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= 039539
(484 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 102 bits (253), Expect = 6e-22, Method: Compositional matrix adjust.
Identities = 82/255 (32%), Positives = 124/255 (48%), Gaps = 23/255 (9%)
Query: 28 IGILSKIQKIGSHLGHGREEDAHEFLRCAVDTM-QSVCLKEFGAK----GKIAEETTLIG 82
I +L+ KI +L ++DAHEF + ++ + QS L AK + ++
Sbjct: 222 IYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQSYVLDLPNAKEVSRANNKQCECIVH 281
Query: 83 LTFGGYLRSKIKCLKCLGKSEL-YERMMDLTVEIDGDIGTLEEALAQFTASEILVGENKY 141
F G L S I C C S+ + +DL+++I D L E L F E L N Y
Sbjct: 282 TVFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIK-DKKKLYECLDSFHKKEQLKDFN-Y 339
Query: 142 YCSRCKSYEKAKKKLTVLEEPNILTIVLKRFE---SGNFGKLNKSVWFPEVLNMAPYMS- 197
+C C S + A K+L + + P++L + LKRFE +G+ KL+ + FP LNM Y S
Sbjct: 340 HCGECNSTQDAIKQLGIHKLPSVLVLQLKRFEHLLNGSNRKLDDFIEFPTYLNMKNYCST 399
Query: 198 -----RTGDGSP---MYSLYAVVVHLDVTNATFSGHYVCYVKNSHEEWFRIDDSTVIPVK 249
+ +G +Y L +V H N GHY+ + K S +WF+ +DS V +
Sbjct: 400 KEKDKHSENGKVPDIIYELIGIVSHKGTVN---EGHYIAFCKISGGQWFKFNDSMVSSIS 456
Query: 250 LERVLSEEAYMLLYA 264
E VL E+AY+L Y
Sbjct: 457 QEEVLKEQAYLLFYT 471
>pdb|3M99|A Chain A, Structure Of The Ubp8-Sgf11-Sgf73-Sus1 Saga Dub Module
Length = 471
Score = 102 bits (253), Expect = 6e-22, Method: Compositional matrix adjust.
Identities = 82/255 (32%), Positives = 124/255 (48%), Gaps = 23/255 (9%)
Query: 28 IGILSKIQKIGSHLGHGREEDAHEFLRCAVDTM-QSVCLKEFGAK----GKIAEETTLIG 82
I +L+ KI +L ++DAHEF + ++ + QS L AK + ++
Sbjct: 217 IYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQSYVLDLPNAKEVSRANNKQCECIVH 276
Query: 83 LTFGGYLRSKIKCLKCLGKSEL-YERMMDLTVEIDGDIGTLEEALAQFTASEILVGENKY 141
F G L S I C C S+ + +DL+++I D L E L F E L N Y
Sbjct: 277 TVFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIK-DKKKLYECLDSFHKKEQLKDFN-Y 334
Query: 142 YCSRCKSYEKAKKKLTVLEEPNILTIVLKRFE---SGNFGKLNKSVWFPEVLNMAPYMS- 197
+C C S + A K+L + + P++L + LKRFE +G+ KL+ + FP LNM Y S
Sbjct: 335 HCGECNSTQDAIKQLGIHKLPSVLVLQLKRFEHLLNGSNRKLDDFIEFPTYLNMKNYCST 394
Query: 198 -----RTGDGSP---MYSLYAVVVHLDVTNATFSGHYVCYVKNSHEEWFRIDDSTVIPVK 249
+ +G +Y L +V H N GHY+ + K S +WF+ +DS V +
Sbjct: 395 KEKDKHSENGKVPDIIYELIGIVSHKGTVN---EGHYIAFCKISGGQWFKFNDSMVSSIS 451
Query: 250 LERVLSEEAYMLLYA 264
E VL E+AY+L Y
Sbjct: 452 QEEVLKEQAYLLFYT 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 = 102 bits (253), Expect = 6e-22, Method: Compositional matrix adjust.
