sbjct  3539  QFTEFVG--TQSIDMLAHRTGVSVEQMLAAIQS-LHAGFQGKTILGQSTLEDEFTPDDVN  3595

Query  298   RQCSGVTFQ  306
              Q  GV  Q
Sbjct  3596  MQVMGVVMQ  3604


> sp|P0C6T5|R1A_BCHK5 Replicase polyprotein 1a OS=Bat coronavirus 
HKU5 OX=694008 GN=1a PE=3 SV=1
Length=4481

 Score =  463 bits (1191),  Expect = 2e-146, Method: Composition-based stats.
 Identities = 154/310 (50%), Positives = 207/310 (67%), Gaps = 8/310 (3%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KMA PSG VE CMVQVTCG+ TLNGLWLD+ V+CPRHV+C ++ + +PNY+ LL+ 
Sbjct  3339  SGLVKMAAPSGVVENCMVQVTCGSMTLNGLWLDNYVWCPRHVMCPADQLSDPNYDALLVS  3398

Query  61    KSNHNFLVQAG---NVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLAC  117
             K+N +F+VQ        LRV+GH+M   +LKL V++ANP+TP Y F  ++PG +FSVLAC
Sbjct  3399  KTNLSFIVQKNVGAPANLRVVGHTMVGTLLKLTVESANPQTPAYTFTTVKPGASFSVLAC  3458

Query  118   YNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDL  177
             YNG P+GV+   MR N TIKGSFL GSCGSVG+  + + ++FCYMH MEL  G H G   
Sbjct  3459  YNGRPTGVFMVNMRQNSTIKGSFLCGSCGSVGYTQEGNVINFCYMHQMELSNGTHTGCAF  3518

Query  178   EGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKY  237
             +G  YG F DRQ  Q   +D   T+N++AWLYAA++NG  WF+    T +  FN  AM  
Sbjct  3519  DGVMYGAFEDRQVHQVQLSDKYCTINIVAWLYAAILNGCNWFVKPNKTGIATFNEWAMSN  3578

Query  238   NYE-PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDV  296
              +   +    VD+   L+ +TG++V  +  +++  L  G  G+TILG+++LEDEFTP DV
Sbjct  3579  QFTEFIGTQSVDM---LAHKTGVSVEQLLYAIQT-LHKGFQGKTILGNSMLEDEFTPDDV  3634

Query  297   VRQCSGVTFQ  306
               Q  GV  Q
Sbjct  3635  NMQVMGVVMQ  3644


> sp|P0C6X2|R1AB_CVHN1 Replicase polyprotein 1ab OS=Human coronavirus 
HKU1 (isolate N1) OX=443239 GN=rep PE=3 SV=1
Length=7182

 Score =  463 bits (1192),  Expect = 2e-146, Method: Composition-based stats.
 Identities = 150/306 (49%), Positives = 193/306 (63%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ K+E C+V VT G+ TLNGLWLDD VYCPRHVIC+S +M  P+Y  LL R
Sbjct  3335  SGIVKMVSPTSKIEPCIVSVTYGSMTLNGLWLDDKVYCPRHVICSSSNMNEPDYSALLCR  3394

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              +  +F + +G + L V+ + MQ C L L V   NP TPKY F  ++PG+TF+VLA YNG
Sbjct  3395  VTLGDFTIMSGRMSLTVVSYQMQGCQLVLTVSLQNPYTPKYTFGNVKPGETFTVLAAYNG  3454

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   MR ++TIKGSFL GSCGSVG+ +  D V F YMH +EL TG H GTD  GN
Sbjct  3455  RPQGAFHVTMRSSYTIKGSFLCGSCGSVGYVLTGDSVKFVYMHQLELSTGCHTGTDFTGN  3514

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D   TVNV+AWLYAA++N   WF+     +  DFN+ AM   + 
Sbjct  3515  FYGPYRDAQVVQLPVKDYVQTVNVIAWLYAAILNNCAWFVQNDVCSTEDFNVWAMANGFS  3574

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  L  L++ TG+++  + A++K L   G  GR ILGS   EDE  P DV +Q 
Sbjct  3575  QVKADLV--LDALASMTGVSIETLLAAIKRLYM-GFQGRQILGSCTFEDELAPSDVYQQL  3631

Query  301   SGVTFQ  306
             +GV  Q
Sbjct  3632  AGVKLQ  3637


> sp|P0C6U3|R1A_CVHN1 Replicase polyprotein 1a OS=Human coronavirus 
HKU1 (isolate N1) OX=443239 GN=1a PE=1 SV=1
Length=4471

 Score =  462 bits (1190),  Expect = 2e-146, Method: Composition-based stats.
 Identities = 150/306 (49%), Positives = 193/306 (63%), Gaps = 3/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM  P+ K+E C+V VT G+ TLNGLWLDD VYCPRHVIC+S +M  P+Y  LL R
Sbjct  3335  SGIVKMVSPTSKIEPCIVSVTYGSMTLNGLWLDDKVYCPRHVICSSSNMNEPDYSALLCR  3394

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              +  +F + +G + L V+ + MQ C L L V   NP TPKY F  ++PG+TF+VLA YNG
Sbjct  3395  VTLGDFTIMSGRMSLTVVSYQMQGCQLVLTVSLQNPYTPKYTFGNVKPGETFTVLAAYNG  3454

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P G +   MR ++TIKGSFL GSCGSVG+ +  D V F YMH +EL TG H GTD  GN
Sbjct  3455  RPQGAFHVTMRSSYTIKGSFLCGSCGSVGYVLTGDSVKFVYMHQLELSTGCHTGTDFTGN  3514

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGP+ D Q  Q    D   TVNV+AWLYAA++N   WF+     +  DFN+ AM   + 
Sbjct  3515  FYGPYRDAQVVQLPVKDYVQTVNVIAWLYAAILNNCAWFVQNDVCSTEDFNVWAMANGFS  3574

