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= 008156
(576 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 = 70.1 bits (170), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 86/340 (25%), Positives = 132/340 (38%), Gaps = 99/340 (29%)
Query: 74 VPGLQNLGNNCFLNVILQALASCTCFLPFLQKVMGE-CEEPDEDLP-LTVALASLLEELC 131
+ GL+NLGN C++N ILQ C C P L C + D + L + EE
Sbjct: 62 LTGLRNLGNTCYMNSILQ----CLCNAPHLADYFNRNCYQDDINRSNLLGHKGEVAEEFG 117
Query: 132 LV------GETRLVLSPQKVMLAMELYIQNFNLTSQQDAEEAFLHLMSSLREEFLES--- 182
++ G+ R + SP+ + + F SQQD++E L LM L E+ ++
Sbjct: 118 IIMKALWTGQYRYI-SPKDFKITIGKINDQFAGYSQQDSQELLLFLMDGLHEDLNKADNR 176
Query: 183 --YSPNESSLVDAFEAASCRILSLKRREVQSEQKRWRKH-------FFGPFDGILGSILT 233
Y + +D F+AA + W+KH F G S +
Sbjct: 177 KRYKEENNDHLDDFKAA---------------EHAWQKHKQLNESIIVALFQGQFKSTVQ 221
Query: 234 CQSCLSQISLDYQFFH-SLPLSPVLDSGSTIPFGCTLEDCLKQFLTAEQLEN---YHCSH 289
C +C + F + SLPL+ CTL+DCL+ F E+L + ++CSH
Sbjct: 222 CLTCHKKSRTFEAFMYLSLPLASTSK--------CTLQDCLRLFSKEEKLTDNNRFYCSH 273
Query: 290 CWHIAAIKYLSITEANEMEIEELRRCSAQDSCNCRSRLHLETLPWSNKFSHTLKKLSISH 349
CR+R +LKK+ I
Sbjct: 274 ---------------------------------CRAR------------RDSLKKIEIWK 288
Query: 350 CPQILCIHLQRVSINEMGELVKIWGHIAFPL-ILDLFPFV 388
P +L +HL+R S + + K+ + FPL LDL +V
Sbjct: 289 LPPVLLVHLKRFSYDGRWK-QKLQTSVDFPLENLDLSQYV 327
Score = 29.3 bits (64), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 18/37 (48%), Gaps = 7/37 (18%)
Query: 501 YRLASVVEHFGRVGSGHYTVY-------RSVRVESHE 530
Y L SV H+G + GHYT Y R + + HE
Sbjct: 337 YNLFSVSNHYGGLDGGHYTAYCKNAARQRWFKFDDHE 373
>pdb|2GFO|A Chain A, Structure Of The Catalytic Domain Of Human Ubiquitin
Carboxyl-terminal Hydrolase 8
Length = 396
Score = 65.9 bits (159), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 85/340 (25%), Positives = 130/340 (38%), Gaps = 99/340 (29%)
Query: 74 VPGLQNLGNNCFLNVILQALASCTCFLPFLQKVMGE-CEEPDEDLP-LTVALASLLEELC 131
+ GL+NLGN C+ N ILQ C C P L C + D + L + EE
Sbjct: 62 LTGLRNLGNTCYXNSILQ----CLCNAPHLADYFNRNCYQDDINRSNLLGHKGEVAEEFG 117
Query: 132 LV------GETRLVLSPQKVMLAMELYIQNFNLTSQQDAEEAFLHLMSSLREEFLES--- 182
++ G+ R + SP+ + + F SQQD++E L L L E+ ++
Sbjct: 118 IIXKALWTGQYRYI-SPKDFKITIGKINDQFAGYSQQDSQELLLFLXDGLHEDLNKADNR 176
Query: 183 --YSPNESSLVDAFEAASCRILSLKRREVQSEQKRWRKH-------FFGPFDGILGSILT 233
Y + +D F+AA + W+KH F G S +
Sbjct: 177 KRYKEENNDHLDDFKAA---------------EHAWQKHKQLNESIIVALFQGQFKSTVQ 221
Query: 234 CQSCLSQISLDYQFFH-SLPLSPVLDSGSTIPFGCTLEDCLKQFLTAEQLEN---YHCSH 289
C +C + F + SLPL+ CTL+DCL+ F E+L + ++CSH
Sbjct: 222 CLTCHKKSRTFEAFXYLSLPLASTSK--------CTLQDCLRLFSKEEKLTDNNRFYCSH 273
Query: 290 CWHIAAIKYLSITEANEMEIEELRRCSAQDSCNCRSRLHLETLPWSNKFSHTLKKLSISH 349
CR+R +LKK+ I
Sbjct: 274 ---------------------------------CRAR------------RDSLKKIEIWK 288
Query: 350 CPQILCIHLQRVSINEMGELVKIWGHIAFPL-ILDLFPFV 388
P +L +HL+R S + + K+ + FPL LDL +V
Sbjct: 289 LPPVLLVHLKRFSYDGRWK-QKLQTSVDFPLENLDLSQYV 327
Score = 29.3 bits (64), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 18/37 (48%), Gaps = 7/37 (18%)
Query: 501 YRLASVVEHFGRVGSGHYTVY-------RSVRVESHE 530
