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= 024898
(261 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 = 90.5 bits (223), Expect = 9e-19, Method: Compositional matrix adjust.
Identities = 73/201 (36%), Positives = 101/201 (50%), Gaps = 25/201 (12%)
Query: 64 FQGILTNETRCLRCETVTARDETFFDLSLDIEQNSSIT--SCLKNFSSTETLNAEDKFFC 121
FQG + +CL C + E F LSL + S T CL+ FS E L ++F+C
Sbjct: 212 FQGQFKSTVQCLTCHKKSRTFEAFMYLSLPLASTSKCTLQDCLRLFSKEEKLTDNNRFYC 271
Query: 122 DKCCSLQEAQKRMKIKKSPHTLVIHLKRFKYIEQLGRYK-KLSYRVVFPLE-LKLSN--- 176
C + +++ K+++I K P L++HLKRF Y GR+K KL V FPLE L LS
Sbjct: 272 SHCRARRDSLKKIEIWKLPPVLLVHLKRFSYD---GRWKQKLQTSVDFPLENLDLSQYVI 328
Query: 177 TAEDADIEYSLFAVVVHVGSGPNHGHYVSLVK--SHNHWLFFDDENVEMIDESAVQTFFG 234
++ +Y+LF+V H G G + GHY + K + W FDD E+ D S
Sbjct: 329 GPKNNLKKYNLFSVSNHYG-GLDGGHYTAYCKNAARQRWFKFDDH--EVSDISVSSVKSS 385
Query: 235 SAQEYSSNTDHGYILFYESLG 255
+A YILFY SLG
Sbjct: 386 AA----------YILFYTSLG 396
>pdb|3M99|A Chain A, Structure Of The Ubp8-Sgf11-Sgf73-Sus1 Saga Dub Module
Length = 471
Score = 89.7 bits (221), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 76/263 (28%), Positives = 112/263 (42%), Gaps = 47/263 (17%)
Query: 3 QDAHEFLNFLLNELVDILXXXXXXXXXXXXXXXXXXTANGPTNGLANGVRKEPLVTWVHK 62
QDAHEF F++N++ N AN + E + VH
Sbjct: 236 QDAHEFWQFIINQI---------------HQSYVLDLPNAKEVSRANNKQCECI---VHT 277
Query: 63 NFQGILTNETRCLRCETVTARD-ETFFDLSLDIEQNSSITSCLKNFSSTETLNAEDKFFC 121
F+G L + C C+ + + F DLSLDI+ + CL +F E L + + C
Sbjct: 278 VFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIKDKKKLYECLDSFHKKEQL-KDFNYHC 336
Query: 122 DKCCSLQEAQKRMKIKKSPHTLVIHLKRFKYIEQLGRYKKLSYRVVFPLELKLSN----- 176
+C S Q+A K++ I K P LV+ LKRF+++ G +KL + FP L + N
Sbjct: 337 GECNSTQDAIKQLGIHKLPSVLVLQLKRFEHLLN-GSNRKLDDFIEFPTYLNMKNYCSTK 395
Query: 177 -------TAEDADIEYSLFAVVVHVGSGPNHGHYVSLVK-SHNHWLFFDDENVEMIDESA 228
+ DI Y L +V H G+ N GHY++ K S W F+D V I +
Sbjct: 396 EKDKHSENGKVPDIIYELIGIVSHKGT-VNEGHYIAFCKISGGQWFKFNDSMVSSISQEE 454
Query: 229 VQTFFGSAQEYSSNTDHGYILFY 251
V + Y+LFY
Sbjct: 455 VL------------KEQAYLLFY 465
>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 = 89.7 bits (221), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 76/264 (28%), Positives = 112/264 (42%), Gaps = 47/264 (17%)
Query: 2 HQDAHEFLNFLLNELVDILXXXXXXXXXXXXXXXXXXTANGPTNGLANGVRKEPLVTWVH 61
QDAHEF F++N++ N AN + E + VH
Sbjct: 240 QQDAHEFWQFIINQI---------------HQSYVLDLPNAKEVSRANNKQCECI---VH 281
Query: 62 KNFQGILTNETRCLRCETVTARD-ETFFDLSLDIEQNSSITSCLKNFSSTETLNAEDKFF 120
