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= 037461
(1077 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2F1Z|A Chain A, Crystal Structure Of Hausp
pdb|2F1Z|B Chain B, Crystal Structure Of Hausp
Length = 522
Score = 379 bits (974), Expect = e-105, Method: Compositional matrix adjust.
Identities = 220/513 (42%), Positives = 303/513 (59%), Gaps = 30/513 (5%)
Query: 34 VAQPETANAVENNQPLDDPPSSR----FTWRIENFSRLNTKKHYSEIFIVGGFKWRVLIF 89
VA + N E + ++D S R F + +E FSRL ++ S V W++++
Sbjct: 8 VALSDGHNTAEED--MEDDTSWRSEATFQFTVERFSRL-SESVLSPPCFVRNLPWKIMVM 64
Query: 90 PK----GNNVDHLSMYLDVADSSSLPYGWSRYAQFSLAVINQIHSKYSVRKDTQHQFNAR 145
P+ + + +L ++ S WS +AQ L +IN + S + H F +
Sbjct: 65 PRFYPDRPHQKSVGFFLQ-CNAESDSTSWSCHAQAVLKIINYRDDEKSFSRRISHLFFHK 123
Query: 146 ESDWGFTSFMPLGELYDPNRGYLVNDTLXXXXXXXXXXXXDYWSYDSKKETGYVGLKNQG 205
E+DWGF++FM E+ DP +G++ +D + ++DSKK TGYVGLKNQG
Sbjct: 124 ENDWGFSNFMAWSEVTDPEKGFIDDDKVTFEVFVQADAPHGV-AWDSKKHTGYVGLKNQG 182
Query: 206 ATCYMNSLLQTLFHIPYFRKAVYHMPTTENDMPSGSIPLALQSLFYKLQYSDSSVATKEL 265
ATCYMNSLLQTLF RKAVY MPT E D S S+PLALQ +FY+LQ+SD V TK+L
Sbjct: 183 ATCYMNSLLQTLFFTNQLRKAVYMMPT-EGDDSSKSVPLALQRVFYELQHSDKPVGTKKL 241
Query: 266 TKSFGWDTYDSFMQHDVQELNRVLSEKLEDKMKGTVVEGTIQQLFEGHHMNYIECINVDY 325
TKSFGW+T DSFMQHDVQEL RVL + +E+KMKGT VEGTI +LF G ++YI+C VDY
Sbjct: 242 TKSFGWETLDSFMQHDVQELCRVLLDNVENKMKGTCVEGTIPKLFRGKMVSYIQCKEVDY 301
Query: 326 KSTRKESFYDLQLDVKGCRDVYASFDKYVEVERLEGDNKYHAEQYGLQDAKKGVLFIDFP 385
+S R+E +YD+QL +KG ++++ SF YV VE+L+GDNKY A ++GLQ+A+KGV F+ P
Sbjct: 302 RSDRREDYYDIQLSIKGKKNIFESFVDYVAVEQLDGDNKYDAGEHGLQEAEKGVKFLTLP 361
Query: 386 PVLQLQLKRFEYDFMRDTMVKINDRYEFPLQLDLDRENGKYLSPDADRSVRNLYTXXXXX 445
PVL LQL RF YD D +KINDR+EFP QL LD ++L + N Y
Sbjct: 362 PVLHLQLMRFMYDPQTDQNIKINDRFEFPEQLPLD----EFLQKTDPKDPAN-YILHAVL 416
Query: 446 XXXXXXXXXXYYAFIRPTLSDQWYKFDDERVTKEDLKRALEEQYGGEEELPQTNPGFNNT 505
Y ++ P +W KFDD+ V++ + A+E YGG ++
Sbjct: 417 VHSGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGGHDD----------- 465
Query: 506 PFKFTKYSNAYMLVYIRESDKDKIICNVDEQDI 538
+NAYMLVYIRES +++ V + DI
Sbjct: 466 DLSVRHCTNAYMLVYIRESKLSEVLQAVTDHDI 498
>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 = 330 bits (845), Expect = 3e-90, Method: Compositional matrix adjust.
Identities = 177/346 (51%), Positives = 226/346 (65%), Gaps = 17/346 (4%)
Query: 193 KKETGYVGLKNQGATCYMNSLLQTLFHIPYFRKAVYHMPTTENDMPSGSIPLALQSLFYK 252
KK TGYVGLKNQGATCYMNSLLQTLF RKAVY MPT E D S S+PLALQ +FY+
Sbjct: 1 KKHTGYVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPT-EGDDSSKSVPLALQRVFYE 59
Query: 253 LQYSDSSVATKELTKSFGWDTYDSFMQHDVQELNRVLSEKLEDKMKGTVVEGTIQQLFEG 312
LQ+SD V TK+LTKSFGW+T DSFMQHDVQEL RVL + +E+KMKGT VEGTI +LF G
Sbjct: 60 LQHSDKPVGTKKLTKSFGWETLDSFMQHDVQELCRVLLDNVENKMKGTCVEGTIPKLFRG 119
Query: 313 HHMNYIECINVDYKSTRKESFYDLQLDVKGCRDVYASFDKYVEVERLEGDNKYHAEQYGL 372
++YI+C VDY+S R+E +YD+QL +KG ++++ SF YV VE+L+GDNKY A ++GL
Sbjct: 120 KMVSYIQCKEVDYRSDRREDYYDIQLSIKGKKNIFESFVDYVAVEQLDGDNKYDAGEHGL 179
Query: 373 QDAKKGVLFIDFPPVLQLQLKRFEYDFMRDTMVKINDRYEFPLQLDLDRENGKYLSPDAD 432
Q+A+KGV F+ PPVL LQL RF YD D +KINDR+EFP QL LD ++L
Sbjct: 180 QEAEKGVKFLTLPPVLHLQLMRFMYDPQTDQNIKINDRFEFPEQLPLD----EFLQKTDP 235
Query: 433 RSVRNLYTXXXXXXXXXXXXXXXYYAFIRPTLSDQWYKFDDERVTKEDLKRALEEQYGGE 492
+ N Y Y ++ P +W KFDD+ V++ + A+E YGG
Sbjct: 236 KDPAN-YILHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGGH 294
Query: 493 EELPQTNPGFNNTPFKFTKYSNAYMLVYIRESDKDKIICNVDEQDI 538
++ +NAYMLVYIRES +++ V + DI
Sbjct: 295 DD-----------DLSVRHCTNAYMLVYIRESKLSEVLQAVTDHDI 329
>pdb|1NB8|A Chain A, Structure Of The Catalytic Domain Of Usp7 (Hausp)
pdb|1NB8|B Chain B, Structure Of The Catalytic Domain Of Usp7 (Hausp)
Length = 353
Score = 318 bits (814), Expect = 1e-86, Method: Compositional matrix adjust.
