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= psy15062
(375 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2HD5|A Chain A, Usp2 In Complex With Ubiquitin
Length = 359
Score = 164 bits (414), Expect = 9e-41, Method: Compositional matrix adjust.
Identities = 119/384 (30%), Positives = 178/384 (46%), Gaps = 65/384 (16%)
Query: 4 GLNGIANAGNTCYINSVLQCLSNTPAFRNVLLNEDI--PIHPDSKSQGQLVDALVNFMKM 61
GL G+ N GNTC++NS+LQCLSNT R+ L +H S + LV+ ++
Sbjct: 8 GLAGLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQT 67
Query: 62 MW-SSGNLVLNTKAILLALRSYTKKFDGNQQQDAQXXXXXXXXXXXXXXKVVP--DQYNG 118
+W SS N V++ ++ Y +F G QQDAQ V + N
Sbjct: 68 IWTSSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNP 127
Query: 119 STYSNTSSKQVGSFRALHYWEKFQTTEASVFSDIFVGQLRSSVRCSNCKRTSTVYEIFWE 178
+ + G W K+ E S D+FVGQ
Sbjct: 128 ENLDHLPDDEKGR----QMWRKYLEREDSRIGDLFVGQ---------------------- 161
Query: 179 LSLPVPPGGGTLYECQLRSSVRCSNCKRTSTVYEIFWELSLPVPPGG---GTLYECLNKF 235
L+SS+ C++C STV++ FW+LSLP+ G TL +C+ F
Sbjct: 162 ----------------LKSSLTCTDCGYCSTVFDPFWDLSLPIAKRGYPEVTLMDCMRLF 205
Query: 236 FNGETLHN----TCQYCKKQSDLVKLYEIQRLPPVLILWFKRFSSNF--TQKVTSPIKFP 289
+ L TC C+ + +K + IQR P +L+L KRFS + T K+T+ + FP
Sbjct: 206 TKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKILVLHLKRFSESRIRTSKLTTFVNFP 265
Query: 290 REGLDMEYYISASGRRVESRYTYDLCAVSNHIGKTALYGHYTAYCRREGTGRWYLYDDTV 349
LD+ + S + Y+L AVSNH G T + GHYTAYCR GTG W+ ++D+
Sbjct: 266 LRDLDLREFASENTNHA----VYNLYAVSNHSG-TTMGGHYTAYCRSPGTGEWHTFNDSS 320
Query: 350 VSPVDAQTVESAEAEHGAYILVYQ 373
V+P+ + V +++ AY+L Y+
Sbjct: 321 VTPMSSSQVRTSD----AYLLFYE 340
>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 = 163 bits (413), Expect = 1e-40, Method: Compositional matrix adjust.
Identities = 119/384 (30%), Positives = 178/384 (46%), Gaps = 65/384 (16%)
Query: 4 GLNGIANAGNTCYINSVLQCLSNTPAFRNVLLNEDI--PIHPDSKSQGQLVDALVNFMKM 61
GL G+ N GNTC++NS+LQCLSNT R+ L +H S + LV+ ++
Sbjct: 27 GLAGLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQT 86
Query: 62 MW-SSGNLVLNTKAILLALRSYTKKFDGNQQQDAQXXXXXXXXXXXXXXKVVP--DQYNG 118
+W SS N V++ ++ Y +F G QQDAQ V + N
Sbjct: 87 IWTSSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNP 146
Query: 119 STYSNTSSKQVGSFRALHYWEKFQTTEASVFSDIFVGQLRSSVRCSNCKRTSTVYEIFWE 178
+ + G W K+ E S D+FVGQ
Sbjct: 147 ENLDHLPDDEKGR----QMWRKYLEREDSRIGDLFVGQ---------------------- 180
Query: 179 LSLPVPPGGGTLYECQLRSSVRCSNCKRTSTVYEIFWELSLPVPPGG---GTLYECLNKF 235
L+SS+ C++C STV++ FW+LSLP+ G TL +C+ F
Sbjct: 181 ----------------LKSSLTCTDCGYCSTVFDPFWDLSLPIAKRGYPEVTLMDCMRLF 224
Query: 236 FNGETLHN----TCQYCKKQSDLVKLYEIQRLPPVLILWFKRFSSNF--TQKVTSPIKFP 289
+ L TC C+ + +K + IQR P +L+L KRFS + T K+T+ + FP
Sbjct: 225 TKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKILVLHLKRFSESRIRTSKLTTFVNFP 284
Query: 290 REGLDMEYYISASGRRVESRYTYDLCAVSNHIGKTALYGHYTAYCRREGTGRWYLYDDTV 349
LD+ + S + Y+L AVSNH G T + GHYTAYCR GTG W+ ++D+
Sbjct: 285 LRDLDLREFASENTNHA----VYNLYAVSNHSG-TTMGGHYTAYCRSPGTGEWHTFNDSS 339
Query: 350 VSPVDAQTVESAEAEHGAYILVYQ 373
V+P+ + V +++ AY+L Y+
Sbjct: 340 VTPMSSSQVRTSD----AYLLFYE 359
>pdb|2IBI|A Chain A, Covalent Ubiquitin-Usp2 Complex
Length = 374
Score = 163 bits (413), Expect = 1e-40, Method: Compositional matrix adjust.
