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= psy12278
(300 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2A25|A Chain A, Crystal Structure Of Siah1 Sbd Bound To The Peptide
Ekpaavvapittg From Sip
Length = 193
Score = 336 bits (861), Expect = 1e-92, Method: Compositional matrix adjust.
Identities = 156/191 (81%), Positives = 171/191 (89%)
Query: 108 VAGTMWFPCRYQMNGCGISLLHTEKPEHEDTCEHRPYLCPCPGASCKWGGALDQVMAHLN 167
VA ++ FPC+Y +GC I+L HTEK +HE+ CE RPY CPCPGASCKW G+LD VM HL
Sbjct: 1 VANSVLFPCKYASSGCEITLPHTEKADHEELCEFRPYSCPCPGASCKWQGSLDAVMPHLM 60
Query: 168 QSHKSITTLQGEDIVFLATDINLPGAVDWVMMQSCFGHHFMLVLEKQEKFDGHQHFFAIV 227
HKSITTLQGEDIVFLATDINLPGAVDWVMMQSCFG HFMLVLEKQEK+DGHQ FFAIV
Sbjct: 61 HQHKSITTLQGEDIVFLATDINLPGAVDWVMMQSCFGFHFMLVLEKQEKYDGHQQFFAIV 120
Query: 228 QLIGSRKQSENFTYRLELNGHRRRLTWEATPRSIHEGVASAIMNSDCLVFDTNIAQLFAD 287
QLIG+RKQ+ENF YRLELNGHRRRLTWEATPRSIHEG+A+AIMNSDCLVFDT+IAQLFA+
Sbjct: 121 QLIGTRKQAENFAYRLELNGHRRRLTWEATPRSIHEGIATAIMNSDCLVFDTSIAQLFAE 180
Query: 288 NGNLGINVTIG 298
NGNLGINVTI
Sbjct: 181 NGNLGINVTIS 191
>pdb|2AN6|A Chain A, Protein-Peptide Complex
pdb|2AN6|B Chain B, Protein-Peptide Complex
pdb|2AN6|C Chain C, Protein-Peptide Complex
pdb|2AN6|D Chain D, Protein-Peptide Complex
Length = 191
Score = 334 bits (857), Expect = 3e-92, Method: Compositional matrix adjust.
Identities = 155/188 (82%), Positives = 169/188 (89%)
Query: 111 TMWFPCRYQMNGCGISLLHTEKPEHEDTCEHRPYLCPCPGASCKWGGALDQVMAHLNQSH 170
++ FPC+Y +GC I+L HTEK EHE+ CE RPY CPCPGASCKW G+LD VM HL H
Sbjct: 2 SVLFPCKYASSGCEITLPHTEKAEHEELCEFRPYSCPCPGASCKWQGSLDAVMPHLMHQH 61
Query: 171 KSITTLQGEDIVFLATDINLPGAVDWVMMQSCFGHHFMLVLEKQEKFDGHQHFFAIVQLI 230
KSITTLQGEDIVFLATDINLPGAVDWVMMQSCFG HFMLVLEKQEK+DGHQ FFAIVQLI
Sbjct: 62 KSITTLQGEDIVFLATDINLPGAVDWVMMQSCFGFHFMLVLEKQEKYDGHQQFFAIVQLI 121
Query: 231 GSRKQSENFTYRLELNGHRRRLTWEATPRSIHEGVASAIMNSDCLVFDTNIAQLFADNGN 290
G+RKQ+ENF YRLELNGHRRRLTWEATPRSIHEG+A+AIMNSDCLVFDT+IAQLFA+NGN
Sbjct: 122 GTRKQAENFAYRLELNGHRRRLTWEATPRSIHEGIATAIMNSDCLVFDTSIAQLFAENGN 181
Query: 291 LGINVTIG 298
LGINVTI
Sbjct: 182 LGINVTIS 189
>pdb|1K2F|A Chain A, Siah, Seven In Absentia Homolog
pdb|1K2F|B Chain B, Siah, Seven In Absentia Homolog
Length = 190
Score = 334 bits (857), Expect = 3e-92, Method: Compositional matrix adjust.
