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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: 346 AA
Date run: 2003-05-01 15:10:09 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) ... 693   0.0
 sp P16342 RRPB_CVMA5 RNA-directed RNA polymerase (EC 2.7.7.48) (... 326 4e-90
 sp P29982 RRPB_CVMJH RNA-directed RNA polymerase (EC 2.7.7.48) (... 319 5e-88
 sp Q05002 R1AB_CVH22 Replicase polyprotein 1ab (pp1ab) (ORF1AB) ... 257 2e-69
 sp P26314 RRPB_IBVB RNA-directed RNA polymerase (ORF1B) (EC 2.7.... 239 4e-64
 sp P18457 RRPB_CVPFS RNA-directed RNA polymerase (ORF1B) (EC 2.7... 181 2e-46
 sp P12723 RRPB_IBVK RNA-directed RNA polymerase (ORF1B) (EC 2.7.... 138 2e-33
 sp P19811 RPOA_EAV POL polyprotein (ORF1A/1B) [Contains: RNA-dir...  40 8e-04
 sp P18458 RRPB_BEV RNA-directed RNA polymerase (EC 2.7.7.48) (OR...  39 0.002
 sp Q04561 RPOA_LELV POL polyprotein (ORF1A/1B) [Contains: RNA-di...  30  0.64




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 =  693 bits (1788), Expect = 0.0
 Identities = 346/346 (100%), Positives = 346/346 (100%)

Query: 1    SLENVAYNVVNKGHFDGHAGEAPVSIINNAVYTKVDGIDVEIFENKTTLPVNVAFELWAK 60
            SLENVAYNVVNKGHFDGHAGEAPVSIINNAVYTKVDGIDVEIFENKTTLPVNVAFELWAK
Sbjct: 6430 SLENVAYNVVNKGHFDGHAGEAPVSIINNAVYTKVDGIDVEIFENKTTLPVNVAFELWAK 6489

Query: 61   RNIKPVPEIKILNNLGVDIAANTVIWDYKREAPAHVSTIGVCTMTDIAKKPTESACSSLT 120
            RNIKPVPEIKILNNLGVDIAANTVIWDYKREAPAHVSTIGVCTMTDIAKKPTESACSSLT
Sbjct: 6490 RNIKPVPEIKILNNLGVDIAANTVIWDYKREAPAHVSTIGVCTMTDIAKKPTESACSSLT 6549

Query: 121  VLFDGRVEGQVDLFRNARNGVLITEGSVKGLTPSKGPAQASVNGVTLIGESVKTQFNYFK 180
            VLFDGRVEGQVDLFRNARNGVLITEGSVKGLTPSKGPAQASVNGVTLIGESVKTQFNYFK
Sbjct: 6550 VLFDGRVEGQVDLFRNARNGVLITEGSVKGLTPSKGPAQASVNGVTLIGESVKTQFNYFK 6609

Query: 181  KVDGIIQQLPETYFTQSRDLEDFKPRSQMETDFLELAMDEFIQRYKLEGYAFEHIVYGDF 240
            KVDGIIQQLPETYFTQSRDLEDFKPRSQMETDFLELAMDEFIQRYKLEGYAFEHIVYGDF
Sbjct: 6610 KVDGIIQQLPETYFTQSRDLEDFKPRSQMETDFLELAMDEFIQRYKLEGYAFEHIVYGDF 6669

Query: 241  SHGQLGGLHLMIGLAKRSQDSPLKLEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLD 300
            SHGQLGGLHLMIGLAKRSQDSPLKLEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLD
Sbjct: 6670 SHGQLGGLHLMIGLAKRSQDSPLKLEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLD 6729

Query: 301  DFVEIIKSQDLSVISKVVKVTIDYAEISFMLWCKDGHVETFYPKLQ 346
            DFVEIIKSQDLSVISKVVKVTIDYAEISFMLWCKDGHVETFYPKLQ
Sbjct: 6730 DFVEIIKSQDLSVISKVVKVTIDYAEISFMLWCKDGHVETFYPKLQ 6775






spP16342
RRPB_CVMA5		RNA-directed RNA polymerase (EC 2.7.7.48) (ORF1B) [F2] [Murine
            coronavirus MHV (strain A59)]		          2733 AA 
align
 Score =  326 bits (835), Expect = 4e-90
 Identities = 174/380 (45%), Positives = 235/380 (61%), Gaps = 40/380 (10%)