Identities = 172/346 (49%), Positives = 221/346 (63%), Gaps = 17/346 (4%)
Query: 193 KKETGYVGLKNQGATCYMNSLLQTLFHIPYFRKAVYHMPTTENDMPSGSIPLALQSLFYK 252
KK TGYVGLKNQGATCY NSLLQTLF RKAVY PT E D S S+PLALQ +FY+
Sbjct: 1 KKHTGYVGLKNQGATCYXNSLLQTLFFTNQLRKAVYXXPT-EGDDSSKSVPLALQRVFYE 59
Query: 253 LQYSDSSVATKELTKSFGWDTYDSFMQHDVQELNRVLSEKLEDKMKGTVVEGTIQQLFEG 312
LQ+SD V TK+LTKSFGW+T DSF QHDVQEL RVL + +E+K KGT VEGTI +LF G
Sbjct: 60 LQHSDKPVGTKKLTKSFGWETLDSFXQHDVQELCRVLLDNVENKXKGTCVEGTIPKLFRG 119
Query: 313 HHMNYIECINVDYKSTRKESFYDLQLDVKGCRDVYASFDKYVEVERLEGDNKYHAEQYGL 372
++YI+C VDY+S R+E +YD+QL +KG ++++ SF YV VE+L+GDNKY A ++GL
Sbjct: 120 KXVSYIQCKEVDYRSDRREDYYDIQLSIKGKKNIFESFVDYVAVEQLDGDNKYDAGEHGL 179
Query: 373 QDAKKGVLFIDFPPVLQLQLKRFEYDFMRDTMVKINDRYEFPLQLDLDRENGKYLSPDAD 432
Q+A+KGV F+ PPVL LQL RF YD D +KINDR+EFP QL LD ++L
Sbjct: 180 QEAEKGVKFLTLPPVLHLQLXRFXYDPQTDQNIKINDRFEFPEQLPLD----EFLQKTDP 235
Query: 433 RSVRNLYTXXXXXXXXXXXXXXXYYAFIRPTLSDQWYKFDDERVTKEDLKRALEEQYGGE 492
+ N Y Y ++ P +W KFDD+ V++ + A+E YGG
Sbjct: 236 KDPAN-YILHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGGH 294
Query: 493 EELPQTNPGFNNTPFKFTKYSNAYMLVYIRESDKDKIICNVDEQDI 538
++ +NAY LVYIRES +++ V + DI
Sbjct: 295 DD-----------DLSVRHCTNAYXLVYIRESKLSEVLQAVTDHDI 329
>pdb|2YLM|A Chain A, Mechanism Of Usp7 (Hausp) Activation By Its C-Terminal
Ubiquitin-Like Domain (Hubl) And Allosteric Regulation By
Gmp-Synthetase
Length = 530
Score = 143 bits (361), Expect = 4e-34, Method: Compositional matrix adjust.
Identities = 110/381 (28%), Positives = 188/381 (49%), Gaps = 15/381 (3%)
Query: 650 DILLFFKLYDPEKEELRYVGRLFVKSTGKPMEYLPKLNEMAGYAPDEEIDLYEEIKFEPS 709
D++LF K+YDP+ L Y G ++ + K + LP + + AG+ D + LYEE+K +
Sbjct: 130 DVMLFLKMYDPKTRSLNYCGHIYTPISCKIRDLLPVMCDRAGFIQDTSLILYEEVKPNLT 189
Query: 710 VMCEPIEKRCTFRASQLEDGDIICFQKSTPIEGVGKFRYPEVPSFLDYVHNRQVVHFRSL 769
+ + +L DGDII FQK P + P + +++R V F
Sbjct: 190 ERIQDYDVSLDKALDELMDGDIIVFQKDDPENDNSEL--PTAKEYFRDLYHRVDVIFCDK 247
Query: 770 EKPKEDDFCLEMSKLYTYDDVVERVAQQLGLDDPSKIRLTSHNCYSQQPKPQPIKYRGVD 829
P + F + +S Y V + VAQ+L D P ++ Y P P+++
Sbjct: 248 TIPNDPGFVVTLSNRMNYFQVAKTVAQRLNTD-PMLLQFFKSQGYRDGPG-NPLRHNYEG 305
Query: 830 HLSDMLIHYN-QTSDVLYYEVLDIPLPELQCLKTLKVAFHHATKDEVSVHTIRLPKQSTV 888
L D+L + + LYY+ L + + + + ++ K + ++ E + T+ K V
Sbjct: 306 TLRDLLQFFKPRQPKKLYYQQLKMKITDFENRRSFKCIWLNSQFREEEI-TLYPDKHGCV 364
Query: 889 GDVINDLKTKVELSQ-PDAELRLLEVFYHKIYKIFPLNEKIENIN-DQYWTLRAEEIPEE 946
D++ + K VEL + +LRLLE+ +KI + +E +E ++ T R EEIP +
Sbjct: 365 RDLLEECKKAVELGEKASGKLRLLEIVSYKIIGVHQEDELLECLSPATSRTFRIEEIPLD 424
Query: 947 EKNLGP-HDRLIHVYHFTKETAQNQMQIQNFGEPFFLVIHEGETLQEIKVRIQRKLQVPD 1005
+ ++ ++ L+ V HF KE FG PF L IH+GE +E+ RIQ L + +
Sbjct: 425 QVDIDKENEMLVTVAHFHKEV------FGTFGIPFLLRIHQGEHFREVMKRIQSLLDIQE 478
Query: 1006 EEFAKWKFAFLSLGRPEYLQD 1026
+EF K+KFA + +GR +Y+ +
Sbjct: 479 KEFEKFKFAIVMMGRHQYINE 499
>pdb|3M99|A Chain A, Structure Of The Ubp8-Sgf11-Sgf73-Sus1 Saga Dub Module
Length = 471
Score = 97.1 bits (240), Expect = 4e-20, Method: Compositional matrix adjust.
Identities = 92/335 (27%), Positives = 138/335 (41%), Gaps = 53/335 (15%)
Query: 197 GYVGLKNQGATCYMNSLLQTLFHIPYFRK---AVYHMPTTENDMPSGSIPLALQSLFYKL 253
G GL N G+TC+M+S+LQ L H PYF + + H + P AL + ++L
Sbjct: 135 GLSGLINMGSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHEL 194
Query: 254 -------QYSDSSVATKELTK-----SFGW---DTYDSFMQHDVQE-----LNRVLSEKL 293
Q S SS +T T + W + Q D E +N++ +
Sbjct: 195 YGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQSYV 254
Query: 294 ED--------KMKGTVVEGTIQQLFEGHHMNYIECINVDYKS-TRKESFYDLQLDVKGCR 344
D + E + +FEG + I C S T + F DL LD+K +
Sbjct: 255 LDLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIKDKK 314
Query: 345 DVYASFDKYVEVERLEGDNKYHAEQYGLQDAKKGVLFIDFPPVLQLQLKRFEYDFMRDTM 404
+Y D + + E+L+ N + E QDA K + P VL LQLKRFE+ + +
Sbjct: 315 KLYECLDSFHKKEQLKDFNYHCGECNSTQDAIKQLGIHKLPSVLVLQLKRFEH-LLNGSN 373
Query: 405 VKINDRYEFPLQLDLDR-----------ENGKYLSPDADRSVRNLYTXXXXXXXXXXXXX 453
K++D EFP L++ ENGK PD +Y
Sbjct: 374 RKLDDFIEFPTYLNMKNYCSTKEKDKHSENGKV--PDI------IYELIGIVSHKGTVNE 425
Query: 454 XXYYAFIRPTLSDQWYKFDDERVTKEDLKRALEEQ 488
Y AF + + QW+KF+D V+ + L+EQ
Sbjct: 426 GHYIAFCKIS-GGQWFKFNDSMVSSISQEEVLKEQ 459
>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 = 97.1 bits (240), Expect = 5e-20, Method: Compositional matrix adjust.