F+G L + C C+ + + F DLSLDI+ + CL +F E L + +
Sbjct: 282 TVFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIKDKKKLYECLDSFHKKEQL-KDFNYH 340
Query: 121 CDKCCSLQEAQKRMKIKKSPHTLVIHLKRFKYIEQLGRYKKLSYRVVFPLELKLSN---- 176
C +C S Q+A K++ I K P LV+ LKRF+++ G +KL + FP L + N
Sbjct: 341 CGECNSTQDAIKQLGIHKLPSVLVLQLKRFEHLLN-GSNRKLDDFIEFPTYLNMKNYCST 399
Query: 177 --------TAEDADIEYSLFAVVVHVGSGPNHGHYVSLVK-SHNHWLFFDDENVEMIDES 227
+ DI Y L +V H G+ N GHY++ K S W F+D V I +
Sbjct: 400 KEKDKHSENGKVPDIIYELIGIVSHKGT-VNEGHYIAFCKISGGQWFKFNDSMVSSISQE 458
Query: 228 AVQTFFGSAQEYSSNTDHGYILFY 251
V + Y+LFY
Sbjct: 459 EVL------------KEQAYLLFY 470
>pdb|2GFO|A Chain A, Structure Of The Catalytic Domain Of Human Ubiquitin
Carboxyl-terminal Hydrolase 8
Length = 396
Score = 89.7 bits (221), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 73/201 (36%), Positives = 101/201 (50%), Gaps = 25/201 (12%)
Query: 64 FQGILTNETRCLRCETVTARDETFFDLSLDIEQNSSIT--SCLKNFSSTETLNAEDKFFC 121
FQG + +CL C + E F LSL + S T CL+ FS E L ++F+C
Sbjct: 212 FQGQFKSTVQCLTCHKKSRTFEAFXYLSLPLASTSKCTLQDCLRLFSKEEKLTDNNRFYC 271
Query: 122 DKCCSLQEAQKRMKIKKSPHTLVIHLKRFKYIEQLGRYK-KLSYRVVFPLE-LKLSN--- 176
C + +++ K+++I K P L++HLKRF Y GR+K KL V FPLE L LS
Sbjct: 272 SHCRARRDSLKKIEIWKLPPVLLVHLKRFSYD---GRWKQKLQTSVDFPLENLDLSQYVI 328
Query: 177 TAEDADIEYSLFAVVVHVGSGPNHGHYVSLVK--SHNHWLFFDDENVEMIDESAVQTFFG 234
++ +Y+LF+V H G G + GHY + K + W FDD E+ D S
Sbjct: 329 GPKNNLKKYNLFSVSNHYG-GLDGGHYTAYCKNAARQRWFKFDDH--EVSDISVSSVKSS 385
Query: 235 SAQEYSSNTDHGYILFYESLG 255
+A YILFY SLG
Sbjct: 386 AA----------YILFYTSLG 396
>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 = 89.7 bits (221), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 76/263 (28%), Positives = 112/263 (42%), Gaps = 47/263 (17%)
Query: 3 QDAHEFLNFLLNELVDILXXXXXXXXXXXXXXXXXXTANGPTNGLANGVRKEPLVTWVHK 62
QDAHEF F++N++ N AN + E + VH
Sbjct: 241 QDAHEFWQFIINQI---------------HQSYVLDLPNAKEVSRANNKQCECI---VHT 282
Query: 63 NFQGILTNETRCLRCETVTARD-ETFFDLSLDIEQNSSITSCLKNFSSTETLNAEDKFFC 121
F+G L + C C+ + + F DLSLDI+ + CL +F E L + + C
Sbjct: 283 VFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIKDKKKLYECLDSFHKKEQL-KDFNYHC 341
Query: 122 DKCCSLQEAQKRMKIKKSPHTLVIHLKRFKYIEQLGRYKKLSYRVVFPLELKLSN----- 176
+C S Q+A K++ I K P LV+ LKRF+++ G +KL + FP L + N
Sbjct: 342 GECNSTQDAIKQLGIHKLPSVLVLQLKRFEHLLN-GSNRKLDDFIEFPTYLNMKNYCSTK 400
Query: 177 -------TAEDADIEYSLFAVVVHVGSGPNHGHYVSLVK-SHNHWLFFDDENVEMIDESA 228
+ DI Y L +V H G+ N GHY++ K S W F+D V I +