Y L SV H+G + GHYT Y R + + HE
Sbjct: 337 YNLFSVSNHYGGLDGGHYTAYCKNAARQRWFKFDDHE 373
>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 = 61.2 bits (147), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 81/321 (25%), Positives = 123/321 (38%), Gaps = 65/321 (20%)
Query: 76 GLQNLGNNCFLNVILQALASCTCFLPFLQKVMGECEEPDEDLP--LTVALASLLEELCLV 133
GL+NLGN CFLN +LQ L+S F + E P LT A A ++ L
Sbjct: 24 GLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQELTEAFADVIGALWHP 83
Query: 134 GETRLVLSPQKVMLAMELYIQNFNLTSQQDAEEAFLHLMSSLREEFLESYSPNESSLVDA 193
V +P + + Y+ +F+ SQQDA+E LM L E L +
Sbjct: 84 DSCEAV-NPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRAPPILANG 142
Query: 194 FEAASCRILS--LKRREVQSEQKR---WRKHF-------FGPFDGILGSILTCQSCLSQI 241
+ R L+ E+ + + W+++ F G L S L CQ+C
Sbjct: 143 PVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKCQAC-GYR 201
Query: 242 SLDYQFF--HSLPLSPVLDSGSTIPFGCTLEDCLKQFLTAEQLENYHCSHCWHIAAIKYL 299
S ++ F SLP+ +G + +L DC F E+LE+ + C
Sbjct: 202 STTFEVFCDLSLPIPKKGFAGGKV----SLRDCFNLFTKEEELESENAPVC--------- 248
Query: 300 SITEANEMEIEELRRCSAQDSCNCRSRLHLETLPWSNKFSHTLKKLSISHCPQILCIHLQ 359
D C ++R + KKL++ P+IL +HL
Sbjct: 249 -------------------DRCRQKTR--------------STKKLTVQRFPRILVLHLN 275
Query: 360 RVSINEMGELVKIWGHIAFPL 380
R S + G + K + FPL
Sbjct: 276 RFSASR-GSIKKSSVGVDFPL 295
Score = 35.8 bits (81), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 36/76 (47%), Gaps = 16/76 (21%)
Query: 500 LYRLASVVEHFGRVGSGHYTVYRSVRVESHEENPNEHFETPLTHWFCISDSQVYSVSVND 559
+Y+L ++ H G V GHYT R + T W +DS+V VS N
Sbjct: 312 VYQLYALCNHSGSVHYGHYTAL--CRCQ--------------TGWHVYNDSRVSPVSENQ 355
Query: 560 VLAAEASLLFYERIIE 575
V ++E +LFY+ + E
Sbjct: 356 VASSEGYVLFYQLMQE 371
>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 = 60.8 bits (146), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 81/321 (25%), Positives = 123/321 (38%), Gaps = 65/321 (20%)
Query: 76 GLQNLGNNCFLNVILQALASCTCFLPFLQKVMGECEEP--DEDLPLTVALASLLEELCLV 133
GL+NLGN CFLN +LQ L+S F + E P LT A A ++ L
Sbjct: 5 GLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQELTEAFADVIGALWHP 64
Query: 134 GETRLVLSPQKVMLAMELYIQNFNLTSQQDAEEAFLHLMSSLREEFLESYSPNESSLVDA 193
V +P + + Y+ +F+ SQQDA+E LM L E L +
Sbjct: 65 DSCEAV-NPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRAPPILANG 123
Query: 194 FEAASCRILS--LKRREVQSEQKR---WRKHF-------FGPFDGILGSILTCQSCLSQI 241
+ R L+ E+ + + W+++ F G L S L CQ+C
Sbjct: 124 PVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKCQAC-GYR 182
Query: 242 SLDYQFF--HSLPLSPVLDSGSTIPFGCTLEDCLKQFLTAEQLENYHCSHCWHIAAIKYL 299
S ++ F SLP+ +G + +L DC F E+LE+ + C
Sbjct: 183 STTFEVFCDLSLPIPKKGFAGGKV----SLRDCFNLFTKEEELESENAPVC--------- 229
Query: 300 SITEANEMEIEELRRCSAQDSCNCRSRLHLETLPWSNKFSHTLKKLSISHCPQILCIHLQ 359
D C ++R + KKL++ P+IL +HL
Sbjct: 230 -------------------DRCRQKTR--------------STKKLTVQRFPRILVLHLN 256
Query: 360 RVSINEMGELVKIWGHIAFPL 380
R S + G + K + FPL
Sbjct: 257 RFSASR-GSIKKSSVGVDFPL 276
Score = 35.8 bits (81), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 36/76 (47%), Gaps = 16/76 (21%)