Identities = 92/335 (27%), Positives = 138/335 (41%), Gaps = 53/335 (15%)
Query: 197 GYVGLKNQGATCYMNSLLQTLFHIPYFRK---AVYHMPTTENDMPSGSIPLALQSLFYKL 253
G GL N G+TC+M+S+LQ L H PYF + + H + P AL + ++L
Sbjct: 140 GLSGLINMGSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHEL 199
Query: 254 -------QYSDSSVATKELTK-----SFGW---DTYDSFMQHDVQE-----LNRVLSEKL 293
Q S SS +T T + W + Q D E +N++ +
Sbjct: 200 YGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQSYV 259
Query: 294 ED--------KMKGTVVEGTIQQLFEGHHMNYIECINVDYKS-TRKESFYDLQLDVKGCR 344
D + E + +FEG + I C S T + F DL LD+K +
Sbjct: 260 LDLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIKDKK 319
Query: 345 DVYASFDKYVEVERLEGDNKYHAEQYGLQDAKKGVLFIDFPPVLQLQLKRFEYDFMRDTM 404
+Y D + + E+L+ N + E QDA K + P VL LQLKRFE+ + +
Sbjct: 320 KLYECLDSFHKKEQLKDFNYHCGECNSTQDAIKQLGIHKLPSVLVLQLKRFEH-LLNGSN 378
Query: 405 VKINDRYEFPLQLDLDR-----------ENGKYLSPDADRSVRNLYTXXXXXXXXXXXXX 453
K++D EFP L++ ENGK PD +Y
Sbjct: 379 RKLDDFIEFPTYLNMKNYCSTKEKDKHSENGKV--PDI------IYELIGIVSHKGTVNE 430
Query: 454 XXYYAFIRPTLSDQWYKFDDERVTKEDLKRALEEQ 488
Y AF + + QW+KF+D V+ + L+EQ
Sbjct: 431 GHYIAFCKIS-GGQWFKFNDSMVSSISQEEVLKEQ 464
>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 = 95.9 bits (237), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 92/335 (27%), Positives = 137/335 (40%), Gaps = 53/335 (15%)
Query: 197 GYVGLKNQGATCYMNSLLQTLFHIPYFRK---AVYHMPTTENDMPSGSIPLALQSLFYKL 253
G GL N G TC+M+S+LQ L H PYF + + H + P AL + ++L
Sbjct: 140 GLSGLINMGNTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHEL 199
Query: 254 -------QYSDSSVATKELTK-----SFGW---DTYDSFMQHDVQE-----LNRVLSEKL 293
Q S SS +T T + W + Q D E +N++ +
Sbjct: 200 YGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQSYV 259
Query: 294 ED--------KMKGTVVEGTIQQLFEGHHMNYIECINVDYKS-TRKESFYDLQLDVKGCR 344
D + E + +FEG + I C S T + F DL LD+K +
Sbjct: 260 LDLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIKDKK 319
Query: 345 DVYASFDKYVEVERLEGDNKYHAEQYGLQDAKKGVLFIDFPPVLQLQLKRFEYDFMRDTM 404
+Y D + + E+L+ N + E QDA K + P VL LQLKRFE+ + +
Sbjct: 320 KLYECLDSFHKKEQLKDFNYHCGECNSTQDAIKQLGIHKLPSVLVLQLKRFEH-LLNGSN 378
Query: 405 VKINDRYEFPLQLDLDR-----------ENGKYLSPDADRSVRNLYTXXXXXXXXXXXXX 453
K++D EFP L++ ENGK PD +Y
Sbjct: 379 RKLDDFIEFPTYLNMKNYCSTKEKDKHSENGKV--PDI------IYELIGIVSHKGTVNE 430
Query: 454 XXYYAFIRPTLSDQWYKFDDERVTKEDLKRALEEQ 488
Y AF + + QW+KF+D V+ + L+EQ
Sbjct: 431 GHYIAFCKIS-GGQWFKFNDSMVSSISQEEVLKEQ 464
>pdb|3N3K|A Chain A, The Catalytic Domain Of Usp8 In Complex With A Usp8
Specific Inhibitor
Length = 396
Score = 68.9 bits (167), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 78/320 (24%), Positives = 125/320 (39%), Gaps = 56/320 (17%)
Query: 199 VGLKNQGATCYMNSLLQTLFHIP----YFRKAVYHMPTTENDMPSGSIPLA-----LQSL 249
GL+N G TCYMNS+LQ L + P YF + Y +++ +A +
Sbjct: 63 TGLRNLGNTCYMNSILQCLCNAPHLADYFNRNCYQDDINRSNLLGHKGEVAEEFGIIMKA 122
Query: 250 FYKLQYSDSSVATKELTKSFGWDTYDSFMQHDVQELNRVLSEKLEDKMKGT--------- 300
+ QY S ++T D + + Q D QEL L + L + +
Sbjct: 123 LWTGQYRYISPKDFKITIGKINDQFAGYSQQDSQELLLFLMDGLHEDLNKADNRKRYKEE 182
Query: 301 --------------------VVEGTIQQLFEGHHMNYIECINVDYKSTRKESFYDLQLDV 340
+ E I LF+G + ++C+ KS E+F L L +
Sbjct: 183 NNDHLDDFKAAEHAWQKHKQLNESIIVALFQGQFKSTVQCLTCHKKSRTFEAFMYLSLPL 242
Query: 341 KG---C--RDVYASFDKYVEVERLEGDNKYHAEQY-GLQDAKKGVLFIDFPPVLQLQLKR 394
C +D F K E+L +N+++ +D+ K + PPVL + LKR
Sbjct: 243 ASTSKCTLQDCLRLFSK---EEKLTDNNRFYCSHCRARRDSLKKIEIWKLPPVLLVHLKR 299
Query: 395 FEYDFMRDTMVKINDRYEFPLQ-LDLDRENGKYLSPDADRSVRNLYTXXXXXXXXXXXXX 453
F YD K+ +FPL+ LDL + + P + NL++
Sbjct: 300 FSYDGRWKQ--KLQTSVDFPLENLDLSQY---VIGPKNNLKKYNLFS---VSNHYGGLDG 351
Query: 454 XXYYAFIRPTLSDQWYKFDD 473
Y A+ + +W+KFDD
Sbjct: 352 GHYTAYCKNAARQRWFKFDD 371
>pdb|2GFO|A Chain A, Structure Of The Catalytic Domain Of Human Ubiquitin
Carboxyl-terminal Hydrolase 8
Length = 396
Score = 66.6 bits (161), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 77/320 (24%), Positives = 124/320 (38%), Gaps = 56/320 (17%)
Query: 199 VGLKNQGATCYMNSLLQTLFHIP----YFRKAVYHMPTTENDMPSGSIPLA-----LQSL 249
GL+N G TCY NS+LQ L + P YF + Y +++ +A +
Sbjct: 63 TGLRNLGNTCYXNSILQCLCNAPHLADYFNRNCYQDDINRSNLLGHKGEVAEEFGIIXKA 122
