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= 026060
(244 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 = 243 bits (619), Expect = 1e-64, Method: Compositional matrix adjust.
Identities = 112/205 (54%), Positives = 148/205 (72%), Gaps = 4/205 (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-WSNDVSSWENCAN 220
+ I+ N TDG WS+D++SW C N
Sbjct: 180 EEDIEGNFTDGIWSDDLASWRECGN 204
>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 = 241 bits (614), Expect = 3e-64, Method: Compositional matrix adjust.
Identities = 111/205 (54%), Positives = 148/205 (72%), Gaps = 4/205 (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-WSNDVSSWENCAN 220
+ I+ + TDG WS+D++SW C N
Sbjct: 180 EEDIEGDFTDGIWSDDLASWRECGN 204
>pdb|1AK0|A Chain A, P1 Nuclease In Complex With A Substrate Analog
Length = 270
Score = 91.3 bits (225), Expect = 5e-19, Method: Compositional matrix adjust.
Identities = 68/194 (35%), Positives = 96/194 (49%), Gaps = 16/194 (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 207
+++ +NI G
Sbjct: 170 ESWAKTLVQNIESG 183
>pdb|1U83|A Chain A, Psl Synthase From Bacillus Subtilis
Length = 276
Score = 28.9 bits (63), Expect = 3.0, 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 = 5.7, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 22/44 (50%), Gaps = 3/44 (6%)
Query: 13 VNGVLGWGKE---GHFAICKIAEGYLTEDALAAVKELLPDSAEG 53
+ + GWG E A+C+ G+LT + A + E LP + G
Sbjct: 47 IAPLPGWGSETLNADIALCQQLPGHLTPEIXATIPEALPAAQFG 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 = 6.0, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 22/44 (50%), Gaps = 3/44 (6%)
Query: 13 VNGVLGWGKE---GHFAICKIAEGYLTEDALAAVKELLPDSAEG 53
+ + GWG E A+C+ G+LT + A + E LP + G
Sbjct: 45 IAPLPGWGSETLNADIALCQQLPGHLTPEIXATIPEALPAAQFG 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 = 6.7, 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 = 27.7 bits (60), Expect = 6.9, 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
0.323 0.137 0.460
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,436,381
Number of Sequences: 62578
Number of extensions: 338515
Number of successful extensions: 714
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 698
Number of HSP's gapped (non-prelim): 9
length of query: 244
length of database: 14,973,337
effective HSP length: 96
effective length of query: 148
effective length of database: 8,965,849
effective search space: 1326945652
effective search space used: 1326945652
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 50 (23.9 bits)