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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: 113 AA
Date run: 2003-05-01 15:03:15 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) ... 234 2e-63
 sp Q05002 R1AB_CVH22 Replicase polyprotein 1ab (pp1ab) (ORF1AB) ...  97 5e-22
 sp P19751 RRPA_CVMJH RNA-directed RNA polymerase (ORF1A) (EC 2.7...  93 1e-20
 sp P27920 VGF1_IBVB F1 protein [F1] [Avian infectious bronchitis...  80 8e-17
 sp Q04538 POLG_POWVL Genome polyprotein [Contains: Capsid protei...  25   3.0
 sp P20988 VA11_VACCC Protein A11 [A11R] [Vaccinia virus (strain ...  24   5.1
 sp P03361 POL_BLVJ POL polyprotein [Contains: Reverse transcript...  24   5.1
 sp P33845 VA22_VARV Protein A22 [A22R] [Variola virus]               23   8.6
 sp P20997 VA22_VACCC Protein A22 [A22R] [Vaccinia virus (strain ...  23   8.6



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 =  234 bits (597), Expect = 2e-63
 Identities = 113/113 (100%), Positives = 113/113 (100%)

Query: 1    NNELSPVALRQMSCAAGTTQTACTDDNALAYYNNSKGGRFVLALLSDHQDLKWARFPKSD 60
            NNELSPVALRQMSCAAGTTQTACTDDNALAYYNNSKGGRFVLALLSDHQDLKWARFPKSD
Sbjct: 4118 NNELSPVALRQMSCAAGTTQTACTDDNALAYYNNSKGGRFVLALLSDHQDLKWARFPKSD 4177

Query: 61   GTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQ 113
            GTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQ
Sbjct: 4178 GTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQ 4230






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 = 97.4 bits (241), Expect = 5e-22
 Identities = 51/113 (45%), Positives = 69/113 (61%), Gaps = 4/113 (3%)

Query: 1    NNELSPVALRQMSCAAGTTQTACTDDNALAYYNNSKGGRFVLALLSDHQDLKWARFPKSD 60
            NNE+ P  ++  +          ++ NAL  YNN  G  F+ A ++    +K+ ++    
Sbjct: 3825 NNEIMPGKMKVKATKGEGDGGITSEGNAL--YNNEGGRAFMYAYVTTKPGMKYVKWEHDS 3882

Query: 61   GTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQ 113
            G  T+  ELEPPCRFV DTP GP++KYLYF+K LNNL RG VLG + ATVRLQ
Sbjct: 3883 GVVTV--ELEPPCRFVIDTPTGPQIKYLYFVKNLNNLRRGAVLGYIGATVRLQ 3933






spP19751
RRPA_CVMJH		RNA-directed RNA polymerase (ORF1A) (EC 2.7.7.48) [Murine coronavirus
            MHV (strain JHM)]		          4488 AA 
align
 Score = 92.8 bits (229), Expect = 1e-20
 Identities = 50/113 (44%), Positives = 66/113 (58%), Gaps = 3/113 (2%)

Query: 1    NNELSPVALRQMSCAAGTTQTACTDDNALAYYNNSKGGRFVLALLSDHQDLKWARFPKSD 60
            NNEL P  LR     +G+            YYN +  G+ V A+LSD   LK+ +  K D
Sbjct: 4228 NNELMPQKLRTQVVNSGSDMNCNIPTQC--YYNTTGTGKIVYAILSDCDGLKYTKIVKED 4285

Query: 61   GTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQ 113
            G   +  EL+PPC+F     KG K+KYLYF+KG N L RG V+G+L++TVRLQ
Sbjct: 4286 GN-CVVLELDPPCKFSVQDVKGLKIKYLYFVKGCNTLARGWVVGTLSSTVRLQ 4337






spP27920
VGF1_IBVB		F1 protein [F1] [Avian infectious bronchitis virus (strain Beaudette)
            (IBV)]		          3951 AA 
align
 Score = 80.1 bits (196), Expect = 8e-17
 Identities = 45/113 (39%), Positives = 63/113 (55%), Gaps = 2/113 (1%)

