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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: 306 AA
Date run: 2003-05-01 14:57:53 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) ... 639   0.0
 sp P19751 RRPA_CVMJH RNA-directed RNA polymerase (ORF1A) (EC 2.7... 306 4e-84
 sp Q05002 R1AB_CVH22 Replicase polyprotein 1ab (pp1ab) (ORF1AB) ... 232 6e-62
 sp P27920 VGF1_IBVB F1 protein [F1] [Avian infectious bronchitis... 227 2e-60
 sp P52437 V120_HSV6U Capsid assembly protein U30 [U30] [Human he...  28   1.6
 sp P30003 V120_HSV6G Capsid assembly protein U30 (Fragment) [U30...  28   1.6
 sp P30202 ADEN_ADEM1 Adenain (EC 3.4.22.39) (Endoprotease) (Late...  28   1.6
 sp Q64761 FIB1_ADEG1 Fiber protein 1 [Avian adenovirus gal1 (str...  28   2.1




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 =  639 bits (1647), Expect = 0.0
 Identities = 306/306 (100%), Positives = 306/306 (100%)

Query: 1    SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLIR 60
            SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLIR
Sbjct: 3241 SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLIR 3300

Query: 61   KSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNG 120
            KSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNG
Sbjct: 3301 KSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNG 3360

Query: 121  SPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGK 180
            SPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGK
Sbjct: 3361 SPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGK 3420

Query: 181  FYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE 240
            FYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE
Sbjct: 3421 FYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE 3480

Query: 241  PLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQC 300
            PLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQC
Sbjct: 3481 PLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQC 3540

Query: 301  SGVTFQ 306
            SGVTFQ
Sbjct: 3541 SGVTFQ 3546






spP19751
RRPA_CVMJH		RNA-directed RNA polymerase (ORF1A) (EC 2.7.7.48) [Murine coronavirus
            MHV (strain JHM)]		          4488 AA 
align
 Score =  306 bits (783), Expect = 4e-84
 Identities = 154/306 (50%), Positives = 198/306 (64%), Gaps = 3/306 (0%)

Query: 1    SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLIR 60
            SG  KM  P+ KVE C+V VT G  TLNGLWLDD VYCPRHVIC++ DM +P+Y +LL R
Sbjct: 3351 SGIVKMVSPTSKVEPCVVSVTYGNMTLNGLWLDDKVYCPRHVICSSADMTDPDYPNLLCR 3410

Query: 61   KSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNG 120
             ++  F V +  + L V+ + MQ  LL L V   NP TPKY F  ++PG+TF+VLA YNG
Sbjct: 3411 VTSSDFCVMSDRMSLTVMSYQMQGSLLVLTVTLQNPNTPKYSFGVVKPGETFTVLAAYNG 3470

Query: 121  SPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGK 180
             P G +   MR +HTIKGSFL GSCGSVG+ +  D V F YMH +EL TG H GTD  G 
Sbjct: 3471 RPQGAFHVVMRSSHTIKGSFLCGSCGSVGYVLTGDSVRFVYMHQLELSTGCHTGTDFSGN 3530

Query: 181  FYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE 240
            FYGP+ D Q  Q    D T T+NV+AWLYAA++N   WF+   + +L +FN+ AM   + 
Sbjct: 3531 FYGPYRDAQVVQLPVQDYTQTVNVVAWLYAAILNRCNWFVQSDSCSLEEFNVWAMTNGFS 3590

Query: 241  PLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQC 300
             +  D V  L  L++ TG+ V  + AA+K  L +G  G+ ILGS +LEDE TP DV +Q 
Sbjct: 3591 SIKADLV--LDALASMTGVTVEQVLAAIKR-LHSGFQGKQILGSCVLEDELTPSDVYQQL 3647

Query: 301  SGVTFQ 306
            +GV  Q
Sbjct: 3648 AGVKLQ 3653






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 =  232 bits (592), Expect = 6e-62
 Identities = 124/307 (40%), Positives = 186/307 (60%), Gaps = 6/307 (1%)

