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= 040797
(280 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3E0C|A Chain A, Crystal Structure Of Dna Damage-Binding Protein 1(Ddb1)
Length = 1140
Score = 33.1 bits (74), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 39/79 (49%), Gaps = 6/79 (7%)
Query: 172 RLLSATVEYEETGWYDGQIWVKTAEVLARDRLLGSFSVKPVLSRLKYTLITLGASLFVCA 231
RL +E EE DG + +K V LLG S+ L+ L ++ +G+ L
Sbjct: 279 RLFMLLLEKEE--QMDGTVTLKDLRV----ELLGETSIAECLTYLDNGVVFVGSRLGDSQ 332
Query: 232 LLLINLEGGQKGSYLTPTE 250
L+ +N++ ++GSY+ E
Sbjct: 333 LVKLNVDSNEQGSYVVAME 351
>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 = 33.1 bits (74), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 39/79 (49%), Gaps = 6/79 (7%)
Query: 172 RLLSATVEYEETGWYDGQIWVKTAEVLARDRLLGSFSVKPVLSRLKYTLITLGASLFVCA 231
RL +E EE DG + +K V LLG S+ L+ L ++ +G+ L
Sbjct: 289 RLFMLLLEKEE--QMDGTVTLKDLRV----ELLGETSIAECLTYLDNGVVFVGSRLGDSQ 342
Query: 232 LLLINLEGGQKGSYLTPTE 250
L+ +N++ ++GSY+ E
Sbjct: 343 LVKLNVDSNEQGSYVVAME 361
>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 = 33.1 bits (74), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 39/79 (49%), Gaps = 6/79 (7%)
Query: 172 RLLSATVEYEETGWYDGQIWVKTAEVLARDRLLGSFSVKPVLSRLKYTLITLGASLFVCA 231
RL +E EE DG + +K V LLG S+ L+ L ++ +G+ L
Sbjct: 283 RLFMLLLEKEE--QMDGTVTLKDLRV----ELLGETSIAECLTYLDNGVVFVGSRLGDSQ 336
Query: 232 LLLINLEGGQKGSYLTPTE 250
L+ +N++ ++GSY+ E
Sbjct: 337 LVKLNVDSNEQGSYVVAME 355
>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 = 33.1 bits (74), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 39/79 (49%), Gaps = 6/79 (7%)
Query: 172 RLLSATVEYEETGWYDGQIWVKTAEVLARDRLLGSFSVKPVLSRLKYTLITLGASLFVCA 231
RL +E EE DG + +K V LLG S+ L+ L ++ +G+ L
Sbjct: 298 RLFMLLLEKEE--QMDGTVTLKDLRV----ELLGETSIAECLTYLDNGVVFVGSRLGDSQ 351
Query: 232 LLLINLEGGQKGSYLTPTE 250
L+ +N++ ++GSY+ E
Sbjct: 352 LVKLNVDSNEQGSYVVAME 370
>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 = 33.1 bits (74), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 39/79 (49%), Gaps = 6/79 (7%)
Query: 172 RLLSATVEYEETGWYDGQIWVKTAEVLARDRLLGSFSVKPVLSRLKYTLITLGASLFVCA 231
RL +E EE DG + +K V LLG S+ L+ L ++ +G+ L
Sbjct: 298 RLFMLLLEKEE--QMDGTVTLKDLRV----ELLGETSIAECLTYLDNGVVFVGSRLGDSQ 351
Query: 232 LLLINLEGGQKGSYLTPTE 250
L+ +N++ ++GSY+ E
Sbjct: 352 LVKLNVDSNEQGSYVVAME 370
>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 = 33.1 bits (74), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 39/79 (49%), Gaps = 6/79 (7%)
Query: 172 RLLSATVEYEETGWYDGQIWVKTAEVLARDRLLGSFSVKPVLSRLKYTLITLGASLFVCA 231
RL +E EE DG + +K V LLG S+ L+ L ++ +G+ L
Sbjct: 298 RLFMLLLEKEE--QMDGTVTLKDLRV----ELLGETSIAECLTYLDNGVVFVGSRLGDSQ 351
Query: 232 LLLINLEGGQKGSYLTPTE 250
L+ +N++ ++GSY+ E
Sbjct: 352 LVKLNVDSNEQGSYVVAME 370
>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 = 33.1 bits (74), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 39/79 (49%), Gaps = 6/79 (7%)
Query: 172 RLLSATVEYEETGWYDGQIWVKTAEVLARDRLLGSFSVKPVLSRLKYTLITLGASLFVCA 231
