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============================================================================

                  Welcome to the SIB BLAST Network Service

If results of this search are reported or published, please mention that
the computation was performed at the SIB using the BLAST network service.
The SIB BLAST network service uses a server developed at SIB and the NCBI
BLAST 2 software. It is implemented on hardware provided by HP.

In case of problems, please contact us.

NCBI BLAST program reference [PMID:9254694]:
Altschul S.F., Madden T.L., Schäffer A.A., Zhang J., Zhang Z., Miller W.,
Lipman D.J.  Gapped BLAST and PSI-BLAST: a new generation of protein
database search programs.  Nucleic Acids Res. 25:3389-3402(1997).

============================================================================

Query length: 298 AA
Date run: 2003-05-01 15:11:16 UTC+0100 on sib-blast.unil.ch
Program: NCBI BLASTP 2.2.5 [Nov-16-2002]
Database: XXswissprot Viruses 
           8482 sequences; 3,552,911 total letters
           Swiss-Prot Release 41.6 of 30-Apr-2003




List of potentially matching sequences
Send selected sequences to

Include query sequence 

  Db AC     Description                                            Score E-value

 sp P59641 R1AB_CVHSA Replicase polyprotein 1ab (pp1ab) (ORF1AB) ... 604 e-174
 sp P16342 RRPB_CVMA5 RNA-directed RNA polymerase (EC 2.7.7.48) (... 389 e-109
 sp P29982 RRPB_CVMJH RNA-directed RNA polymerase (EC 2.7.7.48) (... 387 e-108
 sp Q05002 R1AB_CVH22 Replicase polyprotein 1ab (pp1ab) (ORF1AB) ... 349 4e-97
 sp P18457 RRPB_CVPFS RNA-directed RNA polymerase (ORF1B) (EC 2.7... 344 1e-95
 sp P12723 RRPB_IBVK RNA-directed RNA polymerase (ORF1B) (EC 2.7.... 330 2e-91
 sp P26314 RRPB_IBVB RNA-directed RNA polymerase (ORF1B) (EC 2.7.... 330 2e-91
 sp P36697 RRPB_CVCAI RNA-directed RNA polymerase (EC 2.7.7.48) (... 181 2e-46
 sp Q04158 RRPB_CVPR8 RNA-directed RNA polymerase (ORF1B) (EC 2.7... 126 4e-30
 sp P18458 RRPB_BEV RNA-directed RNA polymerase (EC 2.7.7.48) (OR...  67 4e-12
 sp O56075 POLG_PEMVM Genome polyprotein [Contains: N-terminal pr...  31  0.24
 sp P16472 TOP1_SFVKA DNA topoisomerase I (EC 5.99.1.2) [Shope fi...  28   2.0
 sp Q83949 Y066_NPVOP Hypothetical 98.6 kDa protein (ORF71) [Orgy...  26   9.9



Alignments



spP59641
R1AB_CVHSA		Replicase polyprotein 1ab (pp1ab) (ORF1AB) [Includes: Replicase
            polyprotein 1a (pp1a) (ORF1A)] [Contains: Leader protein;
            p65 homolog; Papain-like proteinase (EC 3.4.24.-) (NSP1);
            3C-like proteinase (EC 3.4.24.-) (3CL-PRO) (NSP2); HD2
            (NSP3); NSP4; NSP5; NSP6; Growth factor-like (NSP7);
            RNA-directed RNA polymerase (EC 2.7.7.48) (RdRp) (NSP9);
            Helicase (Hel) (NSP10); NSP11; NSP12; NSP13] [Human
            coronavirus (strain SARS) (HCoV-SARS)]		          7073 AA 
align
 Score =  604 bits (1558), Expect = e-174
 Identities = 296/298 (99%), Positives = 297/298 (99%)

Query: 1    ASRAWQPGVAMPNLYKMQRMLLEKCDLQNYGENAVIPKGIMMNVAKYTQLCQYLNTLTLA 60
            AS+AWQPGVAMPNLYKMQRMLLEKCDLQNYGENAVIPKGIMMNVAKYTQLCQYLNTLTLA
Sbjct: 6776 ASQAWQPGVAMPNLYKMQRMLLEKCDLQNYGENAVIPKGIMMNVAKYTQLCQYLNTLTLA 6835

