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= 008267
(572 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3M99|A Chain A, Structure Of The Ubp8-Sgf11-Sgf73-Sus1 Saga Dub Module
Length = 471
Score = 168 bits (425), Expect = 8e-42, Method: Compositional matrix adjust.
Identities = 140/558 (25%), Positives = 231/558 (41%), Gaps = 118/558 (21%)
Query: 23 CPHLADFHARNGTKPFRAIQDCLHIKPPGGRAAIRRDSSEVPRCGVCGDSSCPRLYACMA 82
CPH+ +K ++ C + + + +CG C + + + C+
Sbjct: 4 CPHIQQVFQNEKSKD-GVLKTCNAARYILNHSVPKEKFLNTMKCGTCHEINSGATFMCLQ 62
Query: 83 CAAVSCHVPPHSSHVAIHATKTSSACSHEIAVDVDRAELFCCACRDQVYDRDFDAAVVLA 142
C C + SH H+ + H ++ + LFC C D + + D +LA
Sbjct: 63 CGFCGCW---NHSHFLSHSKQIG----HIFGINSNNGLLFCFKCEDYIGNIDLINDAILA 115
Query: 143 HTTSIIQSSKPENLRKRRRIDYRPWSPDLRERSLMVNNASPIDSMSSSXXXXXXXXXXXX 202
+ + + P + R + S + +M S
Sbjct: 116 --------------KYWDDVCTKTMVPSMERR----DGLSGLINMGS------------- 144
Query: 203 XXXXTCFMNSVLQALFHTPPLRNYFLSDRHNRYYCQSKN-GVR---LCLACDLDTMFSAI 258
TCFM+S+LQ L H P YF+ RH+ S N VR C +C LD + +
Sbjct: 145 ----TCFMSSILQCLIHNP----YFI--RHSMSQIHSNNCKVRSPDKCFSCALDKIVHEL 194
Query: 259 FCGDRMPYSPAK---------FLYSW---WRHASNLASYEQQDAHEFFISMLDGIHEKVE 306
+ + + F+Y W+ NLA Y QQDAHEF+ +++ IH+
Sbjct: 195 YGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQSYV 254
Query: 307 KDQHKPRS---QGNGDC-CIAHRVFSGILRSDVMCMACGFTS-TTFDPCVDFSLDLEPNQ 361
D + N C CI H VF G L S ++C C S TT DP +D SLD++ +
Sbjct: 255 LDLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIKDKK 314
Query: 362 GSSMKTSSTKSNHSCNCEADGMNSSQNCGISTLMGCLDRFTRPERLGSDQKFFCQQCQVR 421
L CLD F + E+L D + C +C
Sbjct: 315 -------------------------------KLYECLDSFHKKEQL-KDFNYHCGECNST 342
Query: 422 QESLKQMSIRKLPLVSCFHIKRFEHSSVRKMSRKVDRYLQFPLSLDMAPYLSSSILRSRF 481
Q+++KQ+ I KLP V +KRFEH + +RK+D +++FP L+M Y S+
Sbjct: 343 QDAIKQLGIHKLPSVLVLQLKRFEH-LLNGSNRKLDDFIEFPTYLNMKNYCSTK------ 395
Query: 482 GNRFFPFDGDE-SNTLNEPSSEFELFAVVTHTGKLDAGHYVTYLRLS-NKWYKCDDAWIT 539
+ D+ S P +EL +V+H G ++ GHY+ + ++S +W+K +D+ ++
Sbjct: 396 -------EKDKHSENGKVPDIIYELIGIVSHKGTVNEGHYIAFCKISGGQWFKFNDSMVS 448
Query: 540 EVNENTVRAAQGYMMFYV 557
+++ V Q Y++FY
Sbjct: 449 SISQEEVLKEQAYLLFYT 466
>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 = 168 bits (425), Expect = 9e-42, Method: Compositional matrix adjust.
Identities = 140/558 (25%), Positives = 231/558 (41%), Gaps = 118/558 (21%)
Query: 23 CPHLADFHARNGTKPFRAIQDCLHIKPPGGRAAIRRDSSEVPRCGVCGDSSCPRLYACMA 82
CPH+ +K ++ C + + + +CG C + + + C+
Sbjct: 9 CPHIQQVFQNEKSKD-GVLKTCNAARYILNHSVPKEKFLNTMKCGTCHEINSGATFMCLQ 67
Query: 83 CAAVSCHVPPHSSHVAIHATKTSSACSHEIAVDVDRAELFCCACRDQVYDRDFDAAVVLA 142
C C + SH H+ + H ++ + LFC C D + + D +LA
Sbjct: 68 CGFCGCW---NHSHFLSHSKQIG----HIFGINSNNGLLFCFKCEDYIGNIDLINDAILA 120
Query: 143 HTTSIIQSSKPENLRKRRRIDYRPWSPDLRERSLMVNNASPIDSMSSSXXXXXXXXXXXX 202
+ + + P + R + S + +M S
Sbjct: 121 --------------KYWDDVCTKTMVPSMERR----DGLSGLINMGS------------- 149
Query: 203 XXXXTCFMNSVLQALFHTPPLRNYFLSDRHNRYYCQSKN-GVR---LCLACDLDTMFSAI 258
TCFM+S+LQ L H P YF+ RH+ S N VR C +C LD + +
Sbjct: 150 ----TCFMSSILQCLIHNP----YFI--RHSMSQIHSNNCKVRSPDKCFSCALDKIVHEL 199
Query: 259 FCGDRMPYSPAK---------FLYSW---WRHASNLASYEQQDAHEFFISMLDGIHEKVE 306
+ + + F+Y W+ NLA Y QQDAHEF+ +++ IH+
Sbjct: 200 YGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQSYV 259
Query: 307 KDQHKPRS---QGNGDC-CIAHRVFSGILRSDVMCMACGFTS-TTFDPCVDFSLDLEPNQ 361
D + N C CI H VF G L S ++C C S TT DP +D SLD++ +
Sbjct: 260 LDLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIKDKK 319
Query: 362 GSSMKTSSTKSNHSCNCEADGMNSSQNCGISTLMGCLDRFTRPERLGSDQKFFCQQCQVR 421
L CLD F + E+L D + C +C
Sbjct: 320 -------------------------------KLYECLDSFHKKEQL-KDFNYHCGECNST 347
Query: 422 QESLKQMSIRKLPLVSCFHIKRFEHSSVRKMSRKVDRYLQFPLSLDMAPYLSSSILRSRF 481
Q+++KQ+ I KLP V +KRFEH + +RK+D +++FP L+M Y S+
Sbjct: 348 QDAIKQLGIHKLPSVLVLQLKRFEH-LLNGSNRKLDDFIEFPTYLNMKNYCSTK------ 400
Query: 482 GNRFFPFDGDE-SNTLNEPSSEFELFAVVTHTGKLDAGHYVTYLRLS-NKWYKCDDAWIT 539
+ D+ S P +EL +V+H G ++ GHY+ + ++S +W+K +D+ ++
Sbjct: 401 -------EKDKHSENGKVPDIIYELIGIVSHKGTVNEGHYIAFCKISGGQWFKFNDSMVS 453
Query: 540 EVNENTVRAAQGYMMFYV 557
+++ V Q Y++FY
Sbjct: 454 SISQEEVLKEQAYLLFYT 471
>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 = 167 bits (422), Expect = 2e-41, Method: Compositional matrix adjust.