Identities = 119/384 (30%), Positives = 178/384 (46%), Gaps = 65/384 (16%)
Query: 4 GLNGIANAGNTCYINSVLQCLSNTPAFRNVLLNEDI--PIHPDSKSQGQLVDALVNFMKM 61
GL G+ N GNTC++NS+LQCLSNT R+ L +H S + LV+ ++
Sbjct: 34 GLAGLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQT 93
Query: 62 MW-SSGNLVLNTKAILLALRSYTKKFDGNQQQDAQXXXXXXXXXXXXXXKVVP--DQYNG 118
+W SS N V++ ++ Y +F G QQDAQ V + N
Sbjct: 94 IWTSSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNP 153
Query: 119 STYSNTSSKQVGSFRALHYWEKFQTTEASVFSDIFVGQLRSSVRCSNCKRTSTVYEIFWE 178
+ + G W K+ E S D+FVGQ
Sbjct: 154 ENLDHLPDDEKGR----QMWRKYLEREDSRIGDLFVGQ---------------------- 187
Query: 179 LSLPVPPGGGTLYECQLRSSVRCSNCKRTSTVYEIFWELSLPVPPGG---GTLYECLNKF 235
L+SS+ C++C STV++ FW+LSLP+ G TL +C+ F
Sbjct: 188 ----------------LKSSLTCTDCGYCSTVFDPFWDLSLPIAKRGYPEVTLMDCMRLF 231
Query: 236 FNGETLHN----TCQYCKKQSDLVKLYEIQRLPPVLILWFKRFSSNF--TQKVTSPIKFP 289
+ L TC C+ + +K + IQR P +L+L KRFS + T K+T+ + FP
Sbjct: 232 TKEDVLDGDAAPTCCRCRGRKRCIKKFSIQRFPKILVLHLKRFSESRIRTSKLTTFVNFP 291
Query: 290 REGLDMEYYISASGRRVESRYTYDLCAVSNHIGKTALYGHYTAYCRREGTGRWYLYDDTV 349
LD+ + S + Y+L AVSNH G T + GHYTAYCR GTG W+ ++D+
Sbjct: 292 LRDLDLREFASENTNHA----VYNLYAVSNHSG-TTMGGHYTAYCRSPGTGEWHTFNDSS 346
Query: 350 VSPVDAQTVESAEAEHGAYILVYQ 373
V+P+ + V +++ AY+L Y+
Sbjct: 347 VTPMSSSQVRTSD----AYLLFYE 366
>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 = 160 bits (405), Expect = 1e-39, Method: Compositional matrix adjust.
Identities = 115/386 (29%), Positives = 179/386 (46%), Gaps = 42/386 (10%)
Query: 1 MSPGLNGIANAGNTCYINSVLQCLSNTPAFRNVLLNED--IPIHPDSK--SQGQLVDALV 56
+ PGL G+ N GNT ++NS LQCLSNT + L ++ I+ D+ +G++ +A
Sbjct: 4 IQPGLCGLGNLGNTXFMNSALQCLSNTAPLTDYFLKDEYEAEINRDNPLGMKGEIAEAYA 63
Query: 57 NFMKMMWSSGNLVLNTKAILLALRSYTKKFDGNQQQDAQXXXXXXXX-XXXXXXKVVPDQ 115
+K MWS + + + + + +F G QQQD+Q +V
Sbjct: 64 ELIKQMWSGRDAHVAPRMFKTQVGRFAPQFSGYQQQDSQELLAFLLDGLHEDLNRVKKKP 123
Query: 116 YNGSTYSNTSSKQVGSFRALHYWEKFQTTEASVFSDIFVGQLRSSVRCSNCKRTSTVYEI 175
Y +N V + A WE + SV D F G +S++ C C + S ++
Sbjct: 124 YLELKDANGRPDAVVAKEA---WENHRLRNDSVIVDTFHGLFKSTLVCPECAKVSVTFDP 180
Query: 176 FWELSLPVPPGGGTLYECQLRSSVRCSNCKRTSTVYEIFWELSLPVPPGGGTLYECLNKF 235
F L+LP+P + E + + K+ +TV L +C+ F
Sbjct: 181 FCYLTLPLPLKKDRVMEGPMLQPQK----KKKTTV----------------ALRDCIELF 220