Query: 250 FYKLQYSDSSVATKELTKSFGWDTYDSFMQHDVQELNRVLSEKLEDKMKGT--------- 300
+ QY S ++T D + + Q D QEL L + L + +
Sbjct: 123 LWTGQYRYISPKDFKITIGKINDQFAGYSQQDSQELLLFLXDGLHEDLNKADNRKRYKEE 182
Query: 301 --------------------VVEGTIQQLFEGHHMNYIECINVDYKSTRKESFYDLQLDV 340
+ E I LF+G + ++C+ KS E+F L L +
Sbjct: 183 NNDHLDDFKAAEHAWQKHKQLNESIIVALFQGQFKSTVQCLTCHKKSRTFEAFXYLSLPL 242
Query: 341 KG---C--RDVYASFDKYVEVERLEGDNKYHAEQY-GLQDAKKGVLFIDFPPVLQLQLKR 394
C +D F K E+L +N+++ +D+ K + PPVL + LKR
Sbjct: 243 ASTSKCTLQDCLRLFSK---EEKLTDNNRFYCSHCRARRDSLKKIEIWKLPPVLLVHLKR 299
Query: 395 FEYDFMRDTMVKINDRYEFPLQ-LDLDRENGKYLSPDADRSVRNLYTXXXXXXXXXXXXX 453
F YD K+ +FPL+ LDL + + P + NL++
Sbjct: 300 FSYDGRWKQ--KLQTSVDFPLENLDLSQY---VIGPKNNLKKYNLFS---VSNHYGGLDG 351
Query: 454 XXYYAFIRPTLSDQWYKFDD 473
Y A+ + +W+KFDD
Sbjct: 352 GHYTAYCKNAARQRWFKFDD 371
>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 = 64.3 bits (155), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 79/331 (23%), Positives = 128/331 (38%), Gaps = 50/331 (15%)
Query: 189 SYDSKKETGYVGLKNQGATCYMNSLLQTLFHIPYFRKAVYHMPTTENDMPSGSIPLALQS 248
S +SK G GL+N G TC+MNS+LQ L + R + + AL
Sbjct: 19 SMNSKSAQGLAGLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVE 78
Query: 249 LFYKLQYSDSSVATKELTKSFGWDT--------YDSFMQHDVQELNRVLSEKLEDKMKGT 300
F KL + + + ++ + T + + Q D QE R L + L +++
Sbjct: 79 EFAKLIQTIWTSSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRV 138
Query: 301 VV-----------------------------EGTIQQLFEGHHMNYIECINVDYKSTRKE 331
+ + I LF G + + C + Y ST +
Sbjct: 139 TLRPKSNPENLDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFD 198
Query: 332 SFYDLQLDV--KGCRDVYA--SFDKYVEVERLEGDNK-YHAEQYGLQDAKKGVLFIDFPP 386
F+DL L + +G +V + + + L+GD K G + K FP
Sbjct: 199 PFWDLSLPIAKRGYPEVTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPK 258
Query: 387 VLQLQLKRFEYDFMRDTMVKINDRYEFPLQLDLDRENGKYLSPDADRSVRNLYTXXXXXX 446
+L L LKRF +R + K+ FPL+ DLD ++ S + + +V NLY
Sbjct: 259 ILVLHLKRFSESRIRTS--KLTTFVNFPLR-DLDLR--EFASENTNHAVYNLYAVSNHSG 313
Query: 447 XXXXXXXXXYYAFIRPTLSDQWYKFDDERVT 477
Y A+ R + +W+ F+D VT
Sbjct: 314 TTMGGH---YTAYCRSPGTGEWHTFNDSSVT 341
>pdb|2HD5|A Chain A, Usp2 In Complex With Ubiquitin
Length = 359
Score = 63.2 bits (152), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 78/329 (23%), Positives = 127/329 (38%), Gaps = 50/329 (15%)
Query: 191 DSKKETGYVGLKNQGATCYMNSLLQTLFHIPYFRKAVYHMPTTENDMPSGSIPLALQSLF 250
+SK G GL+N G TC+MNS+LQ L + R + + AL F
Sbjct: 2 NSKSAQGLAGLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEF 61
Query: 251 YKLQYSDSSVATKELTKSFGWDT--------YDSFMQHDVQELNRVLSEKLEDKMKGTVV 302
KL + + + ++ + T + + Q D QE R L + L +++ +
Sbjct: 62 AKLIQTIWTSSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTL 121
Query: 303 -----------------------------EGTIQQLFEGHHMNYIECINVDYKSTRKESF 333
+ I LF G + + C + Y ST + F
Sbjct: 122 RPKSNPENLDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPF 181
Query: 334 YDLQLDV--KGCRDVYA--SFDKYVEVERLEGDNK-YHAEQYGLQDAKKGVLFIDFPPVL 388
+DL L + +G +V + + + L+GD K G + K FP +L
Sbjct: 182 WDLSLPIAKRGYPEVTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKIL 241
Query: 389 QLQLKRFEYDFMRDTMVKINDRYEFPLQLDLDRENGKYLSPDADRSVRNLYTXXXXXXXX 448
L LKRF +R + K+ FPL+ DLD ++ S + + +V NLY
Sbjct: 242 VLHLKRFSESRIRTS--KLTTFVNFPLR-DLDLR--EFASENTNHAVYNLYAVSNHSGTT 296
Query: 449 XXXXXXXYYAFIRPTLSDQWYKFDDERVT 477
Y A+ R + +W+ F+D VT
Sbjct: 297 MGGH---YTAYCRSPGTGEWHTFNDSSVT 322
>pdb|2IBI|A Chain A, Covalent Ubiquitin-Usp2 Complex
Length = 374
Score = 60.8 bits (146), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 77/329 (23%), Positives = 126/329 (38%), Gaps = 50/329 (15%)
Query: 191 DSKKETGYVGLKNQGATCYMNSLLQTLFHIPYFRKAVYHMPTTENDMPSGSIPLALQSLF 250
+SK G GL+N G TC+MNS+LQ L + R + + AL F
Sbjct: 28 NSKSAQGLAGLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEF 87
Query: 251 YKLQYSDSSVATKELTKSFGWDT--------YDSFMQHDVQELNRVLSEKLEDKMKGTVV 302
KL + + + ++ + T + + Q D QE R L + L +++ +
Sbjct: 88 AKLIQTIWTSSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTL 147
Query: 303 -----------------------------EGTIQQLFEGHHMNYIECINVDYKSTRKESF 333
+ I LF G + + C + Y ST + F
Sbjct: 148 RPKSNPENLDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPF 207