Identities = 139/558 (24%), Positives = 231/558 (41%), Gaps = 118/558 (21%)
Query: 23 CPHLADFHARNGTKPFRAIQDCLHIKPPGGRAAIRRDSSEVPRCGVCGDSSCPRLYACMA 82
CPH+ +K ++ C + + + +CG C + + + C+
Sbjct: 9 CPHIQQVFQNEKSKD-GVLKTCNAARYILNHSVPKEKFLNTMKCGTCHEINSGATFMCLQ 67
Query: 83 CAAVSCHVPPHSSHVAIHATKTSSACSHEIAVDVDRAELFCCACRDQVYDRDFDAAVVLA 142
C C + SH H+ + H ++ + LFC C D + + D +LA
Sbjct: 68 CGFCGCW---NHSHFLSHSKQIG----HIFGINSNNGLLFCFKCEDYIGNIDLINDAILA 120
Query: 143 HTTSIIQSSKPENLRKRRRIDYRPWSPDLRERSLMVNNASPIDSMSSSXXXXXXXXXXXX 202
+ + + P + R + S + +M +
Sbjct: 121 --------------KYWDDVCTKTMVPSMERR----DGLSGLINMGN------------- 149
Query: 203 XXXXTCFMNSVLQALFHTPPLRNYFLSDRHNRYYCQSKN-GVR---LCLACDLDTMFSAI 258
TCFM+S+LQ L H P YF+ RH+ S N VR C +C LD + +
Sbjct: 150 ----TCFMSSILQCLIHNP----YFI--RHSMSQIHSNNCKVRSPDKCFSCALDKIVHEL 199
Query: 259 FCGDRMPYSPAK---------FLYSW---WRHASNLASYEQQDAHEFFISMLDGIHEKVE 306
+ + + F+Y W+ NLA Y QQDAHEF+ +++ IH+
Sbjct: 200 YGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQSYV 259
Query: 307 KDQHKPRS---QGNGDC-CIAHRVFSGILRSDVMCMACGFTS-TTFDPCVDFSLDLEPNQ 361
D + N C CI H VF G L S ++C C S TT DP +D SLD++ +
Sbjct: 260 LDLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIKDKK 319
Query: 362 GSSMKTSSTKSNHSCNCEADGMNSSQNCGISTLMGCLDRFTRPERLGSDQKFFCQQCQVR 421
L CLD F + E+L D + C +C
Sbjct: 320 -------------------------------KLYECLDSFHKKEQL-KDFNYHCGECNST 347
Query: 422 QESLKQMSIRKLPLVSCFHIKRFEHSSVRKMSRKVDRYLQFPLSLDMAPYLSSSILRSRF 481
Q+++KQ+ I KLP V +KRFEH + +RK+D +++FP L+M Y S+
Sbjct: 348 QDAIKQLGIHKLPSVLVLQLKRFEH-LLNGSNRKLDDFIEFPTYLNMKNYCSTK------ 400
Query: 482 GNRFFPFDGDE-SNTLNEPSSEFELFAVVTHTGKLDAGHYVTYLRLS-NKWYKCDDAWIT 539
+ D+ S P +EL +V+H G ++ GHY+ + ++S +W+K +D+ ++
Sbjct: 401 -------EKDKHSENGKVPDIIYELIGIVSHKGTVNEGHYIAFCKISGGQWFKFNDSMVS 453
Query: 540 EVNENTVRAAQGYMMFYV 557
+++ V Q Y++FY
Sbjct: 454 SISQEEVLKEQAYLLFYT 471
>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 = 132 bits (333), Expect = 4e-31, Method: Compositional matrix adjust.
