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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: 198 AA (of which 23% low-complexity regions filtered out)
Date run: 2003-05-01 15:02:00 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) ... 288 6e-79
 sp Q05002 R1AB_CVH22 Replicase polyprotein 1ab (pp1ab) (ORF1AB) ... 132 5e-32
 sp P19751 RRPA_CVMJH RNA-directed RNA polymerase (ORF1A) (EC 2.7... 128 8e-31
 sp P27920 VGF1_IBVB F1 protein [F1] [Avian infectious bronchitis... 106 3e-24
 sp P16379 RRPL_VSVJO RNA polymerase beta subunit (EC 2.7.7.48) (...  27   1.8
 sp P13615 RRPL_VSVJH RNA polymerase beta subunit (EC 2.7.7.48) (...  27   1.8
 sp Q04561 RPOA_LELV POL polyprotein (ORF1A/1B) [Contains: RNA-di...  25   9.2
 sp P16900 GAG_OMVVS GAG polyprotein [Contains: Core proteins P16...  25   9.2



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 =  288 bits (736), Expect = 6e-79
 Identities = 152/198 (76%), Positives = 152/198 (76%)

Query: 1    AIASEFSSLPSXXXXXXXXXXXXXXXXNGDXXXXXXXXXXXXXXXXXEFDRDAAMQRKLE 60
            AIASEFSSLPS                NGD                 EFDRDAAMQRKLE
Sbjct: 3920 AIASEFSSLPSYAAYATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLE 3979

Query: 61   KMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKXXXXXXXXXXXXXRDGCVPLNII 120
            KMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRK             RDGCVPLNII
Sbjct: 3980 KMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNII 4039

Query: 121  PLTTAAKLMVVVPDYGTYKNTCDGNTFTYASALWEIQQVVDADSKIVQLSEINMDNSPNL 180
            PLTTAAKLMVVVPDYGTYKNTCDGNTFTYASALWEIQQVVDADSKIVQLSEINMDNSPNL
Sbjct: 4040 PLTTAAKLMVVVPDYGTYKNTCDGNTFTYASALWEIQQVVDADSKIVQLSEINMDNSPNL 4099

Query: 181  AWPLIVTALRANSAVKLQ 198
            AWPLIVTALRANSAVKLQ
Sbjct: 4100 AWPLIVTALRANSAVKLQ 4117






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 =  132 bits (331), Expect = 5e-32
 Identities = 70/198 (35%), Positives = 106/198 (53%), Gaps = 3/198 (1%)

Query: 1    AIASEFSSLPSXXXXXXXXXXXXXXXXNGDXXXXXXXXXXXXXXXXXEFDRDAAMQRKLE 60
            ++AS F  +PS                NG                  EFDR++++Q+K+ 
Sbjct: 3630 SVASSFVGMPSFVAYETARQEYENAVANGSSPQIIKQLKKAMNVAKAEFDRESSVQKKIN 3689

Query: 61   KMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKXXXXXXXXXXXXXRDGCVPLNII 120
            +MA+QA   MYK+AR+ ++++KV SAM ++LF MLR+             R+G VPL++I
Sbjct: 3690 RMAEQAAAAMYKEARAVNRKSKVVSAMHSLLFGMLRRLDMSSVDTILNMARNGVVPLSVI 3749

Query: 121  PLTTAAKLMVVVPDYGTYKNTCDGNTFTYASALWEIQQVVDADSKIVQLSEINMDNSPNL 180
            P T+AA+L+VVVPD+ ++          YA  +W +Q+V D D K V L ++  +N   L
Sbjct: 3750 PATSAARLVVVVPDHDSFVKMMVDGFVHYAGVVWTLQEVKDNDGKNVHLKDVTKENQEIL 3809

Query: 181  AWPLIVTALRANSAVKLQ 198
             WPLI+T  R    VKLQ
Sbjct: 3810 VWPLILTCER---VVKLQ 3824






spP19751
RRPA_CVMJH		RNA-directed RNA polymerase (ORF1A) (EC 2.7.7.48) [Murine coronavirus
            MHV (strain JHM)]		          4488 AA 
align
 Score =  128 bits (321), Expect = 8e-31
 Identities = 69/152 (45%), Positives = 93/152 (61%), Gaps = 6/152 (3%)

Query: 49   FDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKXXXXXXXXXXX 108
            ++RD A+ RKLE+MAD A+T MYK+AR  DK++KV SA+QTMLF+M+RK           
Sbjct: 4080 YERDRAVARKLERMADLALTNMYKEARINDKKSKVVSALQTMLFSMVRKLDNQALNSILD 4139

Query: 109  XXRDGCVPLNIIPLTTAAKLMVVVPDYGTYKNTCDGNTFTYASALWEIQQVVDADSKIVQ 168
                GCVPLN IP  T+  L ++VPD   +    D    TYA  +W IQ + DAD  + Q
Sbjct: 4140 NAVKGCVPLNAIPPLTSNTLTIIVPDKQVFDQVVDNVYVTYAPNVWHIQSIQDADGAVKQ 4199

