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= 021034
(318 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2K4K|A Chain A, Solution Structure Of Gsp13 From Bacillus Subtilis
Length = 130
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 35/58 (60%), Gaps = 1/58 (1%)
Query: 260 AQLGIGSVVIGTVQSLKPYGAFIDIGG-INGLLHVSQISHDRVADIATVLQPGDTLKV 316
A+ +GSV G V L+ YGAF+ + GL+H+S+++H V DI L GD ++V
Sbjct: 3 AKFEVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGFVKDINEHLSVGDEVQV 60
>pdb|4AIM|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
Length = 726
Score = 45.4 bits (106), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 25/56 (44%), Positives = 37/56 (66%), Gaps = 1/56 (1%)
Query: 264 IGSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISHDRVADIATVLQPGDTLKVCL 318
IG + G V + +GAF++ G +GL+HVSQIS++RVA + VL+ G +KV L
Sbjct: 637 IGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKL 692
>pdb|4AID|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
pdb|4AID|B Chain B, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
pdb|4AID|C Chain C, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
Length = 726
Score = 44.7 bits (104), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 24/56 (42%), Positives = 37/56 (66%), Gaps = 1/56 (1%)
Query: 264 IGSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISHDRVADIATVLQPGDTLKVCL 318
+G + G V + +GAF++ G +GL+HVSQIS++RVA + VL+ G +KV L
Sbjct: 637 VGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKL 692
>pdb|4AM3|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rna
pdb|4AM3|B Chain B, Crystal Structure Of C. Crescentus Pnpase Bound To Rna
pdb|4AM3|C Chain C, Crystal Structure Of C. Crescentus Pnpase Bound To Rna
Length = 717
Score = 44.7 bits (104), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 24/56 (42%), Positives = 37/56 (66%), Gaps = 1/56 (1%)
Query: 264 IGSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQISHDRVADIATVLQPGDTLKVCL 318
+G + G V + +GAF++ G +GL+HVSQIS++RVA + VL+ G +KV L
Sbjct: 628 VGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKL 683
>pdb|3CDI|A Chain A, Crystal Structure Of E. Coli Pnpase
Length = 723
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 27/86 (31%), Positives = 46/86 (53%), Gaps = 4/86 (4%)
Query: 232 DLPLKFVEVDEEQSRLVLSNRKAMADSQAQLGIGSVVIGTVQSLKPYGAFIDIGG-INGL 290
D +K D E+++ + + + + A++ +G V G V + +GAF+ IGG GL
Sbjct: 598 DGTVKIAATDGEKAKHAI---RRIEEITAEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGL 654
Query: 291 LHVSQISHDRVADIATVLQPGDTLKV 316
+H+SQI+ RV + LQ G + V
Sbjct: 655 VHISQIADKRVEKVTDYLQMGQEVPV 680
Score = 28.9 bits (63), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 30/52 (57%), Gaps = 5/52 (9%)
Query: 212 GFVPFSQISSKSTAEEL----LGKDLPLKFVEVDEEQSRLVLSNRKAMADSQ 259
G V SQI+ K + +G+++P+K +EVD Q R+ LS ++A SQ
Sbjct: 653 GLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVD-RQGRIRLSIKEATEQSQ 703
>pdb|1SRO|A Chain A, S1 Rna Binding Domain, Nmr, 20 Structures
Length = 76
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 34/58 (58%), Gaps = 1/58 (1%)
Query: 260 AQLGIGSVVIGTVQSLKPYGAFIDIGG-INGLLHVSQISHDRVADIATVLQPGDTLKV 316
A++ +G V G V + +GAF+ IGG GL+H+SQI+ RV + LQ G + V
Sbjct: 1 AEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPV 58
>pdb|3BZC|A Chain A, Crystal Structure Of The Tex Protein From Pseudomonas
Aeruginosa, Crystal Form I
pdb|3BZK|A Chain A, Crystal Structure Of The Tex Protein From Pseudomonas
Aeruginosa, Crystal Form 2
Length = 785
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/61 (39%), Positives = 37/61 (60%), Gaps = 1/61 (1%)
Query: 257 DSQAQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLK 315
+S L G V+ G V ++ +GAF+DIG +GL+H+S +S V D V++ GD +K
Sbjct: 647 ESLKDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVK 706
Query: 316 V 316
V
Sbjct: 707 V 707
>pdb|2OCE|A Chain A, Crystal Structure Of Tex Family Protein Pa5201 From
Pseudomonas Aeruginosa
Length = 780
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/61 (39%), Positives = 37/61 (60%), Gaps = 1/61 (1%)
Query: 257 DSQAQLGIGSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGDTLK 315
+S L G V+ G V ++ +GAF+DIG +GL+H+S +S V D V++ GD +K