Identities = 99/377 (26%), Positives = 165/377 (43%), Gaps = 65/377 (17%)
Query: 207 TCFMNSVLQALFHTPPLRNYFLSDRH----NRYYCQSKNGVRLCLACDLDTMFSAIFCGD 262
T FMNS LQ L +T PL +YFL D + NR + G++ +A + ++ G
Sbjct: 17 TXFMNSALQCLSNTAPLTDYFLKDEYEAEINR---DNPLGMKGEIAEAYAELIKQMWSGR 73
Query: 263 RMPYSPAKFLYSWWRHASNLASYEQQDAHEFFISMLDGIHEKVEKDQHKPR-----SQGN 317
+P F R A + Y+QQD+ E +LDG+HE + + + KP + G
Sbjct: 74 DAHVAPRMFKTQVGRFAPQFSGYQQQDSQELLAFLLDGLHEDLNRVKKKPYLELKDANGR 133
Query: 318 GDCCIA------HRV---------FSGILRSDVMCMACGFTSTTFDPCVDFSLDLEPNQG 362
D +A HR+ F G+ +S ++C C S TFDP +L L +
Sbjct: 134 PDAVVAKEAWENHRLRNDSVIVDTFHGLFKSTLVCPECAKVSVTFDPFCYLTLPLPLKKD 193
Query: 363 SSMKTSSTKSNHSCNCEADGMNSSQNCGISTLMGCLDRFTRPERLGSDQKFFCQQCQVRQ 422
M+ + L C++ FT E LG ++C C+ Q
Sbjct: 194 RVMEGPMLQPQKKKKTTV------------ALRDCIELFTTMETLGEHDPWYCPNCKKHQ 241
Query: 423 ESLKQMSIRKLPLVSCFHIKRFEHSSVRKMSRKVDRYLQFPL-SLDMAPYLSSSILRSRF 481
++ K+ + LP + H+KRF ++ R K+D ++FP+ L+M+ ++ + R
Sbjct: 242 QATKKFDLWSLPKILVVHLKRFSYN--RYWRDKLDTVVEFPIRGLNMSEFVCNLSAR--- 296
Query: 482 GNRFFPFDGDESNTLNEPSSEFELFAVVTHTGKLDAGHYVTYL--RLSNKWYKCDDAWIT 539
P+ ++L AV H G + GHY Y +L+ KWY DD+ ++
Sbjct: 297 -----PY-------------VYDLIAVSNHYGAMGVGHYTAYAKNKLNGKWYYFDDSNVS 338
Query: 540 EVNENTVRAAQGYMMFY 556
+E+ + Y++FY
Sbjct: 339 LASEDQIVTKAAYVLFY 355
>pdb|3N3K|A Chain A, The Catalytic Domain Of Usp8 In Complex With A Usp8
Specific Inhibitor
Length = 396
Score = 127 bits (320), Expect = 1e-29, Method: Compositional matrix adjust.
Identities = 103/378 (27%), Positives = 169/378 (44%), Gaps = 82/378 (21%)
Query: 207 TCFMNSVLQALFHTPPLRNYF----LSDRHNRYYCQSKNGVRLCLACDLDTMFSAIFCGD 262
TC+MNS+LQ L + P L +YF D NR G +A + + A++ G
Sbjct: 71 TCYMNSILQCLCNAPHLADYFNRNCYQDDINRSNLLGHKGE---VAEEFGIIMKALWTGQ 127
Query: 263 RMPYSPAKFLYSWWRHASNLASYEQQDAHEFFISMLDGIHEKVEK-DQHKPRSQGNGDCC 321
SP F + + A Y QQD+ E + ++DG+HE + K D K + N D
Sbjct: 128 YRYISPKDFKITIGKINDQFAGYSQQDSQELLLFLMDGLHEDLNKADNRKRYKEENNDHL 187
Query: 322 -------------------IAHRVFSGILRSDVMCMACGFTSTTFDPCVDFSLDLEPNQG 362
I +F G +S V C+ C S TF+ + SL L
Sbjct: 188 DDFKAAEHAWQKHKQLNESIIVALFQGQFKSTVQCLTCHKKSRTFEAFMYLSLPLA---- 243
Query: 363 SSMKTSSTKSNHSCNCEADGMNSSQNCGISTLMGCLDRFTRPERLGSDQKFFCQQCQVRQ 422
S+ C TL CL F++ E+L + +F+C C+ R+
Sbjct: 244 ----------------------STSKC---TLQDCLRLFSKEEKLTDNNRFYCSHCRARR 278
Query: 423 ESLKQMSIRKLPLVSCFHIKRFEHSSVRKMSRKVDRYLQFPL-SLDMAPYLSSSILRSRF 481
+SLK++ I KLP V H+KRF + + +K+ + FPL +LD++ Y+
Sbjct: 279 DSLKKIEIWKLPPVLLVHLKRFSYDG--RWKQKLQTSVDFPLENLDLSQYVI-------- 328
Query: 482 GNRFFPFDGDESNTLNEPSSEFELFAVVTHTGKLDAGHYVTYLRLS--NKWYKCDDAWIT 539
G ++N ++ LF+V H G LD GHY Y + + +W+K DD ++
Sbjct: 329 --------GPKNNL-----KKYNLFSVSNHYGGLDGGHYTAYCKNAARQRWFKFDDHEVS 375
Query: 540 EVNENTVRAAQGYMMFYV 557
+++ ++V+++ Y++FY
Sbjct: 376 DISVSSVKSSAAYILFYT 393
>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 = 125 bits (313), Expect = 8e-29, Method: Compositional matrix adjust.
Identities = 102/375 (27%), Positives = 161/375 (42%), Gaps = 78/375 (20%)
Query: 207 TCFMNSVLQALFHTPPLRNYFLSDRHNRYYCQSKNGVRLCLACDLDTMFSAIFCGD-RMP 265
TCFMNS+LQ L +T LR+Y L + R N L + + I+
Sbjct: 37 TCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNA-HTALVEEFAKLIQTIWTSSPNDV 95
Query: 266 YSPAKFLYSWWRHASNLASYEQQDAHEFFISMLDGIHEKVEKDQHKPRSQGNG------- 318
SP++F R+A Y QQDA EF +LDG+H +V + +P+S
Sbjct: 96 VSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPENLDHLPDD 155
Query: 319 --------------DCCIAHRVFSGILRSDVMCMACGFTSTTFDPCVDFSLDLEPNQGSS 364
D I +F G L+S + C CG+ ST FDP D SL +
Sbjct: 156 EKGRQMWRKYLEREDSRIGD-LFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPI------- 207
Query: 365 MKTSSTKSNHSCNCEADGMNSSQNCGISTLMGCLDRFTRPERLGSDQKFFCQQCQVRQES 424
+ + TLM C+ FT+ + L D+K C +C+ R+
Sbjct: 208 --------------------AKRGYPEVTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRC 247
Query: 425 LKQMSIRKLPLVSCFHIKRFEHSSVRKMSRKVDRYLQFPL-SLDMAPYLSSSILRSRFGN 483
+K+ SI++ P + H+KRF S +R + K+ ++ FPL LD+ + S
Sbjct: 248 IKKFSIQRFPKILVLHLKRFSESRIR--TSKLTTFVNFPLRDLDLREFASE--------- 296
Query: 484 RFFPFDGDESNTLNEPSSEFELFAVVTHTGKLDAGHYVTYLRL--SNKWYKCDDAWITEV 541
N + + L+AV H+G GHY Y R + +W+ +D+ +T +
Sbjct: 297 -------------NTNHAVYNLYAVSNHSGTTMGGHYTAYCRSPGTGEWHTFNDSSVTPM 343
Query: 542 NENTVRAAQGYMMFY 556
+ + VR + Y++FY
Sbjct: 344 SSSQVRTSDAYLLFY 358
>pdb|2HD5|A Chain A, Usp2 In Complex With Ubiquitin
Length = 359
Score = 125 bits (313), Expect = 9e-29, Method: Compositional matrix adjust.
