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= psy7178
(154 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3N3K|A Chain A, The Catalytic Domain Of Usp8 In Complex With A Usp8
Specific Inhibitor
Length = 396
Score = 62.4 bits (150), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 31/92 (33%), Positives = 46/92 (50%), Gaps = 3/92 (3%)
Query: 65 GVCGLRNLGNTCFMSAGIQSLVAASALVEYFTN---XXXXXXXXXXXXXXXXVDEFALLV 121
+ GLRNLGNTC+M++ +Q L A L +YF +EF +++
Sbjct: 61 ALTGLRNLGNTCYMNSILQCLCNAPHLADYFNRNCYQDDINRSNLLGHKGEVAEEFGIIM 120
Query: 122 RKMWSGQYSIVHPSDFKQILGVHYPQFKDYRQ 153
+ +W+GQY + P DFK +G QF Y Q
Sbjct: 121 KALWTGQYRYISPKDFKITIGKINDQFAGYSQ 152
>pdb|2Y6E|A Chain A, Ubiquitin Specific Protease 4 Is Inhibited By Its
Ubiquitin- Like Domain
pdb|2Y6E|B Chain B, Ubiquitin Specific Protease 4 Is Inhibited By Its
Ubiquitin- Like Domain
pdb|2Y6E|C Chain C, Ubiquitin Specific Protease 4 Is Inhibited By Its
Ubiquitin- Like Domain
pdb|2Y6E|D Chain D, Ubiquitin Specific Protease 4 Is Inhibited By Its
Ubiquitin- Like Domain
pdb|2Y6E|E Chain E, Ubiquitin Specific Protease 4 Is Inhibited By Its
Ubiquitin- Like Domain
pdb|2Y6E|F Chain F, Ubiquitin Specific Protease 4 Is Inhibited By Its
Ubiquitin- Like Domain
Length = 367
Score = 59.3 bits (142), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 33/94 (35%), Positives = 48/94 (51%), Gaps = 3/94 (3%)
Query: 63 QRGVCGLRNLGNTCFMSAGIQSLVAASALVEYFTNXXXXXXXXXXX---XXXXXVDEFAL 119
Q G+CGL NLGNT FM++ +Q L + L +YF + +A
Sbjct: 5 QPGLCGLGNLGNTXFMNSALQCLSNTAPLTDYFLKDEYEAEINRDNPLGMKGEIAEAYAE 64
Query: 120 LVRKMWSGQYSIVHPSDFKQILGVHYPQFKDYRQ 153
L+++MWSG+ + V P FK +G PQF Y+Q
Sbjct: 65 LIKQMWSGRDAHVAPRMFKTQVGRFAPQFSGYQQ 98
>pdb|2GFO|A Chain A, Structure Of The Catalytic Domain Of Human Ubiquitin
Carboxyl-terminal Hydrolase 8
Length = 396
Score = 58.9 bits (141), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 30/92 (32%), Positives = 44/92 (47%), Gaps = 3/92 (3%)
Query: 65 GVCGLRNLGNTCFMSAGIQSLVAASALVEYFTN---XXXXXXXXXXXXXXXXVDEFALLV 121
+ GLRNLGNTC+ ++ +Q L A L +YF +EF ++
Sbjct: 61 ALTGLRNLGNTCYXNSILQCLCNAPHLADYFNRNCYQDDINRSNLLGHKGEVAEEFGIIX 120
Query: 122 RKMWSGQYSIVHPSDFKQILGVHYPQFKDYRQ 153
+ +W+GQY + P DFK +G QF Y Q
Sbjct: 121 KALWTGQYRYISPKDFKITIGKINDQFAGYSQ 152
>pdb|2IBI|A Chain A, Covalent Ubiquitin-Usp2 Complex
Length = 374
Score = 55.8 bits (133), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 34/104 (32%), Positives = 52/104 (50%), Gaps = 2/104 (1%)
Query: 52 SEDNDVSDNCAQRGVCGLRNLGNTCFMSAGIQSLVAASALVEY-FTNXXXXXXXXXXXXX 110
S D ++ + +G+ GLRNLGNTCFM++ +Q L L +Y
Sbjct: 21 SPGRDGMNSKSAQGLAGLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAH 80
Query: 111 XXXVDEFALLVRKMW-SGQYSIVHPSDFKQILGVHYPQFKDYRQ 153
V+EFA L++ +W S +V PS+FK + + P+F Y Q
Sbjct: 81 TALVEEFAKLIQTIWTSSPNDVVSPSEFKTQIQRYAPRFVGYNQ 124
>pdb|2HD5|A Chain A, Usp2 In Complex With Ubiquitin
Length = 359
Score = 55.5 bits (132), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 32/92 (34%), Positives = 47/92 (51%), Gaps = 2/92 (2%)
