BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 022813
(291 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3SNG|A Chain A, X-ray Structure Of Fully Glycosylated Bifunctional
Nuclease Tbn1 From Solanum Lycopersicum (tomato)
Length = 277
Score = 310 bits (794), Expect = 6e-85, Method: Compositional matrix adjust.
Identities = 145/269 (53%), Positives = 193/269 (71%), Gaps = 5/269 (1%)
Query: 19 WGKEGHFAICKIAEGYLTEDALAAVKELLPDSAEGDLANVCSWADEVR--FHMRWSSPLH 76
W KEGH C+IA+G L ++A AVK LLP+ GDL+ +C W D+VR + +W+SPLH
Sbjct: 1 WSKEGHVMTCRIAQGLLNDEAAHAVKMLLPEYVNGDLSALCVWPDQVRHWYKYKWTSPLH 60
Query: 77 YVDTPDFMCNYKYCRDCHDSVGRKNRCVTGAIYNYTMQLKSGYQDSISVEKYNLTEALMF 136
++DTPD CN+ Y RDCHD G K+ CV GAI N+T QL S Y++ S +YN+TEAL+F
Sbjct: 61 FIDTPDKACNFDYERDCHDQHGVKDMCVAGAIQNFTTQL-SHYREGTSDRRYNMTEALLF 119
Query: 137 LSHFIGDVHQPLHVGFIGDKGGNTITVRWYRRKTNLHHVWDTMIIDSALKTYYDSDIAVM 196
LSHF+GD+HQP+HVGF D GGN+I +RW+R K+NLHHVWD II +A K YY DI ++
Sbjct: 120 LSHFMGDIHQPMHVGFTSDAGGNSIDLRWFRHKSNLHHVWDREIILTAAKDYYAKDINLL 179
Query: 197 IQSIQRNITDG-WSNDVSSWENCANNQTVCPNGYASESVSLACKFAYRNATPGTTLEDDY 255
+ I+ N TDG WS+D++SW C N + C N +A+ES+++ACK+ Y+ G TL DDY
Sbjct: 180 EEDIEGNFTDGIWSDDLASWRECGNVFS-CVNKFATESINIACKWGYKGVEAGETLSDDY 238
Query: 256 FLTRLPIVEKRLAQSGIRLAATLNRIFSS 284
F +RLPIV KR+AQ GIRLA LN +F +
Sbjct: 239 FNSRLPIVMKRVAQGGIRLAMLLNNVFGA 267
>pdb|4DJ4|A Chain A, X-ray Structure Of Mutant N211d Of Bifunctional Nuclease
Tbn1 From Solanum Lycopersicum (tomato)
pdb|4DJ4|B Chain B, X-ray Structure Of Mutant N211d Of Bifunctional Nuclease
Tbn1 From Solanum Lycopersicum (tomato)
Length = 277
Score = 308 bits (790), Expect = 2e-84, Method: Compositional matrix adjust.
Identities = 144/269 (53%), Positives = 193/269 (71%), Gaps = 5/269 (1%)
Query: 19 WGKEGHFAICKIAEGYLTEDALAAVKELLPDSAEGDLANVCSWADEVR--FHMRWSSPLH 76
W KEGH C+IA+G L ++A AVK LLP+ GDL+ +C W D+VR + +W+SPLH
Sbjct: 1 WSKEGHVMTCRIAQGLLNDEAAHAVKMLLPEYVNGDLSALCVWPDQVRHWYKYKWTSPLH 60
Query: 77 YVDTPDFMCNYKYCRDCHDSVGRKNRCVTGAIYNYTMQLKSGYQDSISVEKYNLTEALMF 136
++DTPD CN+ Y RDCHD G K+ CV GAI N+T QL S Y++ S +YN+TEAL+F
Sbjct: 61 FIDTPDKACNFDYERDCHDQHGVKDMCVAGAIQNFTTQL-SHYREGTSDRRYNMTEALLF 119
Query: 137 LSHFIGDVHQPLHVGFIGDKGGNTITVRWYRRKTNLHHVWDTMIIDSALKTYYDSDIAVM 196
LSHF+GD+HQP+HVGF D GGN+I +RW+R K+NLHHVWD II +A K YY DI ++
Sbjct: 120 LSHFMGDIHQPMHVGFTSDAGGNSIDLRWFRHKSNLHHVWDREIILTAAKDYYAKDINLL 179
Query: 197 IQSIQRNITDG-WSNDVSSWENCANNQTVCPNGYASESVSLACKFAYRNATPGTTLEDDY 255
+ I+ + TDG WS+D++SW C N + C N +A+ES+++ACK+ Y+ G TL DDY
Sbjct: 180 EEDIEGDFTDGIWSDDLASWRECGNVFS-CVNKFATESINIACKWGYKGVEAGETLSDDY 238
Query: 256 FLTRLPIVEKRLAQSGIRLAATLNRIFSS 284
F +RLPIV KR+AQ GIRLA LN +F +
Sbjct: 239 FNSRLPIVMKRVAQGGIRLAMLLNNVFGA 267
>pdb|1AK0|A Chain A, P1 Nuclease In Complex With A Substrate Analog
Length = 270
Score = 104 bits (260), Expect = 5e-23, Method: Compositional matrix adjust.