Query: 334 YDLQLDV--KGCRDVYA--SFDKYVEVERLEGDNK-YHAEQYGLQDAKKGVLFIDFPPVL 388
+DL L + +G +V + + + L+GD G + K FP +L
Sbjct: 208 WDLSLPIAKRGYPEVTLMDCMRLFTKEDVLDGDAAPTCCRCRGRKRCIKKFSIQRFPKIL 267
Query: 389 QLQLKRFEYDFMRDTMVKINDRYEFPLQLDLDRENGKYLSPDADRSVRNLYTXXXXXXXX 448
L LKRF +R + K+ FPL+ DLD ++ S + + +V NLY
Sbjct: 268 VLHLKRFSESRIRTS--KLTTFVNFPLR-DLDLR--EFASENTNHAVYNLYAVSNHSGTT 322
Query: 449 XXXXXXXYYAFIRPTLSDQWYKFDDERVT 477
Y A+ R + +W+ F+D VT
Sbjct: 323 MGGH---YTAYCRSPGTGEWHTFNDSSVT 348
>pdb|3NHE|A Chain A, High Resolution Structure (1.26a) Of Usp2a In Complex With
Ubiquitin
Length = 348
Score = 58.2 bits (139), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 77/329 (23%), Positives = 126/329 (38%), Gaps = 50/329 (15%)
Query: 191 DSKKETGYVGLKNQGATCYMNSLLQTLFHIPYFRKAVYHMPTTENDMPSGSIPLALQSLF 250
+SK G GL+N G T +MNS+LQ L + R + + AL F
Sbjct: 2 NSKSAQGLAGLRNLGNTXFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEF 61
Query: 251 YKLQYSDSSVATKELTKSFGWDT--------YDSFMQHDVQELNRVLSEKLEDKMKGTVV 302
KL + + + ++ + T + + Q D QE R L + L +++ +
Sbjct: 62 AKLIQTIWTSSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTL 121
Query: 303 -----------------------------EGTIQQLFEGHHMNYIECINVDYKSTRKESF 333
+ I LF G + + C + Y ST + F
Sbjct: 122 RPKSNPENLDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPF 181
Query: 334 YDLQLDV--KGCRDVYA--SFDKYVEVERLEGDNK-YHAEQYGLQDAKKGVLFIDFPPVL 388
+DL L + +G +V + + + L+GD K G + K FP +L
Sbjct: 182 WDLSLPIAKRGYPEVTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKIL 241
Query: 389 QLQLKRFEYDFMRDTMVKINDRYEFPLQLDLDRENGKYLSPDADRSVRNLYTXXXXXXXX 448
L LKRF +R + K+ FPL+ DLD ++ S + + +V NLY
Sbjct: 242 VLHLKRFSESRIRTS--KLTTFVNFPLR-DLDLR--EFASENTNHAVYNLYAVSNHSGTT 296
Query: 449 XXXXXXXYYAFIRPTLSDQWYKFDDERVT 477
Y A+ R + +W+ F+D VT
Sbjct: 297 MGGH---YTAYCRSPGTGEWHTFNDSSVT 322
>pdb|2XXN|A Chain A, Structure Of The Virf4-Hausp Traf Domain Complex
Length = 143
Score = 57.8 bits (138), Expect = 3e-08, Method: Composition-based stats.
Identities = 34/121 (28%), Positives = 61/121 (50%), Gaps = 6/121 (4%)
Query: 57 FTWRIENFSRLNTKKHYSEIFIVGGFKWRVLI----FPKGNNVDHLSMYLDVADSSSLPY 112
F + +E FSRL+ F V W++++ +P + + +L ++ S
Sbjct: 9 FQFTVERFSRLSESVLSPPCF-VRNLPWKIMVMPRFYPDRPHQKSVGFFLQ-CNAESDST 66
Query: 113 GWSRYAQFSLAVINQIHSKYSVRKDTQHQFNARESDWGFTSFMPLGELYDPNRGYLVNDT 172
WS +AQ L +IN + S + H F +E+DWGF++FM E+ DP +G++ +D
Sbjct: 67 SWSCHAQAVLKIINYRDDEKSFSRRISHLFFHKENDWGFSNFMAWSEVTDPEKGFIDDDK 126
Query: 173 L 173
+
Sbjct: 127 V 127
>pdb|2F1X|A Chain A, Crystal Structure Of The Traf-Like Domain Of HauspUSP7
Bound To A P53 Peptide
pdb|2F1X|B Chain B, Crystal Structure Of The Traf-Like Domain Of HauspUSP7
Bound To A P53 Peptide
Length = 161
Score = 57.0 bits (136), Expect = 5e-08, Method: Composition-based stats.
Identities = 34/121 (28%), Positives = 61/121 (50%), Gaps = 6/121 (4%)
Query: 57 FTWRIENFSRLNTKKHYSEIFIVGGFKWRVLI----FPKGNNVDHLSMYLDVADSSSLPY 112
F + +E FSRL+ F V W++++ +P + + +L ++ S
Sbjct: 23 FQFTVERFSRLSESVLSPPCF-VRNLPWKIMVMPRFYPDRPHQKSVGFFLQ-CNAESDST 80
Query: 113 GWSRYAQFSLAVINQIHSKYSVRKDTQHQFNARESDWGFTSFMPLGELYDPNRGYLVNDT 172
WS +AQ L +IN + S + H F +E+DWGF++FM E+ DP +G++ +D
Sbjct: 81 SWSCHAQAVLKIINYRDDEKSFSRRISHLFFHKENDWGFSNFMAWSEVTDPEKGFIDDDK 140
Query: 173 L 173
+
Sbjct: 141 V 141
>pdb|1YY6|A Chain A, The Crystal Strucure Of The N-Terminal Domain Of HauspUSP7
Complexed With An Ebna1 Peptide
pdb|1YZE|A Chain A, Crystal Structure Of The N-Terminal Domain Of Usp7HAUSP.
pdb|1YZE|B Chain B, Crystal Structure Of The N-Terminal Domain Of Usp7HAUSP.
pdb|1YZE|C Chain C, Crystal Structure Of The N-Terminal Domain Of Usp7HAUSP.
pdb|2FOJ|A Chain A, The Crystal Strucure Of The N-Terminal Domain Of HauspUSP7
Complexed With P53 Peptide 364-367
pdb|2FOO|A Chain A, The Crystal Strucure Of The N-Terminal Domain Of HauspUSP7
Complexed With P53 Peptide 359-362
pdb|2FOP|A Chain A, The Crystal Strucure Of The N-Terminal Domain Of HauspUSP7
Complexed With Mdm2 Peptide 147-150
pdb|3MQR|A Chain A, Crystal Structure Of The Usp7:hdmx(Ahss) Complex
pdb|3MQS|C Chain C, Crystal Structure Of The Usp7:hdm2(Psts) Complex
Length = 155
Score = 57.0 bits (136), Expect = 5e-08, Method: Composition-based stats.
