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= 010812
(500 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3N3K|A Chain A, The Catalytic Domain Of Usp8 In Complex With A Usp8
Specific Inhibitor
Length = 396
Score = 86.7 bits (213), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 80/283 (28%), Positives = 122/283 (43%), Gaps = 33/283 (11%)
Query: 203 GLINSGNLCFLNATLQALMSCSPFVQLL-QELRTRDIPKAGYPTLTAFVGFVSDFDTPSG 261
GL N GN C++N+ LQ L + + DI ++ +G + G
Sbjct: 64 GLRNLGNTCYMNSILQCLCNAPHLADYFNRNCYQDDINRSN------LLGHKGEVAEEFG 117
Query: 262 GSSKKKNISVLDIG--RPFSPSMFEAVLKNFTPDVPNSISGRPRQEDAQEFLSFIMDQMH 319
K L G R SP F+ + + + +G Q+D+QE L F+MD +H
Sbjct: 118 IIMK-----ALWTGQYRYISPKDFKITIGK----INDQFAGYS-QQDSQELLLFLMDGLH 167
Query: 320 DELLKLQGESTSINGANTALVSL-AEEDEWETVGPKNKSAVTRTQSFLPSALSDIFGGQL 378
++L K N L A E W+ N+S + +F GQ
Sbjct: 168 EDLNKADNRKRYKEENNDHLDDFKAAEHAWQKHKQLNESIIVA-----------LFQGQF 216
Query: 379 KSVVKA-QGNKASATVQPFLLLHLDIYSEAVHTIEDALRLFSAPENL-EGYRTSSTGNAG 436
KS V+ +K S T + F+ L L + S + T++D LRLFS E L + R +
Sbjct: 217 KSTVQCLTCHKKSRTFEAFMYLSLPLASTSKCTLQDCLRLFSKEEKLTDNNRFYCSHCRA 276
Query: 437 VVTAKKSVKIQTLSKILILHLMRFSYGSQGSTKLHKSVRFPLQ 479
+ K ++I L +L++HL RFSY + KL SV FPL+
Sbjct: 277 RRDSLKKIEIWKLPPVLLVHLKRFSYDGRWKQKLQTSVDFPLE 319
>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 = 86.3 bits (212), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 102/313 (32%), Positives = 138/313 (44%), Gaps = 53/313 (16%)
Query: 199 LLPRG------LINSGNLCFLNATLQALMSCSPF--VQLLQELRTRDIPKAGYPT-LT-A 248
L+PRG L N GN CFLNA LQ L S P L ++ R +++P G LT A
Sbjct: 14 LVPRGSSGHVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFR-QEVPGGGRAQELTEA 72
Query: 249 FVGFVSDFDTPSGGSSKKKNISVLDIGRPFSPSMFEAVLKNFTPDVPNSISGRPRQEDAQ 308
F + P D +P+ F AV + + P S SG Q+DAQ
Sbjct: 73 FADVIGALWHP-------------DSCEAVNPTRFRAVFQKYVP----SFSGYS-QQDAQ 114
Query: 309 EFLSFIMDQMHDELLKLQGESTSINGANTALVS-------LAEEDEWETVGPKN---KSA 358
EFL +M+++H E+ + +G AN + S L EE E N K
Sbjct: 115 EFLKLLMERLHLEINR-RGRRAPPILANGPVPSPPRRGGALLEEPELSDDDRANLMWKRY 173
Query: 359 VTRTQSFLPSALSDIFGGQLKSVVKAQG-NKASATVQPFLLLHLDI----YSEAVHTIED 413
+ R S + D+F GQLKS +K Q S T + F L L I ++ ++ D
Sbjct: 174 LERED----SKIVDLFVGQLKSCLKCQACGYRSTTFEVFCDLSLPIPKKGFAGGKVSLRD 229
Query: 414 ALRLFSAPENLEGYRTSSTGNAGVVT-AKKSVKIQTLSKILILHLMRFSYGSQGSTKLHK 472
LF+ E LE T + K + +Q +IL+LHL RFS S+GS K
Sbjct: 230 CFNLFTKEEELESENAPVCDRCRQKTRSTKKLTVQRFPRILVLHLNRFS-ASRGSIKKSS 288
Query: 473 -SVRFPLQ-LVLG 483
V FPLQ L LG
Sbjct: 289 VGVDFPLQRLSLG 301
