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= 001246
(1115 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 = 380 bits (976), Expect = e-105, Method: Compositional matrix adjust.
Identities = 215/494 (43%), Positives = 295/494 (59%), Gaps = 24/494 (4%)
Query: 55 FTWTIENFSRLNTKKHYSDVFVVGGYKWRILIFPK----GNNVDHLSMYLDVADSGTLPY 110
F +T+E FSRL+ FV W+I++ P+ + + +L ++ +
Sbjct: 33 FQFTVERFSRLSESVLSPPCFV-RNLPWKIMVMPRFYPDRPHQKSVGFFLQ-CNAESDST 90
Query: 111 GWSRYAQFSLAVVNQIHSKYSIRKDTQHQFNARESDWGFTSFMPLGDLYDPSRGYLVNDS 170
WS +AQ L ++N + S + H F +E+DWGF++FM ++ DP +G+ ++D
Sbjct: 91 SWSCHAQAVLKIINYRDDEKSFSRRISHLFFHKENDWGFSNFMAWSEVTDPEKGF-IDDD 149
Query: 171 XXXXXXXXXRKVLDYWSYDSKKETGYVGLKNQGATCYMNSLLQTLYHIPYFRKAVYHMPT 230
++DSKK TGYVGLKNQGATCYMNSLLQTL+ RKAVY MPT
Sbjct: 150 KVTFEVFVQADAPHGVAWDSKKHTGYVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPT 209
Query: 231 TENDLPSGSIPLALQSLFYKLQYNDTSVATKELTKSFGWDTYDSFMQHDVQELNRVLCEK 290
E D S S+PLALQ +FY+LQ++D V TK+LTKSFGW+T DSFMQHDVQEL RVL +
Sbjct: 210 -EGDDSSKSVPLALQRVFYELQHSDKPVGTKKLTKSFGWETLDSFMQHDVQELCRVLLDN 268
Query: 291 LEDKMKGTVVEGTIQQLFEGHHMNYIECINVDYKSTRKESFYDLQLDVKGCRDVYASFDK 350
+E+KMKGT VEGTI +LF G ++YI+C VDY+S R+E +YD+QL +KG ++++ SF
Sbjct: 269 VENKMKGTCVEGTIPKLFRGKMVSYIQCKEVDYRSDRREDYYDIQLSIKGKKNIFESFVD 328
Query: 351 YVEVERLEGDNKYHAEEHGLQDAKKGVLFIDFPPVLQLQLKRFEYDFMRDAMVKINDRYE 410
YV VE+L+GDNKY A EHGLQ+A+KGV F+ PPVL LQL RF YD D +KINDR+E
Sbjct: 329 YVAVEQLDGDNKYDAGEHGLQEAEKGVKFLTLPPVLHLQLMRFMYDPQTDQNIKINDRFE 388
Query: 411 FPLQLDLDRENGKYLSPDADRSVRNLYTXXXXXXXXXXXXXXXYYAFIRPTLSDQWYKFD 470
FP QL LD ++L + N Y Y ++ P +W KFD
Sbjct: 389 FPEQLPLD----EFLQKTDPKDPAN-YILHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFD 443
Query: 471 DERVTKEDVKRALEEQYGGEEELXXXXXXXXXXXXXXXKYSNAYMLVYIRESDKDKIICN 530
D+ V++ + A+E YGG ++ +NAYMLVYIRES +++
Sbjct: 444 DDVVSRCTKEEAIEHNYGGHDD-----------DLSVRHCTNAYMLVYIRESKLSEVLQA 492
Query: 531 VDEKDIAEHLRIRL 544
V + DI + L RL
Sbjct: 493 VTDHDIPQQLVERL 506
>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 = 333 bits (853), Expect = 4e-91, Method: Compositional matrix adjust.
Identities = 180/354 (50%), Positives = 230/354 (64%), Gaps = 17/354 (4%)
Query: 191 KKETGYVGLKNQGATCYMNSLLQTLYHIPYFRKAVYHMPTTENDLPSGSIPLALQSLFYK 250
KK TGYVGLKNQGATCYMNSLLQTL+ RKAVY MPT E D S S+PLALQ +FY+
Sbjct: 1 KKHTGYVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPT-EGDDSSKSVPLALQRVFYE 59
Query: 251 LQYNDTSVATKELTKSFGWDTYDSFMQHDVQELNRVLCEKLEDKMKGTVVEGTIQQLFEG 310
LQ++D V TK+LTKSFGW+T DSFMQHDVQEL RVL + +E+KMKGT VEGTI +LF G
Sbjct: 60 LQHSDKPVGTKKLTKSFGWETLDSFMQHDVQELCRVLLDNVENKMKGTCVEGTIPKLFRG 119
Query: 311 HHMNYIECINVDYKSTRKESFYDLQLDVKGCRDVYASFDKYVEVERLEGDNKYHAEEHGL 370
++YI+C VDY+S R+E +YD+QL +KG ++++ SF YV VE+L+GDNKY A EHGL
Sbjct: 120 KMVSYIQCKEVDYRSDRREDYYDIQLSIKGKKNIFESFVDYVAVEQLDGDNKYDAGEHGL 179
Query: 371 QDAKKGVLFIDFPPVLQLQLKRFEYDFMRDAMVKINDRYEFPLQLDLDRENGKYLSPDAD 430
Q+A+KGV F+ PPVL LQL RF YD D +KINDR+EFP QL LD ++L
Sbjct: 180 QEAEKGVKFLTLPPVLHLQLMRFMYDPQTDQNIKINDRFEFPEQLPLD----EFLQKTDP 235
Query: 431 RSVRNLYTXXXXXXXXXXXXXXXYYAFIRPTLSDQWYKFDDERVTKEDVKRALEEQYGGE 490
+ N Y Y ++ P +W KFDD+ V++ + A+E YGG
Sbjct: 236 KDPAN-YILHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGGH 294
Query: 491 EELXXXXXXXXXXXXXXXKYSNAYMLVYIRESDKDKIICNVDEKDIAEHLRIRL 544
++ +NAYMLVYIRES +++ V + DI + L RL
Sbjct: 295 DD-----------DLSVRHCTNAYMLVYIRESKLSEVLQAVTDHDIPQQLVERL 337
>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 = 321 bits (822), Expect = 2e-87, Method: Compositional matrix adjust.