Identities = 102/375 (27%), Positives = 161/375 (42%), Gaps = 78/375 (20%)
Query: 207 TCFMNSVLQALFHTPPLRNYFLSDRHNRYYCQSKNGVRLCLACDLDTMFSAIFCGD-RMP 265
TCFMNS+LQ L +T LR+Y L + R N L + + I+
Sbjct: 18 TCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNA-HTALVEEFAKLIQTIWTSSPNDV 76
Query: 266 YSPAKFLYSWWRHASNLASYEQQDAHEFFISMLDGIHEKVEKDQHKPRSQGNG------- 318
SP++F R+A Y QQDA EF +LDG+H +V + +P+S
Sbjct: 77 VSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPENLDHLPDD 136
Query: 319 --------------DCCIAHRVFSGILRSDVMCMACGFTSTTFDPCVDFSLDLEPNQGSS 364
D I +F G L+S + C CG+ ST FDP D SL +
Sbjct: 137 EKGRQMWRKYLEREDSRIGD-LFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPI------- 188
Query: 365 MKTSSTKSNHSCNCEADGMNSSQNCGISTLMGCLDRFTRPERLGSDQKFFCQQCQVRQES 424
+ + TLM C+ FT+ + L D+K C +C+ R+
Sbjct: 189 --------------------AKRGYPEVTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRC 228
Query: 425 LKQMSIRKLPLVSCFHIKRFEHSSVRKMSRKVDRYLQFPL-SLDMAPYLSSSILRSRFGN 483
+K+ SI++ P + H+KRF S +R + K+ ++ FPL LD+ + S
Sbjct: 229 IKKFSIQRFPKILVLHLKRFSESRIR--TSKLTTFVNFPLRDLDLREFASE--------- 277
Query: 484 RFFPFDGDESNTLNEPSSEFELFAVVTHTGKLDAGHYVTYLRL--SNKWYKCDDAWITEV 541
N + + L+AV H+G GHY Y R + +W+ +D+ +T +
Sbjct: 278 -------------NTNHAVYNLYAVSNHSGTTMGGHYTAYCRSPGTGEWHTFNDSSVTPM 324
Query: 542 NENTVRAAQGYMMFY 556
+ + VR + Y++FY
Sbjct: 325 SSSQVRTSDAYLLFY 339
>pdb|2GFO|A Chain A, Structure Of The Catalytic Domain Of Human Ubiquitin
Carboxyl-terminal Hydrolase 8
Length = 396
Score = 122 bits (307), Expect = 4e-28, Method: Compositional matrix adjust.
Identities = 102/378 (26%), Positives = 166/378 (43%), Gaps = 82/378 (21%)
Query: 207 TCFMNSVLQALFHTPPLRNYF----LSDRHNRYYCQSKNGVRLCLACDLDTMFSAIFCGD 262
TC+ NS+LQ L + P L +YF D NR G +A + + A++ G
Sbjct: 71 TCYXNSILQCLCNAPHLADYFNRNCYQDDINRSNLLGHKGE---VAEEFGIIXKALWTGQ 127
Query: 263 RMPYSPAKFLYSWWRHASNLASYEQQDAHEFFISMLDGIHEKVEK-DQHKPRSQGNGDCC 321
SP F + + A Y QQD+ E + + DG+HE + K D K + N D
Sbjct: 128 YRYISPKDFKITIGKINDQFAGYSQQDSQELLLFLXDGLHEDLNKADNRKRYKEENNDHL 187
Query: 322 -------------------IAHRVFSGILRSDVMCMACGFTSTTFDPCVDFSLDLEPNQG 362
I +F G +S V C+ C S TF+ SL L
Sbjct: 188 DDFKAAEHAWQKHKQLNESIIVALFQGQFKSTVQCLTCHKKSRTFEAFXYLSLPLA---- 243
Query: 363 SSMKTSSTKSNHSCNCEADGMNSSQNCGISTLMGCLDRFTRPERLGSDQKFFCQQCQVRQ 422
S+ C TL CL F++ E+L + +F+C C+ R+
Sbjct: 244 ----------------------STSKC---TLQDCLRLFSKEEKLTDNNRFYCSHCRARR 278
Query: 423 ESLKQMSIRKLPLVSCFHIKRFEHSSVRKMSRKVDRYLQFPL-SLDMAPYLSSSILRSRF 481
+SLK++ I KLP V H+KRF + + +K+ + FPL +LD++ Y+
Sbjct: 279 DSLKKIEIWKLPPVLLVHLKRFSYDG--RWKQKLQTSVDFPLENLDLSQYVI-------- 328
Query: 482 GNRFFPFDGDESNTLNEPSSEFELFAVVTHTGKLDAGHYVTYLRLS--NKWYKCDDAWIT 539
G ++N ++ LF+V H G LD GHY Y + + +W+K DD ++
Sbjct: 329 --------GPKNNL-----KKYNLFSVSNHYGGLDGGHYTAYCKNAARQRWFKFDDHEVS 375
Query: 540 EVNENTVRAAQGYMMFYV 557
+++ ++V+++ Y++FY
Sbjct: 376 DISVSSVKSSAAYILFYT 393
>pdb|2IBI|A Chain A, Covalent Ubiquitin-Usp2 Complex
Length = 374
Score = 122 bits (305), Expect = 7e-28, Method: Compositional matrix adjust.