Identities = 34/121 (28%), Positives = 61/121 (50%), Gaps = 6/121 (4%)
Query: 57 FTWRIENFSRLNTKKHYSEIFIVGGFKWRVLI----FPKGNNVDHLSMYLDVADSSSLPY 112
F + +E FSRL+ F V W++++ +P + + +L ++ S
Sbjct: 21 FQFTVERFSRLSESVLSPPCF-VRNLPWKIMVMPRFYPDRPHQKSVGFFLQ-CNAESDST 78
Query: 113 GWSRYAQFSLAVINQIHSKYSVRKDTQHQFNARESDWGFTSFMPLGELYDPNRGYLVNDT 172
WS +AQ L +IN + S + H F +E+DWGF++FM E+ DP +G++ +D
Sbjct: 79 SWSCHAQAVLKIINYRDDEKSFSRRISHLFFHKENDWGFSNFMAWSEVTDPEKGFIDDDK 138
Query: 173 L 173
+
Sbjct: 139 V 139
>pdb|2F1Y|A Chain A, Crystal Structure Of The Traf-Like Domain Of HauspUSP7
Bound To A Mdm2 Peptide
Length = 159
Score = 56.6 bits (135), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 34/123 (27%), Positives = 63/123 (51%), Gaps = 6/123 (4%)
Query: 55 SRFTWRIENFSRLNTKKHYSEIFIVGGFKWRVLIFPK----GNNVDHLSMYLDVADSSSL 110
+ F + +E FSRL ++ S V W++++ P+ + + +L ++ S
Sbjct: 21 ATFQFTVERFSRL-SESVLSPPCFVRNLPWKIMVMPRFYPDRPHQKSVGFFLQ-CNAESD 78
Query: 111 PYGWSRYAQFSLAVINQIHSKYSVRKDTQHQFNARESDWGFTSFMPLGELYDPNRGYLVN 170
WS +AQ L +IN + S + H F +E+DWGF++FM E+ DP +G++ +
Sbjct: 79 STSWSCHAQAVLKIINYRDDEKSFSRRISHLFFHKENDWGFSNFMAWSEVTDPEKGFIDD 138
Query: 171 DTL 173
D +
Sbjct: 139 DKV 141
>pdb|2F1W|A Chain A, Crystal Structure Of The Traf-Like Domain Of HauspUSP7
Length = 158
Score = 56.2 bits (134), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 34/123 (27%), Positives = 63/123 (51%), Gaps = 6/123 (4%)
Query: 55 SRFTWRIENFSRLNTKKHYSEIFIVGGFKWRVLIFPK----GNNVDHLSMYLDVADSSSL 110
+ F + +E FSRL ++ S V W++++ P+ + + +L ++ S
Sbjct: 21 ATFQFTVERFSRL-SESVLSPPCFVRNLPWKIMVMPRFYPDRPHQKSVGFFLQ-CNAESD 78
Query: 111 PYGWSRYAQFSLAVINQIHSKYSVRKDTQHQFNARESDWGFTSFMPLGELYDPNRGYLVN 170
WS +AQ L +IN + S + H F +E+DWGF++FM E+ DP +G++ +
Sbjct: 79 STSWSCHAQAVLKIINYRDDEKSFSRRISHLFFHKENDWGFSNFMAWSEVTDPEKGFIDD 138
Query: 171 DTL 173
D +
Sbjct: 139 DKV 141
>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 = 54.7 bits (130), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 78/345 (22%), Positives = 123/345 (35%), Gaps = 72/345 (20%)
Query: 193 KKETGYVGLKNQGATCYMNSLLQTLFHIPYFRKAVYHMPTTENDMPSGS----IPLALQS 248
+ +G+VGL+N G TC++N++LQ L R ++P G + A
Sbjct: 17 RGSSGHVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRR-DFRQEVPGGGRAQELTEAFAD 75
Query: 249 LFYKLQYSDSSVATKELTKSFGWDTY----DSFMQHDVQELNRVLSEKLE---------- 294
+ L + DS A + Y + Q D QE ++L E+L
Sbjct: 76 VIGALWHPDSCEAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRA 135
Query: 295 ------------DKMKGTVVE----------------------GTIQQLFEGHHMNYIEC 320
+ G ++E I LF G + ++C
Sbjct: 136 PPILANGPVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKC 195
Query: 321 INVDYKSTRKESFYDLQLDV------KGCRDVYASFDKYVEVERLEGDNKYHAEQYGLQD 374
Y+ST E F DL L + G + F+ + + E LE +N ++ +
Sbjct: 196 QACGYRSTTFEVFCDLSLPIPKKGFAGGKVSLRDCFNLFTKEEELESENAPVCDRCRQKT 255
Query: 375 AKKGVLFID-FPPVLQLQLKRFEYDFMRDTMVKINDRYEFPLQ-LDLDRENGKYLSPDAD 432
L + FP +L L L RF R ++ K + +FPLQ L L G + S A
Sbjct: 256 RSTKKLTVQRFPRILVLHLNRFSAS--RGSIKKSSVGVDFPLQRLSL----GDFASDKAG 309
Query: 433 RSVRNLYTXXXXXXXXXXXXXXXYYAFIRPTLSDQWYKFDDERVT 477
V LY Y A R W+ ++D RV+
Sbjct: 310 SPVYQLYA---LCNHSGSVHYGHYTALCR--CQTGWHVYNDSRVS 349
>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 = 54.3 bits (129), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 78/342 (22%), Positives = 122/342 (35%), Gaps = 72/342 (21%)
Query: 196 TGYVGLKNQGATCYMNSLLQTLFHIPYFRKAVYHMPTTENDMPSGS----IPLALQSLFY 251
+G+VGL+N G TC++N++LQ L R ++P G + A +
Sbjct: 1 SGHVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRR-DFRQEVPGGGRAQELTEAFADVIG 59
Query: 252 KLQYSDSSVATKELTKSFGWDTY----DSFMQHDVQELNRVLSEKLE------------- 294
L + DS A + Y + Q D QE ++L E+L
Sbjct: 60 ALWHPDSCEAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRAPPI 119
Query: 295 ---------DKMKGTVVE----------------------GTIQQLFEGHHMNYIECINV 323
+ G ++E I LF G + ++C
Sbjct: 120 LANGPVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKCQAC 179
Query: 324 DYKSTRKESFYDLQLDV------KGCRDVYASFDKYVEVERLEGDNKYHAEQYGLQDAKK 377
Y+ST E F DL L + G + F+ + + E LE +N ++ +
Sbjct: 180 GYRSTTFEVFCDLSLPIPKKGFAGGKVSLRDCFNLFTKEEELESENAPVCDRCRQKTRST 239
Query: 378 GVLFID-FPPVLQLQLKRFEYDFMRDTMVKINDRYEFPLQ-LDLDRENGKYLSPDADRSV 435