Sbjct: 401 EKDKHSENGKVPDIIYELIGIVSHKGT-VNEGHYIAFCKISGGQWFKFNDSMVSSISQEE 459
Query: 229 VQTFFGSAQEYSSNTDHGYILFY 251
V + Y+LFY
Sbjct: 460 VL------------KEQAYLLFY 470
>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 = 89.7 bits (221), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 60/191 (31%), Positives = 90/191 (47%), Gaps = 27/191 (14%)
Query: 74 CLRCETVTARD---ETFFDLSLDIEQNS------SITSCLKNFSSTETLNAEDKFFCDKC 124
CL+C+ R E F DLSL I + S+ C F+ E L +E+ CD+C
Sbjct: 192 CLKCQACGYRSTTFEVFCDLSLPIPKKGFAGGKVSLRDCFNLFTKEEELESENAPVCDRC 251
Query: 125 CSLQEAQKRMKIKKSPHTLVIHLKRFKYIEQLGRYKKLSYRVVFPLE-LKLSNTAED--A 181
+ K++ +++ P LV+HL RF G KK S V FPL+ L L + A D
Sbjct: 252 RQKTRSTKKLTVQRFPRILVLHLNRFS--ASRGSIKKSSVGVDFPLQRLSLGDFASDKAG 309
Query: 182 DIEYSLFAVVVHVGSGPNHGHYVSLVKSHNHWLFFDDENVEMIDESAVQTFFGSAQEYSS 241
Y L+A+ H GS ++GHY +L + W ++D V + E+ V
Sbjct: 310 SPVYQLYALCNHSGSV-HYGHYTALCRCQTGWHVYNDSRVSPVSENQVA----------- 357
Query: 242 NTDHGYILFYE 252
+ GY+LFY+
Sbjct: 358 -SSEGYVLFYQ 367
>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 = 89.0 bits (219), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 60/191 (31%), Positives = 90/191 (47%), Gaps = 27/191 (14%)
Query: 74 CLRCETVTARD---ETFFDLSLDIEQNS------SITSCLKNFSSTETLNAEDKFFCDKC 124
CL+C+ R E F DLSL I + S+ C F+ E L +E+ CD+C
Sbjct: 173 CLKCQACGYRSTTFEVFCDLSLPIPKKGFAGGKVSLRDCFNLFTKEEELESENAPVCDRC 232
Query: 125 CSLQEAQKRMKIKKSPHTLVIHLKRFKYIEQLGRYKKLSYRVVFPLE-LKLSNTAED--A 181
+ K++ +++ P LV+HL RF G KK S V FPL+ L L + A D
Sbjct: 233 RQKTRSTKKLTVQRFPRILVLHLNRFS--ASRGSIKKSSVGVDFPLQRLSLGDFASDKAG 290
Query: 182 DIEYSLFAVVVHVGSGPNHGHYVSLVKSHNHWLFFDDENVEMIDESAVQTFFGSAQEYSS 241
Y L+A+ H GS ++GHY +L + W ++D V + E+ V
Sbjct: 291 SPVYQLYALCNHSGSV-HYGHYTALCRCQTGWHVYNDSRVSPVSENQVA----------- 338
Query: 242 NTDHGYILFYE 252
+ GY+LFY+
Sbjct: 339 -SSEGYVLFYQ 348
>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 = 89.0 bits (219), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 60/191 (31%), Positives = 90/191 (47%), Gaps = 27/191 (14%)
Query: 74 CLRCETVTARD---ETFFDLSLDIEQNS------SITSCLKNFSSTETLNAEDKFFCDKC 124
CL+C+ R E F DLSL I + S+ C F+ E L +E+ CD+C
Sbjct: 186 CLKCQACGYRSTTFEVFCDLSLPIPKKGFAGGKVSLRDCFNLFTKEEELESENAPVCDRC 245
Query: 125 CSLQEAQKRMKIKKSPHTLVIHLKRFKYIEQLGRYKKLSYRVVFPLE-LKLSNTAED--A 181
+ K++ +++ P LV+HL RF G KK S V FPL+ L L + A D
Sbjct: 246 RQKTRSTKKLTVQRFPRILVLHLNRFS--ASRGSIKKSSVGVDFPLQRLSLGDFASDKAG 303
Query: 182 DIEYSLFAVVVHVGSGPNHGHYVSLVKSHNHWLFFDDENVEMIDESAVQTFFGSAQEYSS 241