Identities = 175/354 (49%), Positives = 225/354 (63%), Gaps = 17/354 (4%)
Query: 191 KKETGYVGLKNQGATCYMNSLLQTLYHIPYFRKAVYHMPTTENDLPSGSIPLALQSLFYK 250
KK TGYVGLKNQGATCY NSLLQTL+ RKAVY PT E D S S+PLALQ +FY+
Sbjct: 1 KKHTGYVGLKNQGATCYXNSLLQTLFFTNQLRKAVYXXPT-EGDDSSKSVPLALQRVFYE 59
Query: 251 LQYNDTSVATKELTKSFGWDTYDSFMQHDVQELNRVLCEKLEDKMKGTVVEGTIQQLFEG 310
LQ++D V TK+LTKSFGW+T DSF QHDVQEL RVL + +E+K KGT VEGTI +LF G
Sbjct: 60 LQHSDKPVGTKKLTKSFGWETLDSFXQHDVQELCRVLLDNVENKXKGTCVEGTIPKLFRG 119
Query: 311 HHMNYIECINVDYKSTRKESFYDLQLDVKGCRDVYASFDKYVEVERLEGDNKYHAEEHGL 370
++YI+C VDY+S R+E +YD+QL +KG ++++ SF YV VE+L+GDNKY A EHGL
Sbjct: 120 KXVSYIQCKEVDYRSDRREDYYDIQLSIKGKKNIFESFVDYVAVEQLDGDNKYDAGEHGL 179
Query: 371 QDAKKGVLFIDFPPVLQLQLKRFEYDFMRDAMVKINDRYEFPLQLDLDRENGKYLSPDAD 430
Q+A+KGV F+ PPVL LQL RF YD D +KINDR+EFP QL LD ++L
Sbjct: 180 QEAEKGVKFLTLPPVLHLQLXRFXYDPQTDQNIKINDRFEFPEQLPLD----EFLQKTDP 235
Query: 431 RSVRNLYTXXXXXXXXXXXXXXXYYAFIRPTLSDQWYKFDDERVTKEDVKRALEEQYGGE 490
+ N Y Y ++ P +W KFDD+ V++ + A+E YGG
Sbjct: 236 KDPAN-YILHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGGH 294
Query: 491 EELXXXXXXXXXXXXXXXKYSNAYMLVYIRESDKDKIICNVDEKDIAEHLRIRL 544
++ +NAY LVYIRES +++ V + DI + L RL
Sbjct: 295 DD-----------DLSVRHCTNAYXLVYIRESKLSEVLQAVTDHDIPQQLVERL 337
>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 = 164 bits (414), Expect = 4e-40, Method: Compositional matrix adjust.
Identities = 143/516 (27%), Positives = 241/516 (46%), Gaps = 34/516 (6%)
Query: 559 AQAHLYTIIKVARDEDLAEQIGRDIYFDLVDHDKVR--SFRVQKQTSFMAFKEEIAKEFG 616
++AHLY +++ ++ G D+Y D +KV+ F+V K +S F + +++ G
Sbjct: 5 SEAHLYMQVQIVAEDQFCGHQGNDMY----DEEKVKYTVFKVLKNSSLAEFVQSLSQTMG 60
Query: 617 IPIQLQRFWIWAKRQNHTYRPNRPLLPQEEAQTVGQLREVSNKTHTAELRLFLEVEFGPD 676
P R W R N T RP + EA + E+S+ + +FLE P+
Sbjct: 61 FPQDQIRLWPMQARSNGT---KRPAMLDNEADGNKTMIELSDNENP--WTIFLET-VDPE 114
Query: 677 LHPIAP--PDKSKD-DILLFFKLYDPEKGELRYVGRLFLKSSSKPIEILRKLNQMAGXXX 733
L P KD D++LF K+YDP+ L Y G ++ S K ++L + AG
Sbjct: 115 LAASGATLPKFDKDHDVMLFLKMYDPKTRSLNYCGHIYTPISCKIRDLLPVMCDRAGFIQ 174
Query: 734 XXXXXXXXXXXXXXCVMCEHLDKRTSFRLSQIEDGDIICFQKSPPLESEQECRYPDVPSF 793
+ D L ++ DGDII FQK P E P +
Sbjct: 175 DTSLILYEEVKPNLTERIQDYDVSLDKALDELMDGDIIVFQKDDPENDNSE--LPTAKEY 232
Query: 794 LEYVHNRQIVRFRALDRPKEDAFCLELSKQHSYDEVVERVARKIGLDDPSKIRLTPHNCY 853
+++R V F P + F + LS + +Y +V + VA+++ D P ++ Y
Sbjct: 233 FRDLYHRVDVIFCDKTIPNDPGFVVTLSNRMNYFQVAKTVAQRLNTD-PMLLQFFKSQGY 291
Query: 854 SQQPKPQPIKYRGVEHLSDMLVHYN-QTSDILYYEVLDIPLPELQGLKNLKVAFHHAT-- 910
P P+++ L D+L + + LYY+ L + + + + ++ K + ++
Sbjct: 292 RDGPG-NPLRHNYEGTLRDLLQFFKPRQPKKLYYQQLKMKITDFENRRSFKCIWLNSQFR 350
Query: 911 KDEVVIHNIRLPKQSTVGDVINELKTKVELSH-PNAELRLLEVFYHKIYKIFAPNEKIEN 969
++E+ ++ K V D++ E K VEL + +LRLLE+ +KI + +E +E
Sbjct: 351 EEEITLYP---DKHGCVRDLLEECKKAVELGEKASGKLRLLEIVSYKIIGVHQEDELLEC 407
Query: 970 INDQYW-TLRAEEIPEEEKNLGP-NDRLIHVYHFTKESAQNQMQVQNFGEPFFLVIHEGE 1027
++ T R EEIP ++ ++ N+ L+ V HF KE FG PF L IH+GE
Sbjct: 408 LSPATSRTFRIEEIPLDQVDIDKENEMLVTVAHFHKEV------FGTFGIPFLLRIHQGE 461
Query: 1028 TLAEVKERIQRKLQVLDEEFSKWKFAFLSLGRPEYL 1063
EV +RIQ L + ++EF K+KFA + +GR +Y+
Sbjct: 462 HFREVMKRIQSLLDIQEKEFEKFKFAIVMMGRHQYI 497
>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 = 94.0 bits (232), Expect = 4e-19, Method: Compositional matrix adjust.
Identities = 88/335 (26%), Positives = 137/335 (40%), Gaps = 53/335 (15%)
Query: 195 GYVGLKNQGATCYMNSLLQTLYHIPYFRK---AVYHMPTTENDLPSGSIPLALQSLFYKL 251
G GL N G+TC+M+S+LQ L H PYF + + H + P AL + ++L
Sbjct: 140 GLSGLINMGSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHEL 199
Query: 252 -------QYNDTSVATKELTK-----SFGW---DTYDSFMQHDVQELNRVLCEKLE---- 292
Q + +S +T T + W + Q D E + + ++
Sbjct: 200 YGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQSYV 259
Query: 293 ---------DKMKGTVVEGTIQQLFEGHHMNYIECINVDYKS-TRKESFYDLQLDVKGCR 342
+ E + +FEG + I C S T + F DL LD+K +
Sbjct: 260 LDLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIKDKK 319
Query: 343 DVYASFDKYVEVERLEGDNKYHAEEHGLQDAKKGVLFIDFPPVLQLQLKRFEYDFMRDAM 402
+Y D + + E+L+ N + E + QDA K + P VL LQLKRFE+ + +
Sbjct: 320 KLYECLDSFHKKEQLKDFNYHCGECNSTQDAIKQLGIHKLPSVLVLQLKRFEH-LLNGSN 378
Query: 403 VKINDRYEFPLQLDLDR-----------ENGKYLSPDADRSVRNLYTXXXXXXXXXXXXX 451
K++D EFP L++ ENGK PD +Y
Sbjct: 379 RKLDDFIEFPTYLNMKNYCSTKEKDKHSENGKV--PDI------IYELIGIVSHKGTVNE 430
Query: 452 XXYYAFIRPTLSDQWYKFDDERVTKEDVKRALEEQ 486
Y AF + + QW+KF+D V+ + L+EQ
Sbjct: 431 GHYIAFCKIS-GGQWFKFNDSMVSSISQEEVLKEQ 464
>pdb|3M99|A Chain A, Structure Of The Ubp8-Sgf11-Sgf73-Sus1 Saga Dub Module
Length = 471
Score = 94.0 bits (232), Expect = 4e-19, Method: Compositional matrix adjust.
