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= 036912
(445 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3TI2|A Chain A, 1.90 Angstrom Resolution Crystal Structure Of N-Terminal
Domain 3- Phosphoshikimate 1-Carboxyvinyltransferase
From Vibrio Cholerae
pdb|3TI2|B Chain B, 1.90 Angstrom Resolution Crystal Structure Of N-Terminal
Domain 3- Phosphoshikimate 1-Carboxyvinyltransferase
From Vibrio Cholerae
pdb|3TI2|C Chain C, 1.90 Angstrom Resolution Crystal Structure Of N-Terminal
Domain 3- Phosphoshikimate 1-Carboxyvinyltransferase
From Vibrio Cholerae
pdb|3TI2|D Chain D, 1.90 Angstrom Resolution Crystal Structure Of N-Terminal
Domain 3- Phosphoshikimate 1-Carboxyvinyltransferase
From Vibrio Cholerae
Length = 228
Score = 38.1 bits (87), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 40/68 (58%), Gaps = 8/68 (11%)
Query: 255 AEPKVKARTPTHVIHSISKLRRAGIKLNAVKAESFLVVKFRHGAIEMPTITID-----DF 309
EP++K R H++ + LR+AG ++ ++ E+F ++ + ++ T+TID F
Sbjct: 102 GEPRMKERPIGHLVDA---LRQAGAQIEYLEQENFPPLRIQGTGLQAGTVTIDGSISSQF 158
Query: 310 MTSFLLNC 317
+T+FL++
Sbjct: 159 LTAFLMSA 166
>pdb|3NVS|A Chain A, 1.02 Angstrom Resolution Crystal Structure Of
3-Phosphoshikimate 1- Carboxyvinyltransferase From
Vibrio Cholerae In Complex With Shikimate-3-Phosphate
(Partially Photolyzed) And Glyphosate
Length = 450
Score = 37.7 bits (86), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 40/68 (58%), Gaps = 8/68 (11%)
Query: 255 AEPKVKARTPTHVIHSISKLRRAGIKLNAVKAESFLVVKFRHGAIEMPTITID-----DF 309
EP++K R H++ + LR+AG ++ ++ E+F ++ + ++ T+TID F
Sbjct: 141 GEPRMKERPIGHLVDA---LRQAGAQIEYLEQENFPPLRIQGTGLQAGTVTIDGSISSQF 197
Query: 310 MTSFLLNC 317
+T+FL++
Sbjct: 198 LTAFLMSA 205
>pdb|1PZ2|A Chain A, Crystal Structure Of A Transient Covalent Reaction
Intermediate Of A Family 51 Alpha-L-Arabinofuranosidase
pdb|1PZ2|B Chain B, Crystal Structure Of A Transient Covalent Reaction
Intermediate Of A Family 51 Alpha-L-Arabinofuranosidase
pdb|1QW8|A Chain A, Crystal Structure Of A Family 51 Alpha-L-
Arabinofuranosidase In Complex With Ara-Alpha(1,3)-Xyl
pdb|1QW8|B Chain B, Crystal Structure Of A Family 51 Alpha-L-
Arabinofuranosidase In Complex With Ara-Alpha(1,3)-Xyl
pdb|1QW9|A Chain A, Crystal Structure Of A Family 51 Alpha-L-
Arabinofuranosidase In Complex With 4-Nitrophenyl-Ara
pdb|1QW9|B Chain B, Crystal Structure Of A Family 51 Alpha-L-
Arabinofuranosidase In Complex With 4-Nitrophenyl-Ara
Length = 502
Score = 31.2 bits (69), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 36/65 (55%), Gaps = 6/65 (9%)
Query: 77 HGEAHVKIIEEHKWRYLGSLLNRLKNTKSLGLE--DFLKAVESLE--IKARECFSETIHL 132
H HV I H+ Y G+ N N +L LE DF+++V ++ +KA++ +TIHL
Sbjct: 233 HTYDHVDYISLHQ--YYGNRDNDTANYLALSLEMDDFIRSVVAIADYVKAKKRSKKTIHL 290
Query: 133 GTDEF 137
DE+
Sbjct: 291 SFDEW 295
>pdb|1PZ3|A Chain A, Crystal Structure Of A Family 51 (gh51)
Alpha-l-arabinofuranosidase From Geobacillus
Stearothermophilus T6
pdb|1PZ3|B Chain B, Crystal Structure Of A Family 51 (gh51)
Alpha-l-arabinofuranosidase From Geobacillus
Stearothermophilus T6
Length = 502
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 36/65 (55%), Gaps = 6/65 (9%)
Query: 77 HGEAHVKIIEEHKWRYLGSLLNRLKNTKSLGLE--DFLKAVESLE--IKARECFSETIHL 132
H HV I H+ Y G+ N N +L LE DF+++V ++ +KA++ +TIHL
Sbjct: 233 HTYDHVDYISLHQ--YYGNRDNDTANYLALSLEMDDFIRSVVAIADYVKAKKRSKKTIHL 290
Query: 133 GTDEF 137
DE+
Sbjct: 291 SFDEW 295
>pdb|1RL4|A Chain A, Plasmodium Falciparum Peptide Deformylase Complex With
Inhibitor
pdb|1RL4|B Chain B, Plasmodium Falciparum Peptide Deformylase Complex With
Inhibitor
Length = 188
Score = 30.4 bits (67), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 38/77 (49%), Gaps = 11/77 (14%)
Query: 15 ISIWEVKKDRLESMNKRISEPPTLLSNSAGK----QSCCIFRLPQSFININGKSYQPHIV 70