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  D V  L  L++ TG+++  + A++K L   G  GR ILGS   EDE  P DV +Q 
Sbjct  3575  QVKADLV--LDALASMTGVSIETLLAAIKRLYM-GFQGRQILGSCTFEDELAPSDVYQQL  3631

Query  301   SGVTFQ  306
             +GV  Q
Sbjct  3632  AGVKLQ  3637


> sp|P0C6F7|R1A_BC133 Replicase polyprotein 1a OS=Bat coronavirus 
133/2005 OX=389230 GN=1a PE=3 SV=1
Length=4441

 Score =  462 bits (1190),  Expect = 3e-146, Method: Composition-based stats.
 Identities = 152/309 (49%), Positives = 201/309 (65%), Gaps = 6/309 (2%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG  KM+ PSG VE C+VQVTCG+ TLNGLWLD+ V+CPRH++C ++ + +PNY+ LLI 
Sbjct  3299  SGLVKMSAPSGAVENCIVQVTCGSMTLNGLWLDNTVWCPRHIMCPADQLTDPNYDALLIS  3358

Query  61    KSNHNFLVQ---AGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLAC  117
             K+NH+F+VQ        LRV+ HSM   +LKL VD ANP TP Y F  ++PG +FSVLAC
Sbjct  3359  KTNHSFIVQKHIGAQANLRVVAHSMVGVLLKLTVDVANPSTPAYTFSTVKPGASFSVLAC  3418

Query  118   YNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDL  177
             YNG P+GV+   +R N TIKGSFL GSCGSVG+  +   ++F YMH MEL  G H G+  
Sbjct  3419  YNGKPTGVFTVNLRHNSTIKGSFLCGSCGSVGYTENGGVLNFVYMHQMELSNGTHTGSSF  3478

Query  178   EGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKY  237
             +G  YG F D+QT Q   TD   T+NV+AWLYAAV+NG +WF+      +  +N  A+  
Sbjct  3479  DGVMYGAFEDKQTHQLQLTDKYCTINVVAWLYAAVLNGCKWFVKPTRVGIVTYNEWALSN  3538

Query  238   NYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVV  297
              +          +  L+ +TG++V  M A+++  L  G  G+TILG + LEDEFTP DV 
Sbjct  3539  QFTEFVG--TQSIDMLAHRTGVSVEQMLAAIQS-LHAGFQGKTILGQSTLEDEFTPDDVN  3595

Query  298   RQCSGVTFQ  306
              Q  GV  Q
Sbjct  3596  MQVMGVVMQ  3604


> sp|P0C6Y4|R1AB_PEDV7 Replicase polyprotein 1ab OS=Porcine epidemic 
diarrhea virus (strain CV777) OX=229032 GN=rep PE=1 SV=1
Length=6781

 Score =  456 bits (1174),  Expect = 5e-144, Method: Composition-based stats.
 Identities = 137/306 (45%), Positives = 195/306 (64%), Gaps = 4/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             +G RKMA PSG VE C+V+V  G   LNGLWL D+V CPRHVI +S      +Y+  L  
Sbjct  2998  AGLRKMAQPSGVVEKCIVRVCYGNMALNGLWLGDIVMCPRHVIASSTTST-IDYDYALSV  3056

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
                HNF + +GNV L V+  +M+  +L++KV+  N  TPKY +  ++PG++F++LACY+G
Sbjct  3057  LRLHNFSISSGNVFLGVVSATMRGALLQIKVNQNNVHTPKYTYRTVRPGESFNILACYDG  3116

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
             + +GVY   MR N+TI+GSF+NG+CGS G+NI+   V FCY+H +EL +G H G+DL+G 
Sbjct  3117  AAAGVYGVNMRSNYTIRGSFINGACGSPGYNINNGTVEFCYLHQLELGSGCHVGSDLDGV  3176

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
              YG + D+ T Q  G  +  T NVLA+LYAA+ING  W+L+     ++ FN  A+     
Sbjct  3177  MYGGYEDQPTLQVEGASSLFTENVLAFLYAALINGSTWWLSSSRIAVDRFNEWAVHNGMT  3236

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +   + D    L+A+TG+ V  + AS++ L +N   G+ ILG   L DEFT  +VVRQ 
Sbjct  3237  TVG--NTDCFSILAAKTGVDVQRLLASIQSLHKN-FGGKQILGHTSLTDEFTTGEVVRQM  3293

Query  301   SGVTFQ  306
              GV  Q
Sbjct  3294  YGVNLQ  3299


> sp|P0C6V6|R1A_PEDV7 Replicase polyprotein 1a OS=Porcine epidemic 
diarrhea virus (strain CV777) OX=229032 GN=1a PE=1 SV=1
Length=4117

 Score =  455 bits (1172),  Expect = 6e-144, Method: Composition-based stats.
 Identities = 137/306 (45%), Positives = 195/306 (64%), Gaps = 4/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             +G RKMA PSG VE C+V+V  G   LNGLWL D+V CPRHVI +S      +Y+  L  
Sbjct  2998  AGLRKMAQPSGVVEKCIVRVCYGNMALNGLWLGDIVMCPRHVIASSTTST-IDYDYALSV  3056

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
                HNF + +GNV L V+  +M+  +L++KV+  N  TPKY +  ++PG++F++LACY+G
Sbjct  3057  LRLHNFSISSGNVFLGVVSATMRGALLQIKVNQNNVHTPKYTYRTVRPGESFNILACYDG  3116

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
             + +GVY   MR N+TI+GSF+NG+CGS G+NI+   V FCY+H +EL +G H G+DL+G 
Sbjct  3117  AAAGVYGVNMRSNYTIRGSFINGACGSPGYNINNGTVEFCYLHQLELGSGCHVGSDLDGV  3176

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
              YG + D+ T Q  G  +  T NVLA+LYAA+ING  W+L+     ++ FN  A+     
Sbjct  3177  MYGGYEDQPTLQVEGASSLFTENVLAFLYAALINGSTWWLSSSRIAVDRFNEWAVHNGMT  3236