Query: 61   VPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDAYSTLIGDCATVHT 120
            VPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDA STLIGDCATVHT
Sbjct: 6836 VPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHT 6895

Query: 121  ANKWDLIISDMYDPRTKHVTKENDSKEGFFTYLCGFIKQKLALGGSIAVKITEHSWNADL 180
            ANKWDLIISDMYDPRTKHVTKENDSKEGFFTYLCGFIKQKLALGGSIAVKITEHSWNADL
Sbjct: 6896 ANKWDLIISDMYDPRTKHVTKENDSKEGFFTYLCGFIKQKLALGGSIAVKITEHSWNADL 6955

Query: 181  YKLMGHFSWWTAFVTNVNASSSEAFLIGANYLGKPKEQIDGYTMHANYIFWRNTNPIQLS 240
            YKLMGHFSWWTAFVTNVNASSSEAFLIGANYLGKPKEQIDGYTMHANYIFWRNTNPIQLS
Sbjct: 6956 YKLMGHFSWWTAFVTNVNASSSEAFLIGANYLGKPKEQIDGYTMHANYIFWRNTNPIQLS 7015

Query: 241  SYSLFDMSKFPLKLRGTAVMSLKENQINDMIYSLLEKGRLIIRENNRVVVSSDILVNN 298
            SYSLFDMSKFPLKLRGTAVMSLKENQINDMIYSLLEKGRLIIRENNRVVVSSDILVNN
Sbjct: 7016 SYSLFDMSKFPLKLRGTAVMSLKENQINDMIYSLLEKGRLIIRENNRVVVSSDILVNN 7073






spP16342
RRPB_CVMA5		RNA-directed RNA polymerase (EC 2.7.7.48) (ORF1B) [F2] [Murine
            coronavirus MHV (strain A59)]		          2733 AA 
align
 Score =  389 bits (1000), Expect = e-109
 Identities = 187/297 (62%), Positives = 232/297 (78%)

Query: 1    ASRAWQPGVAMPNLYKMQRMLLEKCDLQNYGENAVIPKGIMMNVAKYTQLCQYLNTLTLA 60
            A+  W+PG  MP LYK     LE+ +L NYG+   +P G MMNVAKYTQLCQYL+T TLA
Sbjct: 2435 AAADWKPGYVMPVLYKYLESPLERVNLWNYGKPITLPTGCMMNVAKYTQLCQYLSTTTLA 2494

Query: 61   VPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDAYSTLIGDCATVHT 120
            VP NMRV+H GAGSDKGVAPG+AVLRQWLP G++LVD+D+N FVSD+ ++  G+C T+  
Sbjct: 2495 VPANMRVLHLGAGSDKGVAPGSAVLRQWLPAGSILVDNDVNPFVSDSVASYYGNCITLPF 2554

Query: 121  ANKWDLIISDMYDPRTKHVTKENDSKEGFFTYLCGFIKQKLALGGSIAVKITEHSWNADL 180
              +WDLIISDMYDP TK++ + N SK+GFFTYLC  I+ KLALGGS+A+KITE SWNA+L
Sbjct: 2555 DCQWDLIISDMYDPLTKNIGEYNVSKDGFFTYLCHLIRDKLALGGSVAIKITEFSWNAEL 2614

Query: 181  YKLMGHFSWWTAFVTNVNASSSEAFLIGANYLGKPKEQIDGYTMHANYIFWRNTNPIQLS 240
            Y LMG F++WT F TNVNASSSE FLIG N+L K + +IDG TMHANY+FWRN+      
Sbjct: 2615 YSLMGKFAFWTIFCTNVNASSSEGFLIGINWLNKTRTEIDGKTMHANYLFWRNSTMWNGG 2674

Query: 241  SYSLFDMSKFPLKLRGTAVMSLKENQINDMIYSLLEKGRLIIRENNRVVVSSDILVN 297
            +YSLFDMSKFPLK  GTAV+SLK +QIND++ SL+EKG+L++R+  + V   D LVN
Sbjct: 2675 AYSLFDMSKFPLKAAGTAVVSLKPDQINDLVLSLIEKGKLLVRDTRKEVFVGDSLVN 2731






spP29982
RRPB_CVMJH		RNA-directed RNA polymerase (EC 2.7.7.48) (ORF1B) [Murine coronavirus
            MHV (strain JHM)]		          2731 AA 
align
 Score =  387 bits (995), Expect = e-108
 Identities = 184/297 (61%), Positives = 233/297 (78%)