>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 = 85.9 bits (211), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 99/303 (32%), Positives = 134/303 (44%), Gaps = 47/303 (15%)
Query: 203 GLINSGNLCFLNATLQALMSCSPF--VQLLQELRTRDIPKAGYPT-LT-AFVGFVSDFDT 258
GL N GN CFLNA LQ L S P L ++ R +++P G LT AF +
Sbjct: 18 GLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFR-QEVPGGGRAQELTEAFADVIGALWH 76
Query: 259 PSGGSSKKKNISVLDIGRPFSPSMFEAVLKNFTPDVPNSISGRPRQEDAQEFLSFIMDQM 318
P D +P+ F AV + + P S SG Q+DAQEFL +M+++
Sbjct: 77 P-------------DSCEAVNPTRFRAVFQKYVP----SFSGYS-QQDAQEFLKLLMERL 118
Query: 319 HDELLKLQGESTSINGANTALVS-------LAEEDEWETVGPKN---KSAVTRTQSFLPS 368
H E+ + +G AN + S L EE E N K + R S
Sbjct: 119 HLEINR-RGRRAPPILANGPVPSPPRRGGALLEEPELSDDDRANLMWKRYLERED----S 173
Query: 369 ALSDIFGGQLKSVVKAQG-NKASATVQPFLLLHLDI----YSEAVHTIEDALRLFSAPEN 423
+ D+F GQLKS +K Q S T + F L L I ++ ++ D LF+ E
Sbjct: 174 KIVDLFVGQLKSCLKCQACGYRSTTFEVFCDLSLPIPKKGFAGGKVSLRDCFNLFTKEEE 233
Query: 424 LEGYRTSSTGNAGVVT-AKKSVKIQTLSKILILHLMRFSYGSQGSTKLHK-SVRFPLQ-L 480
LE T + K + +Q +IL+LHL RFS S+GS K V FPLQ L
Sbjct: 234 LESENAPVCDRCRQKTRSTKKLTVQRFPRILVLHLNRFS-ASRGSIKKSSVGVDFPLQRL 292
Query: 481 VLG 483
LG
Sbjct: 293 SLG 295
>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 = 85.9 bits (211), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 99/303 (32%), Positives = 134/303 (44%), Gaps = 47/303 (15%)
Query: 203 GLINSGNLCFLNATLQALMSCSPF--VQLLQELRTRDIPKAGYPT-LT-AFVGFVSDFDT 258
GL N GN CFLNA LQ L S P L ++ R +++P G LT AF +
Sbjct: 5 GLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFR-QEVPGGGRAQELTEAFADVIGALWH 63
Query: 259 PSGGSSKKKNISVLDIGRPFSPSMFEAVLKNFTPDVPNSISGRPRQEDAQEFLSFIMDQM 318
P D +P+ F AV + + P S SG Q+DAQEFL +M+++
Sbjct: 64 P-------------DSCEAVNPTRFRAVFQKYVP----SFSGYS-QQDAQEFLKLLMERL 105
Query: 319 HDELLKLQGESTSINGANTALVS-------LAEEDEWETVGPKN---KSAVTRTQSFLPS 368
H E+ + +G AN + S L EE E N K + R S
Sbjct: 106 HLEINR-RGRRAPPILANGPVPSPPRRGGALLEEPELSDDDRANLMWKRYLERED----S 160
Query: 369 ALSDIFGGQLKSVVKAQG-NKASATVQPFLLLHLDI----YSEAVHTIEDALRLFSAPEN 423
+ D+F GQLKS +K Q S T + F L L I ++ ++ D LF+ E
Sbjct: 161 KIVDLFVGQLKSCLKCQACGYRSTTFEVFCDLSLPIPKKGFAGGKVSLRDCFNLFTKEEE 220
Query: 424 LEGYRTSSTGNAGVVT-AKKSVKIQTLSKILILHLMRFSYGSQGSTKLHK-SVRFPLQ-L 480
LE T + K + +Q +IL+LHL RFS S+GS K V FPLQ L
Sbjct: 221 LESENAPVCDRCRQKTRSTKKLTVQRFPRILVLHLNRFS-ASRGSIKKSSVGVDFPLQRL 279
Query: 481 VLG 483
LG
Sbjct: 280 SLG 282
>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 = 85.5 bits (210), Expect = 6e-17, Method: Compositional matrix adjust.