Identities = 87/280 (31%), Positives = 133/280 (47%), Gaps = 24/280 (8%)
Query: 19 WGKEGHFAICKIAEGYLTEDALAAVKELLPDSAEGDLANVCSWADEVRFHM--RWSSPLH 76
WG GH + +A+ Y++ +A + + +L S+ LA++ SWADE R +WS+ LH
Sbjct: 1 WGALGHATVAYVAQHYVSPEAASWAQGILGSSSSSYLASIASWADEYRLTSAGKWSASLH 60
Query: 77 YVDT---PDFMCNYKYCRDCHDSVGRKNRCVTGAIYNYTMQLKSGYQDSISVEKYNLTEA 133
++D P CN Y RDC S C AI NYT ++ S+ N EA
Sbjct: 61 FIDAEDNPPTNCNVDYERDCGSS-----GCSISAIANYTQRVSDS-----SLSSENHAEA 110
Query: 134 LMFLSHFIGDVHQPLHVGFIGDKGGNTITVRWYRRKTNLHHVWDTMIIDSALKTYYDSDI 193
L FL HFIGD+ QPLH GGN I V + NLH WDT + + + SD
Sbjct: 111 LRFLVHFIGDMTQPLHDEAYA-VGGNKINVTFDGYHDNLHSDWDTYMPQKLIGGHALSDA 169
Query: 194 AVMIQSIQRNITDG-WSNDVSSW---ENCANNQTVCPNGYASESVSLACKFAYRNATPGT 249
+++ +NI G ++ W +N + T +AS++ +L C +
Sbjct: 170 ESWAKTLVQNIESGNYTAQAIGWIKGDNISEPITTATR-WASDANALVCTVVMPHGAAAL 228
Query: 250 TLED---DYFLTRLPIVEKRLAQSGIRLAATLNRIFSSQI 286
D Y+ + + +E ++A+ G RLA +N I S+I
Sbjct: 229 QTGDLYPTYYDSVIDTIELQIAKGGYRLANWINEIHGSEI 268
>pdb|1U83|A Chain A, Psl Synthase From Bacillus Subtilis
Length = 276
Score = 28.5 bits (62), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 10/36 (27%), Positives = 21/36 (58%)
Query: 34 YLTEDALAAVKELLPDSAEGDLANVCSWADEVRFHM 69
Y+ ED A ++++ ++ E +CS + +VRF +
Sbjct: 177 YIVEDXEAGAEKVITEARESGTGGICSSSGDVRFQI 212
>pdb|2OZT|A Chain A, Crystal Structure Of O-Succinylbenzoate Synthase From
Thermosynechococcus Elongatus Bp-1
Length = 332
Score = 27.7 bits (60), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 3/39 (7%)
Query: 18 GWGKE---GHFAICKIAEGYLTEDALAAVKELLPDSAEG 53
GWG E A+C+ G+LT + A + E LP + G
Sbjct: 52 GWGSETLNADIALCQQLPGHLTPEIXATIPEALPAAQFG 90
>pdb|3H7V|A Chain A, Crystal Structure Of O-Succinylbenzoate Synthase From
Thermosynechococcus Elongatus Bp-1 Complexed With Mg In
The Active Site
Length = 330
Score = 27.7 bits (60), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 3/39 (7%)
Query: 18 GWGKE---GHFAICKIAEGYLTEDALAAVKELLPDSAEG 53
GWG E A+C+ G+LT + A + E LP + G
Sbjct: 50 GWGSETLNADIALCQQLPGHLTPEIXATIPEALPAAQFG 88
>pdb|2GE7|A Chain A, Structure Of The C-Terminal Dimerization Domain Of
Infectious Bronchitis Virus Nucleocapsid Protein
pdb|2GE7|B Chain B, Structure Of The C-Terminal Dimerization Domain Of
Infectious Bronchitis Virus Nucleocapsid Protein
Length = 108
Score = 27.7 bits (60), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 25/98 (25%), Positives = 41/98 (41%), Gaps = 14/98 (14%)