Identities = 82/255 (32%), Positives = 124/255 (48%), Gaps = 23/255 (9%)
Query: 28 IGILSKIQKIGSHLGHGREEDAHEFLRCAVDTM-QSVCLKEFGAK----GKIAEETTLIG 82
I +L+ KI +L ++DAHEF + ++ + QS L AK + ++
Sbjct: 222 IYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQSYVLDLPNAKEVSRANNKQCECIVH 281
Query: 83 LTFGGYLRSKIKCLKCLGKSEL-YERMMDLTVEIDGDIGTLEEALAQFTASEILVGENKY 141
F G L S I C C S+ + +DL+++I D L E L F E L N Y
Sbjct: 282 TVFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIK-DKKKLYECLDSFHKKEQLKDFN-Y 339
Query: 142 YCSRCKSYEKAKKKLTVLEEPNILTIVLKRFE---SGNFGKLNKSVWFPEVLNMAPYMS- 197
+C C S + A K+L + + P++L + LKRFE +G+ KL+ + FP LNM Y S
Sbjct: 340 HCGECNSTQDAIKQLGIHKLPSVLVLQLKRFEHLLNGSNRKLDDFIEFPTYLNMKNYCST 399
Query: 198 -----RTGDGSP---MYSLYAVVVHLDVTNATFSGHYVCYVKNSHEEWFRIDDSTVIPVK 249
+ +G +Y L +V H N GHY+ + K S +WF+ +DS V +
Sbjct: 400 KEKDKHSENGKVPDIIYELIGIVSHKGTVN---EGHYIAFCKISGGQWFKFNDSMVSSIS 456
Query: 250 LERVLSEEAYMLLYA 264
E VL E+AY+L Y
Sbjct: 457 QEEVLKEQAYLLFYT 471
>pdb|3N3K|A Chain A, The Catalytic Domain Of Usp8 In Complex With A Usp8
Specific Inhibitor
Length = 396
Score = 92.8 bits (229), Expect = 4e-19, Method: Compositional matrix adjust.
Identities = 77/267 (28%), Positives = 123/267 (46%), Gaps = 31/267 (11%)
Query: 25 VSPIGILSKIQKIGSHLGHGREEDAHEFLRCAVDTMQSVC----------------LKEF 68
+SP I KI ++D+ E L +D + L +F
Sbjct: 131 ISPKDFKITIGKINDQFAGYSQQDSQELLLFLMDGLHEDLNKADNRKRYKEENNDHLDDF 190
Query: 69 GA------KGKIAEETTLIGLTFGGYLRSKIKCLKCLGKSELYERMMDLTVEI-DGDIGT 121
A K K E+ ++ L F G +S ++CL C KS +E M L++ + T
Sbjct: 191 KAAEHAWQKHKQLNESIIVAL-FQGQFKSTVQCLTCHKKSRTFEAFMYLSLPLASTSKCT 249
Query: 122 LEEALAQFTASEILVGENKYYCSRCKSYEKAKKKLTVLEEPNILTIVLKRFE-SGNFG-K 179
L++ L F+ E L N++YCS C++ + KK+ + + P +L + LKRF G + K
Sbjct: 250 LQDCLRLFSKEEKLTDNNRFYCSHCRARRDSLKKIEIWKLPPVLLVHLKRFSYDGRWKQK 309
Query: 180 LNKSVWFP-EVLNMAPYMSRTGDGSPMYSLYAVVVHLDVTNATFSGHYVCYVKN-SHEEW 237
L SV FP E L+++ Y+ + Y+L++V H + GHY Y KN + + W
Sbjct: 310 LQTSVDFPLENLDLSQYVIGPKNNLKKYNLFSVSNHYGGLDG---GHYTAYCKNAARQRW 366
Query: 238 FRIDDSTVIPVKLERVLSEEAYMLLYA 264
F+ DD V + + V S AY+L Y
Sbjct: 367 FKFDDHEVSDISVSSVKSSAAYILFYT 393
>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 = 90.5 bits (223), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 66/196 (33%), Positives = 97/196 (49%), Gaps = 14/196 (7%)
Query: 76 EETTLIGLTFGGYLRSKIKCLKCLGKSELYERMMDLTVEID-----GDIGTLEEALAQFT 130
E++ ++ L F G L+S +KC C +S +E DL++ I G +L + FT
Sbjct: 171 EDSKIVDL-FVGQLKSCLKCQACGYRSTTFEVFCDLSLPIPKKGFAGGKVSLRDCFNLFT 229
Query: 131 ASEILVGENKYYCSRCKSYEKAKKKLTVLEEPNILTIVLKRFES--GNFGKLNKSVWFP- 187
E L EN C RC+ ++ KKLTV P IL + L RF + G+ K + V FP
