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= psy13880
(256 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 41/165 (24%), Positives = 69/165 (41%), Gaps = 17/165 (10%)
Query: 96 LFMYQPEARESNGGHR--LIKKTDFHLGQHVNTFFKIRCKPSPISDAPGARS---RFLTW 150
LF+ Q ++ + R L + FHLG+ VN F C S + G S +
Sbjct: 993 LFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVF----CHGSLVMQNLGETSTPTQGSVL 1048
Query: 151 YASLDGALGFFLPLPEKNYRRLLMLQNVMVTHTSHTGGLNPRAFRTYKGKGYYAGNPSRG 210
+ +++G +G L E Y LL +QN + G + +R++ + P+ G
Sbjct: 1049 FGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTE--RKTEPATG 1106
Query: 211 IIDGSLVWKFLQLSLGERLEICKKI------GSKHNDILDELYDI 249
IDG L+ FL +S + E+ + G K D+L +
Sbjct: 1107 FIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKV 1151
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 41/165 (24%), Positives = 69/165 (41%), Gaps = 17/165 (10%)
Query: 96 LFMYQPEARESNGGHR--LIKKTDFHLGQHVNTFFKIRCKPSPISDAPGARS---RFLTW 150
LF+ Q ++ + R L + FHLG+ VN F C S + G S +
Sbjct: 993 LFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVF----CHGSLVMQNLGETSTPTQGSVL 1048
Query: 151 YASLDGALGFFLPLPEKNYRRLLMLQNVMVTHTSHTGGLNPRAFRTYKGKGYYAGNPSRG 210
+ +++G +G L E Y LL +QN + G + +R++ + P+ G
Sbjct: 1049 FGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTE--RKTEPATG 1106
Query: 211 IIDGSLVWKFLQLSLGERLEICKKI------GSKHNDILDELYDI 249
IDG L+ FL +S + E+ + G K D+L +
Sbjct: 1107 FIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKV 1151
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 41/165 (24%), Positives = 69/165 (41%), Gaps = 17/165 (10%)
Query: 96 LFMYQPEARESNGGHR--LIKKTDFHLGQHVNTFFKIRCKPSPISDAPGARS---RFLTW 150
LF+ Q ++ + R L + FHLG+ VN F C S + G S +
Sbjct: 993 LFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVF----CHGSLVMQNLGETSTPTQGSVL 1048
Query: 151 YASLDGALGFFLPLPEKNYRRLLMLQNVMVTHTSHTGGLNPRAFRTYKGKGYYAGNPSRG 210
+ +++G +G L E Y LL +QN + G + +R++ + P+ G
Sbjct: 1049 FGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTE--RKTEPATG 1106
Query: 211 IIDGSLVWKFLQLSLGERLEICKKI------GSKHNDILDELYDI 249
IDG L+ FL +S + E+ + G K D+L +
Sbjct: 1107 FIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKV 1151
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 41/165 (24%), Positives = 69/165 (41%), Gaps = 17/165 (10%)
Query: 96 LFMYQPEARESNGGHR--LIKKTDFHLGQHVNTFFKIRCKPSPISDAPGARS---RFLTW 150
LF+ Q ++ + R L + FHLG+ VN F C S + G S +
Sbjct: 974 LFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVF----CHGSLVMQNLGETSTPTQGSVL 1029
Query: 151 YASLDGALGFFLPLPEKNYRRLLMLQNVMVTHTSHTGGLNPRAFRTYKGKGYYAGNPSRG 210
+ +++G +G L E Y LL +QN + G + +R++ + P+ G
Sbjct: 1030 FGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTE--RKTEPATG 1087
Query: 211 IIDGSLVWKFLQLSLGERLEICKKI------GSKHNDILDELYDI 249
IDG L+ FL +S + E+ + G K D+L +
Sbjct: 1088 FIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKV 1132
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 41/165 (24%), Positives = 69/165 (41%), Gaps = 17/165 (10%)
Query: 96 LFMYQPEARESNGGHR--LIKKTDFHLGQHVNTFFKIRCKPSPISDAPGARS---RFLTW 150
LF+ Q ++ + R L + FHLG+ VN F C S + G S +
Sbjct: 993 LFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVF----CHGSLVMQNLGETSTPTQGSVL 1048
Query: 151 YASLDGALGFFLPLPEKNYRRLLMLQNVMVTHTSHTGGLNPRAFRTYKGKGYYAGNPSRG 210
+ +++G +G L E Y LL +QN + G + +R++ + P+ G
Sbjct: 1049 FGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTE--RKTEPATG 1106
Query: 211 IIDGSLVWKFLQLSLGERLEICKKI------GSKHNDILDELYDI 249
IDG L+ FL +S + E+ + G K D+L +
Sbjct: 1107 FIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKV 1151
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 41/165 (24%), Positives = 69/165 (41%), Gaps = 17/165 (10%)
Query: 96 LFMYQPEARESNGGHR--LIKKTDFHLGQHVNTFFKIRCKPSPISDAPGARS---RFLTW 150
LF+ Q ++ + R L + FHLG+ VN F C S + G S +
Sbjct: 992 LFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVF----CHGSLVMQNLGETSTPTQGSVL 1047
Query: 151 YASLDGALGFFLPLPEKNYRRLLMLQNVMVTHTSHTGGLNPRAFRTYKGKGYYAGNPSRG 210
+ +++G +G L E Y LL +QN + G + +R++ + P+ G
Sbjct: 1048 FGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTE--RKTEPATG 1105
Query: 211 IIDGSLVWKFLQLSLGERLEICKKI------GSKHNDILDELYDI 249
IDG L+ FL +S + E+ + G K D+L +
Sbjct: 1106 FIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKV 1150
>pdb|3E0C|A Chain A, Crystal Structure Of Dna Damage-Binding Protein 1(Ddb1)
Length = 1140
