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= 008273
(571 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1WID|A Chain A, Solution Structure Of The B3 Dna-Binding Domain Of Rav1
Length = 130
Score = 76.3 bits (186), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 48/123 (39%), Positives = 75/123 (60%), Gaps = 10/123 (8%)
Query: 358 LFEKMLSASDAGRIGRLVLPKKCAEAYFP-PISQ--PEGLPLKVQDSKGKEWIFQFRFWP 414
LFEK ++ SD G++ RLV+PK AE +FP P S +G+ L +D GK W F++ +W
Sbjct: 13 LFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSYW- 71
Query: 415 NNNSRMYVL-EGVTPCIQNMQLQAGDIVTFSRLEPEG-KLVMGFRKASSASASDQDNEAN 472
N+S+ YVL +G + ++ L+AGD+V+FSR + +L +G++ S S SD D
Sbjct: 72 -NSSQSYVLTKGWSRFVKEKNLRAGDVVSFSRSNGQDQQLYIGWK---SRSGSDLDASGP 127
Query: 473 KAG 475
+G
Sbjct: 128 SSG 130
>pdb|1D9X|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb
Length = 658
Score = 30.4 bits (67), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 32/120 (26%), Positives = 49/120 (40%), Gaps = 16/120 (13%)
Query: 116 ARKNVLVAPTPSWPPSL----FYQTPFPERIKDLSVKNWTQLAGSGPVPWRQAPSLFNSS 171
ARK VLV P +L F ++I + + T GP +P +
Sbjct: 356 ARKQVLVDHGFRLPSALDNRPLTFEEFEQKINQIIYVSAT----PGPYELEHSPGVVEQI 411
Query: 172 I-------PQPELRPRLPYEVDLSAGI-DRINASERLSVPSLEKRKLEDFSERLMNGGLK 223
I P ++RP DL I +R+ +ER V +L K+ ED ++ L G+K
Sbjct: 412 IRPTGLLDPTIDVRPTKGQIDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIK 471
>pdb|1D9Z|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb In
Complex With Atp
Length = 657
Score = 30.4 bits (67), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 32/120 (26%), Positives = 49/120 (40%), Gaps = 16/120 (13%)
Query: 116 ARKNVLVAPTPSWPPSL----FYQTPFPERIKDLSVKNWTQLAGSGPVPWRQAPSLFNSS 171
ARK VLV P +L F ++I + + T GP +P +
Sbjct: 355 ARKQVLVDHGFRLPSALDNRPLTFEEFEQKINQIIYVSAT----PGPYELEHSPGVVEQI 410
Query: 172 I-------PQPELRPRLPYEVDLSAGI-DRINASERLSVPSLEKRKLEDFSERLMNGGLK 223
I P ++RP DL I +R+ +ER V +L K+ ED ++ L G+K
Sbjct: 411 IRPTGLLDPTIDVRPTKGQIDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIK 470
>pdb|1T5L|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb Point
Mutant Y96a Revealing A Novel Fold For Domain 2
pdb|1T5L|B Chain B, Crystal Structure Of The Dna Repair Protein Uvrb Point
Mutant Y96a Revealing A Novel Fold For Domain 2
Length = 658
Score = 30.4 bits (67), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 32/120 (26%), Positives = 49/120 (40%), Gaps = 16/120 (13%)
Query: 116 ARKNVLVAPTPSWPPSL----FYQTPFPERIKDLSVKNWTQLAGSGPVPWRQAPSLFNSS 171
ARK VLV P +L F ++I + + T GP +P +
Sbjct: 356 ARKQVLVDHGFRLPSALDNRPLTFEEFEQKINQIIYVSAT----PGPYELEHSPGVVEQI 411
Query: 172 I-------PQPELRPRLPYEVDLSAGI-DRINASERLSVPSLEKRKLEDFSERLMNGGLK 223
I P ++RP DL I +R+ +ER V +L K+ ED ++ L G+K
Sbjct: 412 IRPTGLLDPTIDVRPTKGQIDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIK 471