Query: 13 VNGVLGWGKEGHFAICKIAEGYLTEDALAAVKELLPDSAEGDLANVCSWADEVR------ 66
V G GKEG+F K+ E + + + A+ L+P S + C + V
Sbjct: 16 VFGPRTKGKEGNFGDDKMNEEGIKDGRVTAMLNLVPSS------HACLFGSRVTPKLQPD 69
Query: 67 -FHMRWS-SPLHYVDTPDFMCNYKYCRDCHDSVGRKNR 102
H+++ + + D P F K C C D VG + +
Sbjct: 70 GLHLKFEFTTVVPRDDPQFDNYVKICDQCVDGVGTRPK 107
>pdb|2GE8|A Chain A, Structure Of The C-Terminal Dimerization Domain Of
Infectious Bronchitis Virus Nucleocapsid Protein
pdb|2GE8|B Chain B, Structure Of The C-Terminal Dimerization Domain Of
Infectious Bronchitis Virus Nucleocapsid Protein
pdb|2GE8|F Chain F, Structure Of The C-Terminal Dimerization Domain Of
Infectious Bronchitis Virus Nucleocapsid Protein
pdb|2GE8|G Chain G, Structure Of The C-Terminal Dimerization Domain Of
Infectious Bronchitis Virus Nucleocapsid Protein
pdb|2GE8|C Chain C, Structure Of The C-Terminal Dimerization Domain Of
Infectious Bronchitis Virus Nucleocapsid Protein
pdb|2GE8|D Chain D, Structure Of The C-Terminal Dimerization Domain Of
Infectious Bronchitis Virus Nucleocapsid Protein
pdb|2GE8|I Chain I, Structure Of The C-Terminal Dimerization Domain Of
Infectious Bronchitis Virus Nucleocapsid Protein
pdb|2GE8|J Chain J, Structure Of The C-Terminal Dimerization Domain Of
Infectious Bronchitis Virus Nucleocapsid Protein
Length = 114
Score = 27.3 bits (59), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 25/98 (25%), Positives = 41/98 (41%), Gaps = 14/98 (14%)
Query: 13 VNGVLGWGKEGHFAICKIAEGYLTEDALAAVKELLPDSAEGDLANVCSWADEVR------ 66
V G GKEG+F K+ E + + + A+ L+P S + C + V
Sbjct: 22 VFGPRTKGKEGNFGDDKMNEEGIKDGRVTAMLNLVPSS------HACLFGSRVTPKLQPD 75
Query: 67 -FHMRWS-SPLHYVDTPDFMCNYKYCRDCHDSVGRKNR 102
H+++ + + D P F K C C D VG + +
Sbjct: 76 GLHLKFEFTTVVPRDDPQFDNYVKICDQCVDGVGTRPK 113
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.322 0.135 0.433
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,202,006
Number of Sequences: 62578
Number of extensions: 372824
Number of successful extensions: 759
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 743
Number of HSP's gapped (non-prelim): 10
length of query: 291
length of database: 14,973,337
effective HSP length: 98
effective length of query: 193
effective length of database: 8,840,693
effective search space: 1706253749
effective search space used: 1706253749
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: 51 (24.3 bits)