Query: 1    ASRAWQPGVAMPNLYKMQRMLLEKCDLQNYGENAVIPKGIMMNVAKYTQLCQYLNTLTLA 60
            A+  W+PG  MP LYK     +E+ +L NYG+   +P G MMNVAKYTQLCQYL+T TLA
Sbjct: 2433 AAADWKPGYVMPVLYKYLESPMERVNLWNYGKPITLPTGCMMNVAKYTQLCQYLSTTTLA 2492

Query: 61   VPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDAYSTLIGDCATVHT 120
            VP NMRV+H GAGSDKGVAPG+AVLRQWLP+G++LVD+D+N FVSD+ ++  G+C T+  
Sbjct: 2493 VPANMRVLHLGAGSDKGVAPGSAVLRQWLPSGSILVDNDMNPFVSDSVASYYGNCITLPF 2552

Query: 121  ANKWDLIISDMYDPRTKHVTKENDSKEGFFTYLCGFIKQKLALGGSIAVKITEHSWNADL 180
              +WDLIISDMYDP TK++ + N SK+GFFTYLC  I+ KLALGGS+A+KITE SWNA+L
Sbjct: 2553 DCQWDLIISDMYDPLTKNIGEYNVSKDGFFTYLCHLIRDKLALGGSVAIKITEFSWNAEL 2612

Query: 181  YKLMGHFSWWTAFVTNVNASSSEAFLIGANYLGKPKEQIDGYTMHANYIFWRNTNPIQLS 240
            Y LMG F++WT F TNVNASSSE FLIG N+L + + +IDG TMHANY+FWRN+      
Sbjct: 2613 YSLMGKFAFWTIFCTNVNASSSEGFLIGINWLNRTRNEIDGKTMHANYLFWRNSTMWNGG 2672

Query: 241  SYSLFDMSKFPLKLRGTAVMSLKENQINDMIYSLLEKGRLIIRENNRVVVSSDILVN 297
            +YSLFDM+KFPLK  GTAV+SLK +QIND++ SL+EKG+L++R+  + V   D LVN
Sbjct: 2673 AYSLFDMTKFPLKAAGTAVVSLKPDQINDLVLSLIEKGKLLVRDTRKEVFVGDSLVN 2729






spQ05002
R1AB_CVH22		Replicase polyprotein 1ab (pp1ab) (ORF1AB) [Includes: Replicase
            polyprotein 1a (pp1a) (ORF1A)] [Contains: Protein p9;
            Papain-like proteinase 1 (EC 3.4.24.-); Papain-like
            proteinase 2 (EC 3.4.24.-); 3C-like proteinase (EC
            3.4.24.-) (3CL-PRO); RNA-directed RNA polymerase (EC
            2.7.7.48) (RdRp); Helicase (Hel)] [Human coronavirus
            (strain 229E) (HCoV-229E)]		          6758 AA 
align
 Score =  349 bits (895), Expect = 4e-97
 Identities = 168/298 (56%), Positives = 223/298 (74%), Gaps = 2/298 (0%)

Query: 2    SRAWQPGVAMPNLYKMQRMLLEKCDLQNYGENAVIPKGIMMNVAKYTQLCQYLNTLTLAV 61
            S  W+ G +MP +YK QRM LE C+L NYG    +P GIM NV KYTQLCQY N+ TL V
Sbjct: 6459 SAEWKCGYSMPGIYKTQRMCLEPCNLYNYGAGLKLPSGIMFNVVKYTQLCQYFNSTTLCV 6518

Query: 62   PYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDAYSTLIGDCATVHTA 121
            P+NMRV+H GAGSD GVAPGTAVL++WLP   ++VD+D+ D+VSDA  ++ GDCATV+  
Sbjct: 6519 PHNMRVLHLGAGSDYGVAPGTAVLKRWLPHDAIVVDNDVVDYVSDADFSVTGDCATVYLE 6578

Query: 122  NKWDLIISDMYDPRTKHVTKENDSKEGFFTYLCGFIKQKLALGGSIAVKITEHSWNADLY 181
            +K+DL+ISDMYD RTK +  EN SKEGFFTY+ GFI +KLA+GGSIA+K+TE+SWN  LY
Sbjct: 6579 DKFDLLISDMYDGRTKAIDGENVSKEGFFTYINGFICEKLAIGGSIAIKVTEYSWNKKLY 6638