Query: 236 FNGETL--HNT--CQYCKKQSDLVKLYEIQRLPPVLILWFKRFSSN--FTQKVTSPIKFP 289
ETL H+ C CKK K +++ LP +L++ KRFS N + K+ + ++FP
Sbjct: 221 TTMETLGEHDPWYCPNCKKHQQATKKFDLWSLPKILVVHLKRFSYNRYWRDKLDTVVEFP 280
Query: 290 REGLDMEYYISASGRRVESRYTYDLCAVSNHIGKTALYGHYTAYCRREGTGRWYLYDDTV 349
GL+M ++ R Y YDL AVSNH G + GHYTAY + + G+WY +DD+
Sbjct: 281 IRGLNMSEFVCNLSARP---YVYDLIAVSNHYGAMGV-GHYTAYAKNKLNGKWYYFDDSN 336
Query: 350 VSPVDAQTVESAEAEHGAYILVYQRR 375
VS + + AY+L YQRR
Sbjct: 337 VSLASEDQIVTK----AAYVLFYQRR 358
>pdb|3NHE|A Chain A, High Resolution Structure (1.26a) Of Usp2a In Complex With
Ubiquitin
Length = 348
Score = 159 bits (403), Expect = 2e-39, Method: Compositional matrix adjust.
Identities = 118/384 (30%), Positives = 177/384 (46%), Gaps = 65/384 (16%)
Query: 4 GLNGIANAGNTCYINSVLQCLSNTPAFRNVLLNEDI--PIHPDSKSQGQLVDALVNFMKM 61
GL G+ N GNT ++NS+LQCLSNT R+ L +H S + LV+ ++
Sbjct: 8 GLAGLRNLGNTXFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQT 67
Query: 62 MW-SSGNLVLNTKAILLALRSYTKKFDGNQQQDAQXXXXXXXXXXXXXXKVVP--DQYNG 118
+W SS N V++ ++ Y +F G QQDAQ V + N
Sbjct: 68 IWTSSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNP 127
Query: 119 STYSNTSSKQVGSFRALHYWEKFQTTEASVFSDIFVGQLRSSVRCSNCKRTSTVYEIFWE 178
+ + G W K+ E S D+FVGQ
Sbjct: 128 ENLDHLPDDEKGR----QMWRKYLEREDSRIGDLFVGQ---------------------- 161
Query: 179 LSLPVPPGGGTLYECQLRSSVRCSNCKRTSTVYEIFWELSLPVPPGG---GTLYECLNKF 235
L+SS+ C++C STV++ FW+LSLP+ G TL +C+ F
Sbjct: 162 ----------------LKSSLTCTDCGYCSTVFDPFWDLSLPIAKRGYPEVTLMDCMRLF 205
Query: 236 FNGETLHN----TCQYCKKQSDLVKLYEIQRLPPVLILWFKRFSSNF--TQKVTSPIKFP 289
+ L TC C+ + +K + IQR P +L+L KRFS + T K+T+ + FP
Sbjct: 206 TKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKILVLHLKRFSESRIRTSKLTTFVNFP 265
Query: 290 REGLDMEYYISASGRRVESRYTYDLCAVSNHIGKTALYGHYTAYCRREGTGRWYLYDDTV 349
LD+ + S + Y+L AVSNH G T + GHYTAYCR GTG W+ ++D+
Sbjct: 266 LRDLDLREFASENTNHA----VYNLYAVSNHSG-TTMGGHYTAYCRSPGTGEWHTFNDSS 320
Query: 350 VSPVDAQTVESAEAEHGAYILVYQ 373
V+P+ + V +++ AY+L Y+
Sbjct: 321 VTPMSSSQVRTSD----AYLLFYE 340
>pdb|3N3K|A Chain A, The Catalytic Domain Of Usp8 In Complex With A Usp8
Specific Inhibitor
Length = 396
Score = 144 bits (362), Expect = 9e-35, Method: Compositional matrix adjust.