Query: 1    SLENVAYNVVNKGHFDGHAGEAPVSIINNAVYTKVDGIDVEIFENKTTLPVNVAFELWAK 60
            SLENV YN+VN GHFDG AGE P ++I   V  K+   DV +F+N T  P NVA EL+AK
Sbjct: 2061 SLENVVYNLVNAGHFDGRAGELPCAVIGEKVIAKIQNEDVVVFKNNTPFPTNVAVELFAK 2120

Query: 61   RNIKPVPEIKILNNLGVDIAANTVIWDYKREAPAHVSTIGVCTMTDIAKKPTESACSSLT 120
            R+I+P PE+K+  NL +D+  + V+WDY +++    ST  VC  TD+          SL 
Sbjct: 2121 RSIRPHPELKLFRNLNIDVCWSHVLWDYAKDSVFCSSTYKVCKYTDL------QCIESLN 2174

Query: 121  VLFDGRVEGQVDLFRNARNGVLITEGSVKGLTPSKGPAQASVNGVTL--IGES-VKTQFN 177
            VLFDGR  G ++ F+  RNGV I    +K L+  KGP +A +NGV +  +G+S V+  F 
Sbjct: 2175 VLFDGRDNGALEAFKKCRNGVYINTTKIKSLSMIKGPQRADLNGVVVEKVGDSDVEFWFA 2234

Query: 178  YFKKVDGII-----------QQLPE--------------------TYFTQSRDLEDFKPR 206
              K  D +I            + P+                    T FTQSR L  F PR
Sbjct: 2235 VRKDGDDVIFSRTGSLEPSHYRSPQGNPGGNRVGDLSGNEALARGTIFTQSRLLSSFTPR 2294

Query: 207  SQMETDFLELAMDEFIQRYKLEGYAFEHIVYGDFSHGQLGGLHLMIGLAKRSQDSPLKLE 266
            S+ME DF++L  D FI +Y L+ YAFEH+VYG F+   +GGLHL+IGLA+R Q S L ++
Sbjct: 2295 SEMEKDFMDLDDDVFIAKYSLQDYAFEHVVYGSFNQKIIGGLHLLIGLARRQQKSNLVIQ 2354

Query: 267  DFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVISKVVKVTIDYAE 326
            +F+  DS++ +YFITD  +GSSK VC+VIDLLLDDFV+I+KS +L  +SKVV V +D+ +
Sbjct: 2355 EFVTYDSSIHSYFITDENSGSSKSVCTVIDLLLDDFVDIVKSLNLKCVSKVVNVNVDFKD 2414

Query: 327  ISFMLWCKDGHVETFYPKLQ 346
              FMLWC +  V TFYP+LQ
Sbjct: 2415 FQFMLWCNEEKVMTFYPRLQ 2434






spP29982
RRPB_CVMJH		RNA-directed RNA polymerase (EC 2.7.7.48) (ORF1B) [Murine coronavirus
            MHV (strain JHM)]		          2731 AA 
align
 Score =  319 bits (817), Expect = 5e-88
 Identities = 169/380 (44%), Positives = 234/380 (61%), Gaps = 40/380 (10%)

Query: 1    SLENVAYNVVNKGHFDGHAGEAPVSIINNAVYTKVDGIDVEIFENKTTLPVNVAFELWAK 60
            SLENV YN+VN GHFDG AGE P ++I   V  K+   DV +F+N T  P NVA EL+A+
Sbjct: 2059 SLENVVYNLVNAGHFDGRAGELPCAVIGEKVIAKIQNEDVVVFKNNTPFPTNVAVELFAE 2118