Identities = 92/306 (30%), Positives = 132/306 (43%), Gaps = 44/306 (14%)
Query: 184 VPMKAINEPVKSVKDLLPRGLINSGNLCFLNATLQALMSCSPFVQL-LQELRTRDIPKAG 242
VP ++N KS + L GL N GN CF+N+ LQ L + LQ L RD+
Sbjct: 15 VPRGSMNS--KSAQGLA--GLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGS 70
Query: 243 YPTLTAFVGFVSDFDTPSGGSSKKKNISVLDIGRP---FSPSMFEAVLKNFTPDVPNSIS 299
A V +F K I + P SPS F+ ++ + P
Sbjct: 71 ----NAHTALVEEF---------AKLIQTIWTSSPNDVVSPSEFKTQIQRYAPRFVGY-- 115
Query: 300 GRPRQEDAQEFLSFIMDQMHDELLKLQGESTSINGANTALVSLAEEDEWETVGPKNKSAV 359
Q+DAQEFL F++D +H+E+ ++ S N + +DE K +
Sbjct: 116 ---NQQDAQEFLRFLLDGLHNEVNRVTLRPKS----NPENLDHLPDDE------KGRQMW 162
Query: 360 TRTQSFLPSALSDIFGGQLKSVVKAQGNKASATV-QPFLLLHLDI----YSEAVHTIEDA 414
+ S + D+F GQLKS + +TV PF L L I Y E T+ D
Sbjct: 163 RKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPIAKRGYPEV--TLMDC 220
Query: 415 LRLFSAPENLEG-YRTSSTGNAGVVTAKKSVKIQTLSKILILHLMRFSYGSQGSTKLHKS 473
+RLF+ + L+G + + G K IQ KIL+LHL RFS ++KL
Sbjct: 221 MRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKILVLHLKRFSESRIRTSKLTTF 280
Query: 474 VRFPLQ 479
V FPL+
Sbjct: 281 VNFPLR 286
>pdb|2HD5|A Chain A, Usp2 In Complex With Ubiquitin
Length = 359
Score = 85.1 bits (209), Expect = 8e-17, Method: Compositional matrix adjust.
Identities = 86/287 (29%), Positives = 123/287 (42%), Gaps = 40/287 (13%)
Query: 203 GLINSGNLCFLNATLQALMSCSPFVQL-LQELRTRDIPKAGYPTLTAFVGFVSDFDTPSG 261
GL N GN CF+N+ LQ L + LQ L RD+ A V +F
Sbjct: 11 GLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGS----NAHTALVEEF----- 61
Query: 262 GSSKKKNISVLDIGRP---FSPSMFEAVLKNFTPDVPNSISGRPRQEDAQEFLSFIMDQM 318
K I + P SPS F+ ++ + P Q+DAQEFL F++D +
Sbjct: 62 ----AKLIQTIWTSSPNDVVSPSEFKTQIQRYAPRFVGY-----NQQDAQEFLRFLLDGL 112
Query: 319 HDELLKLQGESTSINGANTALVSLAEEDEWETVGPKNKSAVTRTQSFLPSALSDIFGGQL 378
H+E+ ++ S N + +DE K + + S + D+F GQL
Sbjct: 113 HNEVNRVTLRPKS----NPENLDHLPDDE------KGRQMWRKYLEREDSRIGDLFVGQL 162
Query: 379 KSVVKAQGNKASATV-QPFLLLHLDI----YSEAVHTIEDALRLFSAPENLEG-YRTSST 432
KS + +TV PF L L I Y E T+ D +RLF+ + L+G + +
Sbjct: 163 KSSLTCTDCGYCSTVFDPFWDLSLPIAKRGYPEV--TLMDCMRLFTKEDVLDGDEKPTCC 220
Query: 433 GNAGVVTAKKSVKIQTLSKILILHLMRFSYGSQGSTKLHKSVRFPLQ 479
G K IQ KIL+LHL RFS ++KL V FPL+
Sbjct: 221 RCRGRKRCIKKFSIQRFPKILVLHLKRFSESRIRTSKLTTFVNFPLR 267
>pdb|2IBI|A Chain A, Covalent Ubiquitin-Usp2 Complex
Length = 374
Score = 84.7 bits (208), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 85/287 (29%), Positives = 121/287 (42%), Gaps = 40/287 (13%)