Query: 182  KLMGHFSWWTAFVTNVNASSSEAFLIGANYLGKPKEQ--IDGYTMHANYIFWRNTNPIQL 239
            +L+  FS+WT F T+VN SSSEAF++G NYLG   +   IDG  +HANY+FWRN+  + L
Sbjct: 6639 ELVQRFSFWTMFCTSVNTSSSEAFVVGINYLGDFAQGPFIDGNIIHANYVFWRNSTVMSL 6698

Query: 240  SSYSLFDMSKFPLKLRGTAVMSLKENQINDMIYSLLEKGRLIIRENNRVVVSSDILVN 297
            S  S+ D+SKF  K + T V+ LK++ IN+M+ SL+  G+L++R N + +  S+ LV+
Sbjct: 6699 SYNSVLDLSKFNCKHKATVVVQLKDSDINEMVLSLVRSGKLLVRGNGKCLSFSNHLVS 6756






spP18457
RRPB_CVPFS		RNA-directed RNA polymerase (ORF1B) (EC 2.7.7.48) (Fragment)
           [Porcine transmissible gastroenteritis coronavirus
           (strain FS772/70)]		          533 AA 
align
 Score =  344 bits (882), Expect = 1e-95
 Identities = 162/298 (54%), Positives = 213/298 (71%), Gaps = 2/298 (0%)

Query: 2   SRAWQPGVAMPNLYKMQRMLLEKCDLQNYGENAVIPKGIMMNVAKYTQLCQYLNTLTLAV 61
           S  W PG +MP LYK+QRM LE+C+L NYG    +P GI  NV KYTQLCQYLNT TL V
Sbjct: 234 SAEWNPGYSMPTLYKIQRMCLERCNLYNYGAQVKLPDGITTNVVKYTQLCQYLNTTTLCV 293

Query: 62  PYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDAYSTLIGDCATVHTA 121
           P+ MRV+H GA    GVAPG+ VLR+WLP   +LVD+DL D+VSDA  ++ GDC +++  
Sbjct: 294 PHKMRVLHLGAAGASGVAPGSTVLRRWLPDDAILVDNDLRDYVSDADFSVTGDCTSLYIE 353

Query: 122 NKWDLIISDMYDPRTKHVTKENDSKEGFFTYLCGFIKQKLALGGSIAVKITEHSWNADLY 181
           +K+DL++SD+YD  TK +  EN SK+GFFTY+ GFIK+KL+LGGS+A+KITE SWN DLY
Sbjct: 354 DKFDLLVSDLYDGSTKSIDGENTSKDGFFTYINGFIKEKLSLGGSVAIKITEFSWNKDLY 413

Query: 182 KLMGHFSWWTAFVTNVNASSSEAFLIGANYLGK--PKEQIDGYTMHANYIFWRNTNPIQL 239
           +L+  F +WT F T+VN SSSE FLIG NYLG    K  +DG  MHANYIFWRN+  + L
Sbjct: 414 ELIQRFEYWTVFCTSVNTSSSEGFLIGINYLGPYCDKAIVDGNIMHANYIFWRNSTIMAL 473

Query: 240 SSYSLFDMSKFPLKLRGTAVMSLKENQINDMIYSLLEKGRLIIRENNRVVVSSDILVN 297
           S  S+ D  KF  +     +++LKE ++N+M+  LL KG+L+IR N +++   +  VN
Sbjct: 474 SHNSVLDTPKFKCRCNNALIVNLKEKELNEMVIGLLRKGKLLIRNNGKLLNFGNHFVN 531






spP12723
RRPB_IBVK		RNA-directed RNA polymerase (ORF1B) (EC 2.7.7.48) (Fragment) [F2]
           [Avian infectious bronchitis virus (strain KB8523)
           (IBV)]		          521 AA 
align
 Score =  330 bits (845), Expect = 2e-91
 Identities = 160/298 (53%), Positives = 214/298 (71%), Gaps = 5/298 (1%)

Query: 4   AWQPGVAMPNLYKMQRMLLEKCDLQNYGENAVIPKGIMMNVAKYTQLCQYLNTLTLAVPY 63
           AW  G  MP LYK+Q  ++E C++ NYG    +P GIMMNVAKYTQLCQYL+  T+ VP+
Sbjct: 221 AWTCGYNMPELYKVQNCVMEPCNIPNYGVGITLPSGIMMNVAKYTQLCQYLSKTTVCVPH 280