Query: 500 LYRLASVVEHFGRVGSGHYTVYRSVRVESHEENPNEHFETPLTHWFCISDSQVYSVSVND 559
+Y+L ++ H G V GHYT R + T W +DS+V VS N
Sbjct: 293 VYQLYALCNHSGSVHYGHYTAL--CRCQ--------------TGWHVYNDSRVSPVSENQ 336
Query: 560 VLAAEASLLFYERIIE 575
V ++E +LFY+ + E
Sbjct: 337 VASSEGYVLFYQLMQE 352
>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 = 60.5 bits (145), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 81/321 (25%), Positives = 123/321 (38%), Gaps = 65/321 (20%)
Query: 76 GLQNLGNNCFLNVILQALASCTCFLPFLQKVMGECEEP--DEDLPLTVALASLLEELCLV 133
GL+NLGN CFLN +LQ L+S F + E P LT A A ++ L
Sbjct: 18 GLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQELTEAFADVIGALWHP 77
Query: 134 GETRLVLSPQKVMLAMELYIQNFNLTSQQDAEEAFLHLMSSLREEFLESYSPNESSLVDA 193
V +P + + Y+ +F+ SQQDA+E LM L E L +
Sbjct: 78 DSCEAV-NPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRAPPILANG 136
Query: 194 FEAASCRILS--LKRREVQSEQKR---WRKHF-------FGPFDGILGSILTCQSCLSQI 241
+ R L+ E+ + + W+++ F G L S L CQ+C
Sbjct: 137 PVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKCQAC-GYR 195
Query: 242 SLDYQFF--HSLPLSPVLDSGSTIPFGCTLEDCLKQFLTAEQLENYHCSHCWHIAAIKYL 299
S ++ F SLP+ +G + +L DC F E+LE+ + C
Sbjct: 196 STTFEVFCDLSLPIPKKGFAGGKV----SLRDCFNLFTKEEELESENAPVC--------- 242
Query: 300 SITEANEMEIEELRRCSAQDSCNCRSRLHLETLPWSNKFSHTLKKLSISHCPQILCIHLQ 359
D C ++R + KKL++ P+IL +HL
Sbjct: 243 -------------------DRCRQKTR--------------STKKLTVQRFPRILVLHLN 269
Query: 360 RVSINEMGELVKIWGHIAFPL 380
R S + G + K + FPL
Sbjct: 270 RFSASR-GSIKKSSVGVDFPL 289
Score = 35.8 bits (81), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 36/76 (47%), Gaps = 16/76 (21%)
Query: 500 LYRLASVVEHFGRVGSGHYTVYRSVRVESHEENPNEHFETPLTHWFCISDSQVYSVSVND 559
+Y+L ++ H G V GHYT R + T W +DS+V VS N
Sbjct: 306 VYQLYALCNHSGSVHYGHYTAL--CRCQ--------------TGWHVYNDSRVSPVSENQ 349
Query: 560 VLAAEASLLFYERIIE 575
V ++E +LFY+ + E
Sbjct: 350 VASSEGYVLFYQLMQE 365
>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 = 52.4 bits (124), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 78/321 (24%), Positives = 122/321 (38%), Gaps = 57/321 (17%)
Query: 21 FLPHMKWVSASGLLGILGVAGFVLALKKDAKIGNLS--GFSWLSEKENRLEKLCLVP--- 75
FL H K + + GI G + K + IGN+ + L++ + + +VP
Sbjct: 79 FLSHSKQIGH--IFGINSNNGLLFCFKCEDYIGNIDLINDAILAKYWDDVCTKTMVPSME 136
Query: 76 ------GLQNLGNNCFLNVILQALASCTCFL--PFLQKVMGECEEPDEDLPLTVALASLL 127
GL N+GN CF++ ILQ L F+ Q C+ D + AL ++
Sbjct: 137 RRDGLSGLINMGNTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIV 196
Query: 128 EELCLVGETRLVLSPQKVMLAMELYI----------QNFNLTSQQDAEEAFLHLMSSLRE 177
EL T+ S +I QN SQQDA E + +++ + +
Sbjct: 197 HELYGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQ 256
Query: 178 EFLESYSPNESSLVDAF-EAASCRILSLKRREVQSEQKRWRKHFFGPFDGILGSILTCQS 236
++ PN + A + C + ++ F+G L S + C
Sbjct: 257 SYVLDL-PNAKEVSRANNKQCECIVHTV-------------------FEGSLESSIVCPG 296
Query: 237 CLSQISLDYQFFHSLPLSPVLDSGSTIPFGCTLEDCLKQFLTAEQLE--NYHCSHCWHIA 294
C Q + P LD I L +CL F EQL+ NYHC C
Sbjct: 297 C--------QNNSKTTIDPFLDLSLDIKDKKKLYECLDSFHKKEQLKDFNYHCGECNSTQ 348
Query: 295 -AIKYLSITEANEMEIEELRR 314
AIK L I + + + +L+R