Identities = 101/375 (26%), Positives = 159/375 (42%), Gaps = 78/375 (20%)
Query: 207 TCFMNSVLQALFHTPPLRNYFLSDRHNRYYCQSKNGVRLCLACDLDTMFSAIFCGD-RMP 265
TCFMNS+LQ L +T LR+Y L + R N L + + I+
Sbjct: 44 TCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNA-HTALVEEFAKLIQTIWTSSPNDV 102
Query: 266 YSPAKFLYSWWRHASNLASYEQQDAHEFFISMLDGIHEKVEKDQHKPRSQGNG------- 318
SP++F R+A Y QQDA EF +LDG+H +V + +P+S
Sbjct: 103 VSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPENLDHLPDD 162
Query: 319 --------------DCCIAHRVFSGILRSDVMCMACGFTSTTFDPCVDFSLDLEPNQGSS 364
D I +F G L+S + C CG+ ST FDP D SL +
Sbjct: 163 EKGRQMWRKYLEREDSRIGD-LFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPI------- 214
Query: 365 MKTSSTKSNHSCNCEADGMNSSQNCGISTLMGCLDRFTRPERLGSDQKFFCQQCQVRQES 424
+ + TLM C+ FT+ + L D C +C+ R+
Sbjct: 215 --------------------AKRGYPEVTLMDCMRLFTKEDVLDGDAAPTCCRCRGRKRC 254
Query: 425 LKQMSIRKLPLVSCFHIKRFEHSSVRKMSRKVDRYLQFPL-SLDMAPYLSSSILRSRFGN 483
+K+ SI++ P + H+KRF S +R + K+ ++ FPL LD+ + S
Sbjct: 255 IKKFSIQRFPKILVLHLKRFSESRIR--TSKLTTFVNFPLRDLDLREFASE--------- 303
Query: 484 RFFPFDGDESNTLNEPSSEFELFAVVTHTGKLDAGHYVTYLRL--SNKWYKCDDAWITEV 541
N + + L+AV H+G GHY Y R + +W+ +D+ +T +
Sbjct: 304 -------------NTNHAVYNLYAVSNHSGTTMGGHYTAYCRSPGTGEWHTFNDSSVTPM 350
Query: 542 NENTVRAAQGYMMFY 556
+ + VR + Y++FY
Sbjct: 351 SSSQVRTSDAYLLFY 365
>pdb|3NHE|A Chain A, High Resolution Structure (1.26a) Of Usp2a In Complex With
Ubiquitin
Length = 348
Score = 121 bits (304), Expect = 1e-27, Method: Compositional matrix adjust.
Identities = 101/375 (26%), Positives = 160/375 (42%), Gaps = 78/375 (20%)
Query: 207 TCFMNSVLQALFHTPPLRNYFLSDRHNRYYCQSKNGVRLCLACDLDTMFSAIFCGD-RMP 265
T FMNS+LQ L +T LR+Y L + R N L + + I+
Sbjct: 18 TXFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNA-HTALVEEFAKLIQTIWTSSPNDV 76
Query: 266 YSPAKFLYSWWRHASNLASYEQQDAHEFFISMLDGIHEKVEKDQHKPRSQGNG------- 318
SP++F R+A Y QQDA EF +LDG+H +V + +P+S
Sbjct: 77 VSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPENLDHLPDD 136
Query: 319 --------------DCCIAHRVFSGILRSDVMCMACGFTSTTFDPCVDFSLDLEPNQGSS 364
D I +F G L+S + C CG+ ST FDP D SL +
Sbjct: 137 EKGRQMWRKYLEREDSRIGD-LFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPI------- 188
Query: 365 MKTSSTKSNHSCNCEADGMNSSQNCGISTLMGCLDRFTRPERLGSDQKFFCQQCQVRQES 424
+ + TLM C+ FT+ + L D+K C +C+ R+
Sbjct: 189 --------------------AKRGYPEVTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRC 228
Query: 425 LKQMSIRKLPLVSCFHIKRFEHSSVRKMSRKVDRYLQFPL-SLDMAPYLSSSILRSRFGN 483
+K+ SI++ P + H+KRF S +R + K+ ++ FPL LD+ + S
Sbjct: 229 IKKFSIQRFPKILVLHLKRFSESRIR--TSKLTTFVNFPLRDLDLREFASE--------- 277
Query: 484 RFFPFDGDESNTLNEPSSEFELFAVVTHTGKLDAGHYVTYLRL--SNKWYKCDDAWITEV 541
N + + L+AV H+G GHY Y R + +W+ +D+ +T +
Sbjct: 278 -------------NTNHAVYNLYAVSNHSGTTMGGHYTAYCRSPGTGEWHTFNDSSVTPM 324
Query: 542 NENTVRAAQGYMMFY 556
+ + VR + Y++FY
Sbjct: 325 SSSQVRTSDAYLLFY 339
>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 = 114 bits (286), Expect = 1e-25, Method: Compositional matrix adjust.
Identities = 99/392 (25%), Positives = 167/392 (42%), Gaps = 98/392 (25%)
Query: 207 TCFMNSVLQALFHTPPLRNYFLSDRHNRYYCQSKNGVRLCLACDLDTMFSAIFCGDRMPY 266
TCF+N+VLQ L T PLR++ L + + G R A +L F+ + P
Sbjct: 31 TCFLNAVLQCLSSTRPLRDFCL---RRDFRQEVPGGGR---AQELTEAFADVIGALWHPD 84
Query: 267 S-----PAKFLYSWWRHASNLASYEQQDAHEFFISMLDGIHEKV-EKDQHKPRSQGNGDC 320
S P +F + ++ + + Y QQDA EF +++ +H ++ + + P NG
Sbjct: 85 SCEAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRAPPILANGPV 144
Query: 321 CIAHR----------------------------------VFSGILRSDVMCMACGFTSTT 346
R +F G L+S + C ACG+ STT
Sbjct: 145 PSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKCQACGYRSTT 204
Query: 347 FDPCVDFSLDLEPNQGSSMKTSSTKSNHSCNCEADGMNSSQNCGISTLMGCLDRFTRPER 406
F+ D SL + P +G + G +L C + FT+ E
Sbjct: 205 FEVFCDLSLPI-PKKGFA------------------------GGKVSLRDCFNLFTKEEE 239
Query: 407 LGSDQKFFCQQCQVRQESLKQMSIRKLPLVSCFHIKRFEHS--SVRKMSRKVDRYLQFPL 464
L S+ C +C+ + S K++++++ P + H+ RF S S++K S VD FPL
Sbjct: 240 LESENAPVCDRCRQKTRSTKKLTVQRFPRILVLHLNRFSASRGSIKKSSVGVD----FPL 295
Query: 465 SLDMAPYLSSSILRSRFGNRFFPFDGDESNTLNEPSSEFELFAVVTHTGKLDAGHYVTYL 524
R G+ F D++ S ++L+A+ H+G + GHY
Sbjct: 296 Q------------RLSLGD----FASDKAG-----SPVYQLYALCNHSGSVHYGHYTALC 334
Query: 525 RLSNKWYKCDDAWITEVNENTVRAAQGYMMFY 556
R W+ +D+ ++ V+EN V +++GY++FY
Sbjct: 335 RCQTGWHVYNDSRVSPVSENQVASSEGYVLFY 366
>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 = 114 bits (286), Expect = 1e-25, Method: Compositional matrix adjust.