Query: 64  NMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDAYSTLIGDCATVHTANK 123
           NMRV+HFGAGSDKGVAPG+ VL+QWLP GTLLVD+D+ D+VSDA+ +++ DC    T +K
Sbjct: 281 NMRVMHFGAGSDKGVAPGSTVLKQWLPEGTLLVDTDIVDYVSDAHVSVLSDCNKYKTEHK 340

Query: 124 WDLIISDMY---DPRTKH-VTKENDSKEGFFTYLCGFIKQKLALGGSIAVKITEHSWNAD 179
           +DL+ISDMY   D + KH     N+  +  F YL  F++  LALGGS AVK+TE SW+  
Sbjct: 341 FDLVISDMYTDNDSKRKHGGVIANNGNDDVFIYLSSFLRNNLALGGSFAVKLTETSWHES 400

Query: 180 LYKLMGHFSWWTAFVTNVNASSSEAFLIGANYLG-KPKEQIDGYTMHANYIFWRNTNPIQ 238
           LY +    +WWT F T VNASSSEAFLIG NYLG   K ++ G T+HANYIFWRN N +Q
Sbjct: 401 LYDIAQDCAWWTMFCTAVNASSSEAFLIGVNYLGASVKVKVSGKTLHANYIFWRNCNYLQ 460

Query: 239 LSSYSLFDMSKFPLKLRGTAVMSLKENQINDMIYSLLEKGRLIIRENNRVVVSSDILV 296
            S+YS+FD++KF L+L+ T V++LK  Q  D++++L++ G+L++R+      +SD  V
Sbjct: 461 TSAYSIFDVAKFDLRLKATPVVNLKTEQKTDLVFNLIKCGKLLVRDVGNTSFTSDSFV 518






spP26314
RRPB_IBVB		RNA-directed RNA polymerase (ORF1B) (EC 2.7.7.48) [F2] [Avian
            infectious bronchitis virus (strain Beaudette) (IBV)]		          2652 AA 
align
 Score =  330 bits (845), Expect = 2e-91
 Identities = 159/298 (53%), Positives = 215/298 (72%), Gaps = 5/298 (1%)

Query: 4    AWQPGVAMPNLYKMQRMLLEKCDLQNYGENAVIPKGIMMNVAKYTQLCQYLNTLTLAVPY 63
            AW  G  MP LYK+Q  ++E C++ NYG    +P GI+MNVAKYTQLCQYL+  T+ VP+
Sbjct: 2352 AWTCGYNMPELYKVQNCVMEPCNIPNYGVGITLPSGILMNVAKYTQLCQYLSKTTICVPH 2411

Query: 64   NMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDAYSTLIGDCATVHTANK 123
            NMRV+HFGAGSDKGVAPG+ VL+QWLP GTLLVD+D+ D+VSDA+ +++ DC   +T +K
Sbjct: 2412 NMRVMHFGAGSDKGVAPGSTVLKQWLPEGTLLVDNDIVDYVSDAHVSVLSDCNKYNTEHK 2471

Query: 124  WDLIISDMY---DPRTKHV-TKENDSKEGFFTYLCGFIKQKLALGGSIAVKITEHSWNAD 179
            +DL+ISDMY   D + KH     N+  +  F YL  F++  LALGGS AVK+TE SW+  
Sbjct: 2472 FDLVISDMYTDNDSKRKHEGVIANNGNDDVFIYLSSFLRNNLALGGSFAVKVTETSWHEV 2531

Query: 180  LYKLMGHFSWWTAFVTNVNASSSEAFLIGANYLG-KPKEQIDGYTMHANYIFWRNTNPIQ 238
            LY +    +WWT F T VNASSSEAFLIG NYLG   K ++ G T+HANYIFWRN N +Q
Sbjct: 2532 LYDIAQDCAWWTMFCTAVNASSSEAFLIGVNYLGASEKVKVSGKTLHANYIFWRNCNYLQ 2591

