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= psy14433
(144 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3HA1|A Chain A, Alanine Racemase From Bacillus Anthracis (Ames)
pdb|3HA1|B Chain B, Alanine Racemase From Bacillus Anthracis (Ames)
Length = 397
Score = 29.6 bits (65), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 37/80 (46%), Gaps = 16/80 (20%)
Query: 30 HLKGVYINFANKDEL-VANFDKSTD-------WIWDWSSRPDQAPPKDWKFRHPKSKSYS 81
L+GVY +FA DE+ + FDK + W+ ++ P KF H + + +
Sbjct: 161 ELEGVYTHFATADEVETSYFDKQYNTFLEQLSWLKEFGVDP--------KFVHTANSAAT 212
Query: 82 MRYAKVGKNSLFSKEVMYTL 101
+R+ + N++ MY L
Sbjct: 213 LRFQGITFNAVRIGIAMYGL 232
>pdb|3RJL|A Chain A, Crystal Structure Of 1-Pyrroline-5-Carboxylate
Dehydrogenase From Bacillus Licheniformis (Target
Nysgrc-000337)
pdb|3RJL|B Chain B, Crystal Structure Of 1-Pyrroline-5-Carboxylate
Dehydrogenase From Bacillus Licheniformis (Target
Nysgrc-000337)
pdb|3RJL|C Chain C, Crystal Structure Of 1-Pyrroline-5-Carboxylate
Dehydrogenase From Bacillus Licheniformis (Target
Nysgrc-000337)
pdb|3RJL|D Chain D, Crystal Structure Of 1-Pyrroline-5-Carboxylate
Dehydrogenase From Bacillus Licheniformis (Target
Nysgrc-000337)
pdb|3RJL|E Chain E, Crystal Structure Of 1-Pyrroline-5-Carboxylate
Dehydrogenase From Bacillus Licheniformis (Target
Nysgrc-000337)
pdb|3RJL|F Chain F, Crystal Structure Of 1-Pyrroline-5-Carboxylate
Dehydrogenase From Bacillus Licheniformis (Target
Nysgrc-000337)
pdb|3RJL|G Chain G, Crystal Structure Of 1-Pyrroline-5-Carboxylate
Dehydrogenase From Bacillus Licheniformis (Target
Nysgrc-000337)
pdb|3RJL|H Chain H, Crystal Structure Of 1-Pyrroline-5-Carboxylate
Dehydrogenase From Bacillus Licheniformis (Target
Nysgrc-000337)
Length = 538
Score = 27.7 bits (60), Expect = 2.1, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 27/51 (52%), Gaps = 6/51 (11%)
Query: 32 KGVYINFANKDELVANFDKSTDWIWDWSSRPDQAPPK---DWKFRHPKSKS 79
K V IN ANK+E+V K+T D + + QA K W++ P+ ++
Sbjct: 52 KIVSINPANKEEVVGTVSKATQ---DHAEKAIQAAAKAFETWRYTDPEERA 99
>pdb|3SIL|A Chain A, Sialidase From Salmonella Typhimurium
Length = 379
Score = 26.9 bits (58), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 37/81 (45%), Gaps = 9/81 (11%)
Query: 58 WSSRPDQAPPKDWKFRHPKSKSYSMRYAKVGKNSLFSKEVMYTLFVTN--IISILLGTGV 115
W + D+AP DW KS + ++KV N ++ + N I ++L G G
Sbjct: 125 WGAYRDKAPDTDWDLVLYKSTDDGVTFSKVETN-------IHDIVTKNGTISAMLGGVGS 177
Query: 116 GMWLSRRGMLIASNVAKSKRM 136
G+ L+ ++ + ++K +
Sbjct: 178 GLQLNDGKLVFPVQMVRTKNI 198
>pdb|1DIL|A Chain A, Sialidase From Salmonella Typhimurium Complexed With Apana
And Epana Inhibitors
pdb|1DIM|A Chain A, Sialidase From Salmonella Typhimurium Complexed With Epana
Inhibitor
pdb|2SIL|A Chain A, The Structures Of Salmonella Typhimurium Lt2 Neuraminidase
And Its Complex With A Transition State Analogue At 1.6
Angstroms Resolution
pdb|2SIM|A Chain A, The Structures Of Salmonella Typhimurium Lt2 Neuraminidase
And Its Complex With A Transition State Analogue At 1.6
Angstroms Resolution
Length = 381
Score = 26.9 bits (58), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 37/81 (45%), Gaps = 9/81 (11%)
Query: 58 WSSRPDQAPPKDWKFRHPKSKSYSMRYAKVGKNSLFSKEVMYTLFVTN--IISILLGTGV 115
W + D+AP DW KS + ++KV N ++ + N I ++L G G
Sbjct: 127 WGAYRDKAPDTDWDLVLYKSTDDGVTFSKVETN-------IHDIVTKNGTISAMLGGVGS 179
Query: 116 GMWLSRRGMLIASNVAKSKRM 136
G+ L+ ++ + ++K +
Sbjct: 180 GLQLNDGKLVFPVQMVRTKNI 200
>pdb|2ZE4|A Chain A, Crystal Structure Of Phospholipase D From Streptomyces
Antibioticus
Length = 509
Score = 25.8 bits (55), Expect = 8.7, Method: Composition-based stats.
Identities = 9/21 (42%), Positives = 11/21 (52%)
Query: 50 KSTDWIWDWSSRPDQAPPKDW 70
K D +WDW+ R P K W
Sbjct: 215 KYLDTLWDWTCRNASDPAKVW 235
>pdb|2ZE9|A Chain A, Crystal Structure Of H168a Mutant Of Phospholipase D From
Streptomyces Antibioticus, As A Complex With
Phosphatidylcholine
Length = 509
Score = 25.8 bits (55), Expect = 9.0, Method: Composition-based stats.
Identities = 9/21 (42%), Positives = 11/21 (52%)
Query: 50 KSTDWIWDWSSRPDQAPPKDW 70
K D +WDW+ R P K W
Sbjct: 215 KYLDTLWDWTCRNASDPAKVW 235
>pdb|3UV4|A Chain A, Crystal Structure Of The Second Bromodomain Of Human
Transcription Initiation Factor Tfiid Subunit 1 (Taf1)
pdb|3UV4|B Chain B, Crystal Structure Of The Second Bromodomain Of Human
Transcription Initiation Factor Tfiid Subunit 1 (Taf1)
Length = 158
Score = 25.8 bits (55), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 11/28 (39%), Positives = 14/28 (50%)
Query: 65 APPKDWKFRHPKSKSYSMRYAKVGKNSL 92
A P W F HP +K + Y KV N +
Sbjct: 44 AVPDSWPFHHPVNKKFVPDYYKVIVNPM 71
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
0.321 0.134 0.424
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,982,220
Number of Sequences: 62578
Number of extensions: 146399
Number of successful extensions: 295
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 287
Number of HSP's gapped (non-prelim): 14
length of query: 144
length of database: 14,973,337
effective HSP length: 89
effective length of query: 55
effective length of database: 9,403,895
effective search space: 517214225
effective search space used: 517214225
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: 46 (22.3 bits)