Identities = 99/392 (25%), Positives = 167/392 (42%), Gaps = 98/392 (25%)
Query: 207 TCFMNSVLQALFHTPPLRNYFLSDRHNRYYCQSKNGVRLCLACDLDTMFSAIFCGDRMPY 266
TCF+N+VLQ L T PLR++ L + + G R A +L F+ + P
Sbjct: 25 TCFLNAVLQCLSSTRPLRDFCL---RRDFRQEVPGGGR---AQELTEAFADVIGALWHPD 78
Query: 267 S-----PAKFLYSWWRHASNLASYEQQDAHEFFISMLDGIHEKV-EKDQHKPRSQGNGDC 320
S P +F + ++ + + Y QQDA EF +++ +H ++ + + P NG
Sbjct: 79 SCEAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRAPPILANGPV 138
Query: 321 CIAHR----------------------------------VFSGILRSDVMCMACGFTSTT 346
R +F G L+S + C ACG+ STT
Sbjct: 139 PSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKCQACGYRSTT 198
Query: 347 FDPCVDFSLDLEPNQGSSMKTSSTKSNHSCNCEADGMNSSQNCGISTLMGCLDRFTRPER 406
F+ D SL + P +G + G +L C + FT+ E
Sbjct: 199 FEVFCDLSLPI-PKKGFAG------------------------GKVSLRDCFNLFTKEEE 233
Query: 407 LGSDQKFFCQQCQVRQESLKQMSIRKLPLVSCFHIKRFEHS--SVRKMSRKVDRYLQFPL 464
L S+ C +C+ + S K++++++ P + H+ RF S S++K S VD FPL
Sbjct: 234 LESENAPVCDRCRQKTRSTKKLTVQRFPRILVLHLNRFSASRGSIKKSSVGVD----FPL 289
Query: 465 SLDMAPYLSSSILRSRFGNRFFPFDGDESNTLNEPSSEFELFAVVTHTGKLDAGHYVTYL 524
R G+ F D++ S ++L+A+ H+G + GHY
Sbjct: 290 Q------------RLSLGD----FASDKAG-----SPVYQLYALCNHSGSVHYGHYTALC 328
Query: 525 RLSNKWYKCDDAWITEVNENTVRAAQGYMMFY 556
R W+ +D+ ++ V+EN V +++GY++FY
Sbjct: 329 RCQTGWHVYNDSRVSPVSENQVASSEGYVLFY 360
>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 = 114 bits (286), Expect = 1e-25, Method: Compositional matrix adjust.
Identities = 99/392 (25%), Positives = 167/392 (42%), Gaps = 98/392 (25%)
Query: 207 TCFMNSVLQALFHTPPLRNYFLSDRHNRYYCQSKNGVRLCLACDLDTMFSAIFCGDRMPY 266
TCF+N+VLQ L T PLR++ L + + G R A +L F+ + P
Sbjct: 12 TCFLNAVLQCLSSTRPLRDFCL---RRDFRQEVPGGGR---AQELTEAFADVIGALWHPD 65
Query: 267 S-----PAKFLYSWWRHASNLASYEQQDAHEFFISMLDGIHEKV-EKDQHKPRSQGNGDC 320
S P +F + ++ + + Y QQDA EF +++ +H ++ + + P NG
Sbjct: 66 SCEAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRAPPILANGPV 125
Query: 321 CIAHR----------------------------------VFSGILRSDVMCMACGFTSTT 346
R +F G L+S + C ACG+ STT
Sbjct: 126 PSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKCQACGYRSTT 185
Query: 347 FDPCVDFSLDLEPNQGSSMKTSSTKSNHSCNCEADGMNSSQNCGISTLMGCLDRFTRPER 406
F+ D SL + P +G + G +L C + FT+ E
Sbjct: 186 FEVFCDLSLPI-PKKGFAG------------------------GKVSLRDCFNLFTKEEE 220
Query: 407 LGSDQKFFCQQCQVRQESLKQMSIRKLPLVSCFHIKRFEHS--SVRKMSRKVDRYLQFPL 464
L S+ C +C+ + S K++++++ P + H+ RF S S++K S VD FPL
Sbjct: 221 LESENAPVCDRCRQKTRSTKKLTVQRFPRILVLHLNRFSASRGSIKKSSVGVD----FPL 276
Query: 465 SLDMAPYLSSSILRSRFGNRFFPFDGDESNTLNEPSSEFELFAVVTHTGKLDAGHYVTYL 524
R G+ F D++ S ++L+A+ H+G + GHY
Sbjct: 277 Q------------RLSLGD----FASDKAG-----SPVYQLYALCNHSGSVHYGHYTALC 315
Query: 525 RLSNKWYKCDDAWITEVNENTVRAAQGYMMFY 556
R W+ +D+ ++ V+EN V +++GY++FY
Sbjct: 316 RCQTGWHVYNDSRVSPVSENQVASSEGYVLFY 347
>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 = 52.8 bits (125), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 76/340 (22%), Positives = 121/340 (35%), Gaps = 82/340 (24%)
Query: 207 TCFMNSVLQALFHTPPLRN--YFLSDRHNRYYCQSKNGVRLCLACDLDTMFSAIFCGDRM 264
TC+MNS+LQ LF T LR Y + + S V L L +F + D+
Sbjct: 15 TCYMNSLLQTLFFTNQLRKAVYMMPTEGD----DSSKSVPLALQ----RVFYELQHSDK- 65
Query: 265 PYSPAKFLYSW-WRHASNLASYEQQDAHEFFISMLDGIHEKVEKDQHKPRSQGNGDCCIA 323
P K S+ W L S+ Q D E +LD + K++ G C
Sbjct: 66 PVGTKKLTKSFGW---ETLDSFMQHDVQELCRVLLDNVENKMK-----------GTCVEG 111
Query: 324 H--RVFSGILRSDVMCMACGFTSTTFDPCVDFSLDLEPNQGSSMKTSSTKSNHSCNCEAD 381