Sbjct: 648 ESLKDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVK 707
Query: 316 V 316
V
Sbjct: 708 V 708
>pdb|2KHJ|A Chain A, Nmr Structure Of The Domain 6 Of The E. Coli Ribosomal
Protein S1
Length = 109
Score = 37.4 bits (85), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 28/49 (57%), Gaps = 1/49 (2%)
Query: 265 GSVVIGTVQSLKPYGAFIDIG-GINGLLHVSQISHDRVADIATVLQPGD 312
G++V G V ++ GA +++ G+ G L S+ S DRV D VL GD
Sbjct: 32 GAIVTGKVTAVDAKGATVELADGVEGYLRASEASRDRVEDATLVLSVGD 80
>pdb|2Y0S|E Chain E, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|T Chain T, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|E Chain E, Rnap At 3.2ang
pdb|4B1O|E Chain E, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|T Chain T, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 180
Score = 34.3 bits (77), Expect = 0.094, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 19/22 (86%)
Query: 278 YGAFIDIGGINGLLHVSQISHD 299
YG F+++G ++GL+H+SQI+ D
Sbjct: 95 YGVFVNLGPMDGLVHISQITDD 116
>pdb|1GO3|E Chain E, Structure Of An Archeal Homolog Of The Eukaryotic Rna
Polymerase Ii Rpb4RPB7 COMPLEX
pdb|1GO3|M Chain M, Structure Of An Archeal Homolog Of The Eukaryotic Rna
Polymerase Ii Rpb4RPB7 COMPLEX
Length = 187
Score = 34.3 bits (77), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 23/33 (69%)
Query: 270 GTVQSLKPYGAFIDIGGINGLLHVSQISHDRVA 302
G V + +G+F+ +G ++GL+HVSQI D V+
Sbjct: 87 GEVVDVVEFGSFVRLGPLDGLIHVSQIMDDYVS 119
>pdb|3AEV|A Chain A, Crystal Structure Of AEIF2ALPHA-Adim2p-Rrna Complex From
Pyrococcus Horikoshii Ot3
Length = 275
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 28/50 (56%), Gaps = 3/50 (6%)
Query: 265 GSVVIGTVQSLKPYGAFIDIG---GINGLLHVSQISHDRVADIATVLQPG 311
G V+ TV+ + YGAF+++ G +H+S+++ V +I L+ G
Sbjct: 12 GEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEG 61
>pdb|1YZ6|A Chain A, Crystal Structure Of Intact Alpha Subunit Of Aif2 From
Pyrococcus Abyssi
Length = 274
Score = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 28/50 (56%), Gaps = 3/50 (6%)
Query: 265 GSVVIGTVQSLKPYGAFIDIG---GINGLLHVSQISHDRVADIATVLQPG 311
G V+ TV+ + YGAF+++ G +H+S+++ V +I L+ G
Sbjct: 11 GEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEG 60
>pdb|2PMZ|E Chain E, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|2PMZ|T Chain T, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|3HKZ|E Chain E, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
pdb|3HKZ|Q Chain Q, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
Length = 180
Score = 33.9 bits (76), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 19/22 (86%)
Query: 278 YGAFIDIGGINGLLHVSQISHD 299
YG F+++G ++GL+H+SQI+ D
Sbjct: 95 YGIFVNLGPMDGLVHISQITDD 116
>pdb|2WAQ|E Chain E, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|E Chain E, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|T Chain T, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
Length = 180
Score = 33.9 bits (76), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 19/22 (86%)
Query: 278 YGAFIDIGGINGLLHVSQISHD 299
YG F+++G ++GL+H+SQI+ D
Sbjct: 95 YGIFVNLGPMDGLVHISQITDD 116
>pdb|1E3P|A Chain A, Tungstate Derivative Of Streptomyces Antibioticus Pnpase
Gpsi Enzyme
Length = 757
Score = 33.5 bits (75), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 33/58 (56%), Gaps = 5/58 (8%)
Query: 264 IGSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQI----SHDRVADIATVLQPGDTLKV 316
+G ++G+V +GAF+ + G +GLLH+SQI RV ++ VL G ++V
Sbjct: 667 VGERILGSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQV 724
>pdb|1E3H|A Chain A, Semet Derivative Of Streptomyces Antibioticus PnpaseGPSI
Enzyme
Length = 757
Score = 33.5 bits (75), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 33/58 (56%), Gaps = 5/58 (8%)
Query: 264 IGSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQI----SHDRVADIATVLQPGDTLKV 316
+G ++G+V +GAF+ + G +GLLH+SQI RV ++ VL G ++V
Sbjct: 667 VGERILGSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQV 724
>pdb|2BH8|A Chain A, Combinatorial Protein 1b11
pdb|2BH8|B Chain B, Combinatorial Protein 1b11
Length = 101
Score = 33.1 bits (74), Expect = 0.19, Method: Composition-based stats.