Query: 203 GLINSGNLCFLNATLQALMSCSPFVQL-LQELRTRDIPKAGYPTLTAFVGFVSDFDTPSG 261
GL N GN CF+N+ LQ L + LQ L RD+ A V +F
Sbjct: 37 GLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGS----NAHTALVEEF----- 87
Query: 262 GSSKKKNISVLDIGRP---FSPSMFEAVLKNFTPDVPNSISGRPRQEDAQEFLSFIMDQM 318
K I + P SPS F+ ++ + P Q+DAQEFL F++D +
Sbjct: 88 ----AKLIQTIWTSSPNDVVSPSEFKTQIQRYAPRFVGY-----NQQDAQEFLRFLLDGL 138
Query: 319 HDELLKLQGESTSINGANTALVSLAEEDEWETVGPKNKSAVTRTQSFLPSALSDIFGGQL 378
H+E+ ++ S N + +DE K + + S + D+F GQL
Sbjct: 139 HNEVNRVTLRPKS----NPENLDHLPDDE------KGRQMWRKYLEREDSRIGDLFVGQL 188
Query: 379 KSVVKAQGNKASATV-QPFLLLHLDI----YSEAVHTIEDALRLFSAPENLEGYRTSSTG 433
KS + +TV PF L L I Y E T+ D +RLF+ + L+G +
Sbjct: 189 KSSLTCTDCGYCSTVFDPFWDLSLPIAKRGYPEV--TLMDCMRLFTKEDVLDGDAAPTCC 246
Query: 434 NAGVVTAK-KSVKIQTLSKILILHLMRFSYGSQGSTKLHKSVRFPLQ 479
K IQ KIL+LHL RFS ++KL V FPL+
Sbjct: 247 RCRGRKRCIKKFSIQRFPKILVLHLKRFSESRIRTSKLTTFVNFPLR 293
>pdb|2GFO|A Chain A, Structure Of The Catalytic Domain Of Human Ubiquitin
Carboxyl-terminal Hydrolase 8
Length = 396
Score = 81.3 bits (199), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 79/283 (27%), Positives = 119/283 (42%), Gaps = 33/283 (11%)
Query: 203 GLINSGNLCFLNATLQALMSCSPFVQLL-QELRTRDIPKAGYPTLTAFVGFVSDFDTPSG 261
GL N GN C+ N+ LQ L + + DI ++ +G + G
Sbjct: 64 GLRNLGNTCYXNSILQCLCNAPHLADYFNRNCYQDDINRSN------LLGHKGEVAEEFG 117
Query: 262 GSSKKKNISVLDIG--RPFSPSMFEAVLKNFTPDVPNSISGRPRQEDAQEFLSFIMDQMH 319
K L G R SP F+ + + + +G Q+D+QE L F+ D +H
Sbjct: 118 IIXK-----ALWTGQYRYISPKDFKITIGK----INDQFAGYS-QQDSQELLLFLXDGLH 167
Query: 320 DELLKLQGESTSINGANTALVSL-AEEDEWETVGPKNKSAVTRTQSFLPSALSDIFGGQL 378
++L K N L A E W+ N+S + +F GQ
Sbjct: 168 EDLNKADNRKRYKEENNDHLDDFKAAEHAWQKHKQLNESIIVA-----------LFQGQF 216
Query: 379 KSVVKA-QGNKASATVQPFLLLHLDIYSEAVHTIEDALRLFSAPENL-EGYRTSSTGNAG 436
KS V+ +K S T + F L L + S + T++D LRLFS E L + R +
Sbjct: 217 KSTVQCLTCHKKSRTFEAFXYLSLPLASTSKCTLQDCLRLFSKEEKLTDNNRFYCSHCRA 276
Query: 437 VVTAKKSVKIQTLSKILILHLMRFSYGSQGSTKLHKSVRFPLQ 479
+ K ++I L +L++HL RFSY + KL SV FPL+
Sbjct: 277 RRDSLKKIEIWKLPPVLLVHLKRFSYDGRWKQKLQTSVDFPLE 319
>pdb|3NHE|A Chain A, High Resolution Structure (1.26a) Of Usp2a In Complex With
Ubiquitin
Length = 348
Score = 80.5 bits (197), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 85/287 (29%), Positives = 122/287 (42%), Gaps = 40/287 (13%)
Query: 203 GLINSGNLCFLNATLQALMSCSPFVQL-LQELRTRDIPKAGYPTLTAFVGFVSDFDTPSG 261
GL N GN F+N+ LQ L + LQ L RD+ A V +F
Sbjct: 11 GLRNLGNTXFMNSILQCLSNTRELRDYCLQRLYMRDLHHGS----NAHTALVEEF----- 61
