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= 019942
(333 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1I36|A Chain A, Structure Of Conserved Protein Mth1747 Of Unknown Function
Reveals Structural Similarity With 3-Hydroxyacid
Dehydrogenases
pdb|1I36|B Chain B, Structure Of Conserved Protein Mth1747 Of Unknown Function
Reveals Structural Similarity With 3-Hydroxyacid
Dehydrogenases
Length = 264
Score = 33.9 bits (76), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 27/150 (18%), Positives = 68/150 (45%), Gaps = 18/150 (12%)
Query: 45 LNYQTLSPKD--LAKAVLTQGGWADLLCSGRQSPQSVDVALVFVGRELQ----------S 92
++ +SP+ +A +++ +GG+ D G + D+ ++ GR+ + +
Sbjct: 85 VDINNISPETVRMASSLIEKGGFVDAAIMGSVRRKGADIRIIASGRDAEEFMKLNRYGLN 144
Query: 93 SHISGNKHADLALVDTLKVSFTKSNFSMAFPYIVSAGEETMESSLFS--EFTEACVDDFK 150
+ G + D + + L+ S+TK ++ + + +A +E + E+TE +DF+
Sbjct: 145 IEVRGREPGDASAIKMLRSSYTKGVSALLWETLTAAHRLGLEEDVLEMLEYTEG--NDFR 202
Query: 151 VANVAFSESCTVEGENFLKLADLHSVHDHL 180
+ ++ +S + + ++ V D L
Sbjct: 203 ESAISRLKSSCIHARR--RYEEMKEVQDML 230
>pdb|2AYI|A Chain A, Wild-Type Ampt From Thermus Thermophilus
pdb|2AYI|B Chain B, Wild-Type Ampt From Thermus Thermophilus
pdb|2AYI|C Chain C, Wild-Type Ampt From Thermus Thermophilus
pdb|2AYI|D Chain D, Wild-Type Ampt From Thermus Thermophilus
pdb|2AYI|E Chain E, Wild-Type Ampt From Thermus Thermophilus
Length = 408
Score = 31.2 bits (69), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 32/59 (54%), Gaps = 2/59 (3%)
Query: 150 KVANVAFSESCTVE-GENFLKLADLHSVHDHLRLRAEKSLKGQADLIVVCYGDTQSMKQ 207
K+A +A +E G+ + A + +V D +RL AEK+ + A L V YGD + ++
Sbjct: 10 KLAELAIRVGLNLEKGQEVIATAPIEAV-DFVRLLAEKAYREGASLFTVIYGDQELARK 67
>pdb|1Z3I|X Chain X, Structure Of The Swi2SNF2 CHROMATIN REMODELING DOMAIN OF
EUKARYOTIC Rad54
Length = 644
Score = 29.6 bits (65), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 239 DSVEKSGAKYTVLYVSDPVRS-VQYPSHQELERFLAESVAGNKSANNTGC 287
D ++ K V V DPV S V P +E +FL + V G + N+ GC
Sbjct: 33 DLIKADKEKLPVHVVVDPVLSKVLRPHQREGVKFLWDCVTGRRIENSYGC 82
>pdb|3H1C|A Chain A, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|B Chain B, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|C Chain C, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|G Chain G, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|I Chain I, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|K Chain K, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|M Chain M, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|O Chain O, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|R Chain R, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|T Chain T, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|V Chain V, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|X Chain X, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
Length = 549
Score = 29.6 bits (65), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 28/68 (41%), Gaps = 9/68 (13%)
Query: 122 FPYIVSAGEETMESSLFSEFTEAC------VD---DFKVANVAFSESCTVEGENFLKLAD 172
FPY V E ES+ S C +D K A + EG+N++ L+D
Sbjct: 421 FPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVLSD 480
Query: 173 LHSVHDHL 180
+ DHL
Sbjct: 481 ILGDEDHL 488
>pdb|3CDJ|A Chain A, Crystal Structure Of The E. Coli KhS1 DOMAIN TRUNCATED
Pnpase
Length = 559
Score = 29.3 bits (64), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 28/68 (41%), Gaps = 9/68 (13%)
Query: 122 FPYIVSAGEETMESSLFSEFTEAC------VD---DFKVANVAFSESCTVEGENFLKLAD 172
FPY V E ES+ S C +D K A + EG+N++ L+D
Sbjct: 427 FPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVLSD 486
Query: 173 LHSVHDHL 180
+ DHL
Sbjct: 487 ILGDEDHL 494
>pdb|3GCM|A Chain A, Crystal Structure Of E. Coli Polynucleotide Phosphorylase
Bound To Rna And Rnase E
pdb|3GCM|B Chain B, Crystal Structure Of E. Coli Polynucleotide Phosphorylase
Bound To Rna And Rnase E
pdb|3GCM|C Chain C, Crystal Structure Of E. Coli Polynucleotide Phosphorylase
Bound To Rna And Rnase E
pdb|3GLL|A Chain A, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core
pdb|3GME|A Chain A, Crystal Structure Of Polynucleotide Phosphorylase In
Complex With Rnase E And Manganese
Length = 549
Score = 29.3 bits (64), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 28/68 (41%), Gaps = 9/68 (13%)
Query: 122 FPYIVSAGEETMESSLFSEFTEAC------VD---DFKVANVAFSESCTVEGENFLKLAD 172
FPY V E ES+ S C +D K A + EG+N++ L+D
Sbjct: 421 FPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVLSD 480
Query: 173 LHSVHDHL 180
+ DHL
Sbjct: 481 ILGDEDHL 488
>pdb|3VA6|A Chain A, Crystal Structure Of The Extracellular Domain Of The
Putative Hybrid Two Component System Bt4673 From B.