I +W ++ + N+RI P+++ S K + C SF I GK +P IV
Sbjct: 63 IIVWNALYEKRKEENERIFINPSIVEQSLVKLKLIEGCL------SFPGIEGKVERPSIV 116
Query: 71 SIGPYH-HGEAHVKIIE 86
SI Y +G H+KI++
Sbjct: 117 SISYYDINGYKHLKILK 133
>pdb|1RQC|A Chain A, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1RQC|B Chain B, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1RQC|C Chain C, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1RQC|D Chain D, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1RQC|E Chain E, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1RQC|F Chain F, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1RQC|G Chain G, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1RQC|H Chain H, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1RQC|I Chain I, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
pdb|1RQC|J Chain J, Crystals Of Peptide Deformylase From Plasmodium Falciparum
With Ten Subunits Per Asymmetric Unit Reveal Critical
Characteristics Of The Active Site For Drug Design
Length = 185
Score = 30.0 bits (66), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 38/77 (49%), Gaps = 11/77 (14%)
Query: 15 ISIWEVKKDRLESMNKRISEPPTLLSNSAGK----QSCCIFRLPQSFININGKSYQPHIV 70
I +W ++ + N+RI P+++ S K + C SF I GK +P IV
Sbjct: 57 IIVWNALYEKRKEENERIFINPSIVEQSLVKLKLIEGCL------SFPGIEGKVERPSIV 110
Query: 71 SIGPYH-HGEAHVKIIE 86
SI Y +G H+KI++
Sbjct: 111 SISYYDINGYKHLKILK 127
>pdb|3V7P|A Chain A, Crystal Structure Of Amidohydrolase Nis_0429 (Target
Efi-500396) From Nitratiruptor Sp. Sb155-2
Length = 427
Score = 28.9 bits (63), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 37/148 (25%), Positives = 63/148 (42%), Gaps = 20/148 (13%)
Query: 280 KLNAVKAESFLVVKFRHGAIEMPTITIDDFMTSFLLNCVA--YEQCQSGCSKHITTYATL 337
K+ A+ L+ K+ + A+E S LL A + + +K Y
Sbjct: 26 KIEAIDTVENLIKKYPNAAVEHDE-------NSLLLPGFANPHLHLEFSANKATLQYGDF 78
Query: 338 IDYLVNTAR---DVEYLCDGNIIENNL------GTDAEVALFINNLGKDVAFDMDLCYLS 388
I +L + R D+ LCDG +E L GT A A I++ G+D+ +D
Sbjct: 79 IPWLYSVIRHREDLLPLCDGACLEQTLSSIIQTGTTAIGA--ISSYGEDLQACIDSALKV 136
Query: 389 KLFNDVHDYYSSSRHVQWAAFKYKYFDS 416
FN+V +++ V +A+F ++ S
Sbjct: 137 VYFNEVIGSNAATADVMYASFLERFHQS 164
>pdb|3ER6|A Chain A, Crystal Structure Of A Putative Transcriptional Regulator
Protein From Vibrio Parahaemolyticus
pdb|3ER6|B Chain B, Crystal Structure Of A Putative Transcriptional Regulator
Protein From Vibrio Parahaemolyticus
pdb|3ER6|C Chain C, Crystal Structure Of A Putative Transcriptional Regulator
Protein From Vibrio Parahaemolyticus
pdb|3ER6|D Chain D, Crystal Structure Of A Putative Transcriptional Regulator
Protein From Vibrio Parahaemolyticus
pdb|3ER6|E Chain E, Crystal Structure Of A Putative Transcriptional Regulator
Protein From Vibrio Parahaemolyticus
pdb|3ER6|F Chain F, Crystal Structure Of A Putative Transcriptional Regulator
Protein From Vibrio Parahaemolyticus
Length = 209
Score = 28.5 bits (62), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 30/58 (51%), Gaps = 15/58 (25%)
Query: 60 INGKSYQPHIVSIGPYHHGEAHVKIIEEHKWRYLGSLLNRLKNTKSLGLEDFLKAVES 117
I+G Y +S GPY H ++I+EE Y G K+T++LG FL +ES
Sbjct: 159 IDGNVY----LSSGPYSHSSVMLEIVEE----YFG------KHTRNLG-NQFLSTIES 201
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
0.322 0.137 0.409
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,815,556
Number of Sequences: 62578
Number of extensions: 521485
Number of successful extensions: 1105
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: 1102
Number of HSP's gapped (non-prelim): 14
length of query: 445
length of database: 14,973,337
effective HSP length: 102
effective length of query: 343
effective length of database: 8,590,381
effective search space: 2946500683
effective search space used: 2946500683
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: 53 (25.0 bits)