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= 027578
(221 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3BA3|A Chain A, Crystal Structure Of Pyridoxamine 5'-Phosphate
Oxidase-Like Protein (Np_783940.1) From Lactobacillus
Plantarum At 1.55 A Resolution
pdb|3BA3|B Chain B, Crystal Structure Of Pyridoxamine 5'-Phosphate
Oxidase-Like Protein (Np_783940.1) From Lactobacillus
Plantarum At 1.55 A Resolution
Length = 145
Score = 32.0 bits (71), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 40/76 (52%), Gaps = 12/76 (15%)
Query: 126 NVAFVKVSMDGA---PYLRKVDLKLYKSYQELSDALGKMFSSFTIDYVPTYE---DKDGD 179
++AF+ + DG PYLR +KL +S + +D L + + VP Y+ D G
Sbjct: 63 DIAFITIPNDGTAGNPYLRAQHVKLQRSTKTXTDLLPQYLET-----VPNYQQVWDAIGS 117
Query: 180 WMLVGDVPW-DMFVDS 194
++V ++ D+FVD+
Sbjct: 118 TLVVFELKLTDLFVDA 133
>pdb|2P1N|C Chain C, Mechanism Of Auxin Perception By The Tir1 Ubiqutin Ligase
pdb|2P1N|F Chain F, Mechanism Of Auxin Perception By The Tir1 Ubiqutin Ligase
pdb|2P1O|C Chain C, Mechanism Of Auxin Perception By The Tir1 Ubiquitin Ligase
pdb|2P1Q|C Chain C, Mechanism Of Auxin Perception By The Tir1 Ubiquitin Ligase
Length = 13
Score = 31.2 bits (69), Expect = 0.49, Method: Composition-based stats.
Identities = 11/13 (84%), Positives = 13/13 (100%)
Query: 91 QVVGWPPVRSFRK 103
QVVGWPPVR++RK
Sbjct: 1 QVVGWPPVRNYRK 13
>pdb|3H97|A Chain A, Structure Of A Mutant Methionyl-trna Synthetase With
Modified Specificity
pdb|3H99|A Chain A, Structure Of A Mutant Methionyl-Trna Synthetase With
Modified Specificity Complexed With Methionine
pdb|3H9B|A Chain A, Structure Of A Mutant Methionyl-Trna Synthetase With
Modified Specificity Complexed With Azidonorleucine
Length = 560
Score = 28.9 bits (63), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 27/57 (47%)
Query: 108 VQKDNEEGDNKAXXXXXXNVAFVKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFSS 164
VQ+ N + NK N F+ DG D +LYK++ + ++ +G+ + S
Sbjct: 391 VQRVNADIVNKVVNLASRNAGFINKRFDGVLASELADPQLYKTFTDAAEVIGEAWES 447
>pdb|3H9C|A Chain A, Structure Of Methionyl-Trna Synthetase: Crystal Form 2
Length = 547
Score = 28.9 bits (63), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 27/57 (47%)
Query: 108 VQKDNEEGDNKAXXXXXXNVAFVKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFSS 164
VQ+ N + NK N F+ DG D +LYK++ + ++ +G+ + S
Sbjct: 378 VQRVNADIVNKVVNLASRNAGFINKRFDGVLASELADPQLYKTFTDAAEVIGEAWES 434
>pdb|1P7P|A Chain A, Methionyl-trna Synthetase From Escherichia Coli Complexed
With Methionine Phosphonate
pdb|1PFU|A Chain A, Methionyl-Trna Synthetase From Escherichia Coli Complexed
With Methionine Phosphinate
pdb|1PFV|A Chain A, Methionyl-Trna Synthetase From Escherichia Coli Complexed
With Difluoromethionine
pdb|1PFW|A Chain A, Methionyl-Trna Synthetase From Escherichia Coli Complexed
With Trifluoromethionine
pdb|1PFY|A Chain A, Methionyl-Trna Synthetase From Escherichia Coli Complexed
With Methionyl Sulphamoyl Adenosine
pdb|1PG0|A Chain A, Methionyl-Trna Synthetase From Escherichia Coli Complexed
With Methioninyl Adenylate
pdb|1PG2|A Chain A, Methionyl-Trna Synthetase From Escherichia Coli Complexed
With Methionine And Adenosine
Length = 551
Score = 28.9 bits (63), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 27/57 (47%)
Query: 108 VQKDNEEGDNKAXXXXXXNVAFVKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFSS 164
VQ+ N + NK N F+ DG D +LYK++ + ++ +G+ + S
Sbjct: 378 VQRVNADIVNKVVNLASRNAGFINKRFDGVLASELADPQLYKTFTDAAEVIGEAWES 434
>pdb|1F4L|A Chain A, Crystal Structure Of The E.Coli Methionyl-Trna Synthetase
Complexed With Methionine
Length = 551
Score = 28.9 bits (63), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 27/57 (47%)
Query: 108 VQKDNEEGDNKAXXXXXXNVAFVKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFSS 164
VQ+ N + NK N F+ DG D +LYK++ + ++ +G+ + S
Sbjct: 379 VQRVNADIVNKVVNLASRNAGFINKRFDGVLASELADPQLYKTFTDAAEVIGEAWES 435
>pdb|1QQT|A Chain A, Methionyl-Trna Synthetase From Escherichia Coli
Length = 551
Score = 28.1 bits (61), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 26/57 (45%)
Query: 108 VQKDNEEGDNKAXXXXXXNVAFVKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFSS 164
VQ+ N + NK N F+ DG D LYK++ + ++ +G+ + S
Sbjct: 378 VQRVNADIVNKVVNLASRNAGFINKRFDGVLASELADPALYKTFTDAAEVIGEAWES 434
>pdb|2IBP|A Chain A, Crystal Structure Of Citrate Synthase From Pyrobaculum
Aerophilum
pdb|2IBP|B Chain B, Crystal Structure Of Citrate Synthase From Pyrobaculum
Aerophilum
Length = 409
Score = 26.9 bits (58), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 21/40 (52%), Gaps = 4/40 (10%)
Query: 136 GAPYLRKVDLKLYKSYQELSDALGKMFSSFTIDYVPTYED 175
G P L V ++YK+Y D K+F F+ DYV + D
Sbjct: 280 GGPKLMGVGHRVYKAY----DPRAKIFKEFSRDYVAKFGD 315
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
0.315 0.133 0.387
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,292,287
Number of Sequences: 62578
Number of extensions: 190369
Number of successful extensions: 494
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 488
Number of HSP's gapped (non-prelim): 8
length of query: 221
length of database: 14,973,337
effective HSP length: 95
effective length of query: 126
effective length of database: 9,028,427
effective search space: 1137581802
effective search space used: 1137581802
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)