Identities = 101/357 (28%), Positives = 154/357 (43%), Gaps = 57/357 (15%)
Query: 3 PGLNGIANAGNTCYINSVLQCLSNTPA----FRNVLLNEDIPIHPDSKSQGQLVDALVNF 58
P L G+ N GNTCY+NS+LQCL N P F +DI +G++ +
Sbjct: 60 PALTGLRNLGNTCYMNSILQCLCNAPHLADYFNRNCYQDDINRSNLLGHKGEVAEEFGII 119
Query: 59 MKMMWSSGNLVLNTKAILLALRSYTKKFDGNQQQDAQXXXXXXXXXXXXXXKVVPDQYNG 118
MK +W+ ++ K + + +F G QQD+Q N
Sbjct: 120 MKALWTGQYRYISPKDFKITIGKINDQFAGYSQQDSQELLLFLMDGLHEDLNKAD---NR 176
Query: 119 STYSNTSSKQVGSFRAL-HYWEKFQTTEASVFSDIFVGQLRSSVRCSNCKRTSTVYEIFW 177
Y ++ + F+A H W+K + S+ +F GQ +
Sbjct: 177 KRYKEENNDHLDDFKAAEHAWQKHKQLNESIIVALFQGQFK------------------- 217
Query: 178 ELSLPVPPGGGTLYECQLRSSVRCSNCKRTSTVYEIFWELSLPVPPGGG-TLYECLNKFF 236
S+V+C C + S +E F LSLP+ TL +CL F
Sbjct: 218 -------------------STVQCLTCHKKSRTFEAFMYLSLPLASTSKCTLQDCLRLFS 258
Query: 237 NGETLHNT----CQYCKKQSDLVKLYEIQRLPPVLILWFKRFSSN--FTQKVTSPIKFPR 290
E L + C +C+ + D +K EI +LPPVL++ KRFS + + QK+ + + FP
Sbjct: 259 KEEKLTDNNRFYCSHCRARRDSLKKIEIWKLPPVLLVHLKRFSYDGRWKQKLQTSVDFPL 318
Query: 291 EGLDMEYYISASGRRVESRYTYDLCAVSNHIGKTALYGHYTAYCRREGTGRWYLYDD 347
E LD+ Y+ ++ Y+L +VSNH G GHYTAYC+ RW+ +DD
Sbjct: 319 ENLDLSQYVIGPKNNLKK---YNLFSVSNHYGGLD-GGHYTAYCKNAARQRWFKFDD 371
>pdb|2GFO|A Chain A, Structure Of The Catalytic Domain Of Human Ubiquitin
Carboxyl-terminal Hydrolase 8
Length = 396
Score = 139 bits (350), Expect = 2e-33, Method: Compositional matrix adjust.
Identities = 101/357 (28%), Positives = 153/357 (42%), Gaps = 57/357 (15%)
Query: 3 PGLNGIANAGNTCYINSVLQCLSNTPA----FRNVLLNEDIPIHPDSKSQGQLVDALVNF 58
P L G+ N GNTCY NS+LQCL N P F +DI +G++ +
Sbjct: 60 PALTGLRNLGNTCYXNSILQCLCNAPHLADYFNRNCYQDDINRSNLLGHKGEVAEEFGII 119
Query: 59 MKMMWSSGNLVLNTKAILLALRSYTKKFDGNQQQDAQXXXXXXXXXXXXXXKVVPDQYNG 118
K +W+ ++ K + + +F G QQD+Q N
Sbjct: 120 XKALWTGQYRYISPKDFKITIGKINDQFAGYSQQDSQELLLFLXDGLHEDLNKAD---NR 176
Query: 119 STYSNTSSKQVGSFRAL-HYWEKFQTTEASVFSDIFVGQLRSSVRCSNCKRTSTVYEIFW 177
Y ++ + F+A H W+K + S+ +F GQ +
Sbjct: 177 KRYKEENNDHLDDFKAAEHAWQKHKQLNESIIVALFQGQFK------------------- 217
Query: 178 ELSLPVPPGGGTLYECQLRSSVRCSNCKRTSTVYEIFWELSLPVPPGGG-TLYECLNKFF 236
S+V+C C + S +E F LSLP+ TL +CL F
Sbjct: 218 -------------------STVQCLTCHKKSRTFEAFXYLSLPLASTSKCTLQDCLRLFS 258
Query: 237 NGETLHNT----CQYCKKQSDLVKLYEIQRLPPVLILWFKRFSSN--FTQKVTSPIKFPR 290
E L + C +C+ + D +K EI +LPPVL++ KRFS + + QK+ + + FP
Sbjct: 259 KEEKLTDNNRFYCSHCRARRDSLKKIEIWKLPPVLLVHLKRFSYDGRWKQKLQTSVDFPL 318
Query: 291 EGLDMEYYISASGRRVESRYTYDLCAVSNHIGKTALYGHYTAYCRREGTGRWYLYDD 347
E LD+ Y+ ++ Y+L +VSNH G GHYTAYC+ RW+ +DD
Sbjct: 319 ENLDLSQYVIGPKNNLKK---YNLFSVSNHYGGLD-GGHYTAYCKNAARQRWFKFDD 371
>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 = 137 bits (344), Expect = 1e-32, Method: Compositional matrix adjust.
