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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: 601 AA
Date run: 2003-05-01 15:07:35 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) ... 1232   0.0
 sp P16342 RRPB_CVMA5 RNA-directed RNA polymerase (EC 2.7.7.48) (...  860   0.0
 sp P29982 RRPB_CVMJH RNA-directed RNA polymerase (EC 2.7.7.48) (...  842   0.0
 sp Q05002 R1AB_CVH22 Replicase polyprotein 1ab (pp1ab) (ORF1AB) ...  749   0.0
 sp P26314 RRPB_IBVB RNA-directed RNA polymerase (ORF1B) (EC 2.7....  731   0.0
 sp P18458 RRPB_BEV RNA-directed RNA polymerase (EC 2.7.7.48) (OR...   45 5e-05
 sp P04867 V58K_BSMV 58 kDa protein (Beta-B protein) [Barley stri...   33  0.15
 sp Q04561 RPOA_LELV POL polyprotein (ORF1A/1B) [Contains: RNA-di...   33  0.19
 sp Q82007 VE1_HPV73 Replication protein E1 [E1] [Human papilloma...   31  0.56
 sp P50765 VE1_HPV70 Replication protein E1 [E1] [Human papilloma...   30  0.96
 sp P36327 POLN_EEVV3 Nonstructural polyprotein [Contains: Nonstr...   30  0.96
 sp P36725 VE1_HPV34 Replication protein E1 [E1] [Human papilloma...   30   1.6
 sp Q05112 VE1_HPV30 Replication protein E1 [E1] [Human papilloma...   30   1.6
 sp Q04610 POLN_HEVMY Non-structural polyprotein [Contains: RNA-d...   30   1.6
 sp P27282 POLN_EEVVT Nonstructural polyprotein [Contains: Nonstr...   30   1.6
 sp Q81020 VE1_HPV54 Replication protein E1 [E1] [Human papilloma...   29   2.1
 sp P36727 VE1_HPV40 Replication protein E1 [E1] [Human papilloma...   29   2.1
 sp P24829 VE1_HPV39 Replication protein E1 [E1] [Human papilloma...   28   3.6
 sp P36328 POLN_EEVVP Nonstructural polyprotein [Contains: Nonstr...   28   3.6
 sp P04014 VE1_HPV11 Replication protein E1 [E1] [Human papilloma...   28   4.8
 sp Q02262 VE1_PCPV1 Replication protein E1 [E1] [Pygmy chimpanze...   28   6.2
 sp P81174 VE1_CCPV1 Replication protein E1 [E1] [Common chimpanz...   28   6.2
 sp Q80915 VE1_HPV44 Replication protein E1 [E1] [Human papilloma...   27   8.1
 sp Q02261 VE1_HPV13 Replication protein E1 [E1] [Human papilloma...   27   8.1
 sp Q05133 VE1_HPV07 Replication protein E1 [E1] [Human papilloma...   27   8.1



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 = 1232 bits (3188), Expect = 0.0
 Identities = 601/601 (100%), Positives = 601/601 (100%)

Query: 1    AVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDV 60
            AVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDV
Sbjct: 5302 AVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDV 5361

Query: 61   TQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDY 120
            TQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDY
Sbjct: 5362 TQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDY 5421

Query: 121  ILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNY 180
            ILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNY
Sbjct: 5422 ILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNY 5481

Query: 181  VFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTL 240
            VFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTL
Sbjct: 5482 VFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTL 5541

Query: 241  VPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYP 300
            VPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYP
Sbjct: 5542 VPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYP 5601

Query: 301  SARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTV 360
            SARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTV
Sbjct: 5602 SARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTV 5661

Query: 361  NALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPE 420
            NALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPE
Sbjct: 5662 NALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPE 5721

Query: 421  YFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVI 480
            YFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVI
Sbjct: 5722 YFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVI 5781

Query: 481  THDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSE 540
            THDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSE
Sbjct: 5782 THDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSE 5841

Query: 541  YDYVIFTQTTETAHSCNVNRFNVAITRAKIGILCIMSDRDLYDKLQFTSLEIPRRNVATL 600
            YDYVIFTQTTETAHSCNVNRFNVAITRAKIGILCIMSDRDLYDKLQFTSLEIPRRNVATL
Sbjct: 5842 YDYVIFTQTTETAHSCNVNRFNVAITRAKIGILCIMSDRDLYDKLQFTSLEIPRRNVATL 5901

Query: 601  Q 601
            Q
Sbjct: 5902 Q 5902






spP16342
RRPB_CVMA5		RNA-directed RNA polymerase (EC 2.7.7.48) (ORF1B) [F2] [Murine
            coronavirus MHV (strain A59)]		          2733 AA 
align
 Score =  860 bits (2221), Expect = 0.0
 Identities = 406/603 (67%), Positives = 485/603 (80%), Gaps = 5/603 (0%)