Sbjct: 349 DAIKQLGIHKLPSVLVLQLKR 369
Score = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 31/71 (43%), Gaps = 15/71 (21%)
Query: 500 LYRLASVVEHFGRVGSGHYTVYRSVRVESHEENPNEHFETPLTHWFCISDSQVYSVSVND 559
+Y L +V H G V GHY + + WF +DS V S+S +
Sbjct: 415 IYELIGIVSHKGTVNEGHYIAFCKISG---------------GQWFKFNDSMVSSISQEE 459
Query: 560 VLAAEASLLFY 570
VL +A LLFY
Sbjct: 460 VLKEQAYLLFY 470
>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 = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 62/268 (23%), Positives = 103/268 (38%), Gaps = 40/268 (14%)
Query: 76 GLQNLGNNCFLNVILQALASCTCFLPFLQKVMGECEEPDEDLPLTV------ALASLLEE 129
GL NLGN F+N LQ L++ + K E E + D PL + A A L+++
Sbjct: 10 GLGNLGNTXFMNSALQCLSNTAPLTDYFLKDEYEA-EINRDNPLGMKGEIAEAYAELIKQ 68
Query: 130 LCLVGETRLVLSPQKVMLAMELYIQNFNLTSQQDAEEAFLHLMSSLREEFLESYSPNESS 189
+ + ++P+ + + F+ QQD++E L+ L E+
Sbjct: 69 MWSGRDAH--VAPRMFKTQVGRFAPQFSGYQQQDSQELLAFLLDGLHEDLNRVKKKPYLE 126
Query: 190 LVDAFEAASCRILSLKRREVQSEQKRWRKH-------FFGPFDGILGSILTCQSCLS-QI 241
L DA R + ++ W H F G+ S L C C +
Sbjct: 127 LKDAN----------GRPDAVVAKEAWENHRLRNDSVIVDTFHGLFKSTLVCPECAKVSV 176
Query: 242 SLDYQFFHSLPL---------SPVLDSGSTIPFGCTLEDCLKQFLTAEQL---ENYHCSH 289
+ D + +LPL P+L L DC++ F T E L + ++C +
Sbjct: 177 TFDPFCYLTLPLPLKKDRVMEGPMLQPQKKKKTTVALRDCIELFTTMETLGEHDPWYCPN 236
Query: 290 C-WHIAAIKYLSITEANEMEIEELRRCS 316
C H A K + ++ + L+R S
Sbjct: 237 CKKHQQATKKFDLWSLPKILVVHLKRFS 264
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 34/74 (45%), Gaps = 14/74 (18%)
Query: 499 YLYRLASVVEHFGRVGSGHYTVYRSVRVESHEENPNEHFETPLTHWFCISDSQVYSVSVN 558
Y+Y L +V H+G +G GHYT Y ++ W+ DS V S +
Sbjct: 298 YVYDLIAVSNHYGAMGVGHYTAYAKNKLNG--------------KWYYFDDSNVSLASED 343
Query: 559 DVLAAEASLLFYER 572
++ A +LFY+R
Sbjct: 344 QIVTKAAYVLFYQR 357
>pdb|3M99|A Chain A, Structure Of The Ubp8-Sgf11-Sgf73-Sus1 Saga Dub Module
Length = 471
Score = 50.1 bits (118), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 77/321 (23%), Positives = 122/321 (38%), Gaps = 57/321 (17%)
Query: 21 FLPHMKWVSASGLLGILGVAGFVLALKKDAKIGNLS--GFSWLSEKENRLEKLCLVP--- 75
FL H K + + GI G + K + IGN+ + L++ + + +VP
Sbjct: 74 FLSHSKQIGH--IFGINSNNGLLFCFKCEDYIGNIDLINDAILAKYWDDVCTKTMVPSME 131
Query: 76 ------GLQNLGNNCFLNVILQALASCTCFL--PFLQKVMGECEEPDEDLPLTVALASLL 127
GL N+G+ CF++ ILQ L F+ Q C+ D + AL ++
Sbjct: 132 RRDGLSGLINMGSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIV 191
Query: 128 EELCLVGETRLVLSPQKVMLAMELYI----------QNFNLTSQQDAEEAFLHLMSSLRE 177
EL T+ S +I QN SQQDA E + +++ + +
Sbjct: 192 HELYGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQ 251
Query: 178 EFLESYSPNESSLVDAF-EAASCRILSLKRREVQSEQKRWRKHFFGPFDGILGSILTCQS 236
++ PN + A + C + ++ F+G L S + C
Sbjct: 252 SYVLDL-PNAKEVSRANNKQCECIVHTV-------------------FEGSLESSIVCPG 291
Query: 237 CLSQISLDYQFFHSLPLSPVLDSGSTIPFGCTLEDCLKQFLTAEQLE--NYHCSHCWHIA 294
C Q + P LD I L +CL F EQL+ NYHC C
Sbjct: 292 C--------QNNSKTTIDPFLDLSLDIKDKKKLYECLDSFHKKEQLKDFNYHCGECNSTQ 343
Query: 295 -AIKYLSITEANEMEIEELRR 314
AIK L I + + + +L+R
Sbjct: 344 DAIKQLGIHKLPSVLVLQLKR 364
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 31/71 (43%), Gaps = 15/71 (21%)