Query: 1    NNELSPVALRQMSCAAGTTQTACTDDNALAYYNNSKGGRFVLALLSDHQDLKWARFPKSD 60
            NNEL P  ++  +C AG  Q  C+ ++   YY N  G   V A+ S + +LK A F    
Sbjct: 3673 NNELMPHGVKTKACVAGVDQAHCSVESK-CYYTNISGNSVVAAITSSNPNLKVASFLNEA 3731

Query: 61   GTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQ 113
            G   IY +L+PPC+F        +V YLYFIK   ++ RGMVLG+++  V LQ
Sbjct: 3732 GN-QIYVDLDPPCKFGMKVGVKVEVVYLYFIKNTRSIVRGMVLGAISNVVVLQ 3783






spQ04538
POLG_POWVL		Genome polyprotein [Contains: Capsid protein C (Core protein);
           Matrix protein (Envelope protein M); Major envelope
           protein E; Nonstructural proteins NS1, NS2A, NS2B, NS4A
           and NS4B; Protease/helicase (EC 3.4.21.98) (NS3);
           RNA-directed RNA polymerase (EC 2.7.7.48) (NS5)]
           [Tick-borne powassan virus (strain LB)]		          3415 AA 
align
 Score = 25.0 bits (53), Expect = 3.0
 Identities = 12/35 (34%), Positives = 15/35 (42%), Gaps = 5/35 (14%)

Query: 45  LSDHQDLKWARFPKSDGTGTI-----YTELEPPCR 74
           + D    KW R P   G  T+     YT  + PCR
Sbjct: 584 MCDKAKFKWKRVPVDSGHDTVVMEVSYTGSDKPCR 618






spP20988
VA11_VACCC		Protein A11 [A11R] [Vaccinia virus (strain Copenhagen)]          318 AA 
align
 Score = 24.3 bits (51), Expect = 5.1
 Identities = 19/80 (23%), Positives = 31/80 (38%), Gaps = 10/80 (12%)

Query: 1  NNELSPVALRQMSCAAGTTQTACTDDNALAYYNNSKGGRFVLALLSDHQDLKWARFPKSD 60
          +N+   + LRQMS           + NA    +  +    +      ++DL    FP  D
Sbjct: 24 SNKNYEITLRQMSILTHVNNVVDREHNAAVVSSPEEISSQL------NEDL----FPDDD 73

Query: 61 GTGTIYTELEPPCRFVTDTP 80
             TI   ++P    + DTP
Sbjct: 74 SPATIIERVQPHTTIIDDTP 93






spP03361
POL_BLVJ		POL polyprotein [Contains: Reverse transcriptase (EC 2.7.7.49);
           Endonuclease] [POL] [Bovine leukemia virus (Japanese
           isolate BLV-1) (BLV)]		          852 AA 
align
 Score = 24.3 bits (51), Expect = 5.1
 Identities = 11/29 (37%), Positives = 16/29 (55%), Gaps = 3/29 (10%)

Query: 71  PPCRFVTD---TPKGPKVKYLYFIKGLNN 96
           PP   +++   TPKG    +LY + G NN
Sbjct: 771 PPLAVISEGGETPKGSDKLFLYLLPGQNN 799






spP33845
VA22_VARV		Protein A22 [A22R] [Variola virus]          187 AA 
align
 Score = 23.5 bits (49), Expect = 8.6
 Identities = 8/13 (61%), Positives = 11/13 (84%)

Query: 81 KGPKVKYLYFIKG 93
          + P VK++YFIKG
Sbjct: 86 RSPYVKFIYFIKG 98






spP20997
VA22_VACCC		Protein A22 [A22R] [Vaccinia virus (strain Copenhagen)]          176 AA 
align
 Score = 23.5 bits (49), Expect = 8.6
 Identities = 8/13 (61%), Positives = 11/13 (84%)

Query: 81 KGPKVKYLYFIKG 93
          + P VK++YFIKG
Sbjct: 75 RSPYVKFIYFIKG 87





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
   0.318    0.135    0.405 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 881,432
Number of Sequences: 8482
Number of extensions: 36462
Number of successful extensions: 51
Number of sequences better than 10.0: 9
Number of HSP's better than 10.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 41
Number of HSP's gapped (non-prelim): 9
length of query: 113
length of database: 3,552,911
effective HSP length: 78
effective length of query: 35
effective length of database: 2,891,315
effective search space: 101196025
effective search space used: 101196025
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: 49 (23.5 bits)





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