Identities = 88/335 (26%), Positives = 137/335 (40%), Gaps = 53/335 (15%)
Query: 195 GYVGLKNQGATCYMNSLLQTLYHIPYFRK---AVYHMPTTENDLPSGSIPLALQSLFYKL 251
G GL N G+TC+M+S+LQ L H PYF + + H + P AL + ++L
Sbjct: 135 GLSGLINMGSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHEL 194
Query: 252 -------QYNDTSVATKELTK-----SFGW---DTYDSFMQHDVQELNRVLCEKLE---- 292
Q + +S +T T + W + Q D E + + ++
Sbjct: 195 YGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQSYV 254
Query: 293 ---------DKMKGTVVEGTIQQLFEGHHMNYIECINVDYKS-TRKESFYDLQLDVKGCR 342
+ E + +FEG + I C S T + F DL LD+K +
Sbjct: 255 LDLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIKDKK 314
Query: 343 DVYASFDKYVEVERLEGDNKYHAEEHGLQDAKKGVLFIDFPPVLQLQLKRFEYDFMRDAM 402
+Y D + + E+L+ N + E + QDA K + P VL LQLKRFE+ + +
Sbjct: 315 KLYECLDSFHKKEQLKDFNYHCGECNSTQDAIKQLGIHKLPSVLVLQLKRFEH-LLNGSN 373
Query: 403 VKINDRYEFPLQLDLDR-----------ENGKYLSPDADRSVRNLYTXXXXXXXXXXXXX 451
K++D EFP L++ ENGK PD +Y
Sbjct: 374 RKLDDFIEFPTYLNMKNYCSTKEKDKHSENGKV--PDI------IYELIGIVSHKGTVNE 425
Query: 452 XXYYAFIRPTLSDQWYKFDDERVTKEDVKRALEEQ 486
Y AF + + QW+KF+D V+ + L+EQ
Sbjct: 426 GHYIAFCKIS-GGQWFKFNDSMVSSISQEEVLKEQ 459
>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 = 93.2 bits (230), Expect = 7e-19, Method: Compositional matrix adjust.
Identities = 88/335 (26%), Positives = 136/335 (40%), Gaps = 53/335 (15%)
Query: 195 GYVGLKNQGATCYMNSLLQTLYHIPYFRK---AVYHMPTTENDLPSGSIPLALQSLFYKL 251
G GL N G TC+M+S+LQ L H PYF + + H + P AL + ++L
Sbjct: 140 GLSGLINMGNTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHEL 199
Query: 252 -------QYNDTSVATKELTK-----SFGW---DTYDSFMQHDVQELNRVLCEKLE---- 292
Q + +S +T T + W + Q D E + + ++
Sbjct: 200 YGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQSYV 259
Query: 293 ---------DKMKGTVVEGTIQQLFEGHHMNYIECINVDYKS-TRKESFYDLQLDVKGCR 342
+ E + +FEG + I C S T + F DL LD+K +
Sbjct: 260 LDLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIKDKK 319
Query: 343 DVYASFDKYVEVERLEGDNKYHAEEHGLQDAKKGVLFIDFPPVLQLQLKRFEYDFMRDAM 402
+Y D + + E+L+ N + E + QDA K + P VL LQLKRFE+ + +
Sbjct: 320 KLYECLDSFHKKEQLKDFNYHCGECNSTQDAIKQLGIHKLPSVLVLQLKRFEH-LLNGSN 378
Query: 403 VKINDRYEFPLQLDLDR-----------ENGKYLSPDADRSVRNLYTXXXXXXXXXXXXX 451
K++D EFP L++ ENGK PD +Y
Sbjct: 379 RKLDDFIEFPTYLNMKNYCSTKEKDKHSENGKV--PDI------IYELIGIVSHKGTVNE 430
Query: 452 XXYYAFIRPTLSDQWYKFDDERVTKEDVKRALEEQ 486
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 = 69.7 bits (169), Expect = 9e-12, Method: Compositional matrix adjust.
Identities = 79/320 (24%), Positives = 125/320 (39%), Gaps = 56/320 (17%)
Query: 197 VGLKNQGATCYMNSLLQTLYHIP----YFRKAVYHMPTTENDLPSGSIPLA-----LQSL 247
GL+N G TCYMNS+LQ L + P YF + Y ++L +A +
Sbjct: 63 TGLRNLGNTCYMNSILQCLCNAPHLADYFNRNCYQDDINRSNLLGHKGEVAEEFGIIMKA 122
Query: 248 FYKLQYNDTSVATKELTKSFGWDTYDSFMQHDVQELNRVLCEKLEDKMKGT--------- 298
+ QY S ++T D + + Q D QEL L + L + +
Sbjct: 123 LWTGQYRYISPKDFKITIGKINDQFAGYSQQDSQELLLFLMDGLHEDLNKADNRKRYKEE 182
Query: 299 --------------------VVEGTIQQLFEGHHMNYIECINVDYKSTRKESFYDLQLDV 338
+ E I LF+G + ++C+ KS E+F L L +
Sbjct: 183 NNDHLDDFKAAEHAWQKHKQLNESIIVALFQGQFKSTVQCLTCHKKSRTFEAFMYLSLPL 242
Query: 339 KG---C--RDVYASFDKYVEVERLEGDNKYHAEE-HGLQDAKKGVLFIDFPPVLQLQLKR 392
C +D F K E+L +N+++ +D+ K + PPVL + LKR
Sbjct: 243 ASTSKCTLQDCLRLFSK---EEKLTDNNRFYCSHCRARRDSLKKIEIWKLPPVLLVHLKR 299
Query: 393 FEYDFMRDAMVKINDRYEFPLQ-LDLDRENGKYLSPDADRSVRNLYTXXXXXXXXXXXXX 451
F YD K+ +FPL+ LDL + + P + NL++
Sbjct: 300 FSYDGRWKQ--KLQTSVDFPLENLDLSQY---VIGPKNNLKKYNLFS---VSNHYGGLDG 351
Query: 452 XXYYAFIRPTLSDQWYKFDD 471
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 = 78/320 (24%), Positives = 124/320 (38%), Gaps = 56/320 (17%)
Query: 197 VGLKNQGATCYMNSLLQTLYHIP----YFRKAVYHMPTTENDLPSGSIPLA-----LQSL 247
GL+N G TCY NS+LQ L + P YF + Y ++L +A +
Sbjct: 63 TGLRNLGNTCYXNSILQCLCNAPHLADYFNRNCYQDDINRSNLLGHKGEVAEEFGIIXKA 122
Query: 248 FYKLQYNDTSVATKELTKSFGWDTYDSFMQHDVQELNRVLCEKLEDKMKGT--------- 298
+ QY S ++T D + + Q D QEL L + L + +
Sbjct: 123 LWTGQYRYISPKDFKITIGKINDQFAGYSQQDSQELLLFLXDGLHEDLNKADNRKRYKEE 182
Query: 299 --------------------VVEGTIQQLFEGHHMNYIECINVDYKSTRKESFYDLQLDV 338
+ E I LF+G + ++C+ KS E+F L L +
Sbjct: 183 NNDHLDDFKAAEHAWQKHKQLNESIIVALFQGQFKSTVQCLTCHKKSRTFEAFXYLSLPL 242
Query: 339 KG---C--RDVYASFDKYVEVERLEGDNKYHAEE-HGLQDAKKGVLFIDFPPVLQLQLKR 392
C +D F K E+L +N+++ +D+ K + PPVL + LKR
Sbjct: 243 ASTSKCTLQDCLRLFSK---EEKLTDNNRFYCSHCRARRDSLKKIEIWKLPPVLLVHLKR 299