Query: 500 LYRLASVVEHFGRVGSGHYTVYRSVRVESHEENPNEHFETPLTHWFCISDSQVYSVSVND 559
+Y L +V H G V GHY + + WF +DS V S+S +
Sbjct: 410 IYELIGIVSHKGTVNEGHYIAFCKISG---------------GQWFKFNDSMVSSISQEE 454
Query: 560 VLAAEASLLFY 570
VL +A LLFY
Sbjct: 455 VLKEQAYLLFY 465
>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 = 50.1 bits (118), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 77/321 (23%), Positives = 122/321 (38%), Gaps = 57/321 (17%)
Query: 21 FLPHMKWVSASGLLGILGVAGFVLALKKDAKIGNLS--GFSWLSEKENRLEKLCLVP--- 75
FL H K + + GI G + K + IGN+ + L++ + + +VP
Sbjct: 79 FLSHSKQIGH--IFGINSNNGLLFCFKCEDYIGNIDLINDAILAKYWDDVCTKTMVPSME 136
Query: 76 ------GLQNLGNNCFLNVILQALASCTCFL--PFLQKVMGECEEPDEDLPLTVALASLL 127
GL N+G+ CF++ ILQ L F+ Q C+ D + AL ++
Sbjct: 137 RRDGLSGLINMGSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIV 196
Query: 128 EELCLVGETRLVLSPQKVMLAMELYI----------QNFNLTSQQDAEEAFLHLMSSLRE 177
EL T+ S +I QN SQQDA E + +++ + +
Sbjct: 197 HELYGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQ 256
Query: 178 EFLESYSPNESSLVDAF-EAASCRILSLKRREVQSEQKRWRKHFFGPFDGILGSILTCQS 236
++ PN + A + C + ++ F+G L S + C
Sbjct: 257 SYVLDL-PNAKEVSRANNKQCECIVHTV-------------------FEGSLESSIVCPG 296
Query: 237 CLSQISLDYQFFHSLPLSPVLDSGSTIPFGCTLEDCLKQFLTAEQLE--NYHCSHCWHIA 294
C Q + P LD I L +CL F EQL+ NYHC C
Sbjct: 297 C--------QNNSKTTIDPFLDLSLDIKDKKKLYECLDSFHKKEQLKDFNYHCGECNSTQ 348
Query: 295 -AIKYLSITEANEMEIEELRR 314
AIK L I + + + +L+R
Sbjct: 349 DAIKQLGIHKLPSVLVLQLKR 369
Score = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 31/71 (43%), Gaps = 15/71 (21%)
Query: 500 LYRLASVVEHFGRVGSGHYTVYRSVRVESHEENPNEHFETPLTHWFCISDSQVYSVSVND 559
+Y L +V H G V GHY + + WF +DS V S+S +
Sbjct: 415 IYELIGIVSHKGTVNEGHYIAFCKISG---------------GQWFKFNDSMVSSISQEE 459
Query: 560 VLAAEASLLFY 570
VL +A LLFY
Sbjct: 460 VLKEQAYLLFY 470
>pdb|2IBI|A Chain A, Covalent Ubiquitin-Usp2 Complex
Length = 374
Score = 46.6 bits (109), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 82/329 (24%), Positives = 123/329 (37%), Gaps = 80/329 (24%)
Query: 76 GLQNLGNNCFLNVILQALASCTCFLPF-LQKV-MGECEEPDEDLPLTVALASLLEELCLV 133
GL+NLGN CF+N ILQ L++ + LQ++ M + A +L+EE +
Sbjct: 37 GLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSN------AHTALVEEFAKL 90
Query: 134 GET------RLVLSPQKVMLAMELYIQNFNLTSQQDAEEAFLHLMSSLREEFLESYSPNE 187
+T V+SP + ++ Y F +QQDA+E L+ L E N
Sbjct: 91 IQTIWTSSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEV------NR 144
Query: 188 SSLVDAFEAASCRILSLKRREVQSEQKRWRKHF------FGP-FDGILGSILTCQSCLSQ 240
+L + L + + ++ WRK+ G F G L S LTC C
Sbjct: 145 VTLRPKSNPENLDHLP----DDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDC-GY 199
Query: 241 ISLDYQFFHSLPLSPVLDSGSTIPFGCTLEDCLKQFLTAEQLENYHCSHCWHIAAIKYLS 300
S + F L L P+ G TL DC++ F + L+
Sbjct: 200 CSTVFDPFWDLSL-PIAKRGYP---EVTLMDCMRLFTKEDVLDG---------------- 239
Query: 301 ITEANEMEIEELRRCSAQDSCNCRSRLHLETLPWSNKFSHTLKKLSISHCPQILCIHLQR 360
D+ T +KK SI P+IL +HL+R
Sbjct: 240 ------------------DAA--------PTCCRCRGRKRCIKKFSIQRFPKILVLHLKR 273
Query: 361 VSINEMGELVKIWGHIAFPL-ILDLFPFV 388
