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= 044591
(241 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3AGJ|B Chain B, Crystal Structure Of Archaeal Pelota And Gtp-bound Ef1
Alpha Complex
pdb|3AGJ|D Chain D, Crystal Structure Of Archaeal Pelota And Gtp-bound Ef1
Alpha Complex
pdb|3AGJ|F Chain F, Crystal Structure Of Archaeal Pelota And Gtp-bound Ef1
Alpha Complex
pdb|3AGJ|H Chain H, Crystal Structure Of Archaeal Pelota And Gtp-bound Ef1
Alpha Complex
Length = 358
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 26/100 (26%), Positives = 47/100 (47%), Gaps = 15/100 (15%)
Query: 148 VRGLNLLNGQLTIEASFKIASKSRVDIAYDNSTITPEQLMNMFRKN-------YDLLLGI 200
+R L+++ + +E + +KSR +AY TP +++ + R D LL
Sbjct: 247 LRELSIVEAEGVLEEFLRRIAKSRDTVAY-----TPGEVLAVARMGAVDTVLLVDTLL-- 299
Query: 201 FNPDGWLEISYVDDTMRIGRDDKGNIFILERSSSAGENVV 240
+PD + VD+ +R+ G + I+ S AGE +V
Sbjct: 300 HSPDDAVR-EAVDEALRLVESMGGRVIIIPGDSPAGERLV 338
>pdb|2IEM|A Chain A, Solution Structure Of An Oxidized Form (Cys51-Cys198) Of
E. Coli Methionine Sulfoxide Reductase A (Msra)
Length = 211
Score = 28.9 bits (63), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 19/29 (65%)
Query: 172 VDIAYDNSTITPEQLMNMFRKNYDLLLGI 200
V I YD S I+ EQL+ +F +N+D G+
Sbjct: 96 VRIVYDPSVISYEQLLQVFWENHDPAQGM 124
>pdb|1FF3|A Chain A, Structure Of The Peptide Methionine Sulfoxide Reductase
From Escherichia Coli
pdb|1FF3|B Chain B, Structure Of The Peptide Methionine Sulfoxide Reductase
From Escherichia Coli
pdb|1FF3|C Chain C, Structure Of The Peptide Methionine Sulfoxide Reductase
From Escherichia Coli
Length = 211
Score = 28.9 bits (63), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 19/29 (65%)
Query: 172 VDIAYDNSTITPEQLMNMFRKNYDLLLGI 200
V I YD S I+ EQL+ +F +N+D G+
Sbjct: 96 VRIVYDPSVISYEQLLQVFWENHDPAQGM 124
>pdb|2GT3|A Chain A, Solution Structure And Dynamics Of The Reduced Form Of
Methionine Sulfoxide Reductase A From Escherichia Coli,
A 23 Kda Protein
Length = 212
Score = 28.9 bits (63), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 19/29 (65%)
Query: 172 VDIAYDNSTITPEQLMNMFRKNYDLLLGI 200
V I YD S I+ EQL+ +F +N+D G+
Sbjct: 97 VRIVYDPSVISYEQLLQVFWENHDPAQGM 125
>pdb|2B5L|A Chain A, Crystal Structure Of Ddb1 In Complex With Simian Virus 5 V
Protein
pdb|2B5L|B Chain B, Crystal Structure Of Ddb1 In Complex With Simian Virus 5 V
Protein
pdb|2B5M|A Chain A, Crystal Structure Of Ddb1
pdb|2HYE|A Chain A, Crystal Structure Of The Ddb1-cul4a-rbx1-sv5v Complex
Length = 1140
Score = 27.3 bits (59), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 11/43 (25%), Positives = 25/43 (58%)
Query: 193 NYDLLLGIFNPDGWLEISYVDDTMRIGRDDKGNIFILERSSSA 235
N++ + FNP+ + +DD +G ++ N+F+ ++ S+A
Sbjct: 941 NFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAA 983
>pdb|3E0C|A Chain A, Crystal Structure Of Dna Damage-Binding Protein 1(Ddb1)
Length = 1140
Score = 27.3 bits (59), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 11/43 (25%), Positives = 25/43 (58%)
Query: 193 NYDLLLGIFNPDGWLEISYVDDTMRIGRDDKGNIFILERSSSA 235
N++ + FNP+ + +DD +G ++ N+F+ ++ S+A
Sbjct: 941 NFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAA 983