Sbjct: 230 KEEELESENAPVCDRCRQKTRSTKKLTVQRFPRILVLHLNRFSASRGSIKKSSVGVDFPL 289
Query: 188 EVLNMAPYMSRTGDGSPMYSLYAVVVHLDVTNATFSGHYVCYVKNSHEEWFRIDDSTVIP 247
+ L++ + S GSP+Y LYA+ H + + GHY + W +DS V P
Sbjct: 290 QRLSLGDFASDKA-GSPVYQLYALCNH---SGSVHYGHYTALCR-CQTGWHVYNDSRVSP 344
Query: 248 VKLERVLSEEAYMLLY 263
V +V S E Y+L Y
Sbjct: 345 VSENQVASSEGYVLFY 360
>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 = 90.5 bits (223), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 66/196 (33%), Positives = 97/196 (49%), Gaps = 14/196 (7%)
Query: 76 EETTLIGLTFGGYLRSKIKCLKCLGKSELYERMMDLTVEID-----GDIGTLEEALAQFT 130
E++ ++ L F G L+S +KC C +S +E DL++ I G +L + FT
Sbjct: 177 EDSKIVDL-FVGQLKSCLKCQACGYRSTTFEVFCDLSLPIPKKGFAGGKVSLRDCFNLFT 235
Query: 131 ASEILVGENKYYCSRCKSYEKAKKKLTVLEEPNILTIVLKRFES--GNFGKLNKSVWFP- 187
E L EN C RC+ ++ KKLTV P IL + L RF + G+ K + V FP
Sbjct: 236 KEEELESENAPVCDRCRQKTRSTKKLTVQRFPRILVLHLNRFSASRGSIKKSSVGVDFPL 295
Query: 188 EVLNMAPYMSRTGDGSPMYSLYAVVVHLDVTNATFSGHYVCYVKNSHEEWFRIDDSTVIP 247
+ L++ + S GSP+Y LYA+ H + + GHY + W +DS V P
Sbjct: 296 QRLSLGDFASDKA-GSPVYQLYALCNH---SGSVHYGHYTALCR-CQTGWHVYNDSRVSP 350
Query: 248 VKLERVLSEEAYMLLY 263
V +V S E Y+L Y
Sbjct: 351 VSENQVASSEGYVLFY 366
>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 = 90.5 bits (223), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 66/196 (33%), Positives = 97/196 (49%), Gaps = 14/196 (7%)
Query: 76 EETTLIGLTFGGYLRSKIKCLKCLGKSELYERMMDLTVEID-----GDIGTLEEALAQFT 130
E++ ++ L F G L+S +KC C +S +E DL++ I G +L + FT
Sbjct: 158 EDSKIVDL-FVGQLKSCLKCQACGYRSTTFEVFCDLSLPIPKKGFAGGKVSLRDCFNLFT 216
Query: 131 ASEILVGENKYYCSRCKSYEKAKKKLTVLEEPNILTIVLKRFES--GNFGKLNKSVWFP- 187
E L EN C RC+ ++ KKLTV P IL + L RF + G+ K + V FP
Sbjct: 217 KEEELESENAPVCDRCRQKTRSTKKLTVQRFPRILVLHLNRFSASRGSIKKSSVGVDFPL 276
Query: 188 EVLNMAPYMSRTGDGSPMYSLYAVVVHLDVTNATFSGHYVCYVKNSHEEWFRIDDSTVIP 247
+ L++ + S GSP+Y LYA+ H + + GHY + W +DS V P
Sbjct: 277 QRLSLGDFASDKA-GSPVYQLYALCNH---SGSVHYGHYTALCR-CQTGWHVYNDSRVSP 331
Query: 248 VKLERVLSEEAYMLLY 263
V +V S E Y+L Y
Sbjct: 332 VSENQVASSEGYVLFY 347
>pdb|2GFO|A Chain A, Structure Of The Catalytic Domain Of Human Ubiquitin
Carboxyl-terminal Hydrolase 8
Length = 396
Score = 90.5 bits (223), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 64/199 (32%), Positives = 103/199 (51%), Gaps = 9/199 (4%)
Query: 71 KGKIAEETTLIGLTFGGYLRSKIKCLKCLGKSELYERMMDLTVEI-DGDIGTLEEALAQF 129
K K E+ ++ L F G +S ++CL C KS +E L++ + TL++ L F
Sbjct: 199 KHKQLNESIIVAL-FQGQFKSTVQCLTCHKKSRTFEAFXYLSLPLASTSKCTLQDCLRLF 257
Query: 130 TASEILVGENKYYCSRCKSYEKAKKKLTVLEEPNILTIVLKRFE-SGNFG-KLNKSVWFP 187
+ E L N++YCS C++ + KK+ + + P +L + LKRF G + KL SV FP
Sbjct: 258 SKEEKLTDNNRFYCSHCRARRDSLKKIEIWKLPPVLLVHLKRFSYDGRWKQKLQTSVDFP 317