Query: 262 GSSKKKNISVLDIGRP---FSPSMFEAVLKNFTPDVPNSISGRPRQEDAQEFLSFIMDQM 318
K I + P SPS F+ ++ + P Q+DAQEFL F++D +
Sbjct: 62 ----AKLIQTIWTSSPNDVVSPSEFKTQIQRYAPRFVGY-----NQQDAQEFLRFLLDGL 112
Query: 319 HDELLKLQGESTSINGANTALVSLAEEDEWETVGPKNKSAVTRTQSFLPSALSDIFGGQL 378
H+E+ ++ S N + +DE K + + S + D+F GQL
Sbjct: 113 HNEVNRVTLRPKS----NPENLDHLPDDE------KGRQMWRKYLEREDSRIGDLFVGQL 162
Query: 379 KSVVKAQGNKASATV-QPFLLLHLDI----YSEAVHTIEDALRLFSAPENLEG-YRTSST 432
KS + +TV PF L L I Y E T+ D +RLF+ + L+G + +
Sbjct: 163 KSSLTCTDCGYCSTVFDPFWDLSLPIAKRGYPEV--TLMDCMRLFTKEDVLDGDEKPTCC 220
Query: 433 GNAGVVTAKKSVKIQTLSKILILHLMRFSYGSQGSTKLHKSVRFPLQ 479
G K IQ KIL+LHL RFS ++KL V FPL+
Sbjct: 221 RCRGRKRCIKKFSIQRFPKILVLHLKRFSESRIRTSKLTTFVNFPLR 267
>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 = 74.7 bits (182), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 81/308 (26%), Positives = 127/308 (41%), Gaps = 66/308 (21%)
Query: 203 GLINSGNLCFLNATLQALMSCSPFVQ-LLQELRTRDIPKAGYPTLTAFVGFVSDFDTPSG 261
GL N GN F+N+ LQ L + +P L++ +I + D P G
Sbjct: 10 GLGNLGNTXFMNSALQCLSNTAPLTDYFLKDEYEAEINR----------------DNPLG 53
Query: 262 -----GSSKKKNISVLDIGRP--FSPSMFEAVLKNFTPDVPNSISGRPRQEDAQEFLSFI 314
+ + I + GR +P MF+ + F P SG +Q+D+QE L+F+
Sbjct: 54 MKGEIAEAYAELIKQMWSGRDAHVAPRMFKTQVGRFAP----QFSGY-QQQDSQELLAFL 108
Query: 315 MDQMHDELLKLQG----ESTSINGANTALVSLAEEDEWETVGPKNKSAVTRTQSFLPSAL 370
+D +H++L +++ E NG A+V+ ++ WE +N S +
Sbjct: 109 LDGLHEDLNRVKKKPYLELKDANGRPDAVVA---KEAWENHRLRNDSVIV---------- 155
Query: 371 SDIFGGQLKS-VVKAQGNKASATVQPFLLLHLDIYSEAVHTIE----------------- 412
D F G KS +V + K S T PF L L + + +E
Sbjct: 156 -DTFHGLFKSTLVCPECAKVSVTFDPFCYLTLPLPLKKDRVMEGPMLQPQKKKKTTVALR 214
Query: 413 DALRLFSAPENLEGYRTSSTGNAGV-VTAKKSVKIQTLSKILILHLMRFSYGSQGSTKLH 471
D + LF+ E L + N A K + +L KIL++HL RFSY KL
Sbjct: 215 DCIELFTTMETLGEHDPWYCPNCKKHQQATKKFDLWSLPKILVVHLKRFSYNRYWRDKLD 274
Query: 472 KSVRFPLQ 479
V FP++
Sbjct: 275 TVVEFPIR 282
>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 = 58.2 bits (139), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 71/291 (24%), Positives = 113/291 (38%), Gaps = 55/291 (18%)
Query: 203 GLINSGNLCFLNATLQALMSCSPFVQ--LLQ----ELRTRDIPKAGYPTLTAFV----GF 252
GLIN GN CF+++ LQ L+ F++ + Q + R K L V G
Sbjct: 143 GLINMGNTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHELYGA 202
Query: 253 VSDFDTPSGGSSKKKNISVLDIGRPFSPSMFEAVLKNFTPDVPNSISGRPRQEDAQEFLS 312
++ S +S + + L + +++G Q+DA EF
Sbjct: 203 LNTKQASSSSTSTNRQTGFI-------------YLLTCAWKINQNLAGYS-QQDAHEFWQ 248