Query: 61   RNIKPVPEIKILNNLGVDIAANTVIWDYKREAPAHVSTIGVCTMTDIAKKPTESACSSLT 120
            R+I+P PE+K+  +  + +  N V+WDY +++    ST  VC  TD+          SL 
Sbjct: 2119 RSIRPHPELKLFRSSNIHVCWNHVLWDYAKDSVFCSSTYKVCKYTDL------QCIESLN 2172

Query: 121  VLFDGRVEGQVDLFRNARNGVLITEGSVKGLTPSKGPAQASVNGVTL--IGES-VKTQFN 177
            VLFDGR  G ++ F+  RNGV I    +K L+  KGP +A +NGV +  +G+S V+  F 
Sbjct: 2173 VLFDGRDNGALEAFKKCRNGVYINTTKIKSLSMIKGPQRADLNGVVVEKVGDSDVEFWFA 2232

Query: 178  YFKKVDGII-----------QQLPE--------------------TYFTQSRDLEDFKPR 206
              +  D +I            + P+                    T FTQSR L  F PR
Sbjct: 2233 MRRDGDDVIFSRTGSLEPSHYRSPQGNPGGNRVGDLSGNEALARGTIFTQSRFLSSFSPR 2292

Query: 207  SQMETDFLELAMDEFIQRYKLEGYAFEHIVYGDFSHGQLGGLHLMIGLAKRSQDSPLKLE 266
            S+ME DF++L  D FI +Y L+ YAFEH+VYG F+   +GGLHL+IGLA+R + S L ++
Sbjct: 2293 SEMEKDFMDLDEDVFIAKYSLQDYAFEHVVYGSFNQKIIGGLHLLIGLARRPKKSNLVIQ 2352

Query: 267  DFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVISKVVKVTIDYAE 326
            +F+P DS++ +YFITD  +GSS+ VC+VIDLLLDDFV+I+KS +L  +SKVV V +D+ +
Sbjct: 2353 EFVPYDSSIHSYFITDENSGSSESVCTVIDLLLDDFVDIVKSLNLKCVSKVVNVNVDFKD 2412

Query: 327  ISFMLWCKDGHVETFYPKLQ 346
              FMLWC +  V TFYP+LQ
Sbjct: 2413 FQFMLWCNEEKVMTFYPRLQ 2432






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 =  257 bits (656), Expect = 2e-69
 Identities = 154/357 (43%), Positives = 206/357 (57%), Gaps = 22/357 (6%)

Query: 2    LENVAYNVVNKGHFDGHAGEAPVSIINNAVYTKVDGIDVEIFENKTTLPVNVAFELWAKR 61
            LEN+A+NVVNKG F G  GE PV+I  + V+ +    D  +F NKT+LP N+AFEL+AKR
Sbjct: 6112 LENIAFNVVNKGSFVGADGELPVAISGDKVFVRDGNTDNLVFVNKTSLPTNIAFELFAKR 6171

Query: 62   NIKPVPEIKILNNLGVDIAANTVIWDYKREAPAHVSTIGVCTMTDIAKKPTESACSSLTV 121
             +   P + IL NLGV      V+WDY+ E P    T  VC  TD A    E  C+    
Sbjct: 6172 KVGLTPPLSILKNLGVVATYKFVLWDYEAERPLTSFTKSVCGYTDFA----EDVCT---- 6223

Query: 122  LFDGRVEGQVDLFRNARNGVLITEGSVKGLTPSKGPAQASVNGVTLIGESVKT------- 174
             +D  ++G  + F  + N VL +  +VK  T  K      +N   L G ++ T       
Sbjct: 6224 CYDNSIQGSYERFTLSTNAVLFSATAVK--TGGKSLPAIKLNFGMLNGNAIATVKSEDGN 6281

Query: 175  --QFNYFKKV--DGIIQQLPETYFTQSRDLEDFKPRSQMETDFLELAMDEFIQRYKLEGY 230
                N+F  V  DG      + ++TQ R+L+DF PRS ME DFL + +  FIQ+Y LE +
Sbjct: 6282 IKNINWFVYVRKDGKPVDHYDGFYTQGRNLQDFLPRSTMEEDFLNMDIGVFIQKYGLEDF 6341