Query: 239  LSSYSLFDMSKFPLKLRGTAVMSLKENQINDMIYSLLEKGRLIIRENNRVVVSSDILV 296
             S+YS+FD++KF L+L+ T V++LK  Q  D++++L++ G+L++R+      +SD  V
Sbjct: 2592 TSAYSIFDVAKFDLRLKATPVVNLKTEQKTDLVFNLIKCGKLLVRDVGNTSFTSDSFV 2649






spP36697
RRPB_CVCAI		RNA-directed RNA polymerase (EC 2.7.7.48) (ORF1B) (Fragment)
           [Canine enteric coronavirus (strain Insavc-1) (CCV)]		          168 AA 
align
 Score =  181 bits (458), Expect = 2e-46
 Identities = 87/166 (52%), Positives = 117/166 (70%), Gaps = 2/166 (1%)

Query: 134 PRTKHVTKENDSKEGFFTYLCGFIKQKLALGGSIAVKITEHSWNADLYKLMGHFSWWTAF 193
           P TK +  EN SK+GFFTY+ GFIK+KL+LGGS A+KITE SWN DLY+L+  F +WT F
Sbjct: 1   PNTKSIDGENTSKDGFFTYVNGFIKEKLSLGGSAAIKITEFSWNKDLYELIQRFEYWTVF 60

Query: 194 VTNVNASSSEAFLIGANYLGK--PKEQIDGYTMHANYIFWRNTNPIQLSSYSLFDMSKFP 251
            T+VN SSSE FLIG NYLG    +  +DG  MHANYIFWRN+  + LS  S+ D  KF 
Sbjct: 61  CTSVNTSSSEGFLIGVNYLGPYCDRAIVDGNIMHANYIFWRNSTIMALSHNSVLDTPKFK 120

Query: 252 LKLRGTAVMSLKENQINDMIYSLLEKGRLIIRENNRVVVSSDILVN 297
            +     +++LKE ++N+M+  LL+KG+L+IR N +++   + LVN
Sbjct: 121 CRCNNALIVNLKEKELNEMVIGLLKKGKLLIRNNGKLLNFGNHLVN 166






spQ04158
RRPB_CVPR8		RNA-directed RNA polymerase (ORF1B) (EC 2.7.7.48) (Fragment)
           [Porcine respiratory coronavirus (strain 86/137004 /
           British isolate) (PRCV)]		          131 AA 
align
 Score =  126 bits (317), Expect = 4e-30
 Identities = 61/129 (47%), Positives = 84/129 (65%), Gaps = 2/129 (1%)

Query: 171 ITEHSWNADLYKLMGHFSWWTAFVTNVNASSSEAFLIGANYLGK--PKEQIDGYTMHANY 228
           ITE SWN  LY+L+  F +WT F T+VN SSSE FLIG NYLG    K  +DG  MHANY
Sbjct: 1   ITEFSWNKYLYELIQRFEYWTVFCTSVNTSSSEGFLIGVNYLGPYCDKAIVDGNIMHANY 60

Query: 229 IFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKENQINDMIYSLLEKGRLIIRENNRV 288
           IFWRN+  + LS  S+ D  KF  +     +++LKE ++N+M+  LL KG+L+IR N ++
Sbjct: 61  IFWRNSTIMALSHNSVLDTPKFKCRCNNALIVNLKEKELNEMVIGLLRKGKLLIRNNGKL 120

Query: 289 VVSSDILVN 297
           +   +  +N
Sbjct: 121 LNFGNHFIN 129






spP18458
RRPB_BEV		RNA-directed RNA polymerase (EC 2.7.7.48) (ORF1B) [POL] [Berne virus
            (BEV)]		          2291 AA 
align
 Score = 67.0 bits (162), Expect = 4e-12
 Identities = 61/184 (33%), Positives = 92/184 (50%), Gaps = 24/184 (13%)

Query: 26   DLQNYGENAV-IPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAV 84
            DL+NYG+N   +P+ +  N AKYTQ+C ++    + V  N  V H GA    G +PG  V
Sbjct: 2048 DLKNYGQNPTFMPQPV--NFAKYTQICTFIQD-HVKVARNALVWHLGAAGVDGCSPGDIV 2104

Query: 85   LRQWLPTGTLLVDSDLNDFVSDAYSTLIGDCATVHTANKWDLIISDMYDPRTKHVTKEND 144
            L  +     L+   D+ D     YSTL+ D  +     + +LI+SD+Y+  + +V++  D
Sbjct: 2105 LSSFFKE-CLVYSWDIKD-----YSTLL-DKHSYDCNFRPNLIVSDIYNV-SSNVSEVLD 2156