Query: 313 FIMDQMHDELLKLQGESTSINGANTALVSLAEEDEWETVGPKNKSAVTRTQSFLPSALSD 372
FI++Q+H +S ++ N VS A + E + +
Sbjct: 249 FIINQIH--------QSYVLDLPNAKEVSRANNKQCECI------------------VHT 282
Query: 373 IFGGQLKSVVKAQG--NKASATVQPFLLLHLDIYSEAVHTIEDALRLFSAPENLEGYRTS 430
+F G L+S + G N + T+ PFL L LDI + + + L F E L+ +
Sbjct: 283 VFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIKDKK--KLYECLDSFHKKEQLKDFNYH 340
Query: 431 STGNAGVVTAKKSVKIQTLSKILILHLMRFSYGSQGST-KLHKSVRFPLQL 480
A K + I L +L+L L RF + GS KL + FP L
Sbjct: 341 CGECNSTQDAIKQLGIHKLPSVLVLQLKRFEHLLNGSNRKLDDFIEFPTYL 391
>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 = 55.8 bits (133), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 70/291 (24%), Positives = 113/291 (38%), Gaps = 55/291 (18%)
Query: 203 GLINSGNLCFLNATLQALMSCSPFVQ--LLQ----ELRTRDIPKAGYPTLTAFV----GF 252
GLIN G+ CF+++ LQ L+ F++ + Q + R K L V G
Sbjct: 143 GLINMGSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHELYGA 202
Query: 253 VSDFDTPSGGSSKKKNISVLDIGRPFSPSMFEAVLKNFTPDVPNSISGRPRQEDAQEFLS 312
++ S +S + + L + +++G Q+DA EF
Sbjct: 203 LNTKQASSSSTSTNRQTGFI-------------YLLTCAWKINQNLAGYS-QQDAHEFWQ 248
Query: 313 FIMDQMHDELLKLQGESTSINGANTALVSLAEEDEWETVGPKNKSAVTRTQSFLPSALSD 372
FI++Q+H +S ++ N VS A + E + +
Sbjct: 249 FIINQIH--------QSYVLDLPNAKEVSRANNKQCECI------------------VHT 282
Query: 373 IFGGQLKSVVKAQG--NKASATVQPFLLLHLDIYSEAVHTIEDALRLFSAPENLEGYRTS 430
+F G L+S + G N + T+ PFL L LDI + + + L F E L+ +
Sbjct: 283 VFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIKDKK--KLYECLDSFHKKEQLKDFNYH 340
Query: 431 STGNAGVVTAKKSVKIQTLSKILILHLMRFSYGSQGST-KLHKSVRFPLQL 480
A K + I L +L+L L RF + GS KL + FP L
Sbjct: 341 CGECNSTQDAIKQLGIHKLPSVLVLQLKRFEHLLNGSNRKLDDFIEFPTYL 391
>pdb|3M99|A Chain A, Structure Of The Ubp8-Sgf11-Sgf73-Sus1 Saga Dub Module
Length = 471
Score = 55.8 bits (133), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 69/291 (23%), Positives = 111/291 (38%), Gaps = 55/291 (18%)
Query: 203 GLINSGNLCFLNATLQALMSCSPFVQLLQ------ELRTRDIPKAGYPTLTAFV----GF 252
GLIN G+ CF+++ LQ L+ F++ + R K L V G
Sbjct: 138 GLINMGSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHELYGA 197
Query: 253 VSDFDTPSGGSSKKKNISVLDIGRPFSPSMFEAVLKNFTPDVPNSISGRPRQEDAQEFLS 312
++ S +S + + L + +++G Q+DA EF
Sbjct: 198 LNTKQASSSSTSTNRQTGFI-------------YLLTCAWKINQNLAGYS-QQDAHEFWQ 243
Query: 313 FIMDQMHDELLKLQGESTSINGANTALVSLAEEDEWETVGPKNKSAVTRTQSFLPSALSD 372
FI++Q+H +S ++ N VS A + E + +
Sbjct: 244 FIINQIH--------QSYVLDLPNAKEVSRANNKQCECI------------------VHT 277