Query: 393 FEYDFMRDAMVKINDRYEFPLQ-LDLDRENGKYLSPDADRSVRNLYTXXXXXXXXXXXXX 451
F YD K+ +FPL+ LDL + + P + NL++
Sbjct: 300 FSYDGRWKQ--KLQTSVDFPLENLDLSQY---VIGPKNNLKKYNLFS---VSNHYGGLDG 351
Query: 452 XXYYAFIRPTLSDQWYKFDD 471
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 = 82/332 (24%), Positives = 128/332 (38%), Gaps = 52/332 (15%)
Query: 187 SYDSKKETGYVGLKNQGATCYMNSLLQTLYHIPYFRKAVYHMPTTENDLPSGS-IPLALQ 245
S +SK G GL+N G TC+MNS+LQ L + R DL GS AL
Sbjct: 19 SMNSKSAQGLAGLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMR-DLHHGSNAHTALV 77
Query: 246 SLFYKLQYNDTSVATKELTKSFGWDT--------YDSFMQHDVQELNRVLCEKLEDKMKG 297
F KL + + ++ + T + + Q D QE R L + L +++
Sbjct: 78 EEFAKLIQTIWTSSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNR 137
Query: 298 TVV-----------------------------EGTIQQLFEGHHMNYIECINVDYKSTRK 328
+ + I LF G + + C + Y ST
Sbjct: 138 VTLRPKSNPENLDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVF 197
Query: 329 ESFYDLQLDV--KGCRDVYA--SFDKYVEVERLEGDNKYHAEEHGLQDAKKGVLFID-FP 383
+ F+DL L + +G +V + + + L+GD K + I FP
Sbjct: 198 DPFWDLSLPIAKRGYPEVTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFP 257
Query: 384 PVLQLQLKRFEYDFMRDAMVKINDRYEFPLQLDLDRENGKYLSPDADRSVRNLYTXXXXX 443
+L L LKRF +R + K+ FPL+ DLD ++ S + + +V NLY
Sbjct: 258 KILVLHLKRFSESRIRTS--KLTTFVNFPLR-DLDLR--EFASENTNHAVYNLYAVSNHS 312
Query: 444 XXXXXXXXXXYYAFIRPTLSDQWYKFDDERVT 475
Y A+ R + +W+ F+D VT
Sbjct: 313 GTTMGGH---YTAYCRSPGTGEWHTFNDSSVT 341
>pdb|2HD5|A Chain A, Usp2 In Complex With Ubiquitin
Length = 359
Score = 63.2 bits (152), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 81/330 (24%), Positives = 127/330 (38%), Gaps = 52/330 (15%)
Query: 189 DSKKETGYVGLKNQGATCYMNSLLQTLYHIPYFRKAVYHMPTTENDLPSGS-IPLALQSL 247
+SK G GL+N G TC+MNS+LQ L + R DL GS AL
Sbjct: 2 NSKSAQGLAGLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMR-DLHHGSNAHTALVEE 60
Query: 248 FYKLQYNDTSVATKELTKSFGWDT--------YDSFMQHDVQELNRVLCEKLEDKMKGTV 299
F KL + + ++ + T + + Q D QE R L + L +++
Sbjct: 61 FAKLIQTIWTSSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVT 120
Query: 300 V-----------------------------EGTIQQLFEGHHMNYIECINVDYKSTRKES 330
+ + I LF G + + C + Y ST +
Sbjct: 121 LRPKSNPENLDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDP 180
Query: 331 FYDLQLDV--KGCRDVYA--SFDKYVEVERLEGDNKYHAEEHGLQDAKKGVLFID-FPPV 385
F+DL L + +G +V + + + L+GD K + I FP +
Sbjct: 181 FWDLSLPIAKRGYPEVTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKI 240
Query: 386 LQLQLKRFEYDFMRDAMVKINDRYEFPLQLDLDRENGKYLSPDADRSVRNLYTXXXXXXX 445
L L LKRF +R + K+ FPL+ DLD ++ S + + +V NLY
Sbjct: 241 LVLHLKRFSESRIRTS--KLTTFVNFPLR-DLDLR--EFASENTNHAVYNLYAVSNHSGT 295
Query: 446 XXXXXXXXYYAFIRPTLSDQWYKFDDERVT 475
Y A+ R + +W+ F+D VT
Sbjct: 296 TMGGH---YTAYCRSPGTGEWHTFNDSSVT 322
>pdb|2IBI|A Chain A, Covalent Ubiquitin-Usp2 Complex
Length = 374
Score = 61.2 bits (147), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 80/330 (24%), Positives = 126/330 (38%), Gaps = 52/330 (15%)
Query: 189 DSKKETGYVGLKNQGATCYMNSLLQTLYHIPYFRKAVYHMPTTENDLPSGS-IPLALQSL 247
+SK G GL+N G TC+MNS+LQ L + R DL GS AL
Sbjct: 28 NSKSAQGLAGLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMR-DLHHGSNAHTALVEE 86
Query: 248 FYKLQYNDTSVATKELTKSFGWDT--------YDSFMQHDVQELNRVLCEKLEDKMKGTV 299
F KL + + ++ + T + + Q D QE R L + L +++
Sbjct: 87 FAKLIQTIWTSSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVT 146
Query: 300 V-----------------------------EGTIQQLFEGHHMNYIECINVDYKSTRKES 330
+ + I LF G + + C + Y ST +
Sbjct: 147 LRPKSNPENLDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDP 206
Query: 331 FYDLQLDV--KGCRDVYA--SFDKYVEVERLEGDNKYHAEEHGLQDAKKGVLFID-FPPV 385
F+DL L + +G +V + + + L+GD + I FP +
Sbjct: 207 FWDLSLPIAKRGYPEVTLMDCMRLFTKEDVLDGDAAPTCCRCRGRKRCIKKFSIQRFPKI 266
Query: 386 LQLQLKRFEYDFMRDAMVKINDRYEFPLQLDLDRENGKYLSPDADRSVRNLYTXXXXXXX 445
L L LKRF +R + K+ FPL+ DLD ++ S + + +V NLY
Sbjct: 267 LVLHLKRFSESRIRTS--KLTTFVNFPLR-DLDLR--EFASENTNHAVYNLYAVSNHSGT 321
Query: 446 XXXXXXXXYYAFIRPTLSDQWYKFDDERVT 475
Y A+ R + +W+ F+D VT
Sbjct: 322 TMGGH---YTAYCRSPGTGEWHTFNDSSVT 348
>pdb|3NHE|A Chain A, High Resolution Structure (1.26a) Of Usp2a In Complex With
Ubiquitin
Length = 348
Score = 58.5 bits (140), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 80/330 (24%), Positives = 126/330 (38%), Gaps = 52/330 (15%)
Query: 189 DSKKETGYVGLKNQGATCYMNSLLQTLYHIPYFRKAVYHMPTTENDLPSGS-IPLALQSL 247