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +   + D    L+A+TG+ V  + AS++ L +N   G+ ILG   L DEFT  +VVRQ 
Sbjct  3237  TVG--NTDCFSILAAKTGVDVQRLLASIQSLHKN-FGGKQILGHTSLTDEFTTGEVVRQM  3293

Query  301   SGVTFQ  306
              GV  Q
Sbjct  3294  YGVNLQ  3299


> sp|P0C6T6|R1A_BCHK9 Replicase polyprotein 1a OS=Bat coronavirus 
HKU9 OX=694006 GN=1a PE=3 SV=1
Length=4248

 Score =  455 bits (1172),  Expect = 7e-144, Method: Composition-based stats.
 Identities = 159/306 (52%), Positives = 214/306 (70%), Gaps = 0/306 (0%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             +G  +MA PSG VE C+V+V  G+ TLNG+WLD+ V CPRHV+C+ +++ NP+Y  L +R
Sbjct  3104  AGLTRMAHPSGLVEPCLVKVNYGSMTLNGIWLDNFVICPRHVMCSRDELANPDYPRLSMR  3163

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              +N++F V      +RVIGH+M+  +LKL VD  NPKTP Y F+R+  GQ  S+LACY+G
Sbjct  3164  AANYDFHVSQNGHNIRVIGHTMEGSLLKLTVDVNNPKTPAYSFIRVSTGQAMSLLACYDG  3223

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P+GVY C +R N T++ SFL GSCGS GF ++   V FCY+H +ELP G H GTD  G 
Sbjct  3224  LPTGVYTCTLRSNGTMRASFLCGSCGSPGFVMNGKEVQFCYLHQLELPNGTHTGTDFSGV  3283

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGPF D+Q  Q A  D TITVNVLAWLYAAV++G+ WFL + + +  +FN  A+KY  +
Sbjct  3284  FYGPFEDKQVPQLAAPDCTITVNVLAWLYAAVLSGENWFLTKSSISPAEFNNCAVKYMCQ  3343

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +T + + +L PL+A+TGI+V  M ++LK LL  G  GRTI+GS  LEDE TP+D+ RQ 
Sbjct  3344  SVTSESLQVLQPLAAKTGISVERMLSALKVLLSAGFCGRTIMGSCSLEDEHTPYDIGRQM  3403

Query  301   SGVTFQ  306
              GV  Q
Sbjct  3404  LGVKLQ  3409


> sp|P0C6F6|R1A_BC512 Replicase polyprotein 1a OS=Bat coronavirus 
512/2005 OX=693999 GN=1a PE=3 SV=1
Length=4128

 Score =  455 bits (1171),  Expect = 9e-144, Method: Composition-based stats.
 Identities = 139/306 (45%), Positives = 200/306 (65%), Gaps = 4/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             +G RKMA PSG VEGC+V+V+ G  TLNGLWL D V CPRHVI ++      +Y+  +  
Sbjct  3013  AGLRKMAQPSGIVEGCIVRVSYGNLTLNGLWLGDTVICPRHVIASNTT-NVIDYDHAMSL  3071

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
                HNF + +GN+ L VI  SM+  +L +KV+ +N  TP Y +  ++PG +F++LACY+G
Sbjct  3072  VRLHNFSISSGNMFLGVISASMRGTLLHIKVNQSNVNTPNYTYKVLKPGDSFNILACYDG  3131

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
             S +GVY   MR N+TI+GSF++G+CGS G+NI+   V FCYMHH+EL +G H G+D++G 
Sbjct  3132  SAAGVYGVNMRTNYTIRGSFISGACGSPGYNINNGVVEFCYMHHLELGSGCHVGSDMDGT  3191

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
              YG + D+ T Q  G    +T NV +WLY A+INGDRW+L+  +  ++ +N  A++    
Sbjct  3192  MYGKYEDQPTLQIEGASNLVTENVCSWLYGALINGDRWWLSSVSVGVDTYNEWALRNGMT  3251

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              L   +VD    L A+TG+ V  + AS+++L  N   G++ILG   L DEFT  +VV+Q 
Sbjct  3252  ALK--NVDCFSLLVAKTGVDVGRLLASIQKLHGN-FGGKSILGCTSLCDEFTLSEVVKQM  3308

Query  301   SGVTFQ  306
              GVT Q
Sbjct  3309  YGVTLQ  3314


> sp|P0C6W5|R1AB_BCHK9 Replicase polyprotein 1ab OS=Bat coronavirus 
HKU9 OX=694006 GN=rep PE=1 SV=1
Length=6930

 Score =  455 bits (1172),  Expect = 1e-143, Method: Composition-based stats.
 Identities = 159/306 (52%), Positives = 214/306 (70%), Gaps = 0/306 (0%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             +G  +MA PSG VE C+V+V  G+ TLNG+WLD+ V CPRHV+C+ +++ NP+Y  L +R
Sbjct  3104  AGLTRMAHPSGLVEPCLVKVNYGSMTLNGIWLDNFVICPRHVMCSRDELANPDYPRLSMR  3163

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
              +N++F V      +RVIGH+M+  +LKL VD  NPKTP Y F+R+  GQ  S+LACY+G
Sbjct  3164  AANYDFHVSQNGHNIRVIGHTMEGSLLKLTVDVNNPKTPAYSFIRVSTGQAMSLLACYDG  3223

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P+GVY C +R N T++ SFL GSCGS GF ++   V FCY+H +ELP G H GTD  G 
Sbjct  3224  LPTGVYTCTLRSNGTMRASFLCGSCGSPGFVMNGKEVQFCYLHQLELPNGTHTGTDFSGV  3283

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
             FYGPF D+Q  Q A  D TITVNVLAWLYAAV++G+ WFL + + +  +FN  A+KY  +
Sbjct  3284  FYGPFEDKQVPQLAAPDCTITVNVLAWLYAAVLSGENWFLTKSSISPAEFNNCAVKYMCQ  3343