Query: 1    AVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDV 60
            +VGACV+C+SQTSLRCG+CIR+P LCCKC YDHV+ST HK VLSV+PYVCN+PGCDV DV
Sbjct: 940  SVGACVVCSSQTSLRCGSCIRKPLLCCKCAYDHVMSTDHKYVLSVSPYVCNSPGCDVNDV 999

Query: 61   TQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDY 120
            T+LYLGGMSYYC+ HKP  SF L  NG VFGLYK +C GS  + DFN IA+C WT   DY
Sbjct: 1000 TKLYLGGMSYYCEDHKPQYSFKLVMNGMVFGLYKQSCTGSPYIEDFNKIASCKWTEVDDY 1059

Query: 121  ILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNY 180
            +LAN CTERLKLFAAET KATEE FK  Y  AT+RE++SDREL LSWE+GK RPPLN+NY
Sbjct: 1060 VLANECTERLKLFAAETQKATEEAFKQCYASATIREIVSDRELILSWEIGKVRPPLNKNY 1119

Query: 181  VFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTL 240
            VFTGY  T N K  +GEY F+K +  + V YR TTTYKL+VGD F+LTSH V  LSAPTL
Sbjct: 1120 VFTGYHFTNNGKTVLGEYVFDKSELTNGVYYRATTTYKLSVGDVFILTSHAVSSLSAPTL 1179

Query: 241  VPQEHY--VRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALY 298
            VPQE+Y  +R   +Y   ++ + F +NV NYQ +GM++Y T+QGPPGTGKSH AIGLA+Y
Sbjct: 1180 VPQENYTSIRFASVY---SVPETFQNNVPNYQHIGMKRYCTVQGPPGTGKSHLAIGLAVY 1236

Query: 299  YPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFC 358
            Y +AR+VYTA SHAAVDALCEKA K+L I+ C+RI+PA+ RV+C+DKFKVN T  +YVF 
Sbjct: 1237 YCTARVVYTAASHAAVDALCEKAHKFLNINDCTRIVPAKVRVDCYDKFKVNDTTRKYVFT 1296

Query: 359  TVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLE 418
            T+NALPE   DI+V DE+SM TNY+LSV+N+R+RAKHYVYIGDPAQLPAPR LL KGTLE
Sbjct: 1297 TINALPELVTDIIVVDEVSMLTNYELSVINSRVRAKHYVYIGDPAQLPAPRVLLNKGTLE 1356

Query: 419  PEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKG 478
            P YFNSV +LM  +GPD+FLGTC RCP EIVDTVSALVY+NKLKA  D S+ CFK++YKG
Sbjct: 1357 PRYFNSVTKLMCCLGPDIFLGTCYRCPKEIVDTVSALVYNNKLKAKNDNSSMCFKVYYKG 1416

Query: 479  VITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQG 538
              TH+ SSA+N  QI ++ +FL  NP+W  AVFISPYNSQN VA ++LGL TQTVDS+QG
Sbjct: 1417 QTTHESSSAVNMQQIHLISKFLKANPSWSNAVFISPYNSQNYVAKRVLGLQTQTVDSAQG 1476

Query: 539  SEYDYVIFTQTTETAHSCNVNRFNVAITRAKIGILCIMSDRDLYDKLQFTSLEIPRRNVA 598
            SEYD+VI++QT ETAHS NVNRFNVAITRAK GILC+MS   L++ L FT+L + + N  
Sbjct: 1477 SEYDFVIYSQTAETAHSVNVNRFNVAITRAKKGILCVMSSMQLFESLNFTTLTLDKINNP 1536

Query: 599  TLQ 601
             LQ
Sbjct: 1537 RLQ 1539






spP29982
RRPB_CVMJH		RNA-directed RNA polymerase (EC 2.7.7.48) (ORF1B) [Murine coronavirus
            MHV (strain JHM)]		          2731 AA 
align
 Score =  842 bits (2175), Expect = 0.0
 Identities = 400/603 (66%), Positives = 477/603 (79%), Gaps = 5/603 (0%)

Query: 1    AVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDV 60
            +VGACV+C+SQTSLRCG+CIR+P LCCKC YDHV+ST HK VLSV+PYVCN+PGCDV DV
Sbjct: 940  SVGACVVCSSQTSLRCGSCIRKPLLCCKCAYDHVMSTDHKYVLSVSPYVCNSPGCDVNDV 999

Query: 61   TQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDY 120
            T+LYLGGMSYYC++HKP  SF L  NG VFGLYK +C GS  + DFN IA+C WT   DY
Sbjct: 1000 TKLYLGGMSYYCEAHKPQYSFKLVMNGMVFGLYKQSCTGSPYIEDFNKIASCKWTEVDDY 1059