Y L+A+ H GS ++GHY +L + W ++D V + E+ V
Sbjct: 304 SPVYQLYALCNHSGSV-HYGHYTALCRCQTGWHVYNDSRVSPVSENQVA----------- 351
Query: 242 NTDHGYILFYE 252
+ GY+LFY+
Sbjct: 352 -SSEGYVLFYQ 361
>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 = 73.2 bits (178), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 71/279 (25%), Positives = 109/279 (39%), Gaps = 48/279 (17%)
Query: 2 HQDAHEFLNFLLNELVDILXXXXXXXXXXXXXXXXXXTANGPTNGLAN-GVRKEPLVTWV 60
QD+ E L FLL+ L + L A N +R + ++
Sbjct: 98 QQDSQELLAFLLDGLHEDLNRVKKKPYLELKDANGRPDAVVAKEAWENHRLRNDSVIV-- 155
Query: 61 HKNFQGILTNETRCLRCETVTARDETFFDLSLDI-------------------EQNSSIT 101
F G+ + C C V+ + F L+L + + ++
Sbjct: 156 -DTFHGLFKSTLVCPECAKVSVTFDPFCYLTLPLPLKKDRVMEGPMLQPQKKKKTTVALR 214
Query: 102 SCLKNFSSTETLNAEDKFFCDKCCSLQEAQKRMKIKKSPHTLVIHLKRFKYIEQLGRY-- 159
C++ F++ ETL D ++C C Q+A K+ + P LV+HLKRF Y RY
Sbjct: 215 DCIELFTTMETLGEHDPWYCPNCKKHQQATKKFDLWSLPKILVVHLKRFSY----NRYWR 270
Query: 160 KKLSYRVVFPLE-LKLSNTAEDADIE---YSLFAVVVHVGSGPNHGHYVSLVKS--HNHW 213
KL V FP+ L +S + Y L AV H G+ GHY + K+ + W
Sbjct: 271 DKLDTVVEFPIRGLNMSEFVCNLSARPYVYDLIAVSNHYGAM-GVGHYTAYAKNKLNGKW 329
Query: 214 LFFDDENVEMIDESAVQTFFGSAQEYSSNTDHGYILFYE 252
+FDD NV + E + T Y+LFY+
Sbjct: 330 YYFDDSNVSLASEDQIV------------TKAAYVLFYQ 356
>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 = 72.8 bits (177), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 60/202 (29%), Positives = 99/202 (49%), Gaps = 13/202 (6%)
Query: 60 VHKNFQGILTNETRCLRCETVTARDETFFDLSLDIEQNSSITSCLKNFSSTETLNAEDKF 119
+ K F+G + + +C + + R E ++D+ L I+ +I ++ + E L+ ++K+
Sbjct: 113 IPKLFRGKMVSYIQCKEVDYRSDRREDYYDIQLSIKGKKNIFESFVDYVAVEQLDGDNKY 172
Query: 120 FCDKCCSLQEAQKRMKIKKSPHTLVIHLKRFKYIEQLGRYKKLSYRVVFPLELKLSNTAE 179
+ LQEA+K +K P L + L RF Y Q + K++ R FP +L L +
Sbjct: 173 DAGEH-GLQEAEKGVKFLTLPPVLHLQLMRFMYDPQTDQNIKINDRFEFPEQLPLDEFLQ 231
Query: 180 DADIE----YSLFAVVVHVGSGPNH-GHYVSLV--KSHNHWLFFDDENV-EMIDESAVQT 231
D + Y L AV+VH SG NH GHYV + K W FDD+ V E A++
Sbjct: 232 KTDPKDPANYILHAVLVH--SGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEH 289
Query: 232 FFGSAQEYSS--NTDHGYILFY 251
+G + S + + Y+L Y
Sbjct: 290 NYGGHDDDLSVRHCTNAYMLVY 311
>pdb|2F1Z|A Chain A, Crystal Structure Of Hausp
pdb|2F1Z|B Chain B, Crystal Structure Of Hausp
Length = 522
Score = 72.8 bits (177), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 60/202 (29%), Positives = 99/202 (49%), Gaps = 13/202 (6%)
Query: 60 VHKNFQGILTNETRCLRCETVTARDETFFDLSLDIEQNSSITSCLKNFSSTETLNAEDKF 119