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +T + + +L PL+A+TGI+V  M ++LK LL  G  GRTI+GS  LEDE TP+D+ RQ 
Sbjct  3344  SVTSESLQVLQPLAAKTGISVERMLSALKVLLSAGFCGRTIMGSCSLEDEHTPYDIGRQM  3403

Query  301   SGVTFQ  306
              GV  Q
Sbjct  3404  LGVKLQ  3409


> sp|P0C6V2|R1A_CVPPU Replicase polyprotein 1a OS=Porcine transmissible 
gastroenteritis coronavirus (strain Purdue) OX=11151 
GN=1a PE=1 SV=1
Length=4017

 Score =  454 bits (1169),  Expect = 2e-143, Method: Composition-based stats.
 Identities = 136/306 (44%), Positives = 185/306 (60%), Gaps = 4/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG RKMA PSG VE C+V+V+ G   LNGLWL D V CPRHVI +    +  NYE+ +  
Sbjct  2879  SGLRKMAQPSGLVEPCIVRVSYGNNVLNGLWLGDEVICPRHVIASDTTRV-INYENEMSS  2937

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
                HNF V   NV L V+    +   L LKV+  NP TP++KF  I+ G++F++LACY G
Sbjct  2938  VRLHNFSVSKNNVFLGVVSARYKGVNLVLKVNQVNPNTPEHKFKSIKAGESFNILACYEG  2997

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P  VY   MR   TIKGSF+ G+CGSVG+ ++   + F YMHH+EL  G H G++ EG 
Sbjct  2998  CPGSVYGVNMRSQGTIKGSFIAGTCGSVGYVLENGILYFVYMHHLELGNGSHVGSNFEGE  3057

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
              YG + D+ + Q  GT+   + NV+A+LYAA+ING+RWF+   + +L  +N  A   ++ 
Sbjct  3058  MYGGYEDQPSMQLEGTNVMSSDNVVAFLYAALINGERWFVTNTSMSLESYNTWAKTNSFT  3117

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              L+    D    L+A+TG +V  +  S+   L  G  GRTIL    L DEFTP +V+RQ 
Sbjct  3118  ELSS--TDAFSMLAAKTGQSVEKLLDSIVR-LNKGFGGRTILSYGSLCDEFTPTEVIRQM  3174

Query  301   SGVTFQ  306
              GV  Q
Sbjct  3175  YGVNLQ  3180


> sp|P0C6W0|R1AB_BC512 Replicase polyprotein 1ab OS=Bat coronavirus 
512/2005 OX=693999 GN=rep PE=3 SV=1
Length=6793

 Score =  455 bits (1170),  Expect = 2e-143, Method: Composition-based stats.
 Identities = 139/306 (45%), Positives = 200/306 (65%), Gaps = 4/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             +G RKMA PSG VEGC+V+V+ G  TLNGLWL D V CPRHVI ++      +Y+  +  
Sbjct  3013  AGLRKMAQPSGIVEGCIVRVSYGNLTLNGLWLGDTVICPRHVIASNTT-NVIDYDHAMSL  3071

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
                HNF + +GN+ L VI  SM+  +L +KV+ +N  TP Y +  ++PG +F++LACY+G
Sbjct  3072  VRLHNFSISSGNMFLGVISASMRGTLLHIKVNQSNVNTPNYTYKVLKPGDSFNILACYDG  3131

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
             S +GVY   MR N+TI+GSF++G+CGS G+NI+   V FCYMHH+EL +G H G+D++G 
Sbjct  3132  SAAGVYGVNMRTNYTIRGSFISGACGSPGYNINNGVVEFCYMHHLELGSGCHVGSDMDGT  3191

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
              YG + D+ T Q  G    +T NV +WLY A+INGDRW+L+  +  ++ +N  A++    
Sbjct  3192  MYGKYEDQPTLQIEGASNLVTENVCSWLYGALINGDRWWLSSVSVGVDTYNEWALRNGMT  3251

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              L   +VD    L A+TG+ V  + AS+++L  N   G++ILG   L DEFT  +VV+Q 
Sbjct  3252  ALK--NVDCFSLLVAKTGVDVGRLLASIQKLHGN-FGGKSILGCTSLCDEFTLSEVVKQM  3308

Query  301   SGVTFQ  306
              GVT Q
Sbjct  3309  YGVTLQ  3314


> sp|P0C6Y5|R1AB_CVPPU Replicase polyprotein 1ab OS=Porcine transmissible 
gastroenteritis coronavirus (strain Purdue) OX=11151 
GN=rep PE=1 SV=1
Length=6684

 Score =  454 bits (1169),  Expect = 2e-143, Method: Composition-based stats.
 Identities = 136/306 (44%), Positives = 185/306 (60%), Gaps = 4/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG RKMA PSG VE C+V+V+ G   LNGLWL D V CPRHVI +    +  NYE+ +  
Sbjct  2879  SGLRKMAQPSGLVEPCIVRVSYGNNVLNGLWLGDEVICPRHVIASDTTRV-INYENEMSS  2937

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
                HNF V   NV L V+    +   L LKV+  NP TP++KF  I+ G++F++LACY G
Sbjct  2938  VRLHNFSVSKNNVFLGVVSARYKGVNLVLKVNQVNPNTPEHKFKSIKAGESFNILACYEG  2997

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P  VY   MR   TIKGSF+ G+CGSVG+ ++   + F YMHH+EL  G H G++ EG 
Sbjct  2998  CPGSVYGVNMRSQGTIKGSFIAGTCGSVGYVLENGILYFVYMHHLELGNGSHVGSNFEGE  3057

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
              YG + D+ + Q  GT+   + NV+A+LYAA+ING+RWF+   + +L  +N  A   ++ 
Sbjct  3058  MYGGYEDQPSMQLEGTNVMSSDNVVAFLYAALINGERWFVTNTSMSLESYNTWAKTNSFT  3117