Query: 188 -EVLNMAPYMSRTGDGSPMYSLYAVVVHLDVTNATFSGHYVCYVKN-SHEEWFRIDDSTV 245
E L+++ Y+ + Y+L++V H + GHY Y KN + + WF+ DD V
Sbjct: 318 LENLDLSQYVIGPKNNLKKYNLFSVSNHYGGLDG---GHYTAYCKNAARQRWFKFDDHEV 374
Query: 246 IPVKLERVLSEEAYMLLYA 264
+ + V S AY+L Y
Sbjct: 375 SDISVSSVKSSAAYILFYT 393
>pdb|3NHE|A Chain A, High Resolution Structure (1.26a) Of Usp2a In Complex With
Ubiquitin
Length = 348
Score = 85.9 bits (211), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 80/273 (29%), Positives = 127/273 (46%), Gaps = 34/273 (12%)
Query: 25 VSPIGILSKIQKIGSHLGHGREEDAHEFLRCAVDTMQS----VCLKEFG----------- 69
VSP ++IQ+ ++DA EFLR +D + + V L+
Sbjct: 77 VSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPENLDHLPDD 136
Query: 70 AKGK------IAEETTLIGLTFGGYLRSKIKCLKCLGKSELYERMMDLTVEIDGDIG--- 120
KG+ + E + IG F G L+S + C C S +++ DL++ I G
Sbjct: 137 EKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPI-AKRGYPE 195
Query: 121 -TLEEALAQFTASEILVGENKYYCSRCKSYEKAKKKLTVLEEPNILTIVLKRFESGNF-- 177
TL + + FT ++L G+ K C RC+ ++ KK ++ P IL + LKRF
Sbjct: 196 VTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKILVLHLKRFSESRIRT 255
Query: 178 GKLNKSVWFP-EVLNMAPYMSRTGDGSPMYSLYAVVVHLDVTNATFSGHYVCYVKNSHE- 235
KL V FP L++ + S + + +Y+LYAV H + T GHY Y ++
Sbjct: 256 SKLTTFVNFPLRDLDLREFASENTNHA-VYNLYAVSNH---SGTTMGGHYTAYCRSPGTG 311
Query: 236 EWFRIDDSTVIPVKLERVLSEEAYMLLYARHSP 268
EW +DS+V P+ +V + +AY+L Y SP
Sbjct: 312 EWHTFNDSSVTPMSSSQVRTSDAYLLFYELASP 344
>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 = 85.9 bits (211), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 80/273 (29%), Positives = 127/273 (46%), Gaps = 34/273 (12%)
Query: 25 VSPIGILSKIQKIGSHLGHGREEDAHEFLRCAVDTMQS----VCLKEFG----------- 69
VSP ++IQ+ ++DA EFLR +D + + V L+
Sbjct: 96 VSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPENLDHLPDD 155
Query: 70 AKGK------IAEETTLIGLTFGGYLRSKIKCLKCLGKSELYERMMDLTVEIDGDIG--- 120
KG+ + E + IG F G L+S + C C S +++ DL++ I G
Sbjct: 156 EKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPI-AKRGYPE 214
Query: 121 -TLEEALAQFTASEILVGENKYYCSRCKSYEKAKKKLTVLEEPNILTIVLKRFESGNF-- 177
TL + + FT ++L G+ K C RC+ ++ KK ++ P IL + LKRF
Sbjct: 215 VTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKILVLHLKRFSESRIRT 274
Query: 178 GKLNKSVWFP-EVLNMAPYMSRTGDGSPMYSLYAVVVHLDVTNATFSGHYVCYVKNSHE- 235
KL V FP L++ + S + + +Y+LYAV H + T GHY Y ++
Sbjct: 275 SKLTTFVNFPLRDLDLREFASENTNHA-VYNLYAVSNH---SGTTMGGHYTAYCRSPGTG 330
Query: 236 EWFRIDDSTVIPVKLERVLSEEAYMLLYARHSP 268
EW +DS+V P+ +V + +AY+L Y SP
Sbjct: 331 EWHTFNDSSVTPMSSSQVRTSDAYLLFYELASP 363
>pdb|2HD5|A Chain A, Usp2 In Complex With Ubiquitin
Length = 359