>pdb|3UWX|B Chain B, Crystal Structure Of Uvra-Uvrb Complex
Length = 683
Score = 30.4 bits (67), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 32/120 (26%), Positives = 49/120 (40%), Gaps = 16/120 (13%)
Query: 116 ARKNVLVAPTPSWPPSL----FYQTPFPERIKDLSVKNWTQLAGSGPVPWRQAPSLFNSS 171
ARK VLV P +L F ++I + + T GP +P +
Sbjct: 381 ARKQVLVDHGFRLPSALDNRPLTFEEFEQKINQIIYISAT----PGPYELEHSPGVVEQI 436
Query: 172 I-------PQPELRPRLPYEVDLSAGI-DRINASERLSVPSLEKRKLEDFSERLMNGGLK 223
I P ++RP DL I +R+ +ER V +L K+ ED ++ L G+K
Sbjct: 437 IRPTGLLDPTIDVRPTKGQIDDLIGEIHERVERNERTLVTTLTKKMAEDLTDYLKEAGIK 496
>pdb|2FDC|A Chain A, Structural Basis Of Dna Damage Recognition And Processing
By Uvrb: Crystal Structure Of A UvrbDNA COMPLEX
pdb|2FDC|B Chain B, Structural Basis Of Dna Damage Recognition And Processing
By Uvrb: Crystal Structure Of A UvrbDNA COMPLEX
Length = 658
Score = 30.4 bits (67), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 32/120 (26%), Positives = 49/120 (40%), Gaps = 16/120 (13%)
Query: 116 ARKNVLVAPTPSWPPSL----FYQTPFPERIKDLSVKNWTQLAGSGPVPWRQAPSLFNSS 171
ARK VLV P +L F ++I + + T GP +P +
Sbjct: 356 ARKQVLVDHGFRLPSALDNRPLTFEEFEQKINQIIYVSAT----PGPYELEHSPGVVEQI 411
Query: 172 I-------PQPELRPRLPYEVDLSAGI-DRINASERLSVPSLEKRKLEDFSERLMNGGLK 223
I P ++RP DL I +R+ +ER V +L K+ ED ++ L G+K
Sbjct: 412 IRPTGLLDPTIDVRPTKGQIDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIK 471
>pdb|3LQ2|A Chain A, E. Coli Pyruvate Dehydrogenase Complex E1 E235a Mutant
With Low Tdp Concentration
pdb|3LQ2|B Chain B, E. Coli Pyruvate Dehydrogenase Complex E1 E235a Mutant
With Low Tdp Concentration
pdb|3LQ4|A Chain A, E. Coli Pyruvate Dehydrogenase Complex E1 E235a Mutant
With High Tdp Concentration
pdb|3LQ4|B Chain B, E. Coli Pyruvate Dehydrogenase Complex E1 E235a Mutant
With High Tdp Concentration
Length = 886
Score = 30.0 bits (66), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 32/67 (47%), Gaps = 1/67 (1%)
Query: 170 SSIPQPELRPRLPYEVDLSAGIDRINASERLS-VPSLEKRKLEDFSERLMNGGLKSGSRD 228
SS P P+L P +S G+ I A + + LE R L+D S++ + L G D
Sbjct: 175 SSYPHPKLMPEFWQFPTVSMGLGPIGAIYQAKFLKYLEHRGLKDTSKQTVYAFLGDGEMD 234
Query: 229 IPENANA 235
PE+ A
Sbjct: 235 APESKGA 241
>pdb|2QTA|A Chain A, E. Coli Pyruvate Dehydrogenase E1 Component E401k Mutant
With Thiamin Diphosphate
pdb|2QTA|B Chain B, E. Coli Pyruvate Dehydrogenase E1 Component E401k Mutant
With Thiamin Diphosphate
pdb|2QTC|A Chain A, E. Coli Pyruvate Dehydrogenase E1 Component E401k Mutant
With Phosphonolactylthiamin Diphosphate
pdb|2QTC|B Chain B, E. Coli Pyruvate Dehydrogenase E1 Component E401k Mutant
With Phosphonolactylthiamin Diphosphate
Length = 886
Score = 29.3 bits (64), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 32/67 (47%), Gaps = 1/67 (1%)
Query: 170 SSIPQPELRPRLPYEVDLSAGIDRINASERLS-VPSLEKRKLEDFSERLMNGGLKSGSRD 228
SS P P+L P +S G+ I A + + LE R L+D S++ + L G D