Identities = 114/400 (28%), Positives = 170/400 (42%), Gaps = 79/400 (19%)
Query: 2 SPGLNGIANAGNTCYINSVLQCLSNTPAFRNVLLNEDIPIH-PDSKSQGQLVDALVNFMK 60
S G G+ N GNTC++N+VLQCLS+T R+ L D P +L +A + +
Sbjct: 19 SSGHVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQELTEAFADVIG 78
Query: 61 MMWSSGNL-VLNTKAILLALRSYTKKFDGNQQQDAQX-----XXXXXXXXXXXXXKVVPD 114
+W + +N + Y F G QQDAQ + P
Sbjct: 79 ALWHPDSCEAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRAPPI 138
Query: 115 QYNGSTYSNTSSKQVGSF----------RALHYWEKFQTTEASVFSDIFVGQLRSSVRCS 164
NG S ++ G+ RA W+++ E S D+FVGQL+
Sbjct: 139 LANGPVPS--PPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLK------ 190
Query: 165 NCKRTSTVYEIFWELSLPVPPGGGTLYECQLRSSVRCSNCKRTSTVYEIFWELSLPVPP- 223
S ++C C ST +E+F +LSLP+P
Sbjct: 191 --------------------------------SCLKCQACGYRSTTFEVFCDLSLPIPKK 218
Query: 224 --GGG--TLYECLNKFFNGETLHN----TCQYCKKQSDLVKLYEIQRLPPVLILWFKRFS 275
GG +L +C N F E L + C C++++ K +QR P +L+L RFS
Sbjct: 219 GFAGGKVSLRDCFNLFTKEEELESENAPVCDRCRQKTRSTKKLTVQRFPRILVLHLNRFS 278
Query: 276 SN--FTQKVTSPIKFPREGLDMEYYISASGRRVESRYTYDLCAVSNHIGKTALYGHYTAY 333
++ +K + + FP + L + + S Y L A+ NH G + YGHYTA
Sbjct: 279 ASRGSIKKSSVGVDFPLQRLSLGDFASDKA----GSPVYQLYALCNHSG-SVHYGHYTAL 333
Query: 334 CRREGTGRWYLYDDTVVSPVDAQTVESAEAEHGAYILVYQ 373
CR + TG W++Y+D+ VSPV V S+E Y+L YQ
Sbjct: 334 CRCQ-TG-WHVYNDSRVSPVSENQVASSE----GYVLFYQ 367
>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 = 136 bits (342), Expect = 2e-32, Method: Compositional matrix adjust.
Identities = 113/401 (28%), Positives = 170/401 (42%), Gaps = 79/401 (19%)
Query: 1 MSPGLNGIANAGNTCYINSVLQCLSNTPAFRNVLLNEDIPIH-PDSKSQGQLVDALVNFM 59
+ G G+ N GNTC++N+VLQCLS+T R+ L D P +L +A + +
Sbjct: 12 LGSGHVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQELTEAFADVI 71
Query: 60 KMMWSSGNL-VLNTKAILLALRSYTKKFDGNQQQDAQX-----XXXXXXXXXXXXXKVVP 113
+W + +N + Y F G QQDAQ + P
Sbjct: 72 GALWHPDSCEAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRAPP 131
Query: 114 DQYNGSTYSNTSSKQVGSF----------RALHYWEKFQTTEASVFSDIFVGQLRSSVRC 163
NG S ++ G+ RA W+++ E S D+FVGQL+
Sbjct: 132 ILANGPVPS--PPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLK----- 184
Query: 164 SNCKRTSTVYEIFWELSLPVPPGGGTLYECQLRSSVRCSNCKRTSTVYEIFWELSLPVPP 223
S ++C C ST +E+F +LSLP+P
Sbjct: 185 ---------------------------------SCLKCQACGYRSTTFEVFCDLSLPIPK 211
Query: 224 ---GGG--TLYECLNKFFNGETLHN----TCQYCKKQSDLVKLYEIQRLPPVLILWFKRF 274
GG +L +C N F E L + C C++++ K +QR P +L+L RF
Sbjct: 212 KGFAGGKVSLRDCFNLFTKEEELESENAPVCDRCRQKTRSTKKLTVQRFPRILVLHLNRF 271
Query: 275 SSN--FTQKVTSPIKFPREGLDMEYYISASGRRVESRYTYDLCAVSNHIGKTALYGHYTA 332
S++ +K + + FP + L + + S Y L A+ NH G + YGHYTA
Sbjct: 272 SASRGSIKKSSVGVDFPLQRLSLGDFASDKA----GSPVYQLYALCNHSG-SVHYGHYTA 326
Query: 333 YCRREGTGRWYLYDDTVVSPVDAQTVESAEAEHGAYILVYQ 373
CR + TG W++Y+D+ VSPV V S+E Y+L YQ
Sbjct: 327 LCRCQ-TG-WHVYNDSRVSPVSENQVASSE----GYVLFYQ 361
>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 = 136 bits (342), Expect = 2e-32, Method: Compositional matrix adjust.