Identities = 155/188 (82%), Positives = 169/188 (89%)
Query: 111 TMWFPCRYQMNGCGISLLHTEKPEHEDTCEHRPYLCPCPGASCKWGGALDQVMAHLNQSH 170
++ FPC+Y +GC I+L HTEK EHE+ CE RPY CPCPGASCKW G+LD VM HL H
Sbjct: 1 SVLFPCKYASSGCEITLPHTEKAEHEELCEFRPYSCPCPGASCKWQGSLDAVMPHLMHQH 60
Query: 171 KSITTLQGEDIVFLATDINLPGAVDWVMMQSCFGHHFMLVLEKQEKFDGHQHFFAIVQLI 230
KSITTLQGEDIVFLATDINLPGAVDWVMMQSCFG HFMLVLEKQEK+DGHQ FFAIVQLI
Sbjct: 61 KSITTLQGEDIVFLATDINLPGAVDWVMMQSCFGFHFMLVLEKQEKYDGHQQFFAIVQLI 120
Query: 231 GSRKQSENFTYRLELNGHRRRLTWEATPRSIHEGVASAIMNSDCLVFDTNIAQLFADNGN 290
G+RKQ+ENF YRLELNGHRRRLTWEATPRSIHEG+A+AIMNSDCLVFDT+IAQLFA+NGN
Sbjct: 121 GTRKQAENFAYRLELNGHRRRLTWEATPRSIHEGIATAIMNSDCLVFDTSIAQLFAENGN 180
Query: 291 LGINVTIG 298
LGINVTI
Sbjct: 181 LGINVTIS 188
>pdb|4AUQ|B Chain B, Structure Of Birc7-Ubch5b-Ub Complex.
pdb|4AUQ|E Chain E, Structure Of Birc7-Ubch5b-Ub Complex
Length = 62
Score = 42.0 bits (97), Expect = 4e-04, Method: Composition-based stats.
Identities = 18/39 (46%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 59 CPVCFDYVLPPIIQCQSGHLVCSNCRPKLSCCPTCRGPL 97
C VC D + I+ GHLVC+ C P L CP CR P+
Sbjct: 16 CKVCLDRAVS-IVFVPCGHLVCAECAPGLQLCPICRAPV 53
>pdb|3EB5|A Chain A, Structure Of The Ciap2 Ring Domain
pdb|3EB6|A Chain A, Structure Of The Ciap2 Ring Domain Bound To Ubch5b
Length = 74
Score = 33.9 bits (76), Expect = 0.11, Method: Composition-based stats.
Identities = 19/47 (40%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 59 CPVCFDYVLPPIIQCQSGHLV-CSNCRPKLSCCPTCRGPL-GNIRNL 103
C VC D + I+ GHLV C +C P L CP CR + G +R
Sbjct: 27 CKVCMDKEVS-IVFIPCGHLVVCKDCAPSLRKCPICRSTIKGTVRTF 72
>pdb|3T6P|A Chain A, Iap Antagonist-Induced Conformational Change In Ciap1
Promotes E3 Ligase Activation Via Dimerization
Length = 345
Score = 33.9 bits (76), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 21/48 (43%), Positives = 25/48 (52%), Gaps = 5/48 (10%)
Query: 59 CPVCFDYVLPPI-IQCQSGHLV-CSNCRPKLSCCPTCRGPL-GNIRNL 103
C VC D + + I C GHLV C C P L CP CRG + G +R
Sbjct: 298 CKVCMDKEVSVVFIPC--GHLVVCQECAPSLRKCPICRGIIKGTVRTF 343
>pdb|2CKL|B Chain B, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 165
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 26/56 (46%), Gaps = 5/56 (8%)
Query: 53 LASLFECPVCFDYVLPPIIQCQSGHLVCSNC-----RPKLSCCPTCRGPLGNIRNL 103
L S CP+C D + + + H C++C R CPTCR L + R+L
Sbjct: 51 LHSELMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKRSL 106
>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 = 29.3 bits (64), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 204 GHHFMLVLEKQEKFDGHQHFFAI-VQLIGSRKQSENFTY 241
G FML+LEK+E+ DG + V+L+G +E TY
Sbjct: 296 GRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTY 334
>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 = 29.3 bits (64), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 204 GHHFMLVLEKQEKFDGHQHFFAI-VQLIGSRKQSENFTY 241
G FML+LEK+E+ DG + V+L+G +E TY
Sbjct: 296 GRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTY 334
>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 = 29.3 bits (64), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 204 GHHFMLVLEKQEKFDGHQHFFAI-VQLIGSRKQSENFTY 241
G FML+LEK+E+ DG + V+L+G +E TY
Sbjct: 278 GRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTY 316
>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 = 29.3 bits (64), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 204 GHHFMLVLEKQEKFDGHQHFFAI-VQLIGSRKQSENFTY 241
G FML+LEK+E+ DG + V+L+G +E TY
Sbjct: 282 GRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTY 320
>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 = 29.3 bits (64), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 204 GHHFMLVLEKQEKFDGHQHFFAI-VQLIGSRKQSENFTY 241
G FML+LEK+E+ DG + V+L+G +E TY
Sbjct: 281 GRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTY 319