Query: 64 RGVCGLRNLGNTCFMSAGIQSLVAASALVEY-FTNXXXXXXXXXXXXXXXXVDEFALLVR 122
+G+ GLRNLGNTCFM++ +Q L L +Y V+EFA L++
Sbjct: 7 QGLAGLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQ 66
Query: 123 KMW-SGQYSIVHPSDFKQILGVHYPQFKDYRQ 153
+W S +V PS+FK + + P+F Y Q
Sbjct: 67 TIWTSSPNDVVSPSEFKTQIQRYAPRFVGYNQ 98
>pdb|3V6C|A Chain A, Crystal Structure Of Usp2 In Complex With Mutated
Ubiquitin
pdb|3V6E|A Chain A, Crystal Structure Of Usp2 And A Mutant Form Of Ubiquitin
Length = 367
Score = 55.5 bits (132), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 32/92 (34%), Positives = 47/92 (51%), Gaps = 2/92 (2%)
Query: 64 RGVCGLRNLGNTCFMSAGIQSLVAASALVEY-FTNXXXXXXXXXXXXXXXXVDEFALLVR 122
+G+ GLRNLGNTCFM++ +Q L L +Y V+EFA L++
Sbjct: 26 QGLAGLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQ 85
Query: 123 KMW-SGQYSIVHPSDFKQILGVHYPQFKDYRQ 153
+W S +V PS+FK + + P+F Y Q
Sbjct: 86 TIWTSSPNDVVSPSEFKTQIQRYAPRFVGYNQ 117
>pdb|3NHE|A Chain A, High Resolution Structure (1.26a) Of Usp2a In Complex With
Ubiquitin
Length = 348
Score = 51.6 bits (122), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 31/92 (33%), Positives = 46/92 (50%), Gaps = 2/92 (2%)
Query: 64 RGVCGLRNLGNTCFMSAGIQSLVAASALVEY-FTNXXXXXXXXXXXXXXXXVDEFALLVR 122
+G+ GLRNLGNT FM++ +Q L L +Y V+EFA L++
Sbjct: 7 QGLAGLRNLGNTXFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQ 66
Query: 123 KMW-SGQYSIVHPSDFKQILGVHYPQFKDYRQ 153
+W S +V PS+FK + + P+F Y Q
Sbjct: 67 TIWTSSPNDVVSPSEFKTQIQRYAPRFVGYNQ 98
>pdb|3I3T|A Chain A, Crystal Structure Of Covalent Ubiquitin-usp21 Complex
pdb|3I3T|C Chain C, Crystal Structure Of Covalent Ubiquitin-usp21 Complex
pdb|3I3T|E Chain E, Crystal Structure Of Covalent Ubiquitin-usp21 Complex
pdb|3I3T|G Chain G, Crystal Structure Of Covalent Ubiquitin-usp21 Complex
Length = 355
Score = 44.3 bits (103), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/90 (27%), Positives = 40/90 (44%), Gaps = 1/90 (1%)
Query: 65 GVCGLRNLGNTCFMSAGIQSLVAASALVEYFTNXXXXXXXXXXXXXXXXVDEFALLVRKM 124
G GLRNLGNTCF++A +Q L + L ++ + FA ++ +
Sbjct: 2 GHVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQELTEAFADVIGAL 61
Query: 125 WS-GQYSIVHPSDFKQILGVHYPQFKDYRQ 153
W V+P+ F+ + + P F Y Q
Sbjct: 62 WHPDSCEAVNPTRFRAVFQKYVPSFSGYSQ 91
>pdb|3MTN|A Chain A, Usp21 In Complex With A Ubiquitin-based, Usp21-specific
Inhibitor
pdb|3MTN|C Chain C, Usp21 In Complex With A Ubiquitin-based, Usp21-specific
Inhibitor
Length = 373
Score = 44.3 bits (103), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/90 (27%), Positives = 40/90 (44%), Gaps = 1/90 (1%)
Query: 65 GVCGLRNLGNTCFMSAGIQSLVAASALVEYFTNXXXXXXXXXXXXXXXXVDEFALLVRKM 124
G GLRNLGNTCF++A +Q L + L ++ + FA ++ +
Sbjct: 21 GHVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQELTEAFADVIGAL 80
Query: 125 WS-GQYSIVHPSDFKQILGVHYPQFKDYRQ 153
W V+P+ F+ + + P F Y Q
Sbjct: 81 WHPDSCEAVNPTRFRAVFQKYVPSFSGYSQ 110
>pdb|2Y5B|A Chain A, Structure Of Usp21 In Complex With Linear