++F G + S + C + S + D L ++
Sbjct: 112 TIPKLFRGKMVSYIQCKEVDYRSDRREDYYDIQLSIK----------------------- 148
Query: 382 GMNSSQNCGISTLMGCLDRFTRPERLGSDQKFFCQQCQVRQESLKQMSIRKLPLVSCFHI 441
G + + E+L D K+ + + QE+ K + LP V +
Sbjct: 149 --------GKKNIFESFVDYVAVEQLDGDNKYDAGEHGL-QEAEKGVKFLTLPPVLHLQL 199
Query: 442 KRFEHSSVRKMSRKVDRYLQFPLSLDMAPYLSSSILRSRFGNRFFPFDGDESNTLNEPSS 501
RF + + K++ +FP L + +L + D + N
Sbjct: 200 MRFMYDPQTDQNIKINDRFEFPEQLPLDEFLQKT---------------DPKDPAN---- 240
Query: 502 EFELFAVVTHTGKLDAGHYVTYL--RLSNKWYKCDDAWIT 539
+ L AV+ H+G GHYV YL + KW K DD ++
Sbjct: 241 -YILHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFDDDVVS 279
>pdb|2F1Z|A Chain A, Crystal Structure Of Hausp
pdb|2F1Z|B Chain B, Crystal Structure Of Hausp
Length = 522
Score = 52.4 bits (124), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 76/336 (22%), Positives = 120/336 (35%), Gaps = 82/336 (24%)
Query: 207 TCFMNSVLQALFHTPPLRN--YFLSDRHNRYYCQSKNGVRLCLACDLDTMFSAIFCGDRM 264
TC+MNS+LQ LF T LR Y + + S V L L +F + D+
Sbjct: 184 TCYMNSLLQTLFFTNQLRKAVYMMPTEGD----DSSKSVPLALQ----RVFYELQHSDK- 234
Query: 265 PYSPAKFLYSW-WRHASNLASYEQQDAHEFFISMLDGIHEKVEKDQHKPRSQGNGDCCIA 323
P K S+ W L S+ Q D E +LD + K++ G C
Sbjct: 235 PVGTKKLTKSFGWE---TLDSFMQHDVQELCRVLLDNVENKMK-----------GTCVEG 280
Query: 324 H--RVFSGILRSDVMCMACGFTSTTFDPCVDFSLDLEPNQGSSMKTSSTKSNHSCNCEAD 381
++F G + S + C + S + D L ++
Sbjct: 281 TIPKLFRGKMVSYIQCKEVDYRSDRREDYYDIQLSIK----------------------- 317
Query: 382 GMNSSQNCGISTLMGCLDRFTRPERLGSDQKFFCQQCQVRQESLKQMSIRKLPLVSCFHI 441
G + + E+L D K+ + + QE+ K + LP V +
Sbjct: 318 --------GKKNIFESFVDYVAVEQLDGDNKYDAGEHGL-QEAEKGVKFLTLPPVLHLQL 368
Query: 442 KRFEHSSVRKMSRKVDRYLQFPLSLDMAPYLSSSILRSRFGNRFFPFDGDESNTLNEPSS 501
RF + + K++ +FP L + +L + + D +N +
Sbjct: 369 MRFMYDPQTDQNIKINDRFEFPEQLPLDEFLQKTDPK------------DPANYI----- 411
Query: 502 EFELFAVVTHTGKLDAGHYVTYL--RLSNKWYKCDD 535
L AV+ H+G GHYV YL + KW K DD
Sbjct: 412 ---LHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFDD 444
>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 = 48.1 bits (113), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 73/340 (21%), Positives = 115/340 (33%), Gaps = 82/340 (24%)
Query: 207 TCFMNSVLQALFHTPPLRNYFLSDRHNRYYCQSKNG--VRLCLACDLDTMFSAIFCGDRM 264
TC+ NS+LQ LF T LR Y G + L +F + D+
Sbjct: 15 TCYXNSLLQTLFFTNQLRKAV--------YXXPTEGDDSSKSVPLALQRVFYELQHSDK- 65
Query: 265 PYSPAKFLYSW-WRHASNLASYEQQDAHEFFISMLDGIHEKVEKDQHKPRSQGNGDCCIA 323
P K S+ W L S+ Q D E +LD + K + G C
Sbjct: 66 PVGTKKLTKSFGW---ETLDSFXQHDVQELCRVLLDNVENKXK-----------GTCVEG 111
Query: 324 H--RVFSGILRSDVMCMACGFTSTTFDPCVDFSLDLEPNQGSSMKTSSTKSNHSCNCEAD 381
++F G S + C + S + D L ++
Sbjct: 112 TIPKLFRGKXVSYIQCKEVDYRSDRREDYYDIQLSIK----------------------- 148
Query: 382 GMNSSQNCGISTLMGCLDRFTRPERLGSDQKFFCQQCQVRQESLKQMSIRKLPLVSCFHI 441
G + + E+L D K+ + + QE+ K + LP V +
Sbjct: 149 --------GKKNIFESFVDYVAVEQLDGDNKYDAGEHGL-QEAEKGVKFLTLPPVLHLQL 199
Query: 442 KRFEHSSVRKMSRKVDRYLQFPLSLDMAPYLSSSILRSRFGNRFFPFDGDESNTLNEPSS 501
RF + + K++ +FP L + +L + D + N
Sbjct: 200 XRFXYDPQTDQNIKINDRFEFPEQLPLDEFLQKT---------------DPKDPAN---- 240
Query: 502 EFELFAVVTHTGKLDAGHYVTYL--RLSNKWYKCDDAWIT 539
+ L AV+ H+G GHYV YL + KW K DD ++
Sbjct: 241 -YILHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFDDDVVS 279
>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 = 45.4 bits (106), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 44/169 (26%), Positives = 77/169 (45%), Gaps = 37/169 (21%)