+ K F+G + + +C + + R E ++D+ L I+ +I ++ + E L+ ++K+
Sbjct: 282 IPKLFRGKMVSYIQCKEVDYRSDRREDYYDIQLSIKGKKNIFESFVDYVAVEQLDGDNKY 341
Query: 120 FCDKCCSLQEAQKRMKIKKSPHTLVIHLKRFKYIEQLGRYKKLSYRVVFPLELKLSNTAE 179
+ LQEA+K +K P L + L RF Y Q + K++ R FP +L L +
Sbjct: 342 DAGEH-GLQEAEKGVKFLTLPPVLHLQLMRFMYDPQTDQNIKINDRFEFPEQLPLDEFLQ 400
Query: 180 DADIE----YSLFAVVVHVGSGPNH-GHYVSLV--KSHNHWLFFDDENVEM-IDESAVQT 231
D + Y L AV+VH SG NH GHYV + K W FDD+ V E A++
Sbjct: 401 KTDPKDPANYILHAVLVH--SGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEH 458
Query: 232 FFGSAQEYSS--NTDHGYILFY 251
+G + S + + Y+L Y
Sbjct: 459 NYGGHDDDLSVRHCTNAYMLVY 480
>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 = 72.0 bits (175), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 56/184 (30%), Positives = 90/184 (48%), Gaps = 11/184 (5%)
Query: 60 VHKNFQGILTNETRCLRCETVTARDETFFDLSLDIEQNSSITSCLKNFSSTETLNAEDKF 119
+ K F+G + +C + + R E ++D+ L I+ +I ++ + E L+ ++K+
Sbjct: 113 IPKLFRGKXVSYIQCKEVDYRSDRREDYYDIQLSIKGKKNIFESFVDYVAVEQLDGDNKY 172
Query: 120 FCDKCCSLQEAQKRMKIKKSPHTLVIHLKRFKYIEQLGRYKKLSYRVVFPLELKLSNTAE 179
+ LQEA+K +K P L + L RF Y Q + K++ R FP +L L +
Sbjct: 173 DAGEH-GLQEAEKGVKFLTLPPVLHLQLXRFXYDPQTDQNIKINDRFEFPEQLPLDEFLQ 231
Query: 180 DADIE----YSLFAVVVHVGSGPNH-GHYVSLV--KSHNHWLFFDDENV-EMIDESAVQT 231
D + Y L AV+VH SG NH GHYV + K W FDD+ V E A++
Sbjct: 232 KTDPKDPANYILHAVLVH--SGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEH 289
Query: 232 FFGS 235
+G
Sbjct: 290 NYGG 293
>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 = 66.6 bits (161), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 60/198 (30%), Positives = 93/198 (46%), Gaps = 24/198 (12%)
Query: 64 FQGILTNETRCLRCETVTARDETFFDLSLDIEQNS----SITSCLKNFSSTETLNAEDKF 119
F G L + C C + + F+DLSL I + ++ C++ F+ + L+ ++K
Sbjct: 177 FVGQLKSSLTCTDCGYCSTVFDPFWDLSLPIAKRGYPEVTLMDCMRLFTKEDVLDGDEKP 236
Query: 120 FCDKCCSLQEAQKRMKIKKSPHTLVIHLKRFKYIEQLGRYKKLSYRVVFPL-ELKLSNTA 178
C +C + K+ I++ P LV+HLKRF E R KL+ V FPL +L L A
Sbjct: 237 TCCRCRGRKRCIKKFSIQRFPKILVLHLKRFS--ESRIRTSKLTTFVNFPLRDLDLREFA 294
Query: 179 EDAD--IEYSLFAVVVHVGSGPNHGHYVSLVKSH--NHWLFFDDENVEMIDESAVQTFFG 234
+ Y+L+AV H G+ GHY + +S W F+D +V + S V+
Sbjct: 295 SENTNHAVYNLYAVSNHSGTTMG-GHYTAYCRSPGTGEWHTFNDSSVTPMSSSQVR---- 349
Query: 235 SAQEYSSNTDHGYILFYE 252
T Y+LFYE
Sbjct: 350 --------TSDAYLLFYE 359
>pdb|3NHE|A Chain A, High Resolution Structure (1.26a) Of Usp2a In Complex With
Ubiquitin
Length = 348
Score = 66.6 bits (161), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 60/198 (30%), Positives = 93/198 (46%), Gaps = 24/198 (12%)