Identities = 113/398 (28%), Positives = 169/398 (42%), Gaps = 79/398 (19%)
Query: 4 GLNGIANAGNTCYINSVLQCLSNTPAFRNVLLNEDIPIH-PDSKSQGQLVDALVNFMKMM 62
G G+ N GNTC++N+VLQCLS+T R+ L D P +L +A + + +
Sbjct: 2 GHVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQELTEAFADVIGAL 61
Query: 63 WSSGNL-VLNTKAILLALRSYTKKFDGNQQQDAQX-----XXXXXXXXXXXXXKVVPDQY 116
W + +N + Y F G QQDAQ + P
Sbjct: 62 WHPDSCEAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRAPPILA 121
Query: 117 NGSTYSNTSSKQVGSF----------RALHYWEKFQTTEASVFSDIFVGQLRSSVRCSNC 166
NG S ++ G+ RA W+++ E S D+FVGQL+
Sbjct: 122 NGPVPS--PPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLK-------- 171
Query: 167 KRTSTVYEIFWELSLPVPPGGGTLYECQLRSSVRCSNCKRTSTVYEIFWELSLPVPP--- 223
S ++C C ST +E+F +LSLP+P
Sbjct: 172 ------------------------------SCLKCQACGYRSTTFEVFCDLSLPIPKKGF 201
Query: 224 GGG--TLYECLNKFFNGETLHN----TCQYCKKQSDLVKLYEIQRLPPVLILWFKRFSSN 277
GG +L +C N F E L + C C++++ K +QR P +L+L RFS++
Sbjct: 202 AGGKVSLRDCFNLFTKEEELESENAPVCDRCRQKTRSTKKLTVQRFPRILVLHLNRFSAS 261
Query: 278 --FTQKVTSPIKFPREGLDMEYYISASGRRVESRYTYDLCAVSNHIGKTALYGHYTAYCR 335
+K + + FP + L + + S Y L A+ NH G + YGHYTA CR
Sbjct: 262 RGSIKKSSVGVDFPLQRLSLGDFASDKA----GSPVYQLYALCNHSG-SVHYGHYTALCR 316
Query: 336 REGTGRWYLYDDTVVSPVDAQTVESAEAEHGAYILVYQ 373
+ TG W++Y+D+ VSPV V S+E Y+L YQ
Sbjct: 317 CQ-TG-WHVYNDSRVSPVSENQVASSE----GYVLFYQ 348
>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 = 90.9 bits (224), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 99/398 (24%), Positives = 156/398 (39%), Gaps = 90/398 (22%)
Query: 4 GLNGIANAGNTCYINSVLQCLSNTPAF----RNVLLNEDIPIHPDSKSQGQLVDALVNFM 59
GL+G+ N GNTC+++S+LQCL + P F + + + + + K +D +V+ +
Sbjct: 140 GLSGLINMGNTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHEL 199
Query: 60 -----KMMWSSGNLVLNTKAILLALRSYTKKFDGN----QQQDAQXXXXXXXXXXXXXXK 110
SS + N + + L + K + N QQDA
Sbjct: 200 YGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQS-- 257
Query: 111 VVPDQYNGSTYSNTSSKQVGSFRALHYWEKFQTTEASVFSDIFVGQLRSSVRCSNCKRTS 170
V D N S ++KQ + +F G L SS+ C C+ S
Sbjct: 258 YVLDLPNAKEVSRANNKQC----------------ECIVHTVFEGSLESSIVCPGCQNNS 301
Query: 171 -TVYEIFWELSLPVPPGGGTLYECQLRSSVRCSNCKRTSTVYEIFWELSLPVPPGGGTLY 229
T + F +LSL + LY
Sbjct: 302 KTTIDPFLDLSLDIKD---------------------------------------KKKLY 322
Query: 230 ECLNKFFNGETLHN---TCQYCKKQSDLVKLYEIQRLPPVLILWFKRFS---SNFTQKVT 283
ECL+ F E L + C C D +K I +LP VL+L KRF + +K+
Sbjct: 323 ECLDSFHKKEQLKDFNYHCGECNSTQDAIKQLGIHKLPSVLVLQLKRFEHLLNGSNRKLD 382
Query: 284 SPIKFPREGLDMEYYISASGRRVESR------YTYDLCAVSNHIGKTALYGHYTAYCRRE 337
I+FP L+M+ Y S + S Y+L + +H G T GHY A+C+
Sbjct: 383 DFIEFPTY-LNMKNYCSTKEKDKHSENGKVPDIIYELIGIVSHKG-TVNEGHYIAFCKIS 440
Query: 338 GTGRWYLYDDTVVSPVDAQTVESAEAEHGAYILVYQRR 375
G G+W+ ++D++VS + + V + AY+L Y R
Sbjct: 441 G-GQWFKFNDSMVSSISQEEVLKEQ----AYLLFYTIR 473
>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 = 89.4 bits (220), Expect = 3e-18, Method: Compositional matrix adjust.