Identities = 16/34 (47%), Positives = 24/34 (70%), Gaps = 1/34 (2%)
Query: 265 GSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQIS 297
G V G ++S+ +G FI + GGI+GL+H+S IS
Sbjct: 62 GDRVEGKIKSITDFGIFIGLDGGIDGLVHLSDIS 95
>pdb|2KHI|A Chain A, Nmr Structure Of The Domain 4 Of The E. Coli Ribosomal
Protein S1
Length = 115
Score = 30.8 bits (68), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 23/33 (69%), Gaps = 1/33 (3%)
Query: 265 GSVVIGTVQSLKPYGAFIDI-GGINGLLHVSQI 296
G+ + G V +L YG F++I G+ GL+HVS++
Sbjct: 31 GTKLTGRVTNLTDYGCFVEIEEGVEGLVHVSEM 63
>pdb|1V6C|A Chain A, Crystal Structure Of Psychrophilic Subtilisin-like
Protease Apa1 From Antarctic Psychrotroph
Pseudoalteromonas Sp. As-11
pdb|1V6C|B Chain B, Crystal Structure Of Psychrophilic Subtilisin-like
Protease Apa1 From Antarctic Psychrotroph
Pseudoalteromonas Sp. As-11
pdb|1WVM|A Chain A, Crystal Structure Of Psychrophilic Subtilisin-Like Serine
Protease Apa1 From Antarctic Psychrotroph
Pseudoaleromonas Sp. As-11, Complexed With Inhibitor
Chymostatin
pdb|1WVM|B Chain B, Crystal Structure Of Psychrophilic Subtilisin-Like Serine
Protease Apa1 From Antarctic Psychrotroph
Pseudoaleromonas Sp. As-11, Complexed With Inhibitor
Chymostatin
pdb|1Y9Z|A Chain A, Crystal Structure Of Psychrophilic Subtilisin-like Serine
Protease From Antarctic Psychrotroph Pseudoalteromonas
Sp. As-11 At 0.14 Nm Resolution
pdb|1Y9Z|B Chain B, Crystal Structure Of Psychrophilic Subtilisin-like Serine
Protease From Antarctic Psychrotroph Pseudoalteromonas
Sp. As-11 At 0.14 Nm Resolution
Length = 441
Score = 30.8 bits (68), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 26/105 (24%), Positives = 42/105 (40%), Gaps = 10/105 (9%)
Query: 41 KTIVSAVAISNAETREREELNQLFEEAYERCRTA-PMEGVSFTLEEFHSALEKYDFNSEL 99
+T V A +S+++ R + + Y+R V+ T + N+
Sbjct: 8 QTFVGATVLSDSQAGNRTIC--IIDSGYDRSHNDLNANNVTGTNNSGTGNWYQPGNNNAH 65
Query: 100 GTKVKGTVFCTDNRGALVDITAKSSAYLPTQEACIHKIKHVEEAG 144
GT V GT+ N +V + +P Q A IH +K EAG
Sbjct: 66 GTHVAGTIAAIANNEGVVGV-------MPNQNANIHIVKVFNEAG 103
>pdb|2Z6B|A Chain A, Crystal Structure Analysis Of (Gp27-Gp5)3 Conjugated With
Fe(Iii) Protoporphyrin
Length = 584
Score = 29.3 bits (64), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 19/34 (55%)
Query: 258 SQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLL 291
S A GIG V G V+ + YG F+D NG++
Sbjct: 63 SAAMSGIGGSVTGPVEGTRVYGHFLDKWKTNGIV 96
>pdb|1PDL|A Chain A, Fitting Of Gp5 In The Cryoem Reconstruction Of The
Bacteriophage T4 Baseplate
pdb|1PDL|B Chain B, Fitting Of Gp5 In The Cryoem Reconstruction Of The
Bacteriophage T4 Baseplate
pdb|1PDL|C Chain C, Fitting Of Gp5 In The Cryoem Reconstruction Of The
Bacteriophage T4 Baseplate
Length = 575
Score = 29.3 bits (64), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 19/34 (55%)
Query: 258 SQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLL 291
S A GIG V G V+ + YG F+D NG++
Sbjct: 63 SAAMSGIGGSVTGPVEGTRVYGHFLDKWKTNGIV 96
>pdb|1K28|A Chain A, The Structure Of The Bacteriophage T4 Cell-Puncturing
Device
Length = 584
Score = 29.3 bits (64), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 19/34 (55%)
Query: 258 SQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLL 291
S A GIG V G V+ + YG F+D NG++
Sbjct: 63 SAAMSGIGGSVTGPVEGTRVYGHFLDKWKTNGIV 96
>pdb|1WTH|A Chain A, Crystal Structure Of Gp5-S351l Mutant And Gp27 Complex
Length = 584
Score = 29.3 bits (64), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 19/34 (55%)
Query: 258 SQAQLGIGSVVIGTVQSLKPYGAFIDIGGINGLL 291
S A GIG V G V+ + YG F+D NG++
Sbjct: 63 SAAMSGIGGSVTGPVEGTRVYGHFLDKWKTNGIV 96
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 0.132 0.368
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,649,638
Number of Sequences: 62578
Number of extensions: 272126
Number of successful extensions: 833
Number of sequences better than 100.0: 31
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 806
Number of HSP's gapped (non-prelim): 34
length of query: 318
length of database: 14,973,337
effective HSP length: 99
effective length of query: 219
effective length of database: 8,778,115
effective search space: 1922407185
effective search space used: 1922407185
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: 51 (24.3 bits)