Query: 121  ILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNY 180
            +LAN CTERLKLFAAET KATEE FK  Y  AT+RE++SDREL LSWE+GK RPPLN+NY
Sbjct: 1060 VLANECTERLKLFAAETQKATEEAFKQCYASATIREIVSDRELILSWEIGKVRPPLNKNY 1119

Query: 181  VFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTL 240
            VFTGY  T N K  +GEY F+K +  + V YR TTTYKL+VGD F+LTSH V  LSAPTL
Sbjct: 1120 VFTGYHFTNNGKTVLGEYVFDKSELTNGVYYRATTTYKLSVGDVFILTSHAVSSLSAPTL 1179

Query: 241  VPQEHY--VRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALY 298
            VPQE+Y  VR    Y   ++ + F +NV NYQ +G+++Y T+QGPPGTGKSH AIG A+Y
Sbjct: 1180 VPQENYTSVRFASAY---SVPETFQNNVPNYQHIGIKRYCTVQGPPGTGKSHLAIGHAVY 1236

Query: 299  YPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFC 358
            Y +AR+VYTA SHAAVDALCEKA K+L I+ C+RI+PA+ RV+C+DKF VN T  +YVF 
Sbjct: 1237 YCTARVVYTAASHAAVDALCEKAHKFLNINDCARIVPAKLRVDCYDKFNVNDTTRKYVFT 1296

Query: 359  TVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLE 418
            T+NALPE   DI+V DE+SM TNY+LSV+N+R+RAKHYVYIGDPAQLPAPR LL KGTLE
Sbjct: 1297 TINALPELVTDIIVVDEVSMLTNYELSVINSRVRAKHYVYIGDPAQLPAPRVLLNKGTLE 1356

Query: 419  PEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKG 478
            P YFNSV +LM  +GPD+FLGTC RCP EIVDTVSALVY+NKLKA  D SA CFK++YKG
Sbjct: 1357 PRYFNSVTKLMCCLGPDIFLGTCYRCPKEIVDTVSALVYNNKLKAKNDNSAMCFKVYYKG 1416

Query: 479  VITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQG 538
              TH+ SSA+N  QI ++ + L  NP+W  AVFISPYNSQN VA ++LGL TQT DS+QG
Sbjct: 1417 QTTHESSSAVNMQQIHLISKLLKANPSWSNAVFISPYNSQNYVAKRVLGLQTQTADSAQG 1476

Query: 539  SEYDYVIFTQTTETAHSCNVNRFNVAITRAKIGILCIMSDRDLYDKLQFTSLEIPRRNVA 598
            S YD+VI++QT +TAHS NVNRFNVAITRAK GILC+MS   L     FT+L + + N  
Sbjct: 1477 SAYDFVIYSQTAQTAHSVNVNRFNVAITRAKKGILCVMSSMQLIGVFNFTTLTLDKINNP 1536

Query: 599  TLQ 601
             LQ
Sbjct: 1537 RLQ 1539






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 =  749 bits (1933), Expect = 0.0
 Identities = 357/588 (60%), Positives = 446/588 (75%), Gaps = 1/588 (0%)

Query: 1    AVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDV 60
            A G CV+C SQT LRCG C+RRP LC KC YDHV  T HK +L++ PYVCN  GC+V DV
Sbjct: 4996 AAGLCVVCGSQTVLRCGDCLRRPMLCTKCAYDHVFGTDHKFILAITPYVCNTSGCNVNDV 5055

Query: 61   TQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDY 120
            T+LYLGG++YYC  HKP +SFPLC+ G VFGLYK++ +GS ++  FN ++T DW++  DY
Sbjct: 5056 TKLYLGGLNYYCVDHKPHLSFPLCSAGNVFGLYKSSALGSMDIDVFNKLSTSDWSDIRDY 5115

Query: 121  ILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNY 180
             LAN   E L+LFAAET+KA EE+ K SY  AT++E++  +EL L WE GK +PPLNRN 
Sbjct: 5116 KLANDAKESLRLFAAETVKAKEESVKSSYAYATLKEIVGPKELLLLWESGKAKPPLNRNS 5175

Query: 181  VFTGYRVTKNSKVQIGEYTFEKGDYG-DAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPT 239
            VFT +++TK+SK Q+GE+ FEK DYG D V Y+ T T KL  G  F+LTSH V PL APT
Sbjct: 5176 VFTCFQITKDSKFQVGEFVFEKVDYGSDTVTYKSTATTKLVPGMLFILTSHNVAPLRAPT 5235