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              L+    D    L+A+TG +V  +  S+   L  G  GRTIL    L DEFTP +V+RQ 
Sbjct  3118  ELSS--TDAFSMLAAKTGQSVEKLLDSIVR-LNKGFGGRTILSYGSLCDEFTPTEVIRQM  3174

Query  301   SGVTFQ  306
              GV  Q
Sbjct  3175  YGVNLQ  3180


> sp|Q98VG9|R1AB_FIPV Replicase polyprotein 1ab OS=Feline coronavirus 
(strain FIPV WSU-79/1146) OX=33734 GN=rep PE=1 SV=2
Length=6709

 Score =  452 bits (1164),  Expect = 9e-143, Method: Composition-based stats.
 Identities = 135/306 (44%), Positives = 183/306 (60%), Gaps = 4/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG RKMA PSG VE C+V+V  G   LNGLWL D V CPRHVI +    +  NYE+ L  
Sbjct  2904  SGLRKMAQPSGVVEPCIVRVAYGNNVLNGLWLGDEVICPRHVIASDTSRV-INYENELSS  2962

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
                HNF +   N  L V+    +   L LKV+  NP TP++KF  ++PG++F++LACY G
Sbjct  2963  VRLHNFSIAKNNAFLGVVSAKYKGVNLVLKVNQVNPNTPEHKFKSVRPGESFNILACYEG  3022

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
              P  VY   MR   TIKGSF+ G+CGSVG+ ++   + F YMHH+EL  G H G++LEG 
Sbjct  3023  CPGSVYGVNMRSQGTIKGSFIAGTCGSVGYVLENGTLYFVYMHHLELGNGSHVGSNLEGE  3082

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
              YG + D+ + Q  GT+   + NV+A+LYAA+ING+RWF+   + TL  +N  A   ++ 
Sbjct  3083  MYGGYEDQPSMQLEGTNVMSSDNVVAFLYAALINGERWFVTNTSMTLESYNAWAKTNSFT  3142

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +     D    L+A+TG +V  +   +   L  G  GRTIL    L DEFTP +V+RQ 
Sbjct  3143  EIVS--TDAFNMLAAKTGYSVEKLLECIVR-LNKGFGGRTILSYGSLCDEFTPTEVIRQM  3199

Query  301   SGVTFQ  306
              GV  Q
Sbjct  3200  YGVNLQ  3205


> sp|P0C6U2|R1A_CVH22 Replicase polyprotein 1a OS=Human coronavirus 
229E OX=11137 GN=1a PE=1 SV=1
Length=4085

 Score =  448 bits (1152),  Expect = 3e-141, Method: Composition-based stats.
 Identities = 125/306 (41%), Positives = 183/306 (60%), Gaps = 4/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             +G RKMA PSG VE C+V+V  G T LNGLWL D+VYCPRHVI ++      +Y+     
Sbjct  2966  AGLRKMAQPSGFVEKCVVRVCYGNTVLNGLWLGDIVYCPRHVIASNTT-SAIDYDHEYSI  3024

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
                HNF + +G   L V+G +M    LK+KV   N  TP++ F  ++ G+ F++LACY+G
Sbjct  3025  MRLHNFSIISGTAFLGVVGATMHGVTLKIKVSQTNMHTPRHSFRTLKSGEGFNILACYDG  3084

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
                GV+   MR N+TI+GSF+NG+CGS G+N+    V F YMH +EL +G H G+  +G 
Sbjct  3085  CAQGVFGVNMRTNWTIRGSFINGACGSPGYNLKNGEVEFVYMHQIELGSGSHVGSSFDGV  3144

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
              YG F D+   Q    +  +TVNV+A+LYAA++NG  W+L      +  +N  A    + 
Sbjct  3145  MYGGFEDQPNLQVESANQMLTVNVVAFLYAAILNGCTWWLKGEKLFVEHYNEWAQANGFT  3204

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  +  D    L+A+TG+ V  +  +++ +L NG  G+ ILG + L DEF+  +VV+Q 
Sbjct  3205  AMNGE--DAFSILAAKTGVCVERLLHAIQ-VLNNGFGGKQILGYSSLNDEFSINEVVKQM  3261

Query  301   SGVTFQ  306
              GV  Q
Sbjct  3262  FGVNLQ  3267


> sp|P0C6X1|R1AB_CVH22 Replicase polyprotein 1ab OS=Human coronavirus 
229E OX=11137 GN=rep PE=1 SV=1
Length=6758

 Score =  447 bits (1151),  Expect = 6e-141, Method: Composition-based stats.
 Identities = 125/306 (41%), Positives = 183/306 (60%), Gaps = 4/306 (1%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             +G RKMA PSG VE C+V+V  G T LNGLWL D+VYCPRHVI ++      +Y+     
Sbjct  2966  AGLRKMAQPSGFVEKCVVRVCYGNTVLNGLWLGDIVYCPRHVIASNTT-SAIDYDHEYSI  3024

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
                HNF + +G   L V+G +M    LK+KV   N  TP++ F  ++ G+ F++LACY+G
Sbjct  3025  MRLHNFSIISGTAFLGVVGATMHGVTLKIKVSQTNMHTPRHSFRTLKSGEGFNILACYDG  3084

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN  180
                GV+   MR N+TI+GSF+NG+CGS G+N+    V F YMH +EL +G H G+  +G 
Sbjct  3085  CAQGVFGVNMRTNWTIRGSFINGACGSPGYNLKNGEVEFVYMHQIELGSGSHVGSSFDGV  3144

Query  181   FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE  240
              YG F D+   Q    +  +TVNV+A+LYAA++NG  W+L      +  +N  A    + 
Sbjct  3145  MYGGFEDQPNLQVESANQMLTVNVVAFLYAAILNGCTWWLKGEKLFVEHYNEWAQANGFT  3204

Query  241   PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC  300
              +  +  D    L+A+TG+ V  +  +++ +L NG  G+ ILG + L DEF+  +VV+Q 
Sbjct  3205  AMNGE--DAFSILAAKTGVCVERLLHAIQ-VLNNGFGGKQILGYSSLNDEFSINEVVKQM  3261

