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= 013776
(436 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 66.6 bits (161), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 79/252 (31%), Positives = 109/252 (43%), Gaps = 49/252 (19%)
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 ALRLFSAPENLE 425
LF+ E LE
Sbjct: 230 CFNLFTKEEELE 241
>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 = 66.2 bits (160), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 76/242 (31%), Positives = 105/242 (43%), Gaps = 43/242 (17%)
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 LE 425
LE
Sbjct: 234 LE 235
>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 = 65.9 bits (159), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 76/242 (31%), Positives = 105/242 (43%), Gaps = 43/242 (17%)
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 LE 425
LE
Sbjct: 221 LE 222
>pdb|2IBI|A Chain A, Covalent Ubiquitin-Usp2 Complex
Length = 374
Score = 63.9 bits (154), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 67/233 (28%), Positives = 98/233 (42%), Gaps = 39/233 (16%)
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----YSEAVHTIEDALRLFSAPENLEG 426
KS + +TV PF L L I Y E T+ D +RLF+ + L+G
Sbjct: 189 KSSLTCTDCGYCSTVFDPFWDLSLPIAKRGYPEV--TLMDCMRLFTKEDVLDG 239
>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 = 63.5 bits (153), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 67/233 (28%), Positives = 98/233 (42%), Gaps = 39/233 (16%)
Query: 203 GLINSGNLCFLNATLQALMSCSPFVQL-LQELRTRDIPKAGYPTLTAFVGFVSDFDTPSG 261
GL N GN CF+N+ LQ L + LQ L RD+ A V +F
Sbjct: 30 GLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGS----NAHTALVEEF----- 80
Query: 262 GSSKKKNISVLDIGRP---FSPSMFEAVLKNFTPDVPNSISGRPRQEDAQEFLSFIMDQM 318
K I + P SPS F+ ++ + P Q+DAQEFL F++D +
Sbjct: 81 ----AKLIQTIWTSSPNDVVSPSEFKTQIQRYAPRFVGY-----NQQDAQEFLRFLLDGL 131
Query: 319 HDELLKLQGESTSINGANTALVSLAEEDEWETVGPKNKSAVTRTQSFLPSALSDIFGGQL 378
H+E+ ++ S N + +DE K + + S + D+F GQL
Sbjct: 132 HNEVNRVTLRPKS----NPENLDHLPDDE------KGRQMWRKYLEREDSRIGDLFVGQL 181
Query: 379 KSVVKAQGNKASATV-QPFLLLHLDI----YSEAVHTIEDALRLFSAPENLEG 426
KS + +TV PF L L I Y E T+ D +RLF+ + L+G
Sbjct: 182 KSSLTCTDCGYCSTVFDPFWDLSLPIAKRGYPEV--TLMDCMRLFTKEDVLDG 232
>pdb|2HD5|A Chain A, Usp2 In Complex With Ubiquitin
Length = 359
Score = 63.2 bits (152), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 67/233 (28%), Positives = 98/233 (42%), Gaps = 39/233 (16%)
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 426
KS + +TV PF L L I Y E T+ D +RLF+ + L+G
Sbjct: 163 KSSLTCTDCGYCSTVFDPFWDLSLPIAKRGYPEV--TLMDCMRLFTKEDVLDG 213
>pdb|3N3K|A Chain A, The Catalytic Domain Of Usp8 In Complex With A Usp8
Specific Inhibitor
Length = 396
Score = 60.1 bits (144), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 62/227 (27%), Positives = 94/227 (41%), Gaps = 32/227 (14%)
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 424
KS V+ +K S T + F+ L L + S + T++D LRLFS E L
Sbjct: 217 KSTVQCLTCHKKSRTFEAFMYLSLPLASTSKCTLQDCLRLFSKEEKL 263
>pdb|3NHE|A Chain A, High Resolution Structure (1.26a) Of Usp2a In Complex With
Ubiquitin
Length = 348
Score = 58.5 bits (140), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 66/233 (28%), Positives = 97/233 (41%), Gaps = 39/233 (16%)
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 426
KS + +TV PF L L I Y E T+ D +RLF+ + L+G
Sbjct: 163 KSSLTCTDCGYCSTVFDPFWDLSLPIAKRGYPEV--TLMDCMRLFTKEDVLDG 213
>pdb|2GFO|A Chain A, Structure Of The Catalytic Domain Of Human Ubiquitin
Carboxyl-terminal Hydrolase 8
Length = 396
Score = 55.1 bits (131), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 61/227 (26%), Positives = 91/227 (40%), Gaps = 32/227 (14%)
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 424
KS V+ +K S T + F L L + S + T++D LRLFS E L
Sbjct: 217 KSTVQCLTCHKKSRTFEAFXYLSLPLASTSKCTLQDCLRLFSKEEKL 263
>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 = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 57/212 (26%), Positives = 91/212 (42%), Gaps = 48/212 (22%)
Query: 203 GLINSGNLCFLNATLQALMSCSPFV-QLLQELRTRDIPKAGYPTLTAFVGFVSDFDTPSG 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-VVKAQGNKASATVQPFLLLHL 401
D F G KS +V + K S T PF L L
Sbjct: 156 -DTFHGLFKSTLVCPECAKVSVTFDPFCYLTL 186
>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 = 41.6 bits (96), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 54/237 (22%), Positives = 90/237 (37%), Gaps = 54/237 (22%)
Query: 203 GLINSGNLCFLNATLQALMSCSPFVQLLQ------ELRTRDIPKAGYPTLTAFV----GF 252
GLIN GN CF+++ LQ L+ F++ + 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--NKASATVQPFLLLHLDIYSEAVHTIEDALRLFSAPENLEGY 427
+F G L+S + G N + T+ PFL L LDI + + + L F E L+ +
Sbjct: 283 VFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIKDKK--KLYECLDSFHKKEQLKDF 337
>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 = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 53/237 (22%), Positives = 90/237 (37%), Gaps = 54/237 (22%)
Query: 203 GLINSGNLCFLNATLQALMSCSPFVQLLQ------ELRTRDIPKAGYPTLTAFV----GF 252
GLIN G+ CF+++ LQ L+ F++ + 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--NKASATVQPFLLLHLDIYSEAVHTIEDALRLFSAPENLEGY 427
+F G L+S + G N + T+ PFL L LDI + + + L F E L+ +
Sbjct: 283 VFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIKDKK--KLYECLDSFHKKEQLKDF 337
>pdb|3M99|A Chain A, Structure Of The Ubp8-Sgf11-Sgf73-Sus1 Saga Dub Module
Length = 471
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 53/237 (22%), Positives = 90/237 (37%), Gaps = 54/237 (22%)
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--NKASATVQPFLLLHLDIYSEAVHTIEDALRLFSAPENLEGY 427
+F G L+S + G N + T+ PFL L LDI + + + L F E L+ +
Sbjct: 278 VFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIKDKK--KLYECLDSFHKKEQLKDF 332
>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 = 0.032, 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 = 33.9 bits (76), 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
>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
Length = 854
Score = 33.5 bits (75), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 31/126 (24%), Positives = 57/126 (45%), Gaps = 15/126 (11%)
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 FIMDQM 318
+++ +
Sbjct: 461 HLINMV 466
>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 = 4.7, 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
0.312 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: 13,001,435
Number of Sequences: 62578
Number of extensions: 544029
Number of successful extensions: 1197
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1166
Number of HSP's gapped (non-prelim): 25
length of query: 436
length of database: 14,973,337
effective HSP length: 102
effective length of query: 334
effective length of database: 8,590,381
effective search space: 2869187254
effective search space used: 2869187254
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 53 (25.0 bits)