Query: 145  SKEGFFTYLCGFIKQKLALGGSIAVKITEHSW-NADLYKLMGHFSWWTAFVTNVNASSSE 203
                           +LALGG+I  K TE S  +  L +   +FS    F   VN SSSE
Sbjct: 2157 D-----------CVHRLALGGTIVFKTTESSRPDIQLSQFTKYFSAVQFFTAGVNTSSSE 2205

Query: 204  AFLI 207
             F++
Sbjct: 2206 VFVV 2209






spO56075
POLG_PEMVM		Genome polyprotein [Contains: N-terminal protein (P1); Helper
            component proteinase (EC 3.4.22.45) (HC-Pro); Protein P3;
            6 kDa protein 1 (6K1); Cytoplasmic inclusion protein
            (CI); 6 kDa protein 2 (6K2); Genome-linked protein (VPG);
            Nuclear inclusion protein A (NI-A) (NIA) (EC 3.4.22.44)
            (49 kDa proteinase) (49 kDa-Pro); Nuclear inclusion
            protein B (NI-B) (NIB) (RNA-directed RNA polymerase) (EC
            2.7.7.48); Coat protein (CP)] [Peanut mottle virus
            (strain M)]		          3099 AA 
align
 Score = 31.2 bits (69), Expect = 0.24
 Identities = 19/51 (37%), Positives = 26/51 (50%), Gaps = 4/51 (7%)

Query: 125  DLIISDMYDPRTKHVTKENDSKEGFFTYLCGFIKQKLALGGSIAVKITEHS 175
            +L++  MYD   K +  E  +KE FF Y+C   K    LG  IA +  E S
Sbjct: 1077 ELVVKQMYDQYCK-LANETPTKEEFFQYVC---KMNKELGERIAPEFEEGS 1123






spP16472
TOP1_SFVKA		DNA topoisomerase I (EC 5.99.1.2) [Shope fibroma virus (strain
           Kasza) (SFV)]		          314 AA 
align
 Score = 28.1 bits (61), Expect = 2.0
 Identities = 28/104 (26%), Positives = 47/104 (45%), Gaps = 15/104 (14%)

Query: 198 NASSSEAFLIGANYLGKPKEQIDGYTMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT 257
           N++    F+     + K  + ID    H N + +      QL  + L + S F   +R  
Sbjct: 81  NSARDTIFIKVHRVIDKIHKFIDDTIEHKNDVLF------QLGVFMLMETSFF---IRMG 131

Query: 258 AVMSLKENQINDMIYSLLEKGRLIIRENNRVV---VSSDILVNN 298
            V  LKEN   D +  L  K + I+REN +++   V  D +++N
Sbjct: 132 KVKYLKEN---DTVGLLTLKNKNIVRENRKILIHFVGKDKIIHN 172






spQ83949
Y066_NPVOP		Hypothetical 98.6 kDa protein (ORF71) [Orgyia pseudotsugata
           multicapsid polyhedrosis virus (OpMNPV)]		          875 AA 
align
 Score = 25.8 bits (55), Expect = 9.9
 Identities = 15/59 (25%), Positives = 26/59 (44%)

Query: 85  LRQWLPTGTLLVDSDLNDFVSDAYSTLIGDCATVHTANKWDLIISDMYDPRTKHVTKEN 143
           L+Q   T  L   S LN+ + +  S L    A      KW   + ++Y+   + + +EN
Sbjct: 810 LKQMASTSALEEMSKLNNNIREINSLLSKHAAITEDIFKWKTTMLEVYESLARTMAEEN 868





Database: XXswissprot Viruses
    Posted date:  Apr 29, 2003 11:07 AM
  Number of letters in database: 3,552,911
  Number of sequences in database:  8482
  
Lambda     K      H
   0.320    0.135    0.410 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,194,329
Number of Sequences: 8482
Number of extensions: 93330
Number of successful extensions: 209
Number of sequences better than 10.0: 13
Number of HSP's better than 10.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 188
Number of HSP's gapped (non-prelim): 13
length of query: 298
length of database: 3,552,911
effective HSP length: 91
effective length of query: 207
effective length of database: 2,781,049
effective search space: 575677143
effective search space used: 575677143
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)





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