Identities = 65/200 (32%), Positives = 99/200 (49%), Gaps = 21/200 (10%)
Query: 189 TLYECQLRSSVRCSNCKRTS-TVYEIFWELSLPVPPGGGTLYECLNKFFNGETLHN---T 244
T++E L SS+ C C+ S T + F +LSL + LYECL+ F E L +
Sbjct: 282 TVFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIKDKK-KLYECLDSFHKKEQLKDFNYH 340
Query: 245 CQYCKKQSDLVKLYEIQRLPPVLILWFKRFS---SNFTQKVTSPIKFPREGLDMEYYISA 301
C C D +K I +LP VL+L KRF + +K+ I+FP L+M+ Y S
Sbjct: 341 CGECNSTQDAIKQLGIHKLPSVLVLQLKRFEHLLNGSNRKLDDFIEFPTY-LNMKNYCST 399
Query: 302 SGRRVESR------YTYDLCAVSNHIGKTALYGHYTAYCRREGTGRWYLYDDTVVSPVDA 355
+ S Y+L + +H G T GHY A+C+ G G+W+ ++D++VS +
Sbjct: 400 KEKDKHSENGKVPDIIYELIGIVSHKG-TVNEGHYIAFCKISG-GQWFKFNDSMVSSISQ 457
Query: 356 QTVESAEAEHGAYILVYQRR 375
+ V + AY+L Y R
Sbjct: 458 EEVLKEQ----AYLLFYTIR 473
>pdb|3M99|A Chain A, Structure Of The Ubp8-Sgf11-Sgf73-Sus1 Saga Dub Module
Length = 471
Score = 89.4 bits (220), Expect = 3e-18, Method: Compositional matrix adjust.
Identities = 65/200 (32%), Positives = 99/200 (49%), Gaps = 21/200 (10%)
Query: 189 TLYECQLRSSVRCSNCKRTS-TVYEIFWELSLPVPPGGGTLYECLNKFFNGETLHN---T 244
T++E L SS+ C C+ S T + F +LSL + LYECL+ F E L +
Sbjct: 277 TVFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIKDKK-KLYECLDSFHKKEQLKDFNYH 335
Query: 245 CQYCKKQSDLVKLYEIQRLPPVLILWFKRFS---SNFTQKVTSPIKFPREGLDMEYYISA 301
C C D +K I +LP VL+L KRF + +K+ I+FP L+M+ Y S
Sbjct: 336 CGECNSTQDAIKQLGIHKLPSVLVLQLKRFEHLLNGSNRKLDDFIEFPTY-LNMKNYCST 394
Query: 302 SGRRVESR------YTYDLCAVSNHIGKTALYGHYTAYCRREGTGRWYLYDDTVVSPVDA 355
+ S Y+L + +H G T GHY A+C+ G G+W+ ++D++VS +
Sbjct: 395 KEKDKHSENGKVPDIIYELIGIVSHKG-TVNEGHYIAFCKISG-GQWFKFNDSMVSSISQ 452
Query: 356 QTVESAEAEHGAYILVYQRR 375
+ V + AY+L Y R
Sbjct: 453 EEVLKEQ----AYLLFYTIR 468
>pdb|2F1Z|A Chain A, Crystal Structure Of Hausp
pdb|2F1Z|B Chain B, Crystal Structure Of Hausp
Length = 522
Score = 52.8 bits (125), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 53/206 (25%), Positives = 87/206 (42%), Gaps = 27/206 (13%)
Query: 190 LYECQLRSSVRCSNCKRTSTVYEIFWELSLPVPPGGGTLYECLNKFFNGETLHNTCQYCK 249
L+ ++ S ++C S E ++++ L + G ++E + E L +Y
Sbjct: 285 LFRGKMVSYIQCKEVDYRSDRREDYYDIQLSIK-GKKNIFESFVDYVAVEQLDGDNKYDA 343
Query: 250 KQSDL---VKLYEIQRLPPVLILWFKRF----SSNFTQKVTSPIKFPREGLDMEYYISAS 302
+ L K + LPPVL L RF ++ K+ +FP E L ++ ++ +
Sbjct: 344 GEHGLQEAEKGVKFLTLPPVLHLQLMRFMYDPQTDQNIKINDRFEFP-EQLPLDEFLQKT 402
Query: 303 GRRVESRYTYDLCAVSNHIGKTALYGHYTAYCRREGTGRWYLYDDTVVSPVDAQTVESAE 362
+ + Y L AV H G GHY Y +G G+W +DD VVS + E+ E
Sbjct: 403 DPKDPANYI--LHAVLVHSGDNH-GGHYVVYLNPKGDGKWCKFDDDVVSRCTKE--EAIE 457
Query: 363 AEHG-------------AYILVYQRR 375
+G AY+LVY R
Sbjct: 458 HNYGGHDDDLSVRHCTNAYMLVYIRE 483
>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 = 3e-07, Method: Compositional matrix adjust.