RL +E EE DG + +K V LLG S+ L+ L ++ +G+ L
Sbjct: 297 RLFMLLLEKEE--QMDGTVTLKDLRV----ELLGETSIAECLTYLDNGVVFVGSRLGDSQ 350
Query: 232 LLLINLEGGQKGSYLTPTE 250
L+ +N++ ++GSY+ E
Sbjct: 351 LVKLNVDSNEQGSYVVAME 369
>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 = 33.1 bits (74), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 39/79 (49%), Gaps = 6/79 (7%)
Query: 172 RLLSATVEYEETGWYDGQIWVKTAEVLARDRLLGSFSVKPVLSRLKYTLITLGASLFVCA 231
RL +E EE DG + +K V LLG S+ L+ L ++ +G+ L
Sbjct: 279 RLFMLLLEKEE--QMDGTVTLKDLRV----ELLGETSIAECLTYLDNGVVFVGSRLGDSQ 332
Query: 232 LLLINLEGGQKGSYLTPTE 250
L+ +N++ ++GSY+ E
Sbjct: 333 LVKLNVDSNEQGSYVVAME 351
>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 = 33.1 bits (74), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 39/79 (49%), Gaps = 6/79 (7%)
Query: 172 RLLSATVEYEETGWYDGQIWVKTAEVLARDRLLGSFSVKPVLSRLKYTLITLGASLFVCA 231
RL +E EE DG + +K V LLG S+ L+ L ++ +G+ L
Sbjct: 298 RLFMLLLEKEE--QMDGTVTLKDLRV----ELLGETSIAECLTYLDNGVVFVGSRLGDSQ 351
Query: 232 LLLINLEGGQKGSYLTPTE 250
L+ +N++ ++GSY+ E
Sbjct: 352 LVKLNVDSNEQGSYVVAME 370
>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 = 33.1 bits (74), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 39/79 (49%), Gaps = 6/79 (7%)
Query: 172 RLLSATVEYEETGWYDGQIWVKTAEVLARDRLLGSFSVKPVLSRLKYTLITLGASLFVCA 231
RL +E EE DG + +K V LLG S+ L+ L ++ +G+ L
Sbjct: 282 RLFMLLLEKEE--QMDGTVTLKDLRV----ELLGETSIAECLTYLDNGVVFVGSRLGDSQ 335
Query: 232 LLLINLEGGQKGSYLTPTE 250
L+ +N++ ++GSY+ E
Sbjct: 336 LVKLNVDSNEQGSYVVAME 354
>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 = 33.1 bits (74), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 39/79 (49%), Gaps = 6/79 (7%)
Query: 172 RLLSATVEYEETGWYDGQIWVKTAEVLARDRLLGSFSVKPVLSRLKYTLITLGASLFVCA 231
RL +E EE DG + +K V LLG S+ L+ L ++ +G+ L
Sbjct: 297 RLFMLLLEKEE--QMDGTVTLKDLRV----ELLGETSIAECLTYLDNGVVFVGSRLGDSQ 350
Query: 232 LLLINLEGGQKGSYLTPTE 250
L+ +N++ ++GSY+ E
Sbjct: 351 LVKLNVDSNEQGSYVVAME 369
>pdb|2CS0|A Chain A, Solution Structure Of The Sh2 Domain Of Human Hsh2d
Protein
Length = 119
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 4/66 (6%)
Query: 185 WYDGQIWVKTAEVLARDRLLGSFSVKPVLSRLKYTLITLGASLFVCALLLINLEGGQKGS 244
W+ G I + AE L + LGSF ++ S + YTL + A C ++ L+ G+
Sbjct: 18 WFHGAISREDAENLLESQPLGSFLIRVSHSHVGYTL-SYKAQSSCCHFMVKLLD---DGT 73
Query: 245 YLTPTE 250
++ P E
Sbjct: 74 FMIPGE 79
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
0.320 0.138 0.435
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,841,456
Number of Sequences: 62578
Number of extensions: 316350
Number of successful extensions: 624
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 613
Number of HSP's gapped (non-prelim): 16
length of query: 280
length of database: 14,973,337
effective HSP length: 98
effective length of query: 182
effective length of database: 8,840,693
effective search space: 1609006126
effective search space used: 1609006126
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)