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= 032361
(142 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1WSP|A Chain A, Crystal Structure Of Axin Dix Domain
pdb|1WSP|B Chain B, Crystal Structure Of Axin Dix Domain
pdb|1WSP|C Chain C, Crystal Structure Of Axin Dix Domain
Length = 84
Score = 28.1 bits (61), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 27/47 (57%), Gaps = 5/47 (10%)
Query: 36 KAQRLGHAFKELMDKYGEGELQMKEMADE----LMMDTTKDDEGLLP 78
+A LG FKEL+ K G K+++DE ++ + ++DE +LP
Sbjct: 25 RAVTLGQ-FKELLTKKGSYRYYFKKVSDEFDCGVVFEEVREDEAILP 70
>pdb|2D5G|A Chain A, Structure Of Ubiquitin Fold Protein R767e Mutant
pdb|2D5G|B Chain B, Structure Of Ubiquitin Fold Protein R767e Mutant
pdb|2D5G|C Chain C, Structure Of Ubiquitin Fold Protein R767e Mutant
pdb|2D5G|D Chain D, Structure Of Ubiquitin Fold Protein R767e Mutant
pdb|2D5G|E Chain E, Structure Of Ubiquitin Fold Protein R767e Mutant
pdb|2D5G|F Chain F, Structure Of Ubiquitin Fold Protein R767e Mutant
Length = 85
Score = 28.1 bits (61), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 27/47 (57%), Gaps = 5/47 (10%)
Query: 36 KAQRLGHAFKELMDKYGEGELQMKEMADE----LMMDTTKDDEGLLP 78
+A LG FKEL+ K G K+++DE ++ + ++DE +LP
Sbjct: 26 RAVTLGQ-FKELLTKKGSYRYYFKKVSDEFDCGVVFEEVREDEAILP 71
>pdb|1ZUH|A Chain A, Structural Basis For Shikimate-Binding Specificity Of
Helicobacter Pylori Shikimate Kinase
pdb|1ZUI|A Chain A, Structural Basis For Shikimate-binding Specificity Of
Helicobacter Pylori Shikimate Kinase
pdb|3HR7|A Chain A, Crystal Structure Of The Shikimate Kinase-Sulfate
Complex From Helicobacter Pylori
pdb|3HR7|B Chain B, Crystal Structure Of The Shikimate Kinase-Sulfate
Complex From Helicobacter Pylori
pdb|3MUF|A Chain A, Shikimate Kinase From Helicobacter Pylori In Complex
With Shikimate-3- Phosphate And Adp
Length = 168
Score = 27.7 bits (60), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 35/67 (52%), Gaps = 5/67 (7%)
Query: 1 MVYVTNRSEGGKSIATEVSPGIHVLTNALLDSPWPKAQRLGHAFKELMDKYGEGELQM-- 58
+V + G S+A E+ + + +LD+ ++R+G + +E+ ++ GE +M
Sbjct: 10 LVLIGFMGSGKSSLAQELGLALKL---EVLDTDMIISERVGLSVREIFEELGEDNFRMFE 66
Query: 59 KEMADEL 65
K + DEL
Sbjct: 67 KNLIDEL 73
>pdb|3N2E|A Chain A, Crystal Structure Of Helicobactor Pylori Shikimate
Kinase In Complex With Nsc162535
pdb|3N2E|B Chain B, Crystal Structure Of Helicobactor Pylori Shikimate
Kinase In Complex With Nsc162535
pdb|3N2E|C Chain C, Crystal Structure Of Helicobactor Pylori Shikimate
Kinase In Complex With Nsc162535
Length = 168
Score = 27.7 bits (60), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 35/67 (52%), Gaps = 5/67 (7%)
Query: 1 MVYVTNRSEGGKSIATEVSPGIHVLTNALLDSPWPKAQRLGHAFKELMDKYGEGELQM-- 58
+V + G S+A E+ + + +LD+ ++R+G + +E+ ++ GE +M
Sbjct: 4 LVLIGFMGSGKSSLAQELGLALKL---EVLDTDMIISERVGLSVREIFEELGEDNFRMFE 60
Query: 59 KEMADEL 65
K + DEL
Sbjct: 61 KNLIDEL 67
>pdb|2DF4|A Chain A, Structure Of Trna-Dependent Amidotransferase Gatcab
Complexed With Mn2+
pdb|2DQN|A Chain A, Structure Of Trna-Dependent Amidotransferase Gatcab
Complexed With Asn
pdb|2G5H|A Chain A, Structure Of Trna-Dependent Amidotransferase Gatcab
pdb|2G5I|A Chain A, Structure Of Trna-dependent Amidotransferase Gatcab
Complexed With Adp-alf4
pdb|3IP4|A Chain A, The High Resolution Structure Of Gatcab
pdb|2F2A|A Chain A, Structure Of Trna-Dependent Amidotransferase Gatcab
Complexed With Gln
Length = 485
Score = 25.8 bits (55), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 2 VYVTNRSEG-GKSIATEVSPGIHVLTNALLDSPWPKAQRLGHAFKELMDKYGE 53
+Y +RSEG GK + + G L++ D+ + K+Q++ K DK E
Sbjct: 342 LYKMSRSEGFGKEVKRRIFLGTFALSSGYYDAYYKKSQKVRTLIKNDFDKVFE 394
>pdb|3N8D|A Chain A, Crystal Structure Of Staphylococcus Aureus Vrsa-9
D-Ala:d-Ala Ligase
pdb|3N8D|B Chain B, Crystal Structure Of Staphylococcus Aureus Vrsa-9
D-Ala:d-Ala Ligase
Length = 364
Score = 25.8 bits (55), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 22/42 (52%)
Query: 22 IHVLTNALLDSPWPKAQRLGHAFKELMDKYGEGELQMKEMAD 63
+ VL N ++ WP AF + KY +G++Q+K AD
Sbjct: 223 VAVLGNDYPEATWPGEVVKDVAFYDYKSKYKDGKVQLKIPAD 264
>pdb|3B8C|A Chain A, Crystal Structure Of A Plasma Membrane Proton Pump
pdb|3B8C|B Chain B, Crystal Structure Of A Plasma Membrane Proton Pump
Length = 885
Score = 25.4 bits (54), Expect = 10.0, Method: Composition-based stats.
Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 7/48 (14%)
Query: 47 LMDKYGEGELQMKEMADELMMDTTKDDE-------GLLPHIYPPETES 87
++DKY E L+ +A +++ + TK+ GLLP PP +S
Sbjct: 446 IIDKYAERGLRSLAVARQVVPEKTKESPGAPWEFVGLLPLFDPPRHDS 493
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
0.313 0.132 0.382
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,406,102
Number of Sequences: 62578
Number of extensions: 173925
Number of successful extensions: 336
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 18
Number of HSP's that attempted gapping in prelim test: 335
Number of HSP's gapped (non-prelim): 19
length of query: 142
length of database: 14,973,337
effective HSP length: 89
effective length of query: 53
effective length of database: 9,403,895
effective search space: 498406435
effective search space used: 498406435
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 46 (22.3 bits)