Query: 231  AFEHIVYGDFSHGQLGGLHLMIGLAKRSQDSPLKLEDFI-PMDSTVKNYFITDAQTGSSK 289
             FEH+VYGD S   LGGLHL+I   + S+   LK E+F+   D T+K   +T     SSK
Sbjct: 6342 NFEHVVYGDVSKTTLGGLHLLISQVRLSKMGILKAEEFVAASDITLKCCTVTYLNDPSSK 6401

Query: 290  CVCSVIDLLLDDFVEIIKSQDLSVISKVVKVTIDYAEISFMLWCKDGHVETFYPKLQ 346
             VC+ +DLLLDDFV ++KS DL+V+SKV +V ID     +MLWCKD  V TFYP+LQ
Sbjct: 6402 TVCTYMDLLLDDFVSVLKSLDLTVVSKVHEVIIDNKPWRWMLWCKDNAVATFYPQLQ 6458






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 =  239 bits (611), Expect = 4e-64
 Identities = 140/351 (39%), Positives = 207/351 (58%), Gaps = 18/351 (5%)

Query: 1    SLENVAYNVVNKGHFDGHAGEAPVSIINNAVYTKVDGIDVEIFENKTTLPVNVAFELWAK 60
            S++N+AYN+   GH+D  AGE P  I  + V+    G++  +F N+TTLP +VAFEL+AK
Sbjct: 2013 SIDNIAYNMYKGGHYDAIAGEMPTVITGDKVFVIDQGVEKAVFVNQTTLPTSVAFELYAK 2072

Query: 61   RNIKPVPEIKILNNLGVDIAANTVIWDYKREAPAHVSTIGVCTMTDIAKKPTESACSSLT 120
            RNI+ +P  +IL  LGVD+    VIWDY  + P + +T+ VC  TDI         + L 
Sbjct: 2073 RNIRTLPNNRILKGLGVDVTNGFVIWDYANQTPLYRNTVKVCAYTDIEP-------NGLV 2125

Query: 121  VLFDGRVEGQVDLFRNARNGVLITEGSVKGLTPSKGPAQASV-NGVTLIGESVKTQFNYF 179
            VL+D R  G    F  A N VL++    K  +  + P+   V NG+ L           +
Sbjct: 2126 VLYDDRY-GDYQSFLAADNAVLVSTQCYKRYSYVEIPSNLLVQNGMPL---KDGANLYVY 2181

Query: 180  KKVDGIIQQLPETYFTQSRDLEDFKPRSQMETDFLELAMDEFIQRYKLEGYAFEHIVYGD 239
            K+V+G    LP T  TQ R  E F+PRS +E DFL ++ + F++RY  +    +HI+YG+
Sbjct: 2182 KRVNGAFVTLPNTINTQGRSYETFEPRSDIERDFLAMSEESFVERYG-KDLGLQHILYGE 2240

Query: 240  FSHGQLGGLHLMIGLAKRSQDSPLKLEDFIPMDSTV-KNYFITDAQTGSSKCVCSVIDLL 298
                QLGGLH +IG+ +  + + L  +     DS V +NYF+  +  GS K VC+V+DLL
Sbjct: 2241 VDKPQLGGLHTVIGMYRLLRANKLNAKSVTNSDSDVMQNYFVL-SDNGSYKQVCTVVDLL 2299

Query: 299  LDDFVEIIKS---QDLSVISKVVKVTIDYAEISFMLWCKDGHVETFYPKLQ 346
            LDDF+E++++   +  +  SKVV V+IDY  I+FM W +DG ++T YP+LQ
Sbjct: 2300 LDDFLELLRNILKEYGTNKSKVVTVSIDYHSINFMTWFEDGSIKTCYPQLQ 2350






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 =  181 bits (459), Expect = 2e-46
 Identities = 99/233 (42%), Positives = 145/233 (62%), Gaps = 5/233 (2%)

Query: 117 SSLTVLFDGRVEGQVDLFRNARNGVLITEGSVKGLTPSKGPAQASVNG--VTLIGESVKT 174
           S +   FD  + G  + F   R+ VLI+  +VKGL+  K      +N   V+ +G    T
Sbjct: 3   SEVVTCFDNSIAGSFERFTTTRDAVLISNNAVKGLSAIK-LQYGLLNDLPVSTVGNKPVT 61