Query  301   SGVTFQ  306
              GV  Q
Sbjct  3262  FGVNLQ  3267


> sp|P0C6X5|R1AB_CVHNL Replicase polyprotein 1ab OS=Human coronavirus 
NL63 OX=277944 GN=rep PE=1 SV=1
Length=6729

 Score =  443 bits (1140),  Expect = 2e-139, Method: Composition-based stats.
 Identities = 135/307 (44%), Positives = 191/307 (62%), Gaps = 5/307 (2%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG +KMA PSG VE C+V+V  G+T LNG+WL D V CPRHVI  S  +L  +Y+     
Sbjct  2940  SGLKKMAQPSGCVERCVVRVCYGSTVLNGVWLGDTVTCPRHVIAPSTTVL-IDYDHAYST  2998

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
                HNF V    V L V+G +M   VL++KV  +N  TPK+ F  ++PG +F++LACY G
Sbjct  2999  MRLHNFSVSHNGVFLGVVGVTMHGSVLRIKVSQSNVHTPKHVFKTLKPGDSFNILACYEG  3058

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDY-DCVSFCYMHHMELPTGVHAGTDLEG  179
               SGV+   +R NFTIKGSF+NG+CGS G+N+     V FCY+H +EL +G H G+D  G
Sbjct  3059  IASGVFGVNLRTNFTIKGSFINGACGSPGYNVRNDGTVEFCYLHQIELGSGAHVGSDFTG  3118

Query  180   NFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNY  239
             + YG F D+ + Q    +  ++ NV+A+LYAA++NG RW+L      ++ FN  AM   Y
Sbjct  3119  SVYGNFDDQPSLQVESANLMLSDNVVAFLYAALLNGCRWWLCSTRVNVDGFNEWAMANGY  3178

Query  240   EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQ  299
               ++   V+    L+A+TG++V  + AS++  L  G  G+ ILG + L DEFT  +VV+Q
Sbjct  3179  TSVSS--VECYSILAAKTGVSVEQLLASIQH-LHEGFGGKNILGYSSLCDEFTLAEVVKQ  3235

Query  300   CSGVTFQ  306
               GV  Q
Sbjct  3236  MYGVNLQ  3242


> sp|P0C6U6|R1A_CVHNL Replicase polyprotein 1a OS=Human coronavirus 
NL63 OX=277944 GN=1a PE=1 SV=1
Length=4060

 Score =  442 bits (1138),  Expect = 2e-139, Method: Composition-based stats.
 Identities = 135/307 (44%), Positives = 191/307 (62%), Gaps = 5/307 (2%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SG +KMA PSG VE C+V+V  G+T LNG+WL D V CPRHVI  S  +L  +Y+     
Sbjct  2940  SGLKKMAQPSGCVERCVVRVCYGSTVLNGVWLGDTVTCPRHVIAPSTTVL-IDYDHAYST  2998

Query  61    KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG  120
                HNF V    V L V+G +M   VL++KV  +N  TPK+ F  ++PG +F++LACY G
Sbjct  2999  MRLHNFSVSHNGVFLGVVGVTMHGSVLRIKVSQSNVHTPKHVFKTLKPGDSFNILACYEG  3058

Query  121   SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDY-DCVSFCYMHHMELPTGVHAGTDLEG  179
               SGV+   +R NFTIKGSF+NG+CGS G+N+     V FCY+H +EL +G H G+D  G
Sbjct  3059  IASGVFGVNLRTNFTIKGSFINGACGSPGYNVRNDGTVEFCYLHQIELGSGAHVGSDFTG  3118

Query  180   NFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNY  239
             + YG F D+ + Q    +  ++ NV+A+LYAA++NG RW+L      ++ FN  AM   Y
Sbjct  3119  SVYGNFDDQPSLQVESANLMLSDNVVAFLYAALLNGCRWWLCSTRVNVDGFNEWAMANGY  3178

Query  240   EPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQ  299
               ++   V+    L+A+TG++V  + AS++  L  G  G+ ILG + L DEFT  +VV+Q
Sbjct  3179  TSVSS--VECYSILAAKTGVSVEQLLASIQH-LHEGFGGKNILGYSSLCDEFTLAEVVKQ  3235

Query  300   CSGVTFQ  306
               GV  Q
Sbjct  3236  MYGVNLQ  3242


> sp|P0C6V4|R1A_IBVBC Replicase polyprotein 1a OS=Avian infectious 
bronchitis virus (strain Beaudette CK) OX=160235 GN=1a PE=3 
SV=1
Length=3951

 Score =  398 bits (1023),  Expect = 5e-124, Method: Composition-based stats.
 Identities = 125/313 (40%), Positives = 174/313 (56%), Gaps = 13/313 (4%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SGF+K+  PS  VE C+V V+     LNGLWL D +YCPRHV+          + D+L  
Sbjct  2780  SGFKKLVSPSSAVEKCIVSVSYRGNNLNGLWLGDTIYCPRHVL---GKFSGDQWNDVLNL  2836

Query  61    KSNHNFLVQAGN-VQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYN  119
              +NH F V   + V L V+   ++  VL L+   AN +TPKYKF++   G +F++   Y 
Sbjct  2837  ANNHEFEVTTQHGVTLNVVSRRLKGAVLILQTAVANAETPKYKFIKANCGDSFTIACAYG  2896

Query  120   GSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEG  179
             G+  G+Y   MR N TI+ SFL G+CGSVGFNI+   V+F YMHH+ELP  +H GTDL G
Sbjct  2897  GTVVGLYPVTMRSNGTIRASFLAGACGSVGFNIEKGVVNFFYMHHLELPNALHTGTDLMG  2956

Query  180   NFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRW------FLNRFTTTLNDFNLV  233
              FYG +VD + AQ    D  +T N++AWLYAA+I+          +L   T +++D+N  
Sbjct  2957  EFYGGYVDEEVAQRVPPDNLVTNNIVAWLYAAIISVKESSFSLPKWLESTTVSVDDYNKW  3016