Query: 169  LSEINMDNSPNLAWPLIVTALRAN--SAVKLQ 198
            L+EI++    N  WPL+++A R N  S V LQ
Sbjct: 4200 LNEIDV----NSTWPLVISANRHNEVSTVVLQ 4227






spP27920
VGF1_IBVB		F1 protein [F1] [Avian infectious bronchitis virus (strain Beaudette)
            (IBV)]		          3951 AA 
align
 Score =  106 bits (264), Expect = 3e-24
 Identities = 55/147 (37%), Positives = 83/147 (56%), Gaps = 5/147 (3%)

Query: 49   FDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKXXXXXXXXXXX 108
            FDRD A+Q+KL+ MA++AMT MYK+AR  D+RAK+ S++  +LF+ML+K           
Sbjct: 3515 FDRDLAVQKKLDSMAERAMTTMYKEARVTDRRAKLVSSLHALLFSMLKKIDSEKLNVLFD 3574

Query: 109  XXRDGCVPLNIIPLTTAAKLMVVVPDYGTYKNTCDGNTFTYASALWEIQQVVDADSKIVQ 168
                G VPL  +P+  + KL +V+PD  T+    +G   TY++ +W I  V+DAD   + 
Sbjct: 3575 QASSGVVPLATVPIVCSNKLTLVIPDPETWVKCVEGVHVTYSTVVWNIDTVIDADGTELH 3634

Query: 169  LSEINMD-----NSPNLAWPLIVTALR 190
             +          +  N+AWPL V   R
Sbjct: 3635 PTSTGSGLTYCISGANIAWPLKVNLTR 3661






spP16379
RRPL_VSVJO		RNA polymerase beta subunit (EC 2.7.7.48) (Large structural protein)
            (L protein) [L] [Vesicular stomatitis virus (serotype New
            Jersey / strain Ogden)]		          2109 AA 
align
 Score = 27.3 bits (59), Expect = 1.8
 Identities = 14/53 (26%), Positives = 25/53 (47%)

Query: 120  IPLTTAAKLMVVVPDYGTYKNTCDGNTFTYASALWEIQQVVDADSKIVQLSEI 172
            +P+   +   ++   YGTY  T + N+ T   +L+   Q+V  D      SE+
Sbjct: 1782 VPVLLESDGCLIYKTYGTYIATQEDNSLTLIGSLFHSVQLVQTDLSSSNTSEL 1834






spP13615
RRPL_VSVJH		RNA polymerase beta subunit (EC 2.7.7.48) (Large structural protein)
            (L protein) [L] [Vesicular stomatitis virus (serotype New
            Jersey / strain Hazelhurst)]		          2109 AA 
align
 Score = 27.3 bits (59), Expect = 1.8
 Identities = 14/53 (26%), Positives = 24/53 (45%)

Query: 120  IPLTTAAKLMVVVPDYGTYKNTCDGNTFTYASALWEIQQVVDADSKIVQLSEI 172
            +P+   +   ++   YGTY  T   N+ T   +L+   Q+V  D      SE+
Sbjct: 1782 VPVLLESDCCLIYKTYGTYIATQKDNSLTLIGSLFHSVQLVQTDLSSSNTSEL 1834






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 = 25.0 bits (53), Expect = 9.2
 Identities = 13/62 (20%), Positives = 31/62 (50%), Gaps = 2/62 (3%)

Query: 131  VVPDYGTYKNTCDGNTFTYASALWEIQQVVDADSKIVQLSEINMDNSPNLAWPLIVTALR 190
            + P +G      DG+ + + +A  + +  ++   +I+Q  E+   ++PNL  P  +  +R
Sbjct: 2490 IQPGHGAGNMGVDGSIWDFETAPTKAE--LELSKQIIQACEVRRGDAPNLQLPYKLYPVR 2547

Query: 191  AN 192
             +
Sbjct: 2548 GD 2549






spP16900
GAG_OMVVS		GAG polyprotein [Contains: Core proteins P16, P25, P14] [GAG]
           [Ovine lentivirus (strain SA-OMVV)]		          446 AA 
align
 Score = 25.0 bits (53), Expect = 9.2
 Identities = 11/36 (30%), Positives = 19/36 (52%)

Query: 156 IQQVVDADSKIVQLSEINMDNSPNLAWPLIVTALRA 191
           + Q++       Q S+ NMD +  L    ++TALR+
Sbjct: 237 VDQIMGVGQTNQQASQANMDQARQLCLQWVITALRS 272





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
   0.317    0.127    0.357 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 900,746
Number of Sequences: 8482
Number of extensions: 26861
Number of successful extensions: 63
Number of sequences better than 10.0: 8
Number of HSP's better than 10.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 55
Number of HSP's gapped (non-prelim): 9
length of query: 198
length of database: 3,552,911
effective HSP length: 87
effective length of query: 111
effective length of database: 2,814,977
effective search space: 312462447
effective search space used: 312462447
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)





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