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 41/165 (24%), Positives = 69/165 (41%), Gaps = 17/165 (10%)
Query: 96 LFMYQPEARESNGGHR--LIKKTDFHLGQHVNTFFKIRCKPSPISDAPGARS---RFLTW 150
LF+ Q ++ + R L + FHLG+ VN F C S + G S +
Sbjct: 974 LFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVF----CHGSLVMQNLGETSTPTQGSVL 1029
Query: 151 YASLDGALGFFLPLPEKNYRRLLMLQNVMVTHTSHTGGLNPRAFRTYKGKGYYAGNPSRG 210
+ +++G +G L E Y LL +QN + G + +R++ + P+ G
Sbjct: 1030 FGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTE--RKTEPATG 1087
Query: 211 IIDGSLVWKFLQLSLGERLEICKKI------GSKHNDILDELYDI 249
IDG L+ FL +S + E+ + G K D+L +
Sbjct: 1088 FIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKV 1132
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 41/165 (24%), Positives = 69/165 (41%), Gaps = 17/165 (10%)
Query: 96 LFMYQPEARESNGGHR--LIKKTDFHLGQHVNTFFKIRCKPSPISDAPGARS---RFLTW 150
LF+ Q ++ + R L + FHLG+ VN F C S + G S +
Sbjct: 984 LFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVF----CHGSLVMQNLGETSTPTQGSVL 1039
Query: 151 YASLDGALGFFLPLPEKNYRRLLMLQNVMVTHTSHTGGLNPRAFRTYKGKGYYAGNPSRG 210
+ +++G +G L E Y LL +QN + G + +R++ + P+ G
Sbjct: 1040 FGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTE--RKTEPATG 1097
Query: 211 IIDGSLVWKFLQLSLGERLEICKKI------GSKHNDILDELYDI 249
IDG L+ FL +S + E+ + G K D+L +
Sbjct: 1098 FIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKV 1142
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 41/165 (24%), Positives = 69/165 (41%), Gaps = 17/165 (10%)
Query: 96 LFMYQPEARESNGGHR--LIKKTDFHLGQHVNTFFKIRCKPSPISDAPGARS---RFLTW 150
LF+ Q ++ + R L + FHLG+ VN F C S + G S +
Sbjct: 978 LFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVF----CHGSLVMQNLGETSTPTQGSVL 1033
Query: 151 YASLDGALGFFLPLPEKNYRRLLMLQNVMVTHTSHTGGLNPRAFRTYKGKGYYAGNPSRG 210
+ +++G +G L E Y LL +QN + G + +R++ + P+ G
Sbjct: 1034 FGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTE--RKTEPATG 1091
Query: 211 IIDGSLVWKFLQLSLGERLEICKKI------GSKHNDILDELYDI 249
IDG L+ FL +S + E+ + G K D+L +
Sbjct: 1092 FIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKV 1136
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 41/165 (24%), Positives = 69/165 (41%), Gaps = 17/165 (10%)
Query: 96 LFMYQPEARESNGGHR--LIKKTDFHLGQHVNTFFKIRCKPSPISDAPGARS---RFLTW 150
LF+ Q ++ + R L + FHLG+ VN F C S + G S +
Sbjct: 992 LFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVF----CHGSLVMQNLGETSTPTQGSVL 1047
Query: 151 YASLDGALGFFLPLPEKNYRRLLMLQNVMVTHTSHTGGLNPRAFRTYKGKGYYAGNPSRG 210
+ +++G +G L E Y LL +QN + G + +R++ + P+ G
Sbjct: 1048 FGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTE--RKTEPATG 1105
Query: 211 IIDGSLVWKFLQLSLGERLEICKKI------GSKHNDILDELYDI 249
IDG L+ FL +S + E+ + G K D+L +
Sbjct: 1106 FIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKV 1150
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 41/165 (24%), Positives = 69/165 (41%), Gaps = 17/165 (10%)
Query: 96 LFMYQPEARESNGGHR--LIKKTDFHLGQHVNTFFKIRCKPSPISDAPGARS---RFLTW 150
LF+ Q ++ + R L + FHLG+ VN F C S + G S +
Sbjct: 977 LFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVF----CHGSLVMQNLGETSTPTQGSVL 1032
Query: 151 YASLDGALGFFLPLPEKNYRRLLMLQNVMVTHTSHTGGLNPRAFRTYKGKGYYAGNPSRG 210
+ +++G +G L E Y LL +QN + G + +R++ + P+ G
Sbjct: 1033 FGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTE--RKTEPATG 1090
Query: 211 IIDGSLVWKFLQLSLGERLEICKKI------GSKHNDILDELYDI 249
IDG L+ FL +S + E+ + G K D+L +
Sbjct: 1091 FIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKV 1135
>pdb|4EV1|A Chain A, Anabaena Tic22 (Protein Transport)
Length = 252
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 9/53 (16%)
Query: 88 SDKDKNVVLFMYQPEARESNGGHRLIKKTDFHLGQHVNTF-----FKIRCKPS 135
+ KD N +LF ++P +E G L++++ GQ VN F F +R P
Sbjct: 95 TKKDPNRLLFAFKPVDQEIKGAMDLLRQS----GQQVNQFKSVPMFAVRFAPD 143
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 0.139 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,618,515
Number of Sequences: 62578
Number of extensions: 305868
Number of successful extensions: 455
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 455
Number of HSP's gapped (non-prelim): 12
length of query: 256
length of database: 14,973,337
effective HSP length: 97
effective length of query: 159
effective length of database: 8,903,271
effective search space: 1415620089
effective search space used: 1415620089
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: 50 (23.9 bits)