Query: 240  LVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYY 299
            +  QE Y  I  L+P+ N+SD +++ V  YQ +G Q+ +T+QGPPG+GKSH +IG+ +YY
Sbjct: 5236 MANQEKYSTIYKLHPSFNVSDAYANLVPYYQLIGKQRITTIQGPPGSGKSHCSIGIGVYY 5295

Query: 300  PSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCT 359
            P ARIV+TACSHAAVD+LC KA+    +DKC+RIIPARARVEC+  FK N+   QYVF T
Sbjct: 5296 PGARIVFTACSHAAVDSLCAKAVTAYSVDKCTRIIPARARVECYSGFKPNNNSAQYVFST 5355

Query: 360  VNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEP 419
            VNALPE  ADIVV DE+SM TNYDLSV+N R+  KH VY+GDP QLPAPR L++KG +EP
Sbjct: 5356 VNALPEVNADIVVVDEVSMCTNYDLSVINQRISYKHIVYVGDPQQLPAPRVLISKGVMEP 5415

Query: 420  EYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGV 479
              +N V + M  IGPD+FL  C RCPAEIV+TVS LVY+NK    K+ S QCFK+F +G 
Sbjct: 5416 IDYNVVTQRMCAIGPDVFLHKCYRCPAEIVNTVSELVYENKFVPVKEASKQCFKIFERGS 5475

Query: 480  ITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGS 539
            +  D  S+INR Q+ VV+ F+ +N  W KAVFISPYNSQN VA+++LGL TQTVDS+QGS
Sbjct: 5476 VQVDNGSSINRRQLDVVKRFIHKNSTWSKAVFISPYNSQNYVAARLLGLQTQTVDSAQGS 5535

Query: 540  EYDYVIFTQTTETAHSCNVNRFNVAITRAKIGILCIMSDRDLYDKLQF 587
            EYDYVIF QT++TAH+CN NRFNVAITRAK GI CIMSDR L+D L+F
Sbjct: 5536 EYDYVIFAQTSDTAHACNANRFNVAITRAKKGIFCIMSDRTLFDALKF 5583


 Score = 30.4 bits (67), Expect = 0.96
 Identities = 19/56 (33%), Positives = 25/56 (44%)

Query: 309  CSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALP 364
            CS   +  + E    YLP    SRII A   V+   K      LE+YV   ++A P
Sbjct: 4876 CSQHTMQIVDENGKYYLPYPDPSRIISAGVFVDDITKTDAVILLERYVSLAIDAYP 4931






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 =  731 bits (1886), Expect = 0.0
 Identities = 349/593 (58%), Positives = 442/593 (74%), Gaps = 5/593 (0%)

Query: 3    GACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQ 62
            G CV+CNSQT LRCG CIR+PFLCCKCCYDHV+ T HK VLS+NPY+C+  GC   DVT+
Sbjct: 894  GVCVVCNSQTILRCGNCIRKPFLCCKCCYDHVMHTDHKNVLSINPYICSQLGCGEADVTK 953

Query: 63   LYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYIL 122
            LYLGGMSY+C +HKP +S PL +NG VFG+Y+  C GS+NV DFN +AT +W+    YIL
Sbjct: 954  LYLGGMSYFCGNHKPKLSIPLVSNGTVFGIYRANCAGSENVDDFNQLATTNWSIVEPYIL 1013

Query: 123  ANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVF 182
            AN C++ L+ FAAET+KATEE  K  +  A VREV SDREL LSWE GK RPPLNRNYVF
Sbjct: 1014 ANRCSDSLRRFAAETVKATEELHKQQFASAEVREVFSDRELILSWEPGKTRPPLNRNYVF 1073

Query: 183  TGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVP 242
            TGY  T+ SKVQ+G++TFEKG+  D V Y+ T+T KL+VGD FVLTSH V+ L APTL P
Sbjct: 1074 TGYHFTRTSKVQLGDFTFEKGEGKDVVYYKATSTAKLSVGDIFVLTSHNVVSLVAPTLCP 1133

Query: 243  QEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSA 302
            Q+ + R   L P + + + F +N+  Y  VG QK +T+QGPPG+GKSHFAIGLA+Y+ SA
Sbjct: 1134 QQTFSRFVNLRPNVMVPECFVNNIPLYHLVGKQKRTTVQGPPGSGKSHFAIGLAVYFSSA 1193

Query: 303  RIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNA 362
            R+V+TACSHAAVDALCEKA K+L +D C+RI+P R  V+CF KFK N T ++Y+F T+NA
Sbjct: 1194 RVVFTACSHAAVDALCEKAFKFLKVDDCTRIVPQRTTVDCFSKFKANDTGKKYIFSTINA 1253