Query: 64 FQGILTNETRCLRCETVTARDETFFDLSLDIEQNS----SITSCLKNFSSTETLNAEDKF 119
F G L + C C + + F+DLSL I + ++ C++ F+ + L+ ++K
Sbjct: 158 FVGQLKSSLTCTDCGYCSTVFDPFWDLSLPIAKRGYPEVTLMDCMRLFTKEDVLDGDEKP 217
Query: 120 FCDKCCSLQEAQKRMKIKKSPHTLVIHLKRFKYIEQLGRYKKLSYRVVFPL-ELKLSNTA 178
C +C + K+ I++ P LV+HLKRF E R KL+ V FPL +L L A
Sbjct: 218 TCCRCRGRKRCIKKFSIQRFPKILVLHLKRFS--ESRIRTSKLTTFVNFPLRDLDLREFA 275
Query: 179 EDAD--IEYSLFAVVVHVGSGPNHGHYVSLVKSH--NHWLFFDDENVEMIDESAVQTFFG 234
+ Y+L+AV H G+ GHY + +S W F+D +V + S V+
Sbjct: 276 SENTNHAVYNLYAVSNHSGTTMG-GHYTAYCRSPGTGEWHTFNDSSVTPMSSSQVR---- 330
Query: 235 SAQEYSSNTDHGYILFYE 252
T Y+LFYE
Sbjct: 331 --------TSDAYLLFYE 340
>pdb|2HD5|A Chain A, Usp2 In Complex With Ubiquitin
Length = 359
Score = 66.6 bits (161), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 60/198 (30%), Positives = 93/198 (46%), Gaps = 24/198 (12%)
Query: 64 FQGILTNETRCLRCETVTARDETFFDLSLDIEQNS----SITSCLKNFSSTETLNAEDKF 119
F G L + C C + + F+DLSL I + ++ C++ F+ + L+ ++K
Sbjct: 158 FVGQLKSSLTCTDCGYCSTVFDPFWDLSLPIAKRGYPEVTLMDCMRLFTKEDVLDGDEKP 217
Query: 120 FCDKCCSLQEAQKRMKIKKSPHTLVIHLKRFKYIEQLGRYKKLSYRVVFPL-ELKLSNTA 178
C +C + K+ I++ P LV+HLKRF E R KL+ V FPL +L L A
Sbjct: 218 TCCRCRGRKRCIKKFSIQRFPKILVLHLKRFS--ESRIRTSKLTTFVNFPLRDLDLREFA 275
Query: 179 EDAD--IEYSLFAVVVHVGSGPNHGHYVSLVKSH--NHWLFFDDENVEMIDESAVQTFFG 234
+ Y+L+AV H G+ GHY + +S W F+D +V + S V+
Sbjct: 276 SENTNHAVYNLYAVSNHSGTTMG-GHYTAYCRSPGTGEWHTFNDSSVTPMSSSQVR---- 330
Query: 235 SAQEYSSNTDHGYILFYE 252
T Y+LFYE
Sbjct: 331 --------TSDAYLLFYE 340
>pdb|2IBI|A Chain A, Covalent Ubiquitin-Usp2 Complex
Length = 374
Score = 63.5 bits (153), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 59/198 (29%), Positives = 91/198 (45%), Gaps = 24/198 (12%)
Query: 64 FQGILTNETRCLRCETVTARDETFFDLSLDIEQNS----SITSCLKNFSSTETLNAEDKF 119
F G L + C C + + F+DLSL I + ++ C++ F+ + L+ +
Sbjct: 184 FVGQLKSSLTCTDCGYCSTVFDPFWDLSLPIAKRGYPEVTLMDCMRLFTKEDVLDGDAAP 243
Query: 120 FCDKCCSLQEAQKRMKIKKSPHTLVIHLKRFKYIEQLGRYKKLSYRVVFPL-ELKLSNTA 178
C +C + K+ I++ P LV+HLKRF E R KL+ V FPL +L L A
Sbjct: 244 TCCRCRGRKRCIKKFSIQRFPKILVLHLKRFS--ESRIRTSKLTTFVNFPLRDLDLREFA 301
Query: 179 EDAD--IEYSLFAVVVHVGSGPNHGHYVSLVKSH--NHWLFFDDENVEMIDESAVQTFFG 234
+ Y+L+AV H G+ GHY + +S W F+D +V + S V+
Sbjct: 302 SENTNHAVYNLYAVSNHSGTTMG-GHYTAYCRSPGTGEWHTFNDSSVTPMSSSQVR---- 356
Query: 235 SAQEYSSNTDHGYILFYE 252
T Y+LFYE
Sbjct: 357 --------TSDAYLLFYE 366