S + + K+ + FPL LDL F
Sbjct: 274 FSESRI-RTSKLTTFVNFPLRDLDLREFA 301
Score = 37.0 bits (84), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 33/76 (43%), Gaps = 16/76 (21%)
Query: 497 NTYLYRLASVVEHFGRVGSGHYTVYRSVRVESHEENPNEHFETPLT-HWFCISDSQVYSV 555
N +Y L +V H G GHYT Y +P T W +DS V +
Sbjct: 306 NHAVYNLYAVSNHSGTTMGGHYTAY---------------CRSPGTGEWHTFNDSSVTPM 350
Query: 556 SVNDVLAAEASLLFYE 571
S + V ++A LLFYE
Sbjct: 351 SSSQVRTSDAYLLFYE 366
>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 = 45.8 bits (107), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 82/329 (24%), Positives = 125/329 (37%), Gaps = 80/329 (24%)
Query: 76 GLQNLGNNCFLNVILQALASCTCFLPF-LQKV-MGECEEPDEDLPLTVALASLLEELCLV 133
GL+NLGN CF+N ILQ L++ + LQ++ M + A +L+EE +
Sbjct: 30 GLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSN------AHTALVEEFAKL 83
Query: 134 GET------RLVLSPQKVMLAMELYIQNFNLTSQQDAEEAFLHLMSSLREEFLESYSPNE 187
+T V+SP + ++ Y F +QQDA+E L+ L E N
Sbjct: 84 IQTIWTSSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEV------NR 137
Query: 188 SSLVDAFEAASCRILSLKRREVQSEQKRWRKHF------FGP-FDGILGSILTCQSCLSQ 240
+L + L + + ++ WRK+ G F G L S LTC C
Sbjct: 138 VTLRPKSNPENLDHLP----DDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDC-GY 192
Query: 241 ISLDYQFFHSLPLSPVLDSGSTIPFGCTLEDCLKQFLTAEQLENYHCSHCWHIAAIKYLS 300
S + F L L P+ G TL DC++ F
Sbjct: 193 CSTVFDPFWDLSL-PIAKRGYP---EVTLMDCMRLF------------------------ 224
Query: 301 ITEANEMEIEELRRCSAQDSCNCRSRLHLETLPWSNKFSHTLKKLSISHCPQILCIHLQR 360
T+ + ++ +E T +KK SI P+IL +HL+R
Sbjct: 225 -TKEDVLDGDEK-----------------PTCCRCRGRKRCIKKFSIQRFPKILVLHLKR 266
Query: 361 VSINEMGELVKIWGHIAFPLI-LDLFPFV 388
S + + K+ + FPL LDL F
Sbjct: 267 FSESRI-RTSKLTTFVNFPLRDLDLREFA 294
Score = 37.0 bits (84), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 33/76 (43%), Gaps = 16/76 (21%)
Query: 497 NTYLYRLASVVEHFGRVGSGHYTVYRSVRVESHEENPNEHFETPLT-HWFCISDSQVYSV 555
N +Y L +V H G GHYT Y +P T W +DS V +
Sbjct: 299 NHAVYNLYAVSNHSGTTMGGHYTAY---------------CRSPGTGEWHTFNDSSVTPM 343
Query: 556 SVNDVLAAEASLLFYE 571
S + V ++A LLFYE
Sbjct: 344 SSSQVRTSDAYLLFYE 359
>pdb|2HD5|A Chain A, Usp2 In Complex With Ubiquitin
Length = 359
Score = 45.4 bits (106), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 82/329 (24%), Positives = 125/329 (37%), Gaps = 80/329 (24%)
Query: 76 GLQNLGNNCFLNVILQALASCTCFLPF-LQKV-MGECEEPDEDLPLTVALASLLEELCLV 133
GL+NLGN CF+N ILQ L++ + LQ++ M + A +L+EE +
Sbjct: 11 GLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSN------AHTALVEEFAKL 64
Query: 134 GET------RLVLSPQKVMLAMELYIQNFNLTSQQDAEEAFLHLMSSLREEFLESYSPNE 187
+T V+SP + ++ Y F +QQDA+E L+ L E N
Sbjct: 65 IQTIWTSSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEV------NR 118
Query: 188 SSLVDAFEAASCRILSLKRREVQSEQKRWRKHF------FGP-FDGILGSILTCQSCLSQ 240
+L + L + + ++ WRK+ G F G L S LTC C
Sbjct: 119 VTLRPKSNPENLDHLP----DDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDC-GY 173
Query: 241 ISLDYQFFHSLPLSPVLDSGSTIPFGCTLEDCLKQFLTAEQLENYHCSHCWHIAAIKYLS 300
S + F L L P+ G TL DC++ F