Query: 363  LPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYF 422
            LPE + DI++ DE+SM TNY+LS +N ++  ++ VY+GDPAQLPAPRTLL  G+L P+ +
Sbjct: 1254 LPEVSCDILLVDEVSMLTNYELSFINGKINYQYVVYVGDPAQLPAPRTLL-NGSLSPKDY 1312

Query: 423  NSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFY---KGV 479
            N V  LM  + PD+FL  C RCP EIVDTVS LVYD K  A+  +S +CFK+        
Sbjct: 1313 NVVTNLMVCVKPDIFLAKCYRCPKEIVDTVSTLVYDGKFIANNPESRECFKVIVNNGNSD 1372

Query: 480  ITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGS 539
            + H+  SA N  Q+  V++F+ RN  WR+A+FISPYN+ N  A ++LGL  QTVDSSQGS
Sbjct: 1373 VGHESGSAYNTTQLEFVKDFVCRNKQWREAIFISPYNAMNQRAYRMLGLNVQTVDSSQGS 1432

Query: 540  EYDYVIFTQTTETAHSCNVNRFNVAITRAKIGILCIMSDRD-LYDKLQFTSLE 591
            EYDYVIF  T ++ H+ N+NRFNVA+TRAK GIL +M  RD LY  L+FT L+
Sbjct: 1433 EYDYVIFCVTADSQHALNINRFNVALTRAKRGILVVMRQRDELYSALKFTELD 1485


 Score = 29.6 bits (65), Expect = 1.6
 Identities = 15/42 (35%), Positives = 24/42 (57%)

Query: 323 KYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALP 364
           KYLP    SRI+ A   V+  DK +  + +E+Y+   ++A P
Sbjct: 786 KYLPYPDPSRILGACVFVDDVDKTEPVAVMERYIALAIDAYP 827






spP18458
RRPB_BEV		RNA-directed RNA polymerase (EC 2.7.7.48) (ORF1B) [POL] [Berne virus
            (BEV)]		          2291 AA 
align
 Score = 44.7 bits (104), Expect = 5e-05
 Identities = 46/176 (26%), Positives = 75/176 (42%), Gaps = 15/176 (8%)

Query: 280  LQGPPGTGKSHFAIGLALYYPSA--RIVYTACSHAAVDALCEKALKYLPIDKCSRIIPAR 337
            + GPPGTGK+ F     L   S+  R VY A +H  V  + EK    + +   +      
Sbjct: 1099 VMGPPGTGKTTFVYDTYLSKASSSNRFVYCAPTHRLVGDMDEKVDGAVVVSAYNDRTYRN 1158

Query: 338  ARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYV 397
                  D + V       + CT N LP   + +++ DE+S+   + + +    +  K  V
Sbjct: 1159 PVWNKDDSYGV-------LLCTHNTLPFIKSAVLIADEVSLIPPH-VMIKILSMGFKKVV 1210

Query: 398  YIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVS 453
             +GDP QL +P     K   + + F     L++      +L  C RCP +I+   S
Sbjct: 1211 LLGDPFQL-SPVYKNHKVHFKYDTF----YLLQLATQKRYLTACYRCPPQILSAFS 1261






spP04867
V58K_BSMV		58 kDa protein (Beta-B protein) [Barley stripe mosaic virus (BSMV)]          528 AA 
align
 Score = 33.1 bits (74), Expect = 0.15
 Identities = 15/45 (33%), Positives = 31/45 (68%), Gaps = 1/45 (2%)

Query: 360 VNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQ 404
           ++A+P  T+D+++ DE ++A + ++ ++  RLRA   + +GD AQ
Sbjct: 316 LSAVP-ITSDLLIIDEYTLAESAEILLLQRRLRASMVLLVGDVAQ 359






spQ04561
RPOA_LELV		POL polyprotein (ORF1A/1B) [Contains: RNA-directed RNA polymerase (EC
            2.7.7.48); Helicase; Protease (EC 3.4.21.-)] [POL]
            [Lelystad virus (LV) (Porcine reproductive and
            respiratory syndrome virus)]		          3859 AA 
align
 Score = 32.7 bits (73), Expect = 0.19
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 11/74 (14%)

Query: 499  FLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHSCNV 558
            F TR  A+ +   ++PY+ ++ + S I      T+DSSQG+ +D  I T    +  S N 
Sbjct: 3347 FTTRPVAFGQV--LTPYH-KDRIGSAI------TIDSSQGATFD--IVTLHLPSPKSLNK 3395

Query: 559  NRFNVAITRAKIGI 572
            +R  VAITRA+ G+
Sbjct: 3396 SRALVAITRARHGL 3409






spQ82007
VE1_HPV73		Replication protein E1 [E1] [Human papillomavirus type 73]          650 AA 
align
 Score = 31.2 bits (69), Expect = 0.56
 Identities = 18/52 (34%), Positives = 24/52 (46%), Gaps = 1/52 (1%)