Score = 85.9 bits (211), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 80/273 (29%), Positives = 127/273 (46%), Gaps = 34/273 (12%)
Query: 25 VSPIGILSKIQKIGSHLGHGREEDAHEFLRCAVDTMQS----VCLKEFG----------- 69
VSP ++IQ+ ++DA EFLR +D + + V L+
Sbjct: 77 VSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPENLDHLPDD 136
Query: 70 AKGK------IAEETTLIGLTFGGYLRSKIKCLKCLGKSELYERMMDLTVEIDGDIG--- 120
KG+ + E + IG F G L+S + C C S +++ DL++ I G
Sbjct: 137 EKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPI-AKRGYPE 195
Query: 121 -TLEEALAQFTASEILVGENKYYCSRCKSYEKAKKKLTVLEEPNILTIVLKRFESGNF-- 177
TL + + FT ++L G+ K C RC+ ++ KK ++ P IL + LKRF
Sbjct: 196 VTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKILVLHLKRFSESRIRT 255
Query: 178 GKLNKSVWFP-EVLNMAPYMSRTGDGSPMYSLYAVVVHLDVTNATFSGHYVCYVKNSHE- 235
KL V FP L++ + S + + +Y+LYAV H + T GHY Y ++
Sbjct: 256 SKLTTFVNFPLRDLDLREFASENTNHA-VYNLYAVSNH---SGTTMGGHYTAYCRSPGTG 311
Query: 236 EWFRIDDSTVIPVKLERVLSEEAYMLLYARHSP 268
EW +DS+V P+ +V + +AY+L Y SP
Sbjct: 312 EWHTFNDSSVTPMSSSQVRTSDAYLLFYELASP 344
>pdb|2IBI|A Chain A, Covalent Ubiquitin-Usp2 Complex
Length = 374
Score = 84.0 bits (206), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 79/273 (28%), Positives = 126/273 (46%), Gaps = 34/273 (12%)
Query: 25 VSPIGILSKIQKIGSHLGHGREEDAHEFLRCAVDTMQS----VCLKEFG----------- 69
VSP ++IQ+ ++DA EFLR +D + + V L+
Sbjct: 103 VSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPENLDHLPDD 162
Query: 70 AKGK------IAEETTLIGLTFGGYLRSKIKCLKCLGKSELYERMMDLTVEIDGDIG--- 120
KG+ + E + IG F G L+S + C C S +++ DL++ I G
Sbjct: 163 EKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPI-AKRGYPE 221
Query: 121 -TLEEALAQFTASEILVGENKYYCSRCKSYEKAKKKLTVLEEPNILTIVLKRFESGNF-- 177
TL + + FT ++L G+ C RC+ ++ KK ++ P IL + LKRF
Sbjct: 222 VTLMDCMRLFTKEDVLDGDAAPTCCRCRGRKRCIKKFSIQRFPKILVLHLKRFSESRIRT 281
Query: 178 GKLNKSVWFP-EVLNMAPYMSRTGDGSPMYSLYAVVVHLDVTNATFSGHYVCYVKNSHE- 235
KL V FP L++ + S + + +Y+LYAV H + T GHY Y ++
Sbjct: 282 SKLTTFVNFPLRDLDLREFASENTNHA-VYNLYAVSNH---SGTTMGGHYTAYCRSPGTG 337
Query: 236 EWFRIDDSTVIPVKLERVLSEEAYMLLYARHSP 268
EW +DS+V P+ +V + +AY+L Y SP
Sbjct: 338 EWHTFNDSSVTPMSSSQVRTSDAYLLFYELASP 370
>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 = 80.9 bits (198), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 68/285 (23%), Positives = 120/285 (42%), Gaps = 48/285 (16%)
Query: 25 VSPIGILSKIQKIGSHLGHGREEDAHEFLRCAVDTMQ----------------------S 62
V+P +++ + +++D+ E L +D + +
Sbjct: 77 VAPRMFKTQVGRFAPQFSGYQQQDSQELLAFLLDGLHEDLNRVKKKPYLELKDANGRPDA 136
Query: 63 VCLKEFGAKGKIAEETTLIGLTFGGYLRSKIKCLKCLGKSELYERMMDLTVEI------- 115
V KE ++ ++ ++ TF G +S + C +C S ++ LT+ +