Sbjct: 174 CSTVFDPFWDLSL-PIAKRGYP---EVTLMDCMRLF------------------------ 205
Query: 301 ITEANEMEIEELRRCSAQDSCNCRSRLHLETLPWSNKFSHTLKKLSISHCPQILCIHLQR 360
T+ + ++ +E T +KK SI P+IL +HL+R
Sbjct: 206 -TKEDVLDGDEK-----------------PTCCRCRGRKRCIKKFSIQRFPKILVLHLKR 247
Query: 361 VSINEMGELVKIWGHIAFPLI-LDLFPFV 388
S + + K+ + FPL LDL F
Sbjct: 248 FSESRI-RTSKLTTFVNFPLRDLDLREFA 275
Score = 37.0 bits (84), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 33/76 (43%), Gaps = 16/76 (21%)
Query: 497 NTYLYRLASVVEHFGRVGSGHYTVYRSVRVESHEENPNEHFETPLT-HWFCISDSQVYSV 555
N +Y L +V H G GHYT Y +P T W +DS V +
Sbjct: 280 NHAVYNLYAVSNHSGTTMGGHYTAY---------------CRSPGTGEWHTFNDSSVTPM 324
Query: 556 SVNDVLAAEASLLFYE 571
S + V ++A LLFYE
Sbjct: 325 SSSQVRTSDAYLLFYE 340
>pdb|3NHE|A Chain A, High Resolution Structure (1.26a) Of Usp2a In Complex With
Ubiquitin
Length = 348
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 81/329 (24%), Positives = 124/329 (37%), Gaps = 80/329 (24%)
Query: 76 GLQNLGNNCFLNVILQALASCTCFLPF-LQKV-MGECEEPDEDLPLTVALASLLEELCLV 133
GL+NLGN F+N ILQ L++ + LQ++ M + A +L+EE +
Sbjct: 11 GLRNLGNTXFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSN------AHTALVEEFAKL 64
Query: 134 GET------RLVLSPQKVMLAMELYIQNFNLTSQQDAEEAFLHLMSSLREEFLESYSPNE 187
+T V+SP + ++ Y F +QQDA+E L+ L E N
Sbjct: 65 IQTIWTSSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEV------NR 118
Query: 188 SSLVDAFEAASCRILSLKRREVQSEQKRWRKHF------FGP-FDGILGSILTCQSCLSQ 240
+L + L + + ++ WRK+ G F G L S LTC C
Sbjct: 119 VTLRPKSNPENLDHLP----DDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDC-GY 173
Query: 241 ISLDYQFFHSLPLSPVLDSGSTIPFGCTLEDCLKQFLTAEQLENYHCSHCWHIAAIKYLS 300
S + F L L P+ G TL DC++ F
Sbjct: 174 CSTVFDPFWDLSL-PIAKRGYP---EVTLMDCMRLF------------------------ 205
Query: 301 ITEANEMEIEELRRCSAQDSCNCRSRLHLETLPWSNKFSHTLKKLSISHCPQILCIHLQR 360
T+ + ++ +E T +KK SI P+IL +HL+R
Sbjct: 206 -TKEDVLDGDEK-----------------PTCCRCRGRKRCIKKFSIQRFPKILVLHLKR 247
Query: 361 VSINEMGELVKIWGHIAFPLI-LDLFPFV 388
S + + K+ + FPL LDL F
Sbjct: 248 FSESRI-RTSKLTTFVNFPLRDLDLREFA 275
Score = 37.0 bits (84), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 33/76 (43%), Gaps = 16/76 (21%)
Query: 497 NTYLYRLASVVEHFGRVGSGHYTVYRSVRVESHEENPNEHFETPLT-HWFCISDSQVYSV 555
N +Y L +V H G GHYT Y +P T W +DS V +
Sbjct: 280 NHAVYNLYAVSNHSGTTMGGHYTAY---------------CRSPGTGEWHTFNDSSVTPM 324
Query: 556 SVNDVLAAEASLLFYE 571
S + V ++A LLFYE
Sbjct: 325 SSSQVRTSDAYLLFYE 340
>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
Length = 854
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 37/133 (27%), Positives = 60/133 (45%), Gaps = 21/133 (15%)
Query: 76 GLQNLGNNCFLNVILQALASCTCF----LPFLQKVMGECE-EPDEDLPLTVA-LASLL-- 127
G++NLGN+C+LN ++Q L S F + L+K+ +P +D VA L L
Sbjct: 346 GIRNLGNSCYLNSVVQVLFSIPDFQRKYVDKLEKIFQNAPTDPTQDFSTQVAKLGHGLLS 405
Query: 128 -------------EELCLVGETRLVLSPQKVMLAMELYIQNFNLTSQQDAEEAFLHLMSS 174
E + E + ++P+ + F+ QQDA+E FLHL++
Sbjct: 406 GEYSKPVPESGDGERVPEQKEVQDGIAPRMFKALIGKGHPEFSTNRQQDAQEFFLHLINM 465
Query: 175 LREEFLESYSPNE 187
+ S +PNE
Sbjct: 466 VERNCRSSENPNE 478