>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 = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/95 (25%), Positives = 45/95 (47%), Gaps = 11/95 (11%)
Query: 164 YRVVFPLELKLSNTAEDADIEYSLFAVVVHVGSGPNHGHYVSLVK---SHNHWLFFDDEN 220
Y+ FP L+ E+ Y+L V+ H G+ GHY + ++ N W F+D+
Sbjct: 328 YKKHFPPNLE---KGENPSCVYNLIGVITHQGANSESGHYQAFIRDELDENKWYKFNDDK 384
Query: 221 VEMIDESAVQTFFGSAQEYSSNTDHGYILFYESLG 255
V ++++ +++ G + +D IL Y+ G
Sbjct: 385 VSVVEKEKIESLAGGGE-----SDSALILXYKGFG 414
>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
Length = 854
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 37/85 (43%), Gaps = 14/85 (16%)
Query: 172 LKLSNTAEDADIEYSLFAVVVHVGSGPNHGHYVSLVKSHNHWLFFDDENVEMIDESAVQT 231
+ + D +Y LFA + H+G+ GHYV +K W+ ++D+ V
Sbjct: 784 VPVGPKVRDGPGKYQLFAFISHMGTSTMCGHYVCHIKKEGRWVIYNDQKV---------- 833
Query: 232 FFGSAQEYSSNTDHGYILFYESLGA 256
A E D GYI FY+ + +
Sbjct: 834 ---CASEKPPK-DLGYIYFYQRVAS 854
>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 = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 32/68 (47%), Gaps = 6/68 (8%)
Query: 185 YSLFAVVVHVGSGPNHGHYVSLVK-SHNHWLFFDDENVEMIDESAVQTFFGSAQEYSSNT 243
Y L AV+ H G + GHYVS VK + W+ FDD+ V ++ + G +
Sbjct: 328 YDLQAVLTHQGRSSSSGHYVSWVKRKQDEWIKFDDDKVSIVTPEDILRLSGGG-----DW 382
Query: 244 DHGYILFY 251
Y+L Y
Sbjct: 383 HIAYVLLY 390
>pdb|1GCW|A Chain A, Co Form Hemoglobin From Mustelus Griseus
pdb|1GCW|C Chain C, Co Form Hemoglobin From Mustelus Griseus
pdb|1GCV|A Chain A, Deoxy Form Hemoglobin From Mustelus Griseus
pdb|1GCV|C Chain C, Deoxy Form Hemoglobin From Mustelus Griseus
Length = 140
Score = 28.1 bits (61), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 20/44 (45%)
Query: 200 HGHYVSLVKSHNHWLFFDDENVEMIDESAVQTFFGSAQEYSSNT 243
H H +L +H L D +N M+ E + T E+S +T
Sbjct: 77 HSHLETLALTHGKKLLVDPQNFPMLSECIIVTLATHLTEFSPDT 120
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 0.134 0.397
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,191,475
Number of Sequences: 62578
Number of extensions: 272511
Number of successful extensions: 730
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 21
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 677
Number of HSP's gapped (non-prelim): 29
length of query: 261
length of database: 14,973,337
effective HSP length: 97
effective length of query: 164
effective length of database: 8,903,271
effective search space: 1460136444
effective search space used: 1460136444
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: 50 (23.9 bits)