+SK G GL+N G T +MNS+LQ L + R DL GS AL
Sbjct: 2 NSKSAQGLAGLRNLGNTXFMNSILQCLSNTRELRDYCLQRLYMR-DLHHGSNAHTALVEE 60
Query: 248 FYKLQYNDTSVATKELTKSFGWDT--------YDSFMQHDVQELNRVLCEKLEDKMKGTV 299
F KL + + ++ + T + + Q D QE R L + L +++
Sbjct: 61 FAKLIQTIWTSSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVT 120
Query: 300 V-----------------------------EGTIQQLFEGHHMNYIECINVDYKSTRKES 330
+ + I LF G + + C + Y ST +
Sbjct: 121 LRPKSNPENLDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDP 180
Query: 331 FYDLQLDV--KGCRDVYA--SFDKYVEVERLEGDNKYHAEEHGLQDAKKGVLFID-FPPV 385
F+DL L + +G +V + + + L+GD K + I FP +
Sbjct: 181 FWDLSLPIAKRGYPEVTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKI 240
Query: 386 LQLQLKRFEYDFMRDAMVKINDRYEFPLQLDLDRENGKYLSPDADRSVRNLYTXXXXXXX 445
L L LKRF +R + K+ FPL+ DLD ++ S + + +V NLY
Sbjct: 241 LVLHLKRFSESRIRTS--KLTTFVNFPLR-DLDLR--EFASENTNHAVYNLYAVSNHSGT 295
Query: 446 XXXXXXXXYYAFIRPTLSDQWYKFDDERVT 475
Y A+ R + +W+ F+D VT
Sbjct: 296 TMGGH---YTAYCRSPGTGEWHTFNDSSVT 322
>pdb|2XXN|A Chain A, Structure Of The Virf4-Hausp Traf Domain Complex
Length = 143
Score = 56.6 bits (135), Expect = 8e-08, Method: Composition-based stats.
Identities = 33/119 (27%), Positives = 61/119 (51%), Gaps = 6/119 (5%)
Query: 55 FTWTIENFSRLNTKKHYSDVFVVGGYKWRILI----FPKGNNVDHLSMYLDVADSGTLPY 110
F +T+E FSRL+ FV W+I++ +P + + +L ++ +
Sbjct: 9 FQFTVERFSRLSESVLSPPCFV-RNLPWKIMVMPRFYPDRPHQKSVGFFLQ-CNAESDST 66
Query: 111 GWSRYAQFSLAVVNQIHSKYSIRKDTQHQFNARESDWGFTSFMPLGDLYDPSRGYLVND 169
WS +AQ L ++N + S + H F +E+DWGF++FM ++ DP +G++ +D
Sbjct: 67 SWSCHAQAVLKIINYRDDEKSFSRRISHLFFHKENDWGFSNFMAWSEVTDPEKGFIDDD 125
>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 = 56.2 bits (134), Expect = 1e-07, Method: Composition-based stats.
Identities = 33/119 (27%), Positives = 61/119 (51%), Gaps = 6/119 (5%)
Query: 55 FTWTIENFSRLNTKKHYSDVFVVGGYKWRILI----FPKGNNVDHLSMYLDVADSGTLPY 110
F +T+E FSRL+ FV W+I++ +P + + +L ++ +
Sbjct: 23 FQFTVERFSRLSESVLSPPCFV-RNLPWKIMVMPRFYPDRPHQKSVGFFLQ-CNAESDST 80
Query: 111 GWSRYAQFSLAVVNQIHSKYSIRKDTQHQFNARESDWGFTSFMPLGDLYDPSRGYLVND 169
WS +AQ L ++N + S + H F +E+DWGF++FM ++ DP +G++ +D
Sbjct: 81 SWSCHAQAVLKIINYRDDEKSFSRRISHLFFHKENDWGFSNFMAWSEVTDPEKGFIDDD 139
>pdb|2F1Y|A Chain A, Crystal Structure Of The Traf-Like Domain Of HauspUSP7
Bound To A Mdm2 Peptide
Length = 159
Score = 55.5 bits (132), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 35/120 (29%), Positives = 62/120 (51%), Gaps = 8/120 (6%)
Query: 55 FTWTIENFSRLNTKKHYSDVFVVGGYKWRILIFPK----GNNVDHLSMYLDV-ADSGTLP 109
F +T+E FSRL+ FV W+I++ P+ + + +L A+S +
Sbjct: 23 FQFTVERFSRLSESVLSPPCFV-RNLPWKIMVMPRFYPDRPHQKSVGFFLQCNAESDST- 80
Query: 110 YGWSRYAQFSLAVVNQIHSKYSIRKDTQHQFNARESDWGFTSFMPLGDLYDPSRGYLVND 169
WS +AQ L ++N + S + H F +E+DWGF++FM ++ DP +G++ +D
Sbjct: 81 -SWSCHAQAVLKIINYRDDEKSFSRRISHLFFHKENDWGFSNFMAWSEVTDPEKGFIDDD 139
>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 = 55.5 bits (132), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 35/120 (29%), Positives = 62/120 (51%), Gaps = 8/120 (6%)
Query: 55 FTWTIENFSRLNTKKHYSDVFVVGGYKWRILIFPK----GNNVDHLSMYLDV-ADSGTLP 109
F +T+E FSRL+ FV W+I++ P+ + + +L A+S +
Sbjct: 21 FQFTVERFSRLSESVLSPPCFV-RNLPWKIMVMPRFYPDRPHQKSVGFFLQCNAESDST- 78
Query: 110 YGWSRYAQFSLAVVNQIHSKYSIRKDTQHQFNARESDWGFTSFMPLGDLYDPSRGYLVND 169
WS +AQ L ++N + S + H F +E+DWGF++FM ++ DP +G++ +D
Sbjct: 79 -SWSCHAQAVLKIINYRDDEKSFSRRISHLFFHKENDWGFSNFMAWSEVTDPEKGFIDDD 137
>pdb|2F1W|A Chain A, Crystal Structure Of The Traf-Like Domain Of HauspUSP7
Length = 158
Score = 55.1 bits (131), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 35/120 (29%), Positives = 62/120 (51%), Gaps = 8/120 (6%)
Query: 55 FTWTIENFSRLNTKKHYSDVFVVGGYKWRILIFPK----GNNVDHLSMYLDV-ADSGTLP 109
F +T+E FSRL+ FV W+I++ P+ + + +L A+S +
Sbjct: 23 FQFTVERFSRLSESVLSPPCFV-RNLPWKIMVMPRFYPDRPHQKSVGFFLQCNAESDST- 80
Query: 110 YGWSRYAQFSLAVVNQIHSKYSIRKDTQHQFNARESDWGFTSFMPLGDLYDPSRGYLVND 169
WS +AQ L ++N + S + H F +E+DWGF++FM ++ DP +G++ +D
Sbjct: 81 -SWSCHAQAVLKIINYRDDEKSFSRRISHLFFHKENDWGFSNFMAWSEVTDPEKGFIDDD 139
>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 = 52.4 bits (124), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 77/345 (22%), Positives = 122/345 (35%), Gaps = 72/345 (20%)
Query: 191 KKETGYVGLKNQGATCYMNSLLQTLYHIPYFRKAVYHMPTTENDLPSGS----IPLALQS 246
+ +G+VGL+N G TC++N++LQ L R ++P G + A
Sbjct: 17 RGSSGHVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRR-DFRQEVPGGGRAQELTEAFAD 75