>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 = 33.1 bits (74), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 25/110 (22%), Positives = 46/110 (41%), Gaps = 6/110 (5%)
Query: 76 GLQNLGNNCFLNVILQALASCTCFLPFLQKVMGECEEPDEDLPLTVALASLLEELCLVGE 135
GL NLGN C++N +Q + S L++ G E A+L + + +
Sbjct: 16 GLTNLGNTCYMNATVQCIRSVPELKDALKRYAGALRASGEMASAQYITAALRDLFDSMDK 75
Query: 136 TRLVLSPQKVMLAMELYIQNFNLTS------QQDAEEAFLHLMSSLREEF 179
T + P ++ + + F QQDA E ++ +M L+++
Sbjct: 76 TSSSIPPIILLQFLHMAFPQFAEKGEQGQYLQQDANECWIQMMRVLQQKL 125
>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 = 31.6 bits (70), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 20/30 (66%), Gaps = 1/30 (3%)
Query: 65 ENRLEKLCLVP-GLQNLGNNCFLNVILQAL 93
E ++++ +P G +N GN C+LN LQAL
Sbjct: 14 EQQVQQFAQLPVGFKNXGNTCYLNATLQAL 43
>pdb|3RGF|B Chain B, Crystal Structure Of Human Cdk8CYCC
Length = 285
Score = 31.6 bits (70), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 33/121 (27%), Positives = 53/121 (43%), Gaps = 11/121 (9%)
Query: 27 WVSASGLLGILGVAGFVLALKKDAKIGNLSGFSWLSEKENRLEKLCLVPGLQNLGNNCFL 86
W S+ L IL + +KD K LSE+E ++ +Q LG + L
Sbjct: 8 WQSSHYLQWILDKQDLLKERQKDLKF--------LSEEEYWKLQIFFTNVIQALGEH--L 57
Query: 87 NVILQALASCTCFLP-FLQKVMGECEEPDEDLPLTVALASLLEELCLVGETRLVLSPQKV 145
+ Q +A+ T + F + + +P P V LAS +EE +V TRL+ + V
Sbjct: 58 KLRQQVIATATVYFKRFYARYSLKSIDPVLMAPTCVFLASKVEEFGVVSNTRLIAAATSV 117
Query: 146 M 146
+
Sbjct: 118 L 118
>pdb|1NFI|E Chain E, I-Kappa-B-AlphaNF-Kappa-B Complex
pdb|1NFI|F Chain F, I-Kappa-B-AlphaNF-Kappa-B Complex
Length = 213
Score = 31.2 bits (69), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 25/85 (29%), Positives = 38/85 (44%), Gaps = 5/85 (5%)
Query: 247 FFHSLPLSPVLDSGSTIPFGCTLEDCLKQFL-TAEQLENYHCSHCWHIAAIK-YLSITEA 304
F + PL + G G + C L + + NY+ C H+A+I YL I E
Sbjct: 73 FRGNTPLHLACEQGCLASVGVLTQSCTTPHLHSILKATNYNGHTCLHLASIHGYLGIVE- 131
Query: 305 NEMEIEELRRCSAQDSCNCRSRLHL 329
+ + +AQ+ CN R+ LHL
Sbjct: 132 --LLVSLGADVNAQEPCNGRTALHL 154
>pdb|1IKN|D Chain D, IkappabalphaNF-Kappab Complex
Length = 236
Score = 30.8 bits (68), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 25/85 (29%), Positives = 38/85 (44%), Gaps = 5/85 (5%)
Query: 247 FFHSLPLSPVLDSGSTIPFGCTLEDCLKQFL-TAEQLENYHCSHCWHIAAIK-YLSITEA 304
F + PL + G G + C L + + NY+ C H+A+I YL I E
Sbjct: 76 FRGNTPLHLACEQGCLASVGVLTQSCTTPHLHSILKATNYNGHTCLHLASIHGYLGIVE- 134
Query: 305 NEMEIEELRRCSAQDSCNCRSRLHL 329
+ + +AQ+ CN R+ LHL
Sbjct: 135 --LLVSLGADVNAQEPCNGRTALHL 157
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 0.135 0.409
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,711,716
Number of Sequences: 62578
Number of extensions: 682007
Number of successful extensions: 1496
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1427
Number of HSP's gapped (non-prelim): 51
length of query: 576
length of database: 14,973,337
effective HSP length: 104
effective length of query: 472
effective length of database: 8,465,225
effective search space: 3995586200
effective search space used: 3995586200
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: 54 (25.4 bits)