Query  234   AMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTP  293
             A    + P +      +  LSA TG+ V  +  ++  +  +   G  ILG    EDE TP
Sbjct  3017  AGDNGFTPFSTST--AITKLSAITGVDVCKLLRTIM-VKNSQWGGDPILGQYNFEDELTP  3073

Query  294   FDVVRQCSGVTFQ  306
               V  Q  GV  Q
Sbjct  3074  ESVFNQIGGVRLQ  3086


> sp|P0C6V3|R1A_IBVB Replicase polyprotein 1a OS=Avian infectious 
bronchitis virus (strain Beaudette) OX=11122 GN=1a PE=1 SV=1
Length=3951

 Score =  398 bits (1023),  Expect = 5e-124, Method: Composition-based stats.
 Identities = 125/313 (40%), Positives = 174/313 (56%), Gaps = 13/313 (4%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SGF+K+  PS  VE C+V V+     LNGLWL D +YCPRHV+          + D+L  
Sbjct  2780  SGFKKLVSPSSAVEKCIVSVSYRGNNLNGLWLGDTIYCPRHVL---GKFSGDQWNDVLNL  2836

Query  61    KSNHNFLVQAGN-VQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYN  119
              +NH F V   + V L V+   ++  VL L+   AN +TPKYKF++   G +F++   Y 
Sbjct  2837  ANNHEFEVTTQHGVTLNVVSRRLKGAVLILQTAVANAETPKYKFIKANCGDSFTIACAYG  2896

Query  120   GSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEG  179
             G+  G+Y   MR N TI+ SFL G+CGSVGFNI+   V+F YMHH+ELP  +H GTDL G
Sbjct  2897  GTVVGLYPVTMRSNGTIRASFLAGACGSVGFNIEKGVVNFFYMHHLELPNALHTGTDLMG  2956

Query  180   NFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRW------FLNRFTTTLNDFNLV  233
              FYG +VD + AQ    D  +T N++AWLYAA+I+          +L   T +++D+N  
Sbjct  2957  EFYGGYVDEEVAQRVPPDNLVTNNIVAWLYAAIISVKESSFSLPKWLESTTVSVDDYNKW  3016

Query  234   AMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTP  293
             A    + P +      +  LSA TG+ V  +  ++  +  +   G  ILG    EDE TP
Sbjct  3017  AGDNGFTPFSTST--AITKLSAITGVDVCKLLRTIM-VKNSQWGGDPILGQYNFEDELTP  3073

Query  294   FDVVRQCSGVTFQ  306
               V  Q  GV  Q
Sbjct  3074  ESVFNQIGGVRLQ  3086


> sp|P0C6Y2|R1AB_IBVBC Replicase polyprotein 1ab OS=Avian infectious 
bronchitis virus (strain Beaudette CK) OX=160235 GN=rep 
PE=3 SV=1
Length=6629

 Score =  397 bits (1020),  Expect = 2e-123, Method: Composition-based stats.
 Identities = 125/313 (40%), Positives = 174/313 (56%), Gaps = 13/313 (4%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SGF+K+  PS  VE C+V V+     LNGLWL D +YCPRHV+          + D+L  
Sbjct  2780  SGFKKLVSPSSAVEKCIVSVSYRGNNLNGLWLGDTIYCPRHVL---GKFSGDQWNDVLNL  2836

Query  61    KSNHNFLVQAGN-VQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYN  119
              +NH F V   + V L V+   ++  VL L+   AN +TPKYKF++   G +F++   Y 
Sbjct  2837  ANNHEFEVTTQHGVTLNVVSRRLKGAVLILQTAVANAETPKYKFIKANCGDSFTIACAYG  2896

Query  120   GSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEG  179
             G+  G+Y   MR N TI+ SFL G+CGSVGFNI+   V+F YMHH+ELP  +H GTDL G
Sbjct  2897  GTVVGLYPVTMRSNGTIRASFLAGACGSVGFNIEKGVVNFFYMHHLELPNALHTGTDLMG  2956

Query  180   NFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRW------FLNRFTTTLNDFNLV  233
              FYG +VD + AQ    D  +T N++AWLYAA+I+          +L   T +++D+N  
Sbjct  2957  EFYGGYVDEEVAQRVPPDNLVTNNIVAWLYAAIISVKESSFSLPKWLESTTVSVDDYNKW  3016

Query  234   AMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTP  293
             A    + P +      +  LSA TG+ V  +  ++  +  +   G  ILG    EDE TP
Sbjct  3017  AGDNGFTPFSTST--AITKLSAITGVDVCKLLRTIM-VKNSQWGGDPILGQYNFEDELTP  3073

Query  294   FDVVRQCSGVTFQ  306
               V  Q  GV  Q
Sbjct  3074  ESVFNQIGGVRLQ  3086


> sp|P0C6Y1|R1AB_IBVB Replicase polyprotein 1ab OS=Avian infectious 
bronchitis virus (strain Beaudette) OX=11122 GN=rep PE=1 
SV=1
Length=6629

 Score =  396 bits (1019),  Expect = 2e-123, Method: Composition-based stats.
 Identities = 125/313 (40%), Positives = 174/313 (56%), Gaps = 13/313 (4%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             SGF+K+  PS  VE C+V V+     LNGLWL D +YCPRHV+          + D+L  
Sbjct  2780  SGFKKLVSPSSAVEKCIVSVSYRGNNLNGLWLGDTIYCPRHVL---GKFSGDQWNDVLNL  2836

Query  61    KSNHNFLVQAGN-VQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYN  119
              +NH F V   + V L V+   ++  VL L+   AN +TPKYKF++   G +F++   Y 
Sbjct  2837  ANNHEFEVTTQHGVTLNVVSRRLKGAVLILQTAVANAETPKYKFIKANCGDSFTIACAYG  2896