Query: 247 LFYKLQYNDTSVATKELTKSFGWDTY----DSFMQHDVQELNRVLCEKLE---------- 292
+ L + D+ A + Y + Q D QE ++L E+L
Sbjct: 76 VIGALWHPDSCEAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRA 135
Query: 293 ------------DKMKGTVVE----------------------GTIQQLFEGHHMNYIEC 318
+ G ++E I LF G + ++C
Sbjct: 136 PPILANGPVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKC 195
Query: 319 INVDYKSTRKESFYDLQLDV------KGCRDVYASFDKYVEVERLEGDNKYHAEEHGLQD 372
Y+ST E F DL L + G + F+ + + E LE +N + +
Sbjct: 196 QACGYRSTTFEVFCDLSLPIPKKGFAGGKVSLRDCFNLFTKEEELESENAPVCDRCRQKT 255
Query: 373 AKKGVLFID-FPPVLQLQLKRFEYDFMRDAMVKINDRYEFPLQ-LDLDRENGKYLSPDAD 430
L + FP +L L L RF R ++ K + +FPLQ L L G + S A
Sbjct: 256 RSTKKLTVQRFPRILVLHLNRFSAS--RGSIKKSSVGVDFPLQRLSL----GDFASDKAG 309
Query: 431 RSVRNLYTXXXXXXXXXXXXXXXYYAFIRPTLSDQWYKFDDERVT 475
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 = 51.6 bits (122), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 77/342 (22%), Positives = 121/342 (35%), Gaps = 72/342 (21%)
Query: 194 TGYVGLKNQGATCYMNSLLQTLYHIPYFRKAVYHMPTTENDLPSGS----IPLALQSLFY 249
+G+VGL+N G TC++N++LQ L R ++P G + A +
Sbjct: 1 SGHVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRR-DFRQEVPGGGRAQELTEAFADVIG 59
Query: 250 KLQYNDTSVATKELTKSFGWDTY----DSFMQHDVQELNRVLCEKLE------------- 292
L + D+ A + Y + Q D QE ++L E+L
Sbjct: 60 ALWHPDSCEAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRAPPI 119
Query: 293 ---------DKMKGTVVE----------------------GTIQQLFEGHHMNYIECINV 321
+ G ++E I LF G + ++C
Sbjct: 120 LANGPVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKCQAC 179
Query: 322 DYKSTRKESFYDLQLDV------KGCRDVYASFDKYVEVERLEGDNKYHAEEHGLQDAKK 375
Y+ST E F DL L + G + F+ + + E LE +N + +
Sbjct: 180 GYRSTTFEVFCDLSLPIPKKGFAGGKVSLRDCFNLFTKEEELESENAPVCDRCRQKTRST 239
Query: 376 GVLFID-FPPVLQLQLKRFEYDFMRDAMVKINDRYEFPLQ-LDLDRENGKYLSPDADRSV 433
L + FP +L L L RF R ++ K + +FPLQ L L G + S A V
Sbjct: 240 KKLTVQRFPRILVLHLNRFSAS--RGSIKKSSVGVDFPLQRLSL----GDFASDKAGSPV 293
Query: 434 RNLYTXXXXXXXXXXXXXXXYYAFIRPTLSDQWYKFDDERVT 475
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 = 51.6 bits (122), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 77/342 (22%), Positives = 121/342 (35%), Gaps = 72/342 (21%)
Query: 194 TGYVGLKNQGATCYMNSLLQTLYHIPYFRKAVYHMPTTENDLPSGS----IPLALQSLFY 249
+G+VGL+N G TC++N++LQ L R ++P G + A +
Sbjct: 14 SGHVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRR-DFRQEVPGGGRAQELTEAFADVIG 72
Query: 250 KLQYNDTSVATKELTKSFGWDTY----DSFMQHDVQELNRVLCEKLE------------- 292
L + D+ A + Y + Q D QE ++L E+L
Sbjct: 73 ALWHPDSCEAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRAPPI 132
Query: 293 ---------DKMKGTVVE----------------------GTIQQLFEGHHMNYIECINV 321
+ G ++E I LF G + ++C
Sbjct: 133 LANGPVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKCQAC 192
Query: 322 DYKSTRKESFYDLQLDV------KGCRDVYASFDKYVEVERLEGDNKYHAEEHGLQDAKK 375
Y+ST E F DL L + G + F+ + + E LE +N + +
Sbjct: 193 GYRSTTFEVFCDLSLPIPKKGFAGGKVSLRDCFNLFTKEEELESENAPVCDRCRQKTRST 252
Query: 376 GVLFID-FPPVLQLQLKRFEYDFMRDAMVKINDRYEFPLQ-LDLDRENGKYLSPDADRSV 433
L + FP +L L L RF R ++ K + +FPLQ L L G + S A V
Sbjct: 253 KKLTVQRFPRILVLHLNRFSAS--RGSIKKSSVGVDFPLQRLSL----GDFASDKAGSPV 306
Query: 434 RNLYTXXXXXXXXXXXXXXXYYAFIRPTLSDQWYKFDDERVT 475
LY Y A R W+ ++D RV+
Sbjct: 307 YQLYA---LCNHSGSVHYGHYTALCR--CQTGWHVYNDSRVS 343
>pdb|2KVR|A Chain A, Solution Nmr Structure Of Human Ubiquitin Specific
Protease Usp7 Ubl Domain (Residues 537-664). Nesg Target
Hr4395c SGC-Toronto
Length = 130
Score = 46.6 bits (109), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 28/102 (27%), Positives = 46/102 (45%), Gaps = 6/102 (5%)
Query: 538 EHLRIRLXXXXXXXXXXRRYKAQAHLYTIIKVARDEDLAEQIGRDIYFDLVDHDKVR--S 595
+ L RL R+ + +AHLY +++ ++ G D+Y D +KV+
Sbjct: 4 QQLVERLQEEKRIEAQKRKERQEAHLYMQVQIVAEDQFCGHQGNDMY----DEEKVKYTV 59
Query: 596 FRVQKQTSFMAFKEEIAKEFGIPIQLQRFWIWAKRQNHTYRP 637
F+V K +S F + +++ G P R W R N T RP
Sbjct: 60 FKVLKNSSLAEFVQSLSQTMGFPQDQIRLWPMQARSNGTKRP 101
>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 = 0.002, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 23/29 (79%)
Query: 195 GYVGLKNQGATCYMNSLLQTLYHIPYFRK 223
GY G++N G +CY+NS++Q L+ IP F++
Sbjct: 343 GYTGIRNLGNSCYLNSVVQVLFSIPDFQR 371
>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 = 38.5 bits (88), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 24/43 (55%)