Diubiquitin-Aldehyde
pdb|2Y5B|E Chain E, Structure Of Usp21 In Complex With Linear
Diubiquitin-Aldehyde
Length = 370
Score = 44.3 bits (103), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/90 (27%), Positives = 40/90 (44%), Gaps = 1/90 (1%)
Query: 65 GVCGLRNLGNTCFMSAGIQSLVAASALVEYFTNXXXXXXXXXXXXXXXXVDEFALLVRKM 124
G GLRNLGNTCF++A +Q L + L ++ + FA ++ +
Sbjct: 15 GHVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQELTEAFADVIGAL 74
Query: 125 WS-GQYSIVHPSDFKQILGVHYPQFKDYRQ 153
W V+P+ F+ + + P F Y Q
Sbjct: 75 WHPDSCEAVNPTRFRAVFQKYVPSFSGYSQ 104
>pdb|2AYN|A Chain A, Structure Of Usp14, A Proteasome-Associated
Deubiquitinating Enzyme
pdb|2AYN|B Chain B, Structure Of Usp14, A Proteasome-Associated
Deubiquitinating Enzyme
pdb|2AYN|C Chain C, Structure Of Usp14, A Proteasome-Associated
Deubiquitinating Enzyme
pdb|2AYO|A Chain A, Structure Of Usp14 Bound To Ubquitin Aldehyde
Length = 404
Score = 34.7 bits (78), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 13/25 (52%), Positives = 18/25 (72%)
Query: 67 CGLRNLGNTCFMSAGIQSLVAASAL 91
CGL NLGNTC+M+A +Q + + L
Sbjct: 15 CGLTNLGNTCYMNATVQCIRSVPEL 39
>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
Length = 854
Score = 33.1 bits (74), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 25/110 (22%), Positives = 42/110 (38%), Gaps = 21/110 (19%)
Query: 65 GVCGLRNLGNTCFMSAGIQSLVAASAL-VEYFTNXXXXXXXXXXXXXXXXVDEFALLVRK 123
G G+RNLGN+C++++ +Q L + +Y + A L
Sbjct: 343 GYTGIRNLGNSCYLNSVVQVLFSIPDFQRKYVDKLEKIFQNAPTDPTQDFSTQVAKLGHG 402
Query: 124 MWSGQYSI--------------------VHPSDFKQILGVHYPQFKDYRQ 153
+ SG+YS + P FK ++G +P+F RQ
Sbjct: 403 LLSGEYSKPVPESGDGERVPEQKEVQDGIAPRMFKALIGKGHPEFSTNRQ 452
>pdb|4FIP|A Chain A, Structure Of The Saga Ubp8(S144n)SGF11(1-72,
Delta-Znf)SUS1SGF73 Dub Module
pdb|4FIP|E Chain E, Structure Of The Saga Ubp8(S144n)SGF11(1-72,
Delta-Znf)SUS1SGF73 Dub Module
pdb|4FK5|A Chain A, Structure Of The Saga Ubp8(S144n)SGF11SUS1SGF73 DUB MODULE
Length = 476
Score = 32.7 bits (73), Expect = 0.081, Method: Composition-based stats.
Identities = 13/22 (59%), Positives = 18/22 (81%)
Query: 65 GVCGLRNLGNTCFMSAGIQSLV 86
G+ GL N+GNTCFMS+ +Q L+
Sbjct: 140 GLSGLINMGNTCFMSSILQCLI 161
>pdb|3MHH|A Chain A, Structure Of The Saga Ubp8SGF11SUS1SGF73 DUB MODULE
pdb|3MHS|A Chain A, Structure Of The Saga Ubp8SGF11SUS1SGF73 DUB MODULE BOUND
Ubiquitin Aldehyde
pdb|4FJC|A Chain A, Structure Of The Saga Ubp8SGF11(1-72, Delta-Znf)SUS1SGF73
DUB Module
pdb|4FJC|E Chain E, Structure Of The Saga Ubp8SGF11(1-72, Delta-Znf)SUS1SGF73
DUB Module
Length = 476
Score = 30.8 bits (68), Expect = 0.34, Method: Composition-based stats.
Identities = 12/22 (54%), Positives = 18/22 (81%)
Query: 65 GVCGLRNLGNTCFMSAGIQSLV 86
G+ GL N+G+TCFMS+ +Q L+
Sbjct: 140 GLSGLINMGSTCFMSSILQCLI 161
>pdb|3M99|A Chain A, Structure Of The Ubp8-Sgf11-Sgf73-Sus1 Saga Dub Module
Length = 471
Score = 30.8 bits (68), Expect = 0.34, Method: Composition-based stats.