Query: 373 IFGGQLKSVVKAQG--NKASATVQPFLLLHLDIYSEAVHTIEDALRLFSAPENLEGYRTS 430
+F G L+S + G N + T+ PFL L LDI + + + L F E L+ +
Sbjct: 278 VFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIKDKK--KLYECLDSFHKKEQLKDFNYH 335
Query: 431 STGNAGVVTAKKSVKIQTLSKILILHLMRFSYGSQGST-KLHKSVRFPLQL 480
A K + I L +L+L L RF + GS KL + FP L
Sbjct: 336 CGECNSTQDAIKQLGIHKLPSVLVLQLKRFEHLLNGSNRKLDDFIEFPTYL 386
>pdb|2F1Z|A Chain A, Crystal Structure Of Hausp
pdb|2F1Z|B Chain B, Crystal Structure Of Hausp
Length = 522
Score = 42.7 bits (99), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 26/67 (38%), Positives = 34/67 (50%), Gaps = 2/67 (2%)
Query: 418 FSAPENLEGYRTSSTGNAGVVTAKKSVKIQTLSKILILHLMRFSYGSQ--GSTKLHKSVR 475
+ A E L+G G G+ A+K VK TL +L L LMRF Y Q + K++
Sbjct: 329 YVAVEQLDGDNKYDAGEHGLQEAEKGVKFLTLPPVLHLQLMRFMYDPQTDQNIKINDRFE 388
Query: 476 FPLQLVL 482
FP QL L
Sbjct: 389 FPEQLPL 395
>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 = 42.4 bits (98), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 26/67 (38%), Positives = 34/67 (50%), Gaps = 2/67 (2%)
Query: 418 FSAPENLEGYRTSSTGNAGVVTAKKSVKIQTLSKILILHLMRFSYGSQ--GSTKLHKSVR 475
+ A E L+G G G+ A+K VK TL +L L LMRF Y Q + K++
Sbjct: 160 YVAVEQLDGDNKYDAGEHGLQEAEKGVKFLTLPPVLHLQLMRFMYDPQTDQNIKINDRFE 219
Query: 476 FPLQLVL 482
FP QL L
Sbjct: 220 FPEQLPL 226
>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 = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 33/67 (49%), Gaps = 2/67 (2%)
Query: 418 FSAPENLEGYRTSSTGNAGVVTAKKSVKIQTLSKILILHLMRFSYGSQ--GSTKLHKSVR 475
+ A E L+G G G+ A+K VK TL +L L L RF Y Q + K++
Sbjct: 160 YVAVEQLDGDNKYDAGEHGLQEAEKGVKFLTLPPVLHLQLXRFXYDPQTDQNIKINDRFE 219
Query: 476 FPLQLVL 482
FP QL L
Sbjct: 220 FPEQLPL 226
>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 = 36.6 bits (83), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 15/22 (68%), Positives = 16/22 (72%)
Query: 200 LPRGLINSGNLCFLNATLQALM 221
LP G N GN C+LNATLQAL
Sbjct: 23 LPVGFKNXGNTCYLNATLQALY 44
>pdb|2AYN|A Chain A, Structure Of Usp14, A Proteasome-Associated
Deubiquitinating Enzyme
pdb|2AYN|B Chain B, Structure Of Usp14, A Proteasome-Associated
Deubiquitinating Enzyme
pdb|2AYN|C Chain C, Structure Of Usp14, A Proteasome-Associated
Deubiquitinating Enzyme
pdb|2AYO|A Chain A, Structure Of Usp14 Bound To Ubquitin Aldehyde
Length = 404
Score = 34.3 bits (77), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 13/23 (56%), Positives = 17/23 (73%)
Query: 200 LPRGLINSGNLCFLNATLQALMS 222
LP GL N GN C++NAT+Q + S
Sbjct: 13 LPCGLTNLGNTCYMNATVQCIRS 35