Query: 197 VGLKNQGATCYMNSLLQTLYHIPYFRKAVYHMPTTENDLPSGS 239
VG KN G TCY+N+ LQ LY + R + + ++ SG+
Sbjct: 25 VGFKNXGNTCYLNATLQALYRVNDLRDXILNYNPSQGVSNSGA 67
Score = 30.4 bits (67), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 25/39 (64%), Gaps = 2/39 (5%)
Query: 454 YYAFIRPTL-SDQWYKFDDERVTKEDVKRALEEQYGGEE 491
Y AFIR L ++WYKF+D++V+ + K +E GG E
Sbjct: 364 YQAFIRDELDENKWYKFNDDKVSVVE-KEKIESLAGGGE 401
>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 = 37.0 bits (84), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 59/258 (22%), Positives = 94/258 (36%), Gaps = 44/258 (17%)
Query: 197 VGLKNQGATCYMNSLLQTLYHIPYFRKAVYHMPT---TENDLPSGS-IPLALQSLFYKLQ 252
GL N G TCYMN+ +Q + +P + A+ ++ S I AL+ LF +
Sbjct: 15 CGLTNLGNTCYMNATVQCIRSVPELKDALKRYAGALRASGEMASAQYITAALRDLFDSMD 74
Query: 253 YNDTSVATKELTKSFGW--------DTYDSFMQHDVQE----LNRVLCEKLE----DKMK 296
+S+ L + ++Q D E + RVL +KLE D +K
Sbjct: 75 KTSSSIPPIILLQFLHMAFPQFAEKGEQGQYLQQDANECWIQMMRVLQQKLEAIEDDSVK 134
Query: 297 GTVV-----------EGTIQQLFEGHHMNYIECINVDYKSTRKESFYDLQLDVKGCRDVY 345
T + I Q F ++C + + K LQL ++V
Sbjct: 135 ETDSSSASAATPSKKKSLIDQFFGVEFETTMKCTESEEEEVTKGKENQLQLSCFINQEVK 194
Query: 346 ASFDKYVEVERLEGDNKYHAEEHGLQDAKKGVLFID------FPPVLQLQLKRFEYDFMR 399
F +L + + LQ + L+I P L +Q+ RF Y
Sbjct: 195 YLFTGL----KLRLQEEITKQSPTLQ---RNALYIKSSKISRLPAYLTIQMVRFFYKEKE 247
Query: 400 DAMVKINDRYEFPLQLDL 417
K+ +FPL LD+
Sbjct: 248 SVNAKVLKDVKFPLMLDM 265
>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 = 36.6 bits (83), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 30/121 (24%), Positives = 48/121 (39%), Gaps = 7/121 (5%)
Query: 55 FTWTIENFSRLNTKKH---YSDVFVVGG---YKWRILIFPKGNNVDHLSMYLDVADSGTL 108
+ WTI NFS + S F G KW + + PKG + + +
Sbjct: 9 YMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDEESKDYLSLYLLLVSC 68
Query: 109 PYGWSRYAQFSLAVVNQIHSKYSIRKDTQHQFNARESDWGFTSFMPLGDLYDPSRGYLVN 168
P R A+F +++N + + + + DWGF F+ G L D + G L +
Sbjct: 69 PKSEVR-AKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRGFLLDEANGLLPD 127
Query: 169 D 169
D
Sbjct: 128 D 128
>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 = 35.0 bits (79), Expect = 0.27, Method: Composition-based stats.
Identities = 30/121 (24%), Positives = 48/121 (39%), Gaps = 7/121 (5%)
Query: 55 FTWTIENFSRLNTKKH---YSDVFVVGG---YKWRILIFPKGNNVDHLSMYLDVADSGTL 108
+ WTI NFS + S F G KW + + PKG + + +
Sbjct: 13 YMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDEESKDYLSLYLLLVSC 72
Query: 109 PYGWSRYAQFSLAVVNQIHSKYSIRKDTQHQFNARESDWGFTSFMPLGDLYDPSRGYLVN 168
P R A+F +++N + + + + DWGF F+ G L D + G L +
Sbjct: 73 PKSEVR-AKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRGFLLDEANGLLPD 131
Query: 169 D 169
D
Sbjct: 132 D 132
>pdb|3HXZ|A Chain A, Crystal Structure Of Catalytic Fragment Of E. Coli Alars
G237a In Complex With Alasa
pdb|3HXZ|B Chain B, Crystal Structure Of Catalytic Fragment Of E. Coli Alars
G237a In Complex With Alasa
pdb|3HXZ|C Chain C, Crystal Structure Of Catalytic Fragment Of E. Coli Alars
G237a In Complex With Alasa
pdb|3HXZ|D Chain D, Crystal Structure Of Catalytic Fragment Of E. Coli Alars
G237a In Complex With Alasa
pdb|3HY0|A Chain A, Crystal Structure Of Catalytic Fragment Of E. Coli Alars
G237a In Complex With Glysa
pdb|3HY0|B Chain B, Crystal Structure Of Catalytic Fragment Of E. Coli Alars
G237a In Complex With Glysa
pdb|3HY1|A Chain A, Crystal Structure Of Catalytic Fragment Of E. Coli Alars
G237a In Complex With Sersa
pdb|3HY1|B Chain B, Crystal Structure Of Catalytic Fragment Of E. Coli Alars
G237a In Complex With Sersa
Length = 441
Score = 32.7 bits (73), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 26/106 (24%), Positives = 46/106 (43%), Gaps = 7/106 (6%)
Query: 857 PKPQPIKYRGVEHLSDMLVHYNQTSDILYYEVLDIPLPELQGL-----KNLKVAFHHATK 911
PKP G+E ++ +L H N DI + L + ++ G K+L+V H
Sbjct: 230 PKPSVDTAMGLERIAAVLQHVNSNYDIDLFRTLIQAVAKVTGATDLSNKSLRVIADHIRS 289
Query: 912 DEVVIHNIRLPKQSTVGDVINELKTKVELSHPNAELRLLEVFYHKI 957
+I + +P G V+ + + + H N L E F++K+
Sbjct: 290 CAFLIADGVMPSNENRGYVLRRIIRRA-VRHGNM-LGAKETFFYKL 333
>pdb|3HXU|A Chain A, Crystal Structure Of Catalytic Fragment Of E. Coli Alars
In Complex With Alasa
pdb|3HXV|A Chain A, Crystal Structure Of Catalytic Fragment Of E. Coli Alars
In Complex With Glysa
pdb|3HXW|A Chain A, Crystal Structure Of Catalytic Fragment Of E. Coli Alars
In Complex With Sersa
pdb|3HXX|A Chain A, Crystal Structure Of Catalytic Fragment Of E. Coli Alars