Query: 1    SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICT-AEDMLNPNYEDLLI 59
            +G RKMA PSG VE C+V+V  G T LNGLWL D VYCPRHVI +     ++ ++E  ++
Sbjct: 2966 AGLRKMAQPSGFVEKCVVRVCYGNTVLNGLWLGDIVYCPRHVIASNTTSAIDYDHEYSIM 3025

Query: 60   RKSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYN 119
            R   H+F + +G   L V+G +M    L++KV  +N  TP++ F  ++ G+ F++LACY+
Sbjct: 3026 RL--HNFSIISGTAFLGVVGATMHGVTLKIKVSQTNMHTPRHSFRTLKSGEGFNILACYD 3083

Query: 120  GSPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEG 179
            G   GV+   MR N TI+GSF+NG+CGS G+N+    V F YMH +EL +G H G+  +G
Sbjct: 3084 GCAQGVFGVNMRTNWTIRGSFINGACGSPGYNLKNGEVEFVYMHQIELGSGSHVGSSFDG 3143

Query: 180  KFYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNY 239
              YG F D+   Q    +  +T+NV+A+LYAA++NG  W+L      +  +N  A    +
Sbjct: 3144 VMYGGFEDQPNLQVESANQMLTVNVVAFLYAAILNGCTWWLKGEKLFVEHYNEWAQANGF 3203

Query: 240  EPLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQ 299
              +  +  D    L+A+TG+ V  +  A+ ++L NG  G+ ILG + L DEF+  +VV+Q
Sbjct: 3204 TAMNGE--DAFSILAAKTGVCVERLLHAI-QVLNNGFGGKQILGYSSLNDEFSINEVVKQ 3260

Query: 300  CSGVTFQ 306
              GV  Q
Sbjct: 3261 MFGVNLQ 3267






spP27920
VGF1_IBVB		F1 protein [F1] [Avian infectious bronchitis virus (strain Beaudette)
            (IBV)]		          3951 AA 
align
 Score =  227 bits (579), Expect = 2e-60
 Identities = 127/316 (40%), Positives = 179/316 (56%), Gaps = 19/316 (6%)

Query: 1    SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLIR 60
            SGF+K+  PS  VE C+V V+     LNGLWL DT+YCPRHV+          + D+L  
Sbjct: 2780 SGFKKLVSPSSAVEKCIVSVSYRGNNLNGLWLGDTIYCPRHVL---GKFSGDQWNDVLNL 2836

Query: 61   KSNHSFLVQAGN-VQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYN 119
             +NH F V   + V L V+   ++  +L L+   +N +TPKYKF++   G +F++   Y 
Sbjct: 2837 ANNHEFEVTTQHGVTLNVVSRRLKGAVLILQTAVANAETPKYKFIKANCGDSFTIACAYG 2896

Query: 120  GSPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEG 179
            G+  G+Y   MR N TI+ SFL G+CGSVGFNI+   V+F YMHH+ELP  +H GTDL G
Sbjct: 2897 GTVVGLYPVTMRSNGTIRASFLAGACGSVGFNIEKGVVNFFYMHHLELPNALHTGTDLMG 2956

Query: 180  KFYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVING-------DRWFLNRFTTTLNDFNL 232
            +FYG +VD + AQ    D  +T N++AWLYAA+I+         +W L   T +++D+N 
Sbjct: 2957 EFYGGYVDEEVAQRVPPDNLVTNNIVAWLYAAIISVKESSFSLPKW-LESTTVSVDDYNK 3015

Query: 233  VAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCAALKELL--QNGMNGRTILGSTILEDE 290
             A    + P +      +  LSA TG+   D+C  L+ ++   +   G  ILG    EDE
Sbjct: 3016 WAGDNGFTPFSTS--TAITKLSAITGV---DVCKLLRTIMVKNSQWGGDPILGQYNFEDE 3070