Query: 275 QKYSTLQGPPGTGKSHFAIGLALYYPSARIVY-TACSHAAVDALCEKALKYL 325
           Q    L GPP TGKSHF + L  +     I Y  + SH  +  L +  +  L
Sbjct: 471 QNCIVLYGPPDTGKSHFGMSLIKFIQGVVISYVNSTSHFWLSPLADAKMALL 522






spP50765
VE1_HPV70		Replication protein E1 [E1] [Human papillomavirus type 70]          652 AA 
align
 Score = 30.4 bits (67), Expect = 0.96
 Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 1/47 (2%)

Query: 280 LQGPPGTGKSHFAIGLALYYPSARIVY-TACSHAAVDALCEKALKYL 325
           +QGPP TGKS+F + L  +     I Y  + SH  ++ L +  +  L
Sbjct: 477 IQGPPNTGKSYFCMSLMHFLQGTVISYVNSTSHFWLEPLADAKVAML 523






spP36327
POLN_EEVV3		Nonstructural polyprotein [Contains: Nonstructural protein NSP1;
           Nonstructural protein NSP2; Nonstructural protein NSP3;
           Nonstructural protein NSP4] [Venezuelan equine
           encephalitis virus (strain 3880)]		          2485 AA 
align
 Score = 30.4 bits (67), Expect = 0.96
 Identities = 49/207 (23%), Positives = 70/207 (33%), Gaps = 44/207 (21%)

Query: 328 DKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVV 387
           + C+ II    R++  D   VN+     V       P  T  I   DE        L  +
Sbjct: 747 ENCAEIIRDVKRIKGLD---VNARTVDSVLLNGCKYPVETLYI---DEAFACHAGTLRAL 800

Query: 388 NARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAE 447
            A +R K  V  GDP Q      +  K     E    V    K+I         RRC   
Sbjct: 801 IAIIRPKKAVLCGDPKQCGFFNMMCLKVHFNHEICTQVFH--KSIS--------RRCTKS 850

Query: 448 IVDTVSALVYDNKLKAHKDKSAQ-------------------CFK-------MFYKG--V 479
           +   VS L YD +++    K  +                   CF+       + YKG  V
Sbjct: 851 VTSVVSTLFYDKRMRTTNPKETKIEIDTTGSTKPKQDDLILTCFRGWVKQLQIDYKGNEV 910

Query: 480 ITHDVSSAINRPQIGVVREFLTRNPAW 506
           +T   S  + R  +  VR  +  NP +
Sbjct: 911 MTAAASQGLTRKGVYAVRYKVNENPLY 937






spP36725
VE1_HPV34		Replication protein E1 [E1] [Human papillomavirus type 34]          647 AA 
align
 Score = 29.6 bits (65), Expect = 1.6
 Identities = 17/52 (32%), Positives = 24/52 (46%), Gaps = 1/52 (1%)

Query: 275 QKYSTLQGPPGTGKSHFAIGLALYYPSARIVY-TACSHAAVDALCEKALKYL 325
           Q    + GPP TGKSHF + L  +     I Y  + SH  +  L +  +  L
Sbjct: 468 QNCIVIYGPPDTGKSHFGMSLMQFMQGVVISYVNSNSHFWLSPLADAKMALL 519






spQ05112
VE1_HPV30		Replication protein E1 [E1] [Human papillomavirus type 30]          631 AA 
align
 Score = 29.6 bits (65), Expect = 1.6
 Identities = 22/58 (37%), Positives = 28/58 (48%), Gaps = 3/58 (5%)

Query: 280 LQGPPGTGKSHFAIGLALYYPSARIVY-TACSHAAVDALCEKALKYL--PIDKCSRII 334
           L GPP TGKS FA+ L  ++  + I Y  + SH  +  L    L  L    D C R I
Sbjct: 457 LYGPPNTGKSCFAMSLIQFFQGSVISYVNSHSHFWLQPLDNAKLGMLDDATDACWRYI 514






spQ04610
POLN_HEVMY		Non-structural polyprotein [Contains: RNA-directed RNA polymerase (EC
            2.7.7.48); Helicase] [Hepatitis E virus (strain Myanmar)
            (HEV)]		          1693 AA 
align
 Score = 29.6 bits (65), Expect = 1.6
 Identities = 47/221 (21%), Positives = 78/221 (35%), Gaps = 60/221 (27%)

Query: 238  PTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKV-GMQKYSTLQGPPGTGKSHFAIGLA 296
            PTL   E   R   L   L+ + +     A  +   G+ +Y    G PG+GKS       
Sbjct: 930  PTLTITEDVARTANLAIELDSATDVGRACAGCRVTPGVVQYQFTAGVPGSGKSR------ 983