>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 = 29.3 bits (64), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 204 GHHFMLVLEKQEKFDGHQHFFAI-VQLIGSRKQSENFTY 241
G FML+LEK+E+ DG + V+L+G +E TY
Sbjct: 297 GRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTY 335
>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 = 29.3 bits (64), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 204 GHHFMLVLEKQEKFDGHQHFFAI-VQLIGSRKQSENFTY 241
G FML+LEK+E+ DG + V+L+G +E TY
Sbjct: 297 GRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTY 335
>pdb|3E0C|A Chain A, Crystal Structure Of Dna Damage-Binding Protein 1(Ddb1)
Length = 1140
Score = 29.3 bits (64), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 204 GHHFMLVLEKQEKFDGHQHFFAI-VQLIGSRKQSENFTY 241
G FML+LEK+E+ DG + V+L+G +E TY
Sbjct: 278 GRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTY 316
>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 = 29.3 bits (64), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 204 GHHFMLVLEKQEKFDGHQHFFAI-VQLIGSRKQSENFTY 241
G FML+LEK+E+ DG + V+L+G +E TY
Sbjct: 288 GRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTY 326
>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 = 29.3 bits (64), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 204 GHHFMLVLEKQEKFDGHQHFFAI-VQLIGSRKQSENFTY 241
G FML+LEK+E+ DG + V+L+G +E TY
Sbjct: 297 GRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTY 335
>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 = 29.3 bits (64), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 204 GHHFMLVLEKQEKFDGHQHFFAI-VQLIGSRKQSENFTY 241
G FML+LEK+E+ DG + V+L+G +E TY
Sbjct: 297 GRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTY 335
>pdb|1JM7|A Chain A, Solution Structure Of The Brca1/bard1 Ring-domain
Heterodimer
Length = 112
Score = 28.9 bits (63), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 14/52 (26%), Positives = 24/52 (46%), Gaps = 8/52 (15%)
Query: 53 LASLFECPVCFDYVLPPIIQCQSGHLVCSNCRPKL-------SCCPTCRGPL 97
+ + ECP+C + + P + + H+ C C KL S CP C+ +
Sbjct: 18 MQKILECPICLELIKEP-VSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDI 68
>pdb|2H0D|B Chain B, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 100
Score = 28.5 bits (62), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 26/56 (46%), Gaps = 5/56 (8%)
Query: 53 LASLFECPVCFDYVLPPIIQCQSGHLVCSNC-----RPKLSCCPTCRGPLGNIRNL 103
L S CP+C D + + + H C++C R CPTCR L + R+L
Sbjct: 31 LHSELMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKRSL 86
>pdb|3RPG|C Chain C, Bmi1RING1B-Ubch5c Complex Structure
Length = 121
Score = 28.5 bits (62), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 26/56 (46%), Gaps = 5/56 (8%)
Query: 53 LASLFECPVCFDYVLPPIIQCQSGHLVCSNC-----RPKLSCCPTCRGPLGNIRNL 103
L S CP+C D + + + H C++C R CPTCR L + R+L
Sbjct: 50 LHSELMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKRSL 105
>pdb|2CT2|A Chain A, Solution Structure Of The Ring Domain Of The Tripartite
Motif Protein 32
Length = 88
Score = 27.3 bits (59), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 10/49 (20%)
Query: 47 AGTSTDLASL---FECPVCF-----DYVLPPIIQCQSGHLVCSNCRPKL 87
+G+S +L +L ECP+C + + P ++ C GH +C C KL
Sbjct: 3 SGSSGNLDALREVLECPICMESFTEEQLRPKLLHC--GHTICRQCLEKL 49
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
0.323 0.138 0.452
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,154,130
Number of Sequences: 62578
Number of extensions: 345556
Number of successful extensions: 577
Number of sequences better than 100.0: 37
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 31
Number of HSP's that attempted gapping in prelim test: 567
Number of HSP's gapped (non-prelim): 38
length of query: 300
length of database: 14,973,337
effective HSP length: 98
effective length of query: 202
effective length of database: 8,840,693
effective search space: 1785819986
effective search space used: 1785819986
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: 51 (24.3 bits)