Query: 175 QFNYFKKVDGIIQQLPETYFTQSRDLEDFKPRSQMETDFLELAMDEFIQRYKLEGYAFEH 234
            + Y +K    ++Q+ ++Y+TQ R  E FKPRS ME DFL +    FIQ+Y LE Y FEH
Sbjct: 62  WYIYVRKNGEYVEQI-DSYYTQGRTFETFKPRSTMEEDFLSMDTTLFIQKYGLEDYGFEH 120

Query: 235 IVYGDFSHGQLGGLHLMIGLAKRSQDSPLKLEDFIP-MDSTVKNYFITDAQTGSSKCVCS 293
           +V+GD S   +GG+HL+I   + ++     +++F+   DST+K+  IT A   SSK VC+
Sbjct: 121 VVFGDVSKTTIGGMHLLISQVRLAKMGLFSVQEFMNNSDSTLKSCCITYADDPSSKNVCT 180

Query: 294 VIDLLLDDFVEIIKSQDLSVISKVVKVTIDYAEISFMLWCKDGHVETFYPKLQ 346
            +D+LLDDFV IIKS DL+V+SKVV V +D     +MLWC++ H++TFYP+LQ
Sbjct: 181 YMDILLDDFVTIIKSLDLNVVSKVVDVIVDCKAWKWMLWCENSHIKTFYPQLQ 233






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 =  138 bits (347), Expect = 2e-33
 Identities = 85/219 (38%), Positives = 131/219 (59%), Gaps = 12/219 (5%)

Query: 134 FRNARNGVLITEGSVKGLTPSKGPAQASVNGVTLIGESVKTQFNYF--KKVDGIIQQLPE 191
           F  A N VL++    K  +  + P+   V      G S+K   N +  K+V+G    LP 
Sbjct: 7   FLAADNAVLVSTQCYKRHSYVEIPSNLLVQN----GMSLKDGANLYVYKRVNGAFVTLPN 62

Query: 192 TYFTQSRDLEDFKPRSQMETDFLELAMDEFIQRYKLEGYAFEHIVYGDFSHGQLGGLHLM 251
           T  TQ R  E F+PRS +E DFL+++ ++F+++Y  +    +HI+YG+    QLGGLH +
Sbjct: 63  TLNTQGRSYETFEPRSDVERDFLDMSEEDFVEKYGKD-LGLQHILYGEVDKPQLGGLHTV 121

Query: 252 IGLAKRSQDSPLKLEDFIPMDSTV-KNYFITDAQTGSSKCVCSVIDLLLDDFVEIIK--- 307
           IG+ +  + + L  +     DS V +NYF+  A  GS K VC+V+DLLLDDF+E+++   
Sbjct: 122 IGMYRLLRANKLNAKSVTNSDSDVMQNYFVL-ADNGSYKQVCTVVDLLLDDFLELLRNIL 180

Query: 308 SQDLSVISKVVKVTIDYAEISFMLWCKDGHVETFYPKLQ 346
           ++  +  SKVV V+IDY  I+FM W +DG ++T YP+LQ
Sbjct: 181 NEYGTNKSKVVTVSIDYHSINFMTWFEDGSIKTCYPQLQ 219






spP19811
RPOA_EAV		POL polyprotein (ORF1A/1B) [Contains: RNA-directed RNA polymerase (EC
            2.7.7.48); Helicase; Protease (EC 3.4.21.-)] [POL]
            [Equine arteritis virus (EAV)]		          3175 AA 
align
 Score = 39.7 bits (91), Expect = 8e-04
 Identities = 43/173 (24%), Positives = 75/173 (43%), Gaps = 36/173 (20%)

Query: 167  LIGESV------KTQFNYFKKVDGIIQQLPETYFTQSRDLEDFKPRSQMETDFLELAMDE 220
            ++G+SV       T +   + VDG  + LP++ F+  R    F+  S+    FL+ A ++
Sbjct: 2904 MVGQSVFVQTPGVTSYWLTEWVDGKARALPDSLFSSGR----FETNSRA---FLDEAEEK 2956