Query: 297  LYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYV 356
                       + + A VD +               ++P R         ++ +   +  
Sbjct: 984  -----------SITQADVDVV---------------VVPTR---------ELRNAWRRRG 1008

Query: 357  FCTVNALPETTADI-----VVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTL 411
            F   N  P T A +     VV DE      + L +   R    H   +GDP Q+PA    
Sbjct: 1009 FAAFN--PHTAARVTQGRRVVIDEAPSLPPHLLLLHMQRAATVHL--LGDPNQIPA---- 1060

Query: 412  LTKGTLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTV 452
                 ++ E+   V  +   +GP  +     RCPA++ + +
Sbjct: 1061 -----IDFEHAGLVPAIRPDLGPTSWWHVTHRCPADVCELI 1096






spP27282
POLN_EEVVT		Nonstructural polyprotein [Contains: Nonstructural protein NSP1;
           Nonstructural protein NSP2; Nonstructural protein NSP3;
           Nonstructural protein NSP4] [Venezuelan equine
           encephalitis virus (strain Trinidad donkey)]		          2492 AA 
align
 Score = 29.6 bits (65), Expect = 1.6
 Identities = 36/151 (23%), Positives = 52/151 (34%), Gaps = 38/151 (25%)

Query: 384 LSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPDMFLGTCRR 443
           L  + A +R K  V  GDP Q      +  K     E    V    K+I         RR
Sbjct: 797 LRALIAIIRPKKAVLCGDPKQCGFFNMMCLKVHFNHEICTQVFH--KSIS--------RR 846

Query: 444 CPAEIVDTVSALVYDNKLKAHKDKSAQ-------------------CFK-------MFYK 477
           C   +   VS L YD K++    K  +                   CF+       + YK
Sbjct: 847 CTKSVTSVVSTLFYDKKMRTTNPKETKIVIDTTGSTKPKQDDLILTCFRGWVKQLQIDYK 906

Query: 478 G--VITHDVSSAINRPQIGVVREFLTRNPAW 506
           G  ++T   S  + R  +  VR  +  NP +
Sbjct: 907 GNEIMTAAASQGLTRKGVYAVRYKVNENPLY 937






spQ81020
VE1_HPV54		Replication protein E1 [E1] [Human papillomavirus type 54]          633 AA 
align
 Score = 29.3 bits (64), Expect = 2.1
 Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 1/47 (2%)

Query: 280 LQGPPGTGKSHFAIGLALYYPSARIVY-TACSHAAVDALCEKALKYL 325
           L GPP TGKS+FA+ L  +     + Y  + SH  ++ L +  +  L
Sbjct: 458 LYGPPDTGKSNFAMSLISFLGGVVLSYVNSSSHFWLEPLADAKIAML 504






spP36727
VE1_HPV40		Replication protein E1 [E1] [Human papillomavirus type 40]          647 AA 
align
 Score = 29.3 bits (64), Expect = 2.1
 Identities = 16/45 (35%), Positives = 23/45 (51%), Gaps = 1/45 (2%)

Query: 282 GPPGTGKSHFAIGLALYYPSARIVY-TACSHAAVDALCEKALKYL 325
           GPP TGKS F + L  +     I Y  +CSH  + +L +  +  L
Sbjct: 477 GPPDTGKSCFGMSLMHFMQGTIISYVNSCSHFWLQSLADAKVAML 521






spP24829
VE1_HPV39		Replication protein E1 [E1] [Human papillomavirus type 39]          647 AA 
align
 Score = 28.5 bits (62), Expect = 3.6
 Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 1/47 (2%)

Query: 280 LQGPPGTGKSHFAIGLALYYPSARIVY-TACSHAAVDALCEKALKYL 325
           + GP  TGKSHF + L  +     I Y  + SH  ++ L +  L  L
Sbjct: 472 IYGPANTGKSHFCMSLMHFLQGTVISYVNSTSHFWLEPLADAKLAML 518






spP36328
POLN_EEVVP		Nonstructural polyprotein [Contains: Nonstructural protein NSP1;
           Nonstructural protein NSP2; Nonstructural protein NSP3;
           Nonstructural protein NSP4] [Venezuelan equine
           encephalitis virus (strain P676)]		          2492 AA 
align
 Score = 28.5 bits (62), Expect = 3.6
 Identities = 35/151 (23%), Positives = 52/151 (34%), Gaps = 38/151 (25%)

Query: 384 LSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPDMFLGTCRR 443
           L  + A +R K  V  GDP Q      +  K     E    V    K+I         RR
Sbjct: 797 LRALIAIIRPKKAVLCGDPKQCGFFNMMCLKVHFNHEICTQVFH--KSIS--------RR 846