Sbjct: 175 SSYPHPKLMPEFWQFPTVSMGLGPIGAIYQAKFLKYLEHRGLKDTSKQTVYAFLGDGEMD 234
Query: 229 IPENANA 235
PE+ A
Sbjct: 235 EPESKGA 241
>pdb|1L8A|A Chain A, E. Coli Pyruvate Dehydrogenase
pdb|1L8A|B Chain B, E. Coli Pyruvate Dehydrogenase
pdb|1RP7|A Chain A, E. Coli Pyruvate Dehydrogenase Inhibitor Complex
pdb|1RP7|B Chain B, E. Coli Pyruvate Dehydrogenase Inhibitor Complex
pdb|2G25|A Chain A, E. Coli Pyruvate Dehydrogenase Phosphonolactylthiamin
Diphosphate Complex
pdb|2G25|B Chain B, E. Coli Pyruvate Dehydrogenase Phosphonolactylthiamin
Diphosphate Complex
pdb|2G28|A Chain A, E. Coli Pyruvate Dehydrogenase H407a Variant
Phosphonolactylthiamin Diphosphate Complex
pdb|2G28|B Chain B, E. Coli Pyruvate Dehydrogenase H407a Variant
Phosphonolactylthiamin Diphosphate Complex
pdb|2G67|A Chain A, E. Coli Pyruvate Dehydrogenase E1 Component (Apoenzyme)
pdb|2G67|B Chain B, E. Coli Pyruvate Dehydrogenase E1 Component (Apoenzyme)
pdb|2IEA|A Chain A, E. Coli Pyruvate Dehydrogenase
pdb|2IEA|B Chain B, E. Coli Pyruvate Dehydrogenase
Length = 886
Score = 29.3 bits (64), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 32/67 (47%), Gaps = 1/67 (1%)
Query: 170 SSIPQPELRPRLPYEVDLSAGIDRINASERLS-VPSLEKRKLEDFSERLMNGGLKSGSRD 228
SS P P+L P +S G+ I A + + LE R L+D S++ + L G D
Sbjct: 175 SSYPHPKLMPEFWQFPTVSMGLGPIGAIYQAKFLKYLEHRGLKDTSKQTVYAFLGDGEMD 234
Query: 229 IPENANA 235
PE+ A
Sbjct: 235 EPESKGA 241
>pdb|1V9N|A Chain A, Structure Of Malate Dehydrogenase From Pyrococcus
Horikoshii Ot3
Length = 360
Score = 29.3 bits (64), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 19/31 (61%)
Query: 264 HFGLAVSYASPSETNSQIGVSGSHLRPVVQP 294
H+G+A YA + IG+S ++ RP+V P
Sbjct: 127 HYGIAGYYALXAAEEGXIGISXTNSRPLVAP 157
>pdb|3LPL|A Chain A, E. Coli Pyruvate Dehydrogenase Complex E1 Component E571a
Mutant
pdb|3LPL|B Chain B, E. Coli Pyruvate Dehydrogenase Complex E1 Component E571a
Mutant
Length = 886
Score = 29.3 bits (64), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 32/67 (47%), Gaps = 1/67 (1%)
Query: 170 SSIPQPELRPRLPYEVDLSAGIDRINASERLS-VPSLEKRKLEDFSERLMNGGLKSGSRD 228
SS P P+L P +S G+ I A + + LE R L+D S++ + L G D
Sbjct: 175 SSYPHPKLMPEFWQFPTVSMGLGPIGAIYQAKFLKYLEHRGLKDTSKQTVYAFLGDGEMD 234
Query: 229 IPENANA 235
PE+ A
Sbjct: 235 EPESKGA 241
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
0.318 0.134 0.411
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,207,685
Number of Sequences: 62578
Number of extensions: 735890
Number of successful extensions: 1502
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1498
Number of HSP's gapped (non-prelim): 11
length of query: 571
length of database: 14,973,337
effective HSP length: 104
effective length of query: 467
effective length of database: 8,465,225
effective search space: 3953260075
effective search space used: 3953260075
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: 54 (25.4 bits)