>pdb|4E54|A Chain A, Damaged Dna Induced Uv-Damaged Dna-Binding Protein
(Uv-Ddb) Dimerization And Its Roles In Chromatinized Dna
Repair
pdb|4E5Z|A Chain A, Damaged Dna Induced Uv-Damaged Dna-Binding Protein
(Uv-Ddb) Dimerization And Its Roles In Chromatinized Dna
Repair
Length = 1150
Score = 27.3 bits (59), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 11/43 (25%), Positives = 25/43 (58%)
Query: 193 NYDLLLGIFNPDGWLEISYVDDTMRIGRDDKGNIFILERSSSA 235
N++ + FNP+ + +DD +G ++ N+F+ ++ S+A
Sbjct: 951 NFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAA 993
>pdb|4A0L|A Chain A, Structure Of Ddb1-Ddb2-Cul4b-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
pdb|4A0L|C Chain C, Structure Of Ddb1-Ddb2-Cul4b-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
Length = 1144
Score = 27.3 bits (59), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 11/43 (25%), Positives = 25/43 (58%)
Query: 193 NYDLLLGIFNPDGWLEISYVDDTMRIGRDDKGNIFILERSSSA 235
N++ + FNP+ + +DD +G ++ N+F+ ++ S+A
Sbjct: 945 NFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAA 987
>pdb|2C9K|A Chain A, Structure Of The Functional Form Of The
Mosquito-Larvicidal Cry4aa Toxin From Bacillus
Thuringiensis At 2.8 A Resolution
Length = 612
Score = 27.3 bits (59), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 19/38 (50%), Gaps = 8/38 (21%)
Query: 54 QVVQGINRGIFGVPSAKKSEIEALVELLESQNPTPHPT 91
Q+ +N+ IFG+P K+ E E NPT PT
Sbjct: 397 QITYDVNKNIFGLPILKRRE--------EQGNPTLFPT 426
>pdb|4A0B|A Chain A, Structure Of Hsddb1-Drddb2 Bound To A 16 Bp Cpd-Duplex (
Pyrimidine At D-1 Position) At 3.8 A Resolution (Cpd 4)
pdb|4A0B|C Chain C, Structure Of Hsddb1-Drddb2 Bound To A 16 Bp Cpd-Duplex (
Pyrimidine At D-1 Position) At 3.8 A Resolution (Cpd 4)
Length = 1159
Score = 27.3 bits (59), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 11/43 (25%), Positives = 25/43 (58%)
Query: 193 NYDLLLGIFNPDGWLEISYVDDTMRIGRDDKGNIFILERSSSA 235
N++ + FNP+ + +DD +G ++ N+F+ ++ S+A
Sbjct: 960 NFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAA 1002
>pdb|4A0A|A Chain A, Structure Of Hsddb1-Drddb2 Bound To A 16 Bp Cpd-Duplex (
Pyrimidine At D-1 Position) At 3.6 A Resolution (Cpd 3)
Length = 1159
Score = 27.3 bits (59), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 11/43 (25%), Positives = 25/43 (58%)
Query: 193 NYDLLLGIFNPDGWLEISYVDDTMRIGRDDKGNIFILERSSSA 235
N++ + FNP+ + +DD +G ++ N+F+ ++ S+A
Sbjct: 960 NFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAA 1002
>pdb|4A08|A Chain A, Structure Of Hsddb1-Drddb2 Bound To A 13 Bp Cpd-Duplex (
Purine At D-1 Position) At 3.0 A Resolution (Cpd 1)
pdb|4A09|A Chain A, Structure Of Hsddb1-Drddb2 Bound To A 15 Bp Cpd-Duplex
(Purine At D-1 Position) At 3.1 A Resolution (Cpd 2)
Length = 1159
Score = 27.3 bits (59), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 11/43 (25%), Positives = 25/43 (58%)
Query: 193 NYDLLLGIFNPDGWLEISYVDDTMRIGRDDKGNIFILERSSSA 235
N++ + FNP+ + +DD +G ++ N+F+ ++ S+A
Sbjct: 960 NFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAA 1002
>pdb|4A11|A Chain A, Structure Of The Hsddb1-Hscsa Complex
pdb|4A0K|C Chain C, Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