Query: 221  FIQRYKLEGYAFEHIVYGDFSHGQLGGLHLMIGLAKRSQDSPLKLEDFIPMDSTVKNYFI 280
            F         A  H   G+ +   +GG H +      SQ  P      +P D+      +
Sbjct: 2957 FAA-------AHPHACLGEINKSTVGGSHFIF-----SQYLP----PLLPADAVA---LV 2997

Query: 281  TDAQTG-SSKCVCSVIDLLLDDFVEIIKSQDLSVISKVVKVTIDYAEISFMLW 332
              +  G ++K  CSV+D+    F   +  + L   S+V K+ ID+     M+W
Sbjct: 2998 GASLAGKAAKAACSVVDVYAPSFEPYLHPETL---SRVYKIMIDFKPCRLMVW 3047






spP18458
RRPB_BEV		RNA-directed RNA polymerase (EC 2.7.7.48) (ORF1B) [POL] [Berne virus
            (BEV)]		          2291 AA 
align
 Score = 38.5 bits (88), Expect = 0.002
 Identities = 38/165 (23%), Positives = 73/165 (44%), Gaps = 30/165 (18%)

Query: 188  QLPETYFTQSRDLEDFKPRSQMETDFLELAMDEFIQRYKLEGYAFEHIVYGDFSH--GQL 245
            +LP+T F+  R L +    +    +  +LA++     +        H+  GDF+     +
Sbjct: 1884 ELPDTLFSTGR-LYNLDHDAAQNFNVKQLAIETMPNNH--------HVFSGDFTEVGTDI 1934

Query: 246  GGLHLMIGLAKRSQDSPLKLEDFIPMDSTVKNYFITDA----QTGSSKCVCSVIDLLLDD 301
            GG+H ++ L                  S + NY    A      G +    +++D+  + 
Sbjct: 1935 GGVHHVVALNGYK-------------GSIIPNYVKPIATGLINVGRAVKRTTLVDVCANQ 1981

Query: 302  FVEIIKSQDLSV-ISKVVKVTIDYAEISFMLWCK-DGHVETFYPK 344
              E +K Q   V +SKV+ V ID+ ++ FM++   +  ++TFYP+
Sbjct: 1982 LYEKVKQQLEGVKVSKVIFVNIDFQDVQFMVFANGEDDIQTFYPQ 2026






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 = 30.0 bits (66), Expect = 0.64
 Identities = 34/151 (22%), Positives = 62/151 (41%), Gaps = 28/151 (18%)

Query: 182  VDGIIQQLPETYFTQSRDLEDFKPRSQMETDFLELAMDEFIQRYKLEGYAFEHIVYGDFS 241
            + G  Q LPET  +  R   D +       ++L+ A +E  +          H   GD  
Sbjct: 3575 IRGEPQALPETLVSTGRIATDCR-------EYLDAAEEEAAKE-------LPHAFIGDVK 3620

Query: 242  HGQLGGLHLMIGLAKRSQDSPLKLEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDD 301
               +GG H +      S+  P  L    P DS       +  +  ++K VC++ D+ L +
Sbjct: 3621 GTTVGGCHHIT-----SKYLPRSL----PKDSVAVVGVSSPGR--AAKAVCTLTDVYLPE 3669

Query: 302  FVEIIKSQDLSVISKVVKVTIDYAEISFMLW 332
                ++ +     SK  K+ +D+ ++  M+W
Sbjct: 3670 LRPYLQPE---TASKCWKLKLDFRDVRLMVW 3697





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
   0.319    0.137    0.396 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,448,182
Number of Sequences: 8482
Number of extensions: 102419
Number of successful extensions: 226
Number of sequences better than 10.0: 10
Number of HSP's better than 10.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 204
Number of HSP's gapped (non-prelim): 13
length of query: 346
length of database: 3,552,911
effective HSP length: 92
effective length of query: 254
effective length of database: 2,772,567
effective search space: 704232018
effective search space used: 704232018
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 bits)





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