L + FP +L L L RF R ++ K + +FPLQ L L G + S A V
Sbjct: 240 KKLTVQRFPRILVLHLNRFSAS--RGSIKKSSVGVDFPLQRLSL----GDFASDKAGSPV 293
Query: 436 RNLYTXXXXXXXXXXXXXXXYYAFIRPTLSDQWYKFDDERVT 477
LY Y A R W+ ++D RV+
Sbjct: 294 YQLYA---LCNHSGSVHYGHYTALCR--CQTGWHVYNDSRVS 330
>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 = 53.9 bits (128), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 78/342 (22%), Positives = 122/342 (35%), Gaps = 72/342 (21%)
Query: 196 TGYVGLKNQGATCYMNSLLQTLFHIPYFRKAVYHMPTTENDMPSGS----IPLALQSLFY 251
+G+VGL+N G TC++N++LQ L R ++P G + A +
Sbjct: 14 SGHVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRR-DFRQEVPGGGRAQELTEAFADVIG 72
Query: 252 KLQYSDSSVATKELTKSFGWDTY----DSFMQHDVQELNRVLSEKLE------------- 294
L + DS A + Y + Q D QE ++L E+L
Sbjct: 73 ALWHPDSCEAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRAPPI 132
Query: 295 ---------DKMKGTVVE----------------------GTIQQLFEGHHMNYIECINV 323
+ G ++E I LF G + ++C
Sbjct: 133 LANGPVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKCQAC 192
Query: 324 DYKSTRKESFYDLQLDV------KGCRDVYASFDKYVEVERLEGDNKYHAEQYGLQDAKK 377
Y+ST E F DL L + G + F+ + + E LE +N ++ +
Sbjct: 193 GYRSTTFEVFCDLSLPIPKKGFAGGKVSLRDCFNLFTKEEELESENAPVCDRCRQKTRST 252
Query: 378 GVLFID-FPPVLQLQLKRFEYDFMRDTMVKINDRYEFPLQ-LDLDRENGKYLSPDADRSV 435
L + FP +L L L RF R ++ K + +FPLQ L L G + S A V
Sbjct: 253 KKLTVQRFPRILVLHLNRFSAS--RGSIKKSSVGVDFPLQRLSL----GDFASDKAGSPV 306
Query: 436 RNLYTXXXXXXXXXXXXXXXYYAFIRPTLSDQWYKFDDERVT 477
LY Y A R W+ ++D RV+
Sbjct: 307 YQLYA---LCNHSGSVHYGHYTALCR--CQTGWHVYNDSRVS 343
>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
Length = 854
Score = 42.7 bits (99), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 15/29 (51%), Positives = 23/29 (79%)
Query: 197 GYVGLKNQGATCYMNSLLQTLFHIPYFRK 225
GY G++N G +CY+NS++Q LF IP F++
Sbjct: 343 GYTGIRNLGNSCYLNSVVQVLFSIPDFQR 371
>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 = 39.7 bits (91), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 61/258 (23%), Positives = 95/258 (36%), Gaps = 44/258 (17%)
Query: 199 VGLKNQGATCYMNSLLQTLFHIPYFRKAVYHMPT---TENDMPSGS-IPLALQSLFYKLQ 254
GL N G TCYMN+ +Q + +P + A+ +M S I AL+ LF +
Sbjct: 15 CGLTNLGNTCYMNATVQCIRSVPELKDALKRYAGALRASGEMASAQYITAALRDLFDSMD 74
Query: 255 YSDSSVATKELTKSFGW--------DTYDSFMQHDVQE----LNRVLSEKLE----DKMK 298
+ SS+ L + ++Q D E + RVL +KLE D +K
Sbjct: 75 KTSSSIPPIILLQFLHMAFPQFAEKGEQGQYLQQDANECWIQMMRVLQQKLEAIEDDSVK 134
Query: 299 GTVV-----------EGTIQQLFEGHHMNYIECINVDYKSTRKESFYDLQLDVKGCRDVY 347
T + I Q F ++C + + K LQL ++V
Sbjct: 135 ETDSSSASAATPSKKKSLIDQFFGVEFETTMKCTESEEEEVTKGKENQLQLSCFINQEVK 194
Query: 348 ASFDKYVEVERLEGDNKYHAEQYGLQDAKKGVLFID------FPPVLQLQLKRFEYDFMR 401
F +L + + LQ + L+I P L +Q+ RF Y
Sbjct: 195 YLFTGL----KLRLQEEITKQSPTLQ---RNALYIKSSKISRLPAYLTIQMVRFFYKEKE 247
Query: 402 DTMVKINDRYEFPLQLDL 419
K+ +FPL LD+
Sbjct: 248 SVNAKVLKDVKFPLMLDM 265
>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 = 37.4 bits (85), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 24/43 (55%)
Query: 199 VGLKNQGATCYMNSLLQTLFHIPYFRKAVYHMPTTENDMPSGS 241
VG KN G TCY+N+ LQ L+ + R + + ++ SG+
Sbjct: 25 VGFKNXGNTCYLNATLQALYRVNDLRDXILNYNPSQGVSNSGA 67
Score = 30.4 bits (67), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 25/39 (64%), Gaps = 2/39 (5%)
Query: 456 YYAFIRPTL-SDQWYKFDDERVTKEDLKRALEEQYGGEE 493
Y AFIR L ++WYKF+D++V+ + K +E GG E
Sbjct: 364 YQAFIRDELDENKWYKFNDDKVSVVE-KEKIESLAGGGE 401
>pdb|3HQI|A Chain A, Structures Of Spop-Substrate Complexes: Insights Into
Molecular Architectures Of Btb-Cul3 Ubiquitin Ligases:
SpopmathxBTB3-Box-Pucsbc1
pdb|3HQI|B Chain B, Structures Of Spop-Substrate Complexes: Insights Into
Molecular Architectures Of Btb-Cul3 Ubiquitin Ligases:
SpopmathxBTB3-Box-Pucsbc1
pdb|3HU6|A Chain A, Structures Of Spop-Substrate Complexes: Insights Into
Molecular Architectures Of Btb-Cul3 Ubiquitin Ligases:
SpopmathxBTB3-Box-Pucsbc1
pdb|3HU6|B Chain B, Structures Of Spop-Substrate Complexes: Insights Into
Molecular Architectures Of Btb-Cul3 Ubiquitin Ligases:
SpopmathxBTB3-Box-Pucsbc1
Length = 312
Score = 33.9 bits (76), Expect = 0.45, Method: Composition-based stats.