Sbjct: 137 VVAKEAWENHRLRNDSVIVD-TFHGLFKSTLVCPECAKVSVTFDPFCYLTLPLPLKKDRV 195
Query: 116 -DGDI----------GTLEEALAQFTASEILVGENKYYCSRCKSYEKAKKKLTVLEEPNI 164
+G + L + + FT E L + +YC CK +++A KK + P I
Sbjct: 196 MEGPMLQPQKKKKTTVALRDCIELFTTMETLGEHDPWYCPNCKKHQQATKKFDLWSLPKI 255
Query: 165 LTIVLKRFESGNF--GKLNKSVWFP-EVLNMAPYMSRTGDGSPMYSLYAVVVHLDVTNAT 221
L + LKRF + KL+ V FP LNM+ ++ +Y L AV H A
Sbjct: 256 LVVHLKRFSYNRYWRDKLDTVVEFPIRGLNMSEFVCNLSARPYVYDLIAVSNHY---GAM 312
Query: 222 FSGHYVCYVKNS-HEEWFRIDDSTVIPVKLERVLSEEAYMLLYAR 265
GHY Y KN + +W+ DDS V ++++++ AY+L Y R
Sbjct: 313 GVGHYTAYAKNKLNGKWYYFDDSNVSLASEDQIVTKAAYVLFYQR 357
>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 = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/65 (38%), Positives = 34/65 (52%), Gaps = 9/65 (13%)
Query: 206 YSLYAVVVHLDVTNATFSGHYVCYVKNSHEEWFRIDDSTVIPVKLERVLSEE-------A 258
Y L AV+ H +++ SGHYV +VK +EW + DD V V E +L A
Sbjct: 328 YDLQAVLTHQGRSSS--SGHYVSWVKRKQDEWIKFDDDKVSIVTPEDILRLSGGGDWHIA 385
Query: 259 YMLLY 263
Y+LLY
Sbjct: 386 YVLLY 390
>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
Length = 854
Score = 35.8 bits (81), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 32/73 (43%), Gaps = 5/73 (6%)
Query: 193 APYMSRTGDGSPMYSLYAVVVHLDVTNATFSGHYVCYVKNSHEEWFRIDDSTVIPVKLER 252
P + DG Y L+A + H+ + T GHYVC++K W +D V E+
Sbjct: 784 VPVGPKVRDGPGKYQLFAFISHMGTS--TMCGHYVCHIKKEG-RWVIYNDQKV--CASEK 838
Query: 253 VLSEEAYMLLYAR 265
+ Y+ Y R
Sbjct: 839 PPKDLGYIYFYQR 851
>pdb|3HR4|A Chain A, Human Inos Reductase And Calmodulin Complex
pdb|3HR4|C Chain C, Human Inos Reductase And Calmodulin Complex
pdb|3HR4|E Chain E, Human Inos Reductase And Calmodulin Complex
pdb|3HR4|G Chain G, Human Inos Reductase And Calmodulin Complex
Length = 219
Score = 32.0 bits (71), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 32/66 (48%), Gaps = 4/66 (6%)
Query: 153 KKKLTVLEEPNILTIVLKRFESG----NFGKLNKSVWFPEVLNMAPYMSRTGDGSPMYSL 208
K +L+ LEE +L +V F +G N KL KS++ + LN + G GS MY
Sbjct: 78 KYRLSCLEEERLLLVVTSTFGNGDCPGNGEKLKKSLFMLKELNNKFRYAVFGLGSSMYPR 137
Query: 209 YAVVVH 214
+ H
Sbjct: 138 FCAFAH 143
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
0.316 0.133 0.398
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,051,767
Number of Sequences: 62578
Number of extensions: 570754
Number of successful extensions: 1496
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1451
Number of HSP's gapped (non-prelim): 19
length of query: 484
length of database: 14,973,337
effective HSP length: 103
effective length of query: 381
effective length of database: 8,527,803
effective search space: 3249092943
effective search space used: 3249092943
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)