In Complex With Amppcp
pdb|3HXY|A Chain A, Crystal Structure Of Catalytic Fragment Of E. Coli Alars
In Complex With Amppcp, Ala-Amp And Pcp
Length = 441
Score = 32.3 bits (72), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 26/106 (24%), Positives = 46/106 (43%), Gaps = 7/106 (6%)
Query: 857 PKPQPIKYRGVEHLSDMLVHYNQTSDILYYEVLDIPLPELQGL-----KNLKVAFHHATK 911
PKP G+E ++ +L H N DI + L + ++ G K+L+V H
Sbjct: 230 PKPSVDTGMGLERIAAVLQHVNSNYDIDLFRTLIQAVAKVTGATDLSNKSLRVIADHIRS 289
Query: 912 DEVVIHNIRLPKQSTVGDVINELKTKVELSHPNAELRLLEVFYHKI 957
+I + +P G V+ + + + H N L E F++K+
Sbjct: 290 CAFLIADGVMPSNENRGYVLRRIIRRA-VRHGNM-LGAKETFFYKL 333
>pdb|2CR2|A Chain A, Solution Structure Of N-Terminal Domain Of Speckle-Type
Poz Protein
Length = 159
Score = 32.3 bits (72), Expect = 1.5, Method: Composition-based stats.
Identities = 29/121 (23%), Positives = 47/121 (38%), Gaps = 7/121 (5%)
Query: 55 FTWTIENFSRLNTKKH---YSDVFVVGG---YKWRILIFPKGNNVDHLSMYLDVADSGTL 108
+ WTI NFS + S F G KW + + PKG + + +
Sbjct: 14 YMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDEESKDYLSLYLLLVSC 73
Query: 109 PYGWSRYAQFSLAVVNQIHSKYSIRKDTQHQFNARESDWGFTSFMPLGDLYDPSRGYLVN 168
P R A+F +++N + + + + DWGF F+ L D + G L +
Sbjct: 74 PKSEVR-AKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRDFLLDEANGLLPD 132
Query: 169 D 169
D
Sbjct: 133 D 133
>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 = 32.0 bits (71), Expect = 2.2, Method: Composition-based stats.
Identities = 29/121 (23%), Positives = 47/121 (38%), Gaps = 7/121 (5%)
Query: 55 FTWTIENFSRLNTKKH---YSDVFVVGG---YKWRILIFPKGNNVDHLSMYLDVADSGTL 108
+ WTI NFS + S F G KW + + PKG + + +
Sbjct: 13 YMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDEESKDYLSLYLLLVSC 72
Query: 109 PYGWSRYAQFSLAVVNQIHSKYSIRKDTQHQFNARESDWGFTSFMPLGDLYDPSRGYLVN 168
P R A+F +++N + + + + DWGF F+ L D + G L +
Sbjct: 73 PKSEVR-AKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRDFLLDEANGLLPD 131
Query: 169 D 169
D
Sbjct: 132 D 132
>pdb|1UA2|A Chain A, Crystal Structure Of Human Cdk7
pdb|1UA2|B Chain B, Crystal Structure Of Human Cdk7
pdb|1UA2|C Chain C, Crystal Structure Of Human Cdk7
pdb|1UA2|D Chain D, Crystal Structure Of Human Cdk7
Length = 346
Score = 30.8 bits (68), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 22/52 (42%), Positives = 27/52 (51%), Gaps = 6/52 (11%)
Query: 910 TKDEVVIHNIRLPKQSTVGDVIN-----ELKTKVELSHPNAELRLLEVFYHK 956
T V I I+L +S D IN E+K ELSHPN + LL+ F HK
Sbjct: 34 TNQIVAIKKIKLGHRSEAKDGINRTALREIKLLQELSHPNI-IGLLDAFGHK 84
>pdb|3MW2|A Chain A, Crystal Structure Of Beta-Neurexin 1 With The Splice Insert
4
pdb|3MW2|B Chain B, Crystal Structure Of Beta-Neurexin 1 With The Splice Insert
4
Length = 207
Score = 29.6 bits (65), Expect = 9.1, Method: Composition-based stats.
Identities = 22/69 (31%), Positives = 36/69 (52%), Gaps = 3/69 (4%)
Query: 980 EEIPEEEKNLGPNDRLIHVYHFTKESAQNQMQVQNFG--EPFFLVIHEGETLAEVKERIQ 1037
++I EE N ND HV FT+ +QV ++ E + ++ E LA ++RI
Sbjct: 76 DDIAIEESNAIINDGKYHVVRFTRSGGNATLQVDSWPVIERYPAGNNDNERLAIARQRIP 135
Query: 1038 RKL-QVLDE 1045
+L +V+DE
Sbjct: 136 YRLGRVVDE 144
>pdb|2R1B|A Chain A, Crystal Structure Of Rat Neurexin 1beta With A Splice Insert
At Ss#4
pdb|2R1B|B Chain B, Crystal Structure Of Rat Neurexin 1beta With A Splice Insert
At Ss#4
Length = 220
Score = 29.6 bits (65), Expect = 9.1, Method: Composition-based stats.
Identities = 22/69 (31%), Positives = 36/69 (52%), Gaps = 3/69 (4%)
Query: 980 EEIPEEEKNLGPNDRLIHVYHFTKESAQNQMQVQNFG--EPFFLVIHEGETLAEVKERIQ 1037
++I EE N ND HV FT+ +QV ++ E + ++ E LA ++RI
Sbjct: 83 DDIAIEESNAIINDGKYHVVRFTRSGGNATLQVDSWPVIERYPAGNNDNERLAIARQRIP 142
Query: 1038 RKL-QVLDE 1045
+L +V+DE
Sbjct: 143 YRLGRVVDE 151
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 0.410
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 32,885,909
Number of Sequences: 62578
Number of extensions: 1387210
Number of successful extensions: 3522
Number of sequences better than 100.0: 36
Number of HSP's better than 100.0 without gapping: 25
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 3448
Number of HSP's gapped (non-prelim): 51
length of query: 1115
length of database: 14,973,337
effective HSP length: 109
effective length of query: 1006
effective length of database: 8,152,335
effective search space: 8201249010
effective search space used: 8201249010
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: 57 (26.6 bits)