Length = 1159
Score = 27.3 bits (59), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 11/43 (25%), Positives = 25/43 (58%)
Query: 193 NYDLLLGIFNPDGWLEISYVDDTMRIGRDDKGNIFILERSSSA 235
N++ + FNP+ + +DD +G ++ N+F+ ++ S+A
Sbjct: 960 NFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAA 1002
>pdb|3I7H|A Chain A, Crystal Structure Of Ddb1 In Complex With The H-Box Motif
Of Hbx
pdb|3I7K|A Chain A, Crystal Structure Of Ddb1 In Complex With The H-Box Motif
Of Whx
pdb|3I7L|A Chain A, Crystal Structure Of Ddb1 In Complex With The H-Box Motif
Of Ddb2
pdb|3I7N|A Chain A, Crystal Structure Of Ddb1 In Complex With The H-Box Motif
Of Wdtc1
pdb|3I7O|A Chain A, Crystal Structure Of Ddb1 In Complex With The H-Box Motif
Of Iqwd1
pdb|3I7P|A Chain A, Crystal Structure Of Ddb1 In Complex With The H-Box Motif
Of Wdr40a
pdb|3I89|A Chain A, Crystal Structure Of Ddb1 In Complex With The H-Box Motif
Of Wdr22
pdb|3I8C|A Chain A, Crystal Structure Of Ddb1 In Complex With The H-Box Motif
Of Wdr21a
pdb|3I8E|A Chain A, Crystal Structure Of Ddb1 In Complex With The H-Box Motif
Of Wdr42a
pdb|3I8E|B Chain B, Crystal Structure Of Ddb1 In Complex With The H-Box Motif
Of Wdr42a
Length = 1143
Score = 27.3 bits (59), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 11/43 (25%), Positives = 25/43 (58%)
Query: 193 NYDLLLGIFNPDGWLEISYVDDTMRIGRDDKGNIFILERSSSA 235
N++ + FNP+ + +DD +G ++ N+F+ ++ S+A
Sbjct: 944 NFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAA 986
>pdb|3EI1|A Chain A, Structure Of Hsddb1-Drddb2 Bound To A 14 Bp 6-4 Photoproduct
Containing Dna-Duplex
pdb|3EI2|A Chain A, Structure Of Hsddb1-Drddb2 Bound To A 16 Bp Abasic Site
Containing Dna-Duplex
pdb|3EI3|A Chain A, Structure Of The Hsddb1-Drddb2 Complex
Length = 1158
Score = 27.3 bits (59), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 11/43 (25%), Positives = 25/43 (58%)
Query: 193 NYDLLLGIFNPDGWLEISYVDDTMRIGRDDKGNIFILERSSSA 235
N++ + FNP+ + +DD +G ++ N+F+ ++ S+A
Sbjct: 959 NFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAA 1001
>pdb|3EI4|A Chain A, Structure Of The Hsddb1-Hsddb2 Complex
pdb|3EI4|C Chain C, Structure Of The Hsddb1-Hsddb2 Complex
pdb|3EI4|E Chain E, Structure Of The Hsddb1-Hsddb2 Complex
Length = 1158
Score = 27.3 bits (59), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 11/43 (25%), Positives = 25/43 (58%)
Query: 193 NYDLLLGIFNPDGWLEISYVDDTMRIGRDDKGNIFILERSSSA 235
N++ + FNP+ + +DD +G ++ N+F+ ++ S+A
Sbjct: 959 NFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAA 1001
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
0.316 0.134 0.375
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,757,077
Number of Sequences: 62578
Number of extensions: 266944
Number of successful extensions: 965
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 951
Number of HSP's gapped (non-prelim): 17
length of query: 241
length of database: 14,973,337
effective HSP length: 96
effective length of query: 145
effective length of database: 8,965,849
effective search space: 1300048105
effective search space used: 1300048105
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: 50 (23.9 bits)