Query  120   GSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEG  179
             G+  G+Y   MR N TI+ SFL G+CGSVGFNI+   V+F YMHH+ELP  +H GTDL G
Sbjct  2897  GTVVGLYPVTMRSNGTIRASFLAGACGSVGFNIEKGVVNFFYMHHLELPNALHTGTDLMG  2956

Query  180   NFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRW------FLNRFTTTLNDFNLV  233
              FYG +VD + AQ    D  +T N++AWLYAA+I+          +L   T +++D+N  
Sbjct  2957  EFYGGYVDEEVAQRVPPDNLVTNNIVAWLYAAIISVKESSFSLPKWLESTTVSVDDYNKW  3016

Query  234   AMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTP  293
             A    + P +      +  LSA TG+ V  +  ++  +  +   G  ILG    EDE TP
Sbjct  3017  AGDNGFTPFSTST--AITKLSAITGVDVCKLLRTIM-VKNSQWGGDPILGQYNFEDELTP  3073

Query  294   FDVVRQCSGVTFQ  306
               V  Q  GV  Q
Sbjct  3074  ESVFNQIGGVRLQ  3086


> sp|P0C6V5|R1A_IBVM Replicase polyprotein 1a OS=Avian infectious 
bronchitis virus (strain M41) OX=11127 GN=1a PE=1 SV=1
Length=3953

 Score =  393 bits (1010),  Expect = 3e-122, Method: Composition-based stats.
 Identities = 125/313 (40%), Positives = 171/313 (55%), Gaps = 13/313 (4%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             +GF+K+  PS  VE C+V V+     LNGLWL D +YCPRHV+          + D+L  
Sbjct  2782  AGFKKLVSPSSAVEKCIVSVSYRGNNLNGLWLGDSIYCPRHVL---GKFSGDQWGDVLNL  2838

Query  61    KSNHNFLVQAGN-VQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYN  119
              +NH F V   N V L V+   ++  VL L+   AN +TPKYKFV+   G +F++   Y 
Sbjct  2839  ANNHEFEVVTQNGVTLNVVSRRLKGAVLILQTAVANAETPKYKFVKANCGDSFTIACSYG  2898

Query  120   GSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEG  179
             G+  G+Y   MR N TI+ SFL G+CGSVGFNI+   V+F YMHH+ELP  +H GTDL G
Sbjct  2899  GTVIGLYPVTMRSNGTIRASFLAGACGSVGFNIEKGVVNFFYMHHLELPNALHTGTDLMG  2958

Query  180   NFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRW------FLNRFTTTLNDFNLV  233
              FYG +VD + AQ    D  +T N++AWLYAA+I+          +L   T ++ D+N  
Sbjct  2959  EFYGGYVDEEVAQRVPPDNLVTNNIVAWLYAAIISVKESSFSQPKWLESTTVSIEDYNRW  3018

Query  234   AMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTP  293
             A    + P +      +  LSA TG+ V  +  ++  +         ILG    EDE TP
Sbjct  3019  ASDNGFTPFSTST--AITKLSAITGVDVCKLLRTIM-VKSAQWGSDPILGQYNFEDELTP  3075

Query  294   FDVVRQCSGVTFQ  306
               V  Q  GV  Q
Sbjct  3076  ESVFNQVGGVRLQ  3088


> sp|P0C6Y3|R1AB_IBVM Replicase polyprotein 1ab OS=Avian infectious 
bronchitis virus (strain M41) OX=11127 GN=rep PE=1 SV=1
Length=6631

 Score =  392 bits (1007),  Expect = 1e-121, Method: Composition-based stats.
 Identities = 125/313 (40%), Positives = 171/313 (55%), Gaps = 13/313 (4%)

Query  1     SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR  60
             +GF+K+  PS  VE C+V V+     LNGLWL D +YCPRHV+          + D+L  
Sbjct  2782  AGFKKLVSPSSAVEKCIVSVSYRGNNLNGLWLGDSIYCPRHVL---GKFSGDQWGDVLNL  2838

Query  61    KSNHNFLVQAGN-VQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYN  119
              +NH F V   N V L V+   ++  VL L+   AN +TPKYKFV+   G +F++   Y 
Sbjct  2839  ANNHEFEVVTQNGVTLNVVSRRLKGAVLILQTAVANAETPKYKFVKANCGDSFTIACSYG  2898

Query  120   GSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEG  179
             G+  G+Y   MR N TI+ SFL G+CGSVGFNI+   V+F YMHH+ELP  +H GTDL G
Sbjct  2899  GTVIGLYPVTMRSNGTIRASFLAGACGSVGFNIEKGVVNFFYMHHLELPNALHTGTDLMG  2958

Query  180   NFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRW------FLNRFTTTLNDFNLV  233
              FYG +VD + AQ    D  +T N++AWLYAA+I+          +L   T ++ D+N  
Sbjct  2959  EFYGGYVDEEVAQRVPPDNLVTNNIVAWLYAAIISVKESSFSQPKWLESTTVSIEDYNRW  3018

Query  234   AMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTP  293
             A    + P +      +  LSA TG+ V  +  ++  +         ILG    EDE TP
Sbjct  3019  ASDNGFTPFSTST--AITKLSAITGVDVCKLLRTIM-VKSAQWGSDPILGQYNFEDELTP  3075

Query  294   FDVVRQCSGVTFQ  306
               V  Q  GV  Q
Sbjct  3076  ESVFNQVGGVRLQ  3088



Lambda      K        H        a         alpha
   0.321    0.148    0.452    0.792     4.96 

Gapped
Lambda      K        H        a         alpha    sigma
   0.267   0.0452    0.140     1.90     42.6     43.6 

Effective search space used: 25877591208

Search has CONVERGED!


  Database: uniprot_sprot.fasta
    Posted date:  Aug 19, 2020  9:15 PM
  Number of letters in database: 202,799,066
  Number of sequences in database:  563,082



Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Neighboring words threshold: 11
Window for multiple hits: 40