Query: 425 LKQMSIRKLPLVSCFHIKRFEHSSVRKMSRKVDRYLQFPLSLDM----APYLSSSIL--R 478
+K I +LP + RF + ++ KV + ++FPL LDM P L ++ R
Sbjct: 222 IKSSKISRLPAYLTIQMVRFFYKEKESVNAKVLKDVKFPLMLDMYELCTPELQEKMVSFR 281
Query: 479 SRFGNRFFPFDGDESNTLNEPSSE----------------------FELFAVVTHTGK-L 515
S+F + + NT ++ SS ++L AV+TH G+
Sbjct: 282 SKFKDLEDKKVNQQPNTSDKKSSPQKEVKYEPFSFADDIGSNNCGYYDLQAVLTHQGRSS 341
Query: 516 DAGHYVTYL-RLSNKWYKCDDAWITEVN-ENTVRAAQG------YMMFY 556
+GHYV+++ R ++W K DD ++ V E+ +R + G Y++ Y
Sbjct: 342 SSGHYVSWVKRKQDEWIKFDDDKVSIVTPEDILRLSGGGDWHIAYVLLY 390
>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
Length = 854
Score = 38.9 bits (89), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 51/289 (17%), Positives = 106/289 (36%), Gaps = 48/289 (16%)
Query: 207 TCFMNSVLQALFHTPPLRNYFL-----------SDRHNRYYCQSKNGVRLCLACDLDTMF 255
+C++NSV+Q LF P + ++ +D + Q L+ +
Sbjct: 353 SCYLNSVVQVLFSIPDFQRKYVDKLEKIFQNAPTDPTQDFSTQVAKLGHGLLSGEYSKPV 412
Query: 256 SAIFCGDRMP--------YSPAKFLYSWWRHASNLASYEQQDAHEFFISMLDGIHEKVEK 307
G+R+P +P F + ++ QQDA EFF+ +++ +
Sbjct: 413 PESGDGERVPEQKEVQDGIAPRMFKALIGKGHPEFSTNRQQDAQEFFLHLINMVERNC-- 470
Query: 308 DQHKPRSQGNGDCCIAHRVFSGILRSDVMCMACGFTSTTFDPCVDFSLDLEPNQGSSMKT 367
RS N + VF ++ + C+A + VD+ + L +++
Sbjct: 471 -----RSSEN-----PNEVFRFLVEEKIKCLAT--EKVKYTQRVDYIMQLPVPMDAALNK 518
Query: 368 SSTKSNHSCNCEADGMNSSQNCGISTLM-------GCLDRFTRPERLGSDQKFFCQQCQV 420
+A+ + + L+ CL+ + PE++ F+ Q
Sbjct: 519 EELLEYEEKKRQAE----EEKMALPELVRAQVPFSSCLEAYGAPEQV---DDFWSTALQA 571
Query: 421 RQESLKQMSIRKLPLVSCFHIKRFEHSSVRKMSRKVDRYLQFPLSLDMA 469
+ ++K P IK+F + + +K+D ++ P LD++
Sbjct: 572 KSVAVKTTRFASFPDYLVIQIKKFTF-GLDWVPKKLDVSIEMPEELDIS 619
Score = 28.5 bits (62), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 30/57 (52%), Gaps = 3/57 (5%)
Query: 501 SEFELFAVVTHTGKLDA-GHYVTYLRLSNKWYKCDDAWITEVNENTVRAAQGYMMFY 556
+++LFA ++H G GHYV +++ +W +D + +E + GY+ FY
Sbjct: 795 GKYQLFAFISHMGTSTMCGHYVCHIKKEGRWVIYNDQKVC-ASEKPPKDL-GYIYFY 849
>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 = 38.1 bits (87), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 4/57 (7%)
Query: 499 PSSEFELFAVVTHTG-KLDAGHYVTYLRLS---NKWYKCDDAWITEVNENTVRAAQG 551
PS + L V+TH G ++GHY ++R NKWYK +D ++ V + + + G
Sbjct: 342 PSCVYNLIGVITHQGANSESGHYQAFIRDELDENKWYKFNDDKVSVVEKEKIESLAG 398
>pdb|2UZG|A Chain A, Zf-Ubp Domain Of Vdu1
Length = 97
Score = 29.3 bits (64), Expect = 5.9, Method: Composition-based stats.
Identities = 20/69 (28%), Positives = 32/69 (46%), Gaps = 9/69 (13%)
Query: 67 GVCGDSSC--PRLYACMA--CAAVSCHVPPHSSHVAIHATKTSSACSHEIAVDVDRAELF 122
G C D P L+AC+ C+ V C H IH+ +T H + V++ ++
Sbjct: 26 GTCQDCKVQGPNLWACLENRCSYVGCG-ESQVDHSTIHSQETK----HYLTVNLTTLRVW 80
Query: 123 CCACRDQVY 131
C AC +V+
Sbjct: 81 CYACSKEVF 89
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.323 0.133 0.425
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,339,704
Number of Sequences: 62578
Number of extensions: 632297
Number of successful extensions: 1748
Number of sequences better than 100.0: 28
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 1643
Number of HSP's gapped (non-prelim): 60
length of query: 572
length of database: 14,973,337
effective HSP length: 104
effective length of query: 468
effective length of database: 8,465,225
effective search space: 3961725300
effective search space used: 3961725300
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 54 (25.4 bits)