Identities = 12/22 (54%), Positives = 18/22 (81%)
Query: 65 GVCGLRNLGNTCFMSAGIQSLV 86
G+ GL N+G+TCFMS+ +Q L+
Sbjct: 135 GLSGLINMGSTCFMSSILQCLI 156
>pdb|1VJV|A Chain A, Crystal Structure Of Ubiquitin Carboxyl-terminal
Hydrolase 6 (yfr010w) From Saccharomyces Cerevisiae At
1.74 A Resolution
Length = 415
Score = 30.4 bits (67), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 19/31 (61%)
Query: 67 CGLRNLGNTCFMSAGIQSLVAASALVEYFTN 97
G +N GNTC+++A +Q+L + L + N
Sbjct: 25 VGFKNXGNTCYLNATLQALYRVNDLRDXILN 55
>pdb|2F1Z|A Chain A, Crystal Structure Of Hausp
pdb|2F1Z|B Chain B, Crystal Structure Of Hausp
Length = 522
Score = 30.4 bits (67), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 5/65 (7%)
Query: 32 SDVCEGPENFTGELSSLFEISEDNDVS-----DNCAQRGVCGLRNLGNTCFMSAGIQSLV 86
S+V + + F + FE+ D D+ G GL+N G TC+M++ +Q+L
Sbjct: 136 SEVTDPEKGFIDDDKVTFEVFVQADAPHGVAWDSKKHTGYVGLKNQGATCYMNSLLQTLF 195
Query: 87 AASAL 91
+ L
Sbjct: 196 FTNQL 200
>pdb|1NBF|A Chain A, Crystal Structure Of A Ubp-Family Deubiquitinating
Enzyme In Isolation And In Complex With Ubiquitin
Aldehyde
pdb|1NBF|B Chain B, Crystal Structure Of A Ubp-Family Deubiquitinating
Enzyme In Isolation And In Complex With Ubiquitin
Aldehyde
pdb|1NBF|E Chain E, Crystal Structure Of A Ubp-Family Deubiquitinating
Enzyme In Isolation And In Complex With Ubiquitin
Aldehyde
Length = 353
Score = 28.9 bits (63), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 11/27 (40%), Positives = 18/27 (66%)
Query: 65 GVCGLRNLGNTCFMSAGIQSLVAASAL 91
G GL+N G TC+M++ +Q+L + L
Sbjct: 5 GYVGLKNQGATCYMNSLLQTLFFTNQL 31
>pdb|3GEH|A Chain A, Crystal Structure Of Mnme From Nostoc In Complex With Gdp,
Folinic Acid And Zn
Length = 462
Score = 28.9 bits (63), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 16/74 (21%), Positives = 29/74 (39%)
Query: 11 ECFSTASAASSFPIPLPPPTSSDVCEGPENFTGELSSLFEISEDNDVSDNCAQRGVCGLR 70
+ + A F LPP + EN E+S L + ++ + + G
Sbjct: 174 DILAEIEARIDFEEDLPPLDDEAIISDIENIAAEISQLLATKDKGELLRTGLKVAIVGRP 233
Query: 71 NLGNTCFMSAGIQS 84
N+G + ++A QS
Sbjct: 234 NVGKSSLLNAWSQS 247
>pdb|4AAY|A Chain A, Crystal Structure Of The Arsenite Oxidase Protein Complex
From Rhizobium Species Strain Nt-26
pdb|4AAY|C Chain C, Crystal Structure Of The Arsenite Oxidase Protein Complex
From Rhizobium Species Strain Nt-26
pdb|4AAY|E Chain E, Crystal Structure Of The Arsenite Oxidase Protein Complex
From Rhizobium Species Strain Nt-26
pdb|4AAY|G Chain G, Crystal Structure Of The Arsenite Oxidase Protein Complex
From Rhizobium Species Strain Nt-26
Length = 845
Score = 26.2 bits (56), Expect = 8.8, Method: Composition-based stats.
Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 3/73 (4%)
Query: 2 GIENTWSQDECFSTASAASSFPIPLPPPTSSDVCEGPENFTGELSSLFEISEDNDVSDNC 61
G ENTW + + A + I P +S+V + GEL++ + ED +++D
Sbjct: 176 GYENTWGTGKLYFEAMKVKNIRIHNRPAYNSEVHGTRDMGVGELNNCY---EDAELADTI 232
Query: 62 AQRGVCGLRNLGN 74
G L N
Sbjct: 233 VAVGTNALETQTN 245
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 0.133 0.408
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,094,466
Number of Sequences: 62578
Number of extensions: 124380
Number of successful extensions: 225
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 20
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 195
Number of HSP's gapped (non-prelim): 20
length of query: 154
length of database: 14,973,337
effective HSP length: 90
effective length of query: 64
effective length of database: 9,341,317
effective search space: 597844288
effective search space used: 597844288
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: 47 (22.7 bits)