Query: 291  FTPFDVVRQCSGVTFQ 306
             TP  V  Q  GV  Q
Sbjct: 3071 LTPESVFNQIGGVRLQ 3086






spP52437
V120_HSV6U		Capsid assembly protein U30 [U30] [Human herpesvirus (type 6 /
           strain Uganda-1102) (HHV6)]		          1082 AA 
align
 Score = 28.5 bits (62), Expect = 1.6
 Identities = 28/109 (25%), Positives = 47/109 (43%), Gaps = 17/109 (15%)

Query: 200 ITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGP--LSAQT 257
           + L+ +AWLYA  IN D   L  FT   +    +A          DH++++     S +T
Sbjct: 743 LLLHYMAWLYAFSINVDHIDLGTFTVIKSVIFKIA----------DHINVMTHTIYSPET 792

Query: 258 GIAVLDMCAALKELLQNGMN---GRTILGSTILEDEFTPFDVVRQCSGV 303
            + V  +  A    LQ  +N    +TI  +  L   +  F   +QC+ +
Sbjct: 793 NLLVSILLNAYTNYLQKYVNPWIKQTITANFSLIQTYITF--TKQCASI 839






spP30003
V120_HSV6G		Capsid assembly protein U30 (Fragment) [U30] [Human herpesvirus
           (type 6 / strain GS) (HHV6)]		          798 AA 
align
 Score = 28.5 bits (62), Expect = 1.6
 Identities = 28/109 (25%), Positives = 47/109 (43%), Gaps = 17/109 (15%)

Query: 200 ITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGP--LSAQT 257
           + L+ +AWLYA  IN D   L  FT   +    +A          DH++++     S +T
Sbjct: 459 LLLHYMAWLYAFSINVDHIDLGTFTVIKSVIFKIA----------DHINVMTHTIYSPET 508

Query: 258 GIAVLDMCAALKELLQNGMN---GRTILGSTILEDEFTPFDVVRQCSGV 303
            + V  +  A    LQ  +N    +TI  +  L   +  F   +QC+ +
Sbjct: 509 NLLVSILLNAYTNYLQKYVNPWIKQTITANFSLIQTYITF--TKQCASI 555






spP30202
ADEN_ADEM1		Adenain (EC 3.4.22.39) (Endoprotease) (Late L3 23 kDa protein)
           [Mouse adenovirus type 1 (MAV-1)]		          204 AA 
align
 Score = 28.5 bits (62), Expect = 1.6
 Identities = 15/42 (35%), Positives = 21/42 (50%)

Query: 242 LTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILG 283
           L + H  + GP SA  G+  +   AA  +  QN MN   I+G
Sbjct: 106 LVKSHQTVQGPHSAACGLFCVLFLAAFGKYPQNPMNNNPIMG 147






spQ64761
FIB1_ADEG1		Fiber protein 1 [Avian adenovirus gal1 (strain Phelps) (Fowl
           adenovirus 1) (CELO)]		          710 AA 
align
 Score = 28.1 bits (61), Expect = 2.1
 Identities = 24/77 (31%), Positives = 36/77 (46%), Gaps = 2/77 (2%)

Query: 184 PFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLT 243
           P    Q A A  TD+T+TLN    L  ++  GD   LN    ++N  +   + +N     
Sbjct: 4   PLTLSQRALALKTDSTLTLNTQGQLGVSLTPGDGLVLNTNGLSIN-ADPQTLAFNNSGAL 62

Query: 244 QDHVDILGPLS-AQTGI 259
           + ++D  GP S   TGI
Sbjct: 63  EVNLDPDGPWSKTATGI 79





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
   0.323    0.138    0.433 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,375,740
Number of Sequences: 8482
Number of extensions: 106381
Number of successful extensions: 165
Number of sequences better than 10.0: 8
Number of HSP's better than 10.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 152
Number of HSP's gapped (non-prelim): 9
length of query: 306
length of database: 3,552,911
effective HSP length: 91
effective length of query: 215
effective length of database: 2,781,049
effective search space: 597925535
effective search space used: 597925535
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 56 (26.2 bits)





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