Thetaiotaomicron
pdb|3VA6|B Chain B, Crystal Structure Of The Extracellular Domain Of The
Putative Hybrid Two Component System Bt4673 From B.
Thetaiotaomicron
Length = 758
Score = 29.3 bits (64), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 230 AGEVISELIDSVEKSGAKYTVLYVSDPVRSVQYPSHQELERFLAESVAGNKSANNTGCDE 289
+G I+++I E G + +LY + + + P +E+ + A+ + G KS N CDE
Sbjct: 470 SGMFINQIIPDNE--GNVWVLLYNNKGIDKIN-PRTREVTKLFADELTGEKSPNYLLCDE 526
>pdb|3OTT|A Chain A, Crystal Structure Of The Extracellular Domain Of The
Putative One Component System Bt4673 From B.
Thetaiotaomicron
pdb|3OTT|B Chain B, Crystal Structure Of The Extracellular Domain Of The
Putative One Component System Bt4673 From B.
Thetaiotaomicron
Length = 758
Score = 29.3 bits (64), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 230 AGEVISELIDSVEKSGAKYTVLYVSDPVRSVQYPSHQELERFLAESVAGNKSANNTGCDE 289
+G I+++I E G + +LY + + + P +E+ + A+ + G KS N CDE
Sbjct: 470 SGMFINQIIPDNE--GNVWVLLYNNKGIDKIN-PRTREVTKLFADELTGEKSPNYLLCDE 526
>pdb|3CDI|A Chain A, Crystal Structure Of E. Coli Pnpase
Length = 723
Score = 29.3 bits (64), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 28/68 (41%), Gaps = 9/68 (13%)
Query: 122 FPYIVSAGEETMESSLFSEFTEAC------VD---DFKVANVAFSESCTVEGENFLKLAD 172
FPY V E ES+ S C +D K A + EG+N++ L+D
Sbjct: 427 FPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVLSD 486
Query: 173 LHSVHDHL 180
+ DHL
Sbjct: 487 ILGDEDHL 494
>pdb|3EPN|A Chain A, Crystal Structure Of Caulobacter Crescentus Thic Complexed
With Imidazole Ribonucleotide
pdb|3EPN|B Chain B, Crystal Structure Of Caulobacter Crescentus Thic Complexed
With Imidazole Ribonucleotide
pdb|3EPO|A Chain A, Crystal Structure Of Caulobacter Crescentus Thic Complexed
With Hmp-P
pdb|3EPO|B Chain B, Crystal Structure Of Caulobacter Crescentus Thic Complexed
With Hmp-P
Length = 612
Score = 28.5 bits (62), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 27/56 (48%), Gaps = 1/56 (1%)
Query: 180 LRLRAEKSLKGQADLIVVCYGDTQSMKQPKQPRPETWG-NQRSWVHPWFIHAGEVI 234
+++ EK L + +VV GD + + P+Q +PE G Q + P F G I
Sbjct: 67 IQIDIEKGLPRTREALVVARGDVEEVADPRQVKPEDNGFAQGKHLAPEFPDTGRKI 122
>pdb|3EPM|A Chain A, Crystal Structure Of Caulobacter Crescentus Thic
pdb|3EPM|B Chain B, Crystal Structure Of Caulobacter Crescentus Thic
Length = 612
Score = 28.5 bits (62), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 27/56 (48%), Gaps = 1/56 (1%)
Query: 180 LRLRAEKSLKGQADLIVVCYGDTQSMKQPKQPRPETWG-NQRSWVHPWFIHAGEVI 234
+++ EK L + +VV GD + + P+Q +PE G Q + P F G I
Sbjct: 67 IQIDIEKGLPRTREALVVARGDVEEVADPRQVKPEDNGFAQGKHLAPEFPDTGRKI 122
>pdb|2P0Y|A Chain A, Crystal Structure Of Q88yi3_lacpl From Lactobacillus
Plantarum. Northeast Structural Genomics Consortium
Target Lpr6
Length = 341
Score = 28.5 bits (62), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 34/66 (51%), Gaps = 4/66 (6%)
Query: 130 EETMESSLFSEFTEACVDDFKVANVAFSESCTVEGENFLKLADLHSVHDHLRLRAE-KSL 188
E+ + F+E ++ DF+ ++C V NFLKL D + HD ++ AE +L
Sbjct: 269 EDYXDFHKFNEVSKQVSHDFRGLR---EQNCRVISSNFLKLRDNGAFHDGDQVVAELXNL 325
Query: 189 KGQADL 194
G +D+
Sbjct: 326 VGHSDV 331
>pdb|2XE4|A Chain A, Structure Of Oligopeptidase B From Leishmania Major
Length = 751
Score = 28.1 bits (61), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 10/76 (13%)
Query: 31 LWSTHHQKISSNNALNYQTLSPKDLAKAVLTQGGWADLLCSGRQSPQSVDVALVFVGREL 90
+W K+ S + Y+ +P L A + + + LC G QSP++ +V L+ + +
Sbjct: 249 VWRHVMGKLQSEDVCLYEEHNP--LFSAFMYKAADTNTLCIGSQSPETAEVHLLDLRK-- 304
Query: 91 QSSHISGNKHADLALV 106
GN H L +V
Sbjct: 305 ------GNAHNTLEIV 314
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
0.317 0.130 0.384
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,025,130
Number of Sequences: 62578
Number of extensions: 335917
Number of successful extensions: 716
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 713
Number of HSP's gapped (non-prelim): 13
length of query: 333
length of database: 14,973,337
effective HSP length: 99
effective length of query: 234
effective length of database: 8,778,115
effective search space: 2054078910
effective search space used: 2054078910
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: 52 (24.6 bits)