Score = 30.8 bits (68), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 27/51 (52%), Gaps = 4/51 (7%)
Query: 442 KSVKIQTLSKILILHLMRFSYGSQGST--KLHKSVRFPLQLVLGRDLLVTP 490
KS KI L L + ++RF Y + S K+ K V+FPL L + L TP
Sbjct: 223 KSSKISRLPAYLTIQMVRFFYKEKESVNAKVLKDVKFPLMLDMYE--LCTP 271
>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
Length = 854
Score = 33.9 bits (76), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 57/289 (19%), Positives = 114/289 (39%), Gaps = 29/289 (10%)
Query: 203 GLINSGNLCFLNATLQALMSCSPF----VQLLQEL--RTRDIPKAGYPTLTAFVG---FV 253
G+ N GN C+LN+ +Q L S F V L+++ P + T A +G
Sbjct: 346 GIRNLGNSCYLNSVVQVLFSIPDFQRKYVDKLEKIFQNAPTDPTQDFSTQVAKLGHGLLS 405
Query: 254 SDFDTPSGGSSKKKNI-SVLDIGRPFSPSMFEAVLKNFTPDVPNSISGRPRQEDAQEFLS 312
++ P S + + ++ +P MF+A++ P+ + RQ+DAQEF
Sbjct: 406 GEYSKPVPESGDGERVPEQKEVQDGIAPRMFKALIGKGHPEFSTN-----RQQDAQEFFL 460
Query: 313 FIMDQMHDELLKLQGESTSINGANTALVSLAEEDEWETVGPKNKSAVTRTQSFLPSALSD 372
+++ ++ S N L EE + + + + R + +
Sbjct: 461 HLINM-------VERNCRSSENPNEVFRFLVEE-KIKCLATEKVKYTQRVDYIMQLPVPM 512
Query: 373 IFGGQLKSVVKAQGNKASATVQPFLLLHLDIYSEAVHTIEDALRLFSAPENLEGYRTSST 432
+ +++ + K A + L L A L + APE ++ + +++
Sbjct: 513 DAALNKEELLEYEEKKRQAEEEKMALPEL---VRAQVPFSSCLEAYGAPEQVDDFWSTAL 569
Query: 433 GNAGVVTAKKSVKIQTLSKILILHLMRFSYGSQG-STKLHKSVRFPLQL 480
V A K+ + + L++ + +F++G KL S+ P +L
Sbjct: 570 QAKSV--AVKTTRFASFPDYLVIQIKKFTFGLDWVPKKLDVSIEMPEEL 616
>pdb|2ENW|A Chain A, Mutant Y92h Structure Of Tthb049 From Thermus Thermophilus
Hb8
pdb|2ENW|B Chain B, Mutant Y92h Structure Of Tthb049 From Thermus Thermophilus
Hb8
Length = 177
Score = 29.3 bits (64), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 23/46 (50%)
Query: 348 WETVGPKNKSAVTRTQSFLPSALSDIFGGQLKSVVKAQGNKASATV 393
WET+ P++K A+ R Q F P + Q + +G KA A +
Sbjct: 85 WETLDPRHKEALLRFQGFHPPGGESLSAFQERVFRFLEGLKAPAVL 130
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
0.313 0.130 0.368
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,481,469
Number of Sequences: 62578
Number of extensions: 598594
Number of successful extensions: 1325
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 18
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1273
Number of HSP's gapped (non-prelim): 34
length of query: 500
length of database: 14,973,337
effective HSP length: 103
effective length of query: 397
effective length of database: 8,527,803
effective search space: 3385537791
effective search space used: 3385537791
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (25.0 bits)