Identities = 31/123 (25%), Positives = 47/123 (38%), Gaps = 7/123 (5%)
Query: 57 FTWRIENFSRLNTKKH---YSEIFIVGG---FKWRVLIFPKGNNVDHLSMYLDVADSSSL 110
+ W I NFS + S F G KW + + PKG + + S
Sbjct: 9 YMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDEESKDYLSLYLLLVSC 68
Query: 111 PYGWSRYAQFSLAVINQIHSKYSVRKDTQHQFNARESDWGFTSFMPLGELYDPNRGYLVN 170
P R A+F +++N + + + + DWGF F+ G L D G L +
Sbjct: 69 PKSEVR-AKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRGFLLDEANGLLPD 127
Query: 171 DTL 173
D L
Sbjct: 128 DKL 130
>pdb|3HQH|A Chain A, Structures Of Spop-Substrate Complexes: Insights Into
Molecular Architectures Of Btb-Cul3 Ubiquitin Ligases:
Spopmathx-Macroh2asbcpep1
pdb|3HQL|A Chain A, Structures Of Spop-Substrate Complexes: Insights Into
Molecular Architectures Of Btb-Cul3 Ubiquitin
Ligases:spopmathx-Pucsbc1_pep2
pdb|3HQL|B Chain B, Structures Of Spop-Substrate Complexes: Insights Into
Molecular Architectures Of Btb-Cul3 Ubiquitin
Ligases:spopmathx-Pucsbc1_pep2
pdb|3HQM|A Chain A, Structures Of Spop-Substrate Complexes: Insights Into
Molecular Architectures Of Btb-Cul3 Ubiquitin Ligases:
Spopmathx-Cisbc2
pdb|3HQM|B Chain B, Structures Of Spop-Substrate Complexes: Insights Into
Molecular Architectures Of Btb-Cul3 Ubiquitin Ligases:
Spopmathx-Cisbc2
pdb|3HSV|A Chain A, Structures Of Spop-Substrate Complexes: Insights Into
Molecular Architectures Of Btb-Cul3 Ubiquitin Ligases:
Spopmathx-Macroh2asbcpep2
pdb|3HSV|B Chain B, Structures Of Spop-Substrate Complexes: Insights Into
Molecular Architectures Of Btb-Cul3 Ubiquitin Ligases:
Spopmathx-Macroh2asbcpep2
Length = 145
Score = 33.9 bits (76), Expect = 0.56, Method: Composition-based stats.
Identities = 31/123 (25%), Positives = 47/123 (38%), Gaps = 7/123 (5%)
Query: 57 FTWRIENFSRLNTKKH---YSEIFIVGG---FKWRVLIFPKGNNVDHLSMYLDVADSSSL 110
+ W I NFS + S F G KW + + PKG + + S
Sbjct: 13 YMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDEESKDYLSLYLLLVSC 72
Query: 111 PYGWSRYAQFSLAVINQIHSKYSVRKDTQHQFNARESDWGFTSFMPLGELYDPNRGYLVN 170
P R A+F +++N + + + + DWGF F+ G L D G L +
Sbjct: 73 PKSEVR-AKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRGFLLDEANGLLPD 131
Query: 171 DTL 173
D L
Sbjct: 132 DKL 134
>pdb|2CR2|A Chain A, Solution Structure Of N-Terminal Domain Of Speckle-Type
Poz Protein
Length = 159
Score = 31.2 bits (69), Expect = 3.3, Method: Composition-based stats.
Identities = 30/123 (24%), Positives = 46/123 (37%), Gaps = 7/123 (5%)
Query: 57 FTWRIENFSRLNTKKH---YSEIFIVGG---FKWRVLIFPKGNNVDHLSMYLDVADSSSL 110
+ W I NFS + S F G KW + + PKG + + S
Sbjct: 14 YMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDEESKDYLSLYLLLVSC 73
Query: 111 PYGWSRYAQFSLAVINQIHSKYSVRKDTQHQFNARESDWGFTSFMPLGELYDPNRGYLVN 170
P R A+F +++N + + + + DWGF F+ L D G L +
Sbjct: 74 PKSEVR-AKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRDFLLDEANGLLPD 132
Query: 171 DTL 173
D L
Sbjct: 133 DKL 135
>pdb|1GVF|A Chain A, Structure Of Tagatose-1,6-Bisphosphate Aldolase
pdb|1GVF|B Chain B, Structure Of Tagatose-1,6-Bisphosphate Aldolase
Length = 286
Score = 30.8 bits (68), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 28/128 (21%), Positives = 55/128 (42%), Gaps = 6/128 (4%)
Query: 751 VPSFLDYVHNRQVVHFRSLEK--PKEDDFCLEMSKLYTYD-DVVERVAQQLGLDDPSKIR 807
V S +D+ H++ L + EDD ++ + D +R + G+D +
Sbjct: 117 VKSVVDFCHSQDCSVEAELGRLGGVEDDMSVDAESAFLTDPQEAKRFVELTGVDSLAVAI 176
Query: 808 LTSHNCYSQQPKPQPIKYRGVDHLSDMLIHYNQTSDV---LYYEVLDIPLPELQCLKTLK 864
T+H YS+ PK + + + D+ + + SDV +++ + ++ LK
Sbjct: 177 GTAHGLYSKTPKIDFQRLAEIREVVDVPLVLHGASDVPDEFVRRTIELGVTKVNVATELK 236
Query: 865 VAFHHATK 872
+AF A K
Sbjct: 237 IAFAGAVK 244
>pdb|3IVB|A Chain A, Structures Of Spop-Substrate Complexes: Insights Into
Architectures Of Btb-Cul3 Ubiquitin Ligases: Spopmath-
Macroh2asbcpep1
pdb|3IVQ|A Chain A, Structures Of Spop-Substrate Complexes: Insights Into
Molecular Architectures Of Btb-Cul3 Ubiquitin Ligases:
Spopmath-Cisbc2
pdb|3IVQ|B Chain B, Structures Of Spop-Substrate Complexes: Insights Into
Molecular Architectures Of Btb-Cul3 Ubiquitin Ligases:
Spopmath-Cisbc2
pdb|3IVV|A Chain A, Structures Of Spop-Substrate Complexes: Insights Into
Molecular Architectures Of Btb-Cul3 Ubiquitin Ligases:
Spopmath-Pucsbc1_pep1
Length = 145
Score = 30.8 bits (68), Expect = 4.7, Method: Composition-based stats.
Identities = 30/123 (24%), Positives = 46/123 (37%), Gaps = 7/123 (5%)
Query: 57 FTWRIENFSRLNTKKH---YSEIFIVGG---FKWRVLIFPKGNNVDHLSMYLDVADSSSL 110
+ W I NFS + S F G KW + + PKG + + S
Sbjct: 13 YMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDEESKDYLSLYLLLVSC 72
Query: 111 PYGWSRYAQFSLAVINQIHSKYSVRKDTQHQFNARESDWGFTSFMPLGELYDPNRGYLVN 170
P R A+F +++N + + + + DWGF F+ L D G L +
Sbjct: 73 PKSEVR-AKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRDFLLDEANGLLPD 131
Query: 171 DTL 173
D L
Sbjct: 132 DKL 134
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
0.319 0.137 0.408
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 32,634,250
Number of Sequences: 62578
Number of extensions: 1418683
Number of successful extensions: 3223
Number of sequences better than 100.0: 33
Number of HSP's better than 100.0 without gapping: 24
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 3153
Number of HSP's gapped (non-prelim): 49
length of query: 1077
length of database: 14,973,337
effective HSP length: 109
effective length of query: 968
effective length of database: 8,152,335
effective search space: 7891460280
effective search space used: 7891460280
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 57 (26.6 bits)