Query: 444 CPAEIVDTVSALVYDNKLKAHKDKSAQ-------------------CFK-------MFYK 477
           C   +   VS L YD +++    K  +                   CF+       + YK
Sbjct: 847 CTKSVTSVVSTLFYDKRMRTTNPKETKIVIDTTGSTKPKQDDLILTCFRGWVKQLQIDYK 906

Query: 478 G--VITHDVSSAINRPQIGVVREFLTRNPAW 506
           G  ++T   S  + R  +  VR  +  NP +
Sbjct: 907 GNEIMTAAASQGLTRKGVYAVRYKVNENPLY 937






spP04014
VE1_HPV11		Replication protein E1 [E1] [Human papillomavirus type 11]          649 AA 
align
 Score = 28.1 bits (61), Expect = 4.8
 Identities = 16/45 (35%), Positives = 22/45 (48%), Gaps = 1/45 (2%)

Query: 282 GPPGTGKSHFAIGLALYYPSARIVY-TACSHAAVDALCEKALKYL 325
           GPP TGKS F + L  +     I Y  +CSH  +  L +  +  L
Sbjct: 478 GPPDTGKSCFCMSLIKFLGGTVISYVNSCSHFWLQPLTDAKVALL 522






spQ02262
VE1_PCPV1		Replication protein E1 [E1] [Pygmy chimpanzee papillomavirus type
           1]		          648 AA 
align
 Score = 27.7 bits (60), Expect = 6.2
 Identities = 16/45 (35%), Positives = 21/45 (46%), Gaps = 1/45 (2%)

Query: 282 GPPGTGKSHFAIGLALYYPSARIVY-TACSHAAVDALCEKALKYL 325
           GPP TGKS F + L  +     I Y  + SH  +  LC   +  L
Sbjct: 477 GPPDTGKSMFCMSLIKFLGGTVISYVNSSSHFWLQPLCNTKVALL 521






spP81174
VE1_CCPV1		Replication protein E1 [E1] [Common chimpanzee papillomavirus type
           1]		          648 AA 
align
 Score = 27.7 bits (60), Expect = 6.2
 Identities = 16/45 (35%), Positives = 21/45 (46%), Gaps = 1/45 (2%)

Query: 282 GPPGTGKSHFAIGLALYYPSARIVY-TACSHAAVDALCEKALKYL 325
           GPP TGKS F + L  +     I Y  + SH  +  LC   +  L
Sbjct: 477 GPPDTGKSAFCMSLIKFLGGTVISYVNSSSHFWLQPLCNAKVALL 521






spQ80915
VE1_HPV44		Replication protein E1 [E1] [Human papillomavirus type 44]          643 AA 
align
 Score = 27.3 bits (59), Expect = 8.1
 Identities = 16/45 (35%), Positives = 21/45 (46%), Gaps = 1/45 (2%)

Query: 282 GPPGTGKSHFAIGLALYYPSARIVY-TACSHAAVDALCEKALKYL 325
           GPP TGKS F + L  +     I Y  + SH  +  LC   +  L
Sbjct: 472 GPPDTGKSCFCMSLIKFLGGTVISYVNSSSHFWLQPLCNAKVALL 516






spQ02261
VE1_HPV13		Replication protein E1 [E1] [Human papillomavirus type 13]          646 AA 
align
 Score = 27.3 bits (59), Expect = 8.1
 Identities = 16/45 (35%), Positives = 21/45 (46%), Gaps = 1/45 (2%)

Query: 282 GPPGTGKSHFAIGLALYYPSARIVY-TACSHAAVDALCEKALKYL 325
           GPP TGKS F + L  +     I Y  + SH  +  LC   +  L
Sbjct: 475 GPPDTGKSCFCMSLIKFLGGTVISYVNSSSHFWLQPLCNAKVALL 519






spQ05133
VE1_HPV07		Replication protein E1 [E1] [Human papillomavirus type 7]          646 AA 
align
 Score = 27.3 bits (59), Expect = 8.1
 Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 1/45 (2%)

Query: 282 GPPGTGKSHFAIGLALYYPSARIVY-TACSHAAVDALCEKALKYL 325
           GPP TGKS F + L  +     I +  +CSH  + +L +  +  L
Sbjct: 476 GPPDTGKSCFGMSLMHFLQGTIISFVNSCSHFWLQSLVDAKVAML 520





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
   0.322    0.136    0.415 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,464,853
Number of Sequences: 8482
Number of extensions: 197886
Number of successful extensions: 501
Number of sequences better than 10.0: 25
Number of HSP's better than 10.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 470
Number of HSP's gapped (non-prelim): 38
length of query: 601
length of database: 3,552,911
effective HSP length: 97
effective length of query: 504
effective length of database: 2,730,157
effective search space: 1375999128
effective search space used: 1375999128
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 59 (27.3 bits)





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