Identities = 53/205 (25%), Positives = 87/205 (42%), Gaps = 27/205 (13%)
Query: 190 LYECQLRSSVRCSNCKRTSTVYEIFWELSLPVPPGGGTLYECLNKFFNGETLHNTCQYCK 249
L+ ++ S ++C S E ++++ L + G ++E + E L +Y
Sbjct: 116 LFRGKMVSYIQCKEVDYRSDRREDYYDIQLSIK-GKKNIFESFVDYVAVEQLDGDNKYDA 174
Query: 250 KQSDL---VKLYEIQRLPPVLILWFKRF----SSNFTQKVTSPIKFPREGLDMEYYISAS 302
+ L K + LPPVL L RF ++ K+ +FP E L ++ ++ +
Sbjct: 175 GEHGLQEAEKGVKFLTLPPVLHLQLMRFMYDPQTDQNIKINDRFEFP-EQLPLDEFLQKT 233
Query: 303 GRRVESRYTYDLCAVSNHIGKTALYGHYTAYCRREGTGRWYLYDDTVVSPVDAQTVESAE 362
+ + Y L AV H G GHY Y +G G+W +DD VVS + E+ E
Sbjct: 234 DPKDPANYI--LHAVLVHSGDNH-GGHYVVYLNPKGDGKWCKFDDDVVSRCTKE--EAIE 288
Query: 363 AEHG-------------AYILVYQR 374
+G AY+LVY R
Sbjct: 289 HNYGGHDDDLSVRHCTNAYMLVYIR 313
>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 = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 53/205 (25%), Positives = 85/205 (41%), Gaps = 27/205 (13%)
Query: 190 LYECQLRSSVRCSNCKRTSTVYEIFWELSLPVPPGGGTLYECLNKFFNGETLHNTCQYCK 249
L+ + S ++C S E ++++ L + G ++E + E L +Y
Sbjct: 116 LFRGKXVSYIQCKEVDYRSDRREDYYDIQLSIK-GKKNIFESFVDYVAVEQLDGDNKYDA 174
Query: 250 KQSDL---VKLYEIQRLPPVLILWFKRF----SSNFTQKVTSPIKFPREGLDMEYYISAS 302
+ L K + LPPVL L RF ++ K+ +FP E L ++ ++ +
Sbjct: 175 GEHGLQEAEKGVKFLTLPPVLHLQLXRFXYDPQTDQNIKINDRFEFP-EQLPLDEFLQKT 233
Query: 303 GRRVESRYTYDLCAVSNHIGKTALYGHYTAYCRREGTGRWYLYDDTVVSPVDAQTVESAE 362
+ + Y L AV H G GHY Y +G G+W +DD VVS + E+ E
Sbjct: 234 DPKDPANYI--LHAVLVHSGDNH-GGHYVVYLNPKGDGKWCKFDDDVVSRCTKE--EAIE 288
Query: 363 AEHG-------------AYILVYQR 374
+G AY LVY R
Sbjct: 289 HNYGGHDDDLSVRHCTNAYXLVYIR 313
Score = 30.4 bits (67), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 17/31 (54%)
Query: 4 GLNGIANAGNTCYINSVLQCLSNTPAFRNVL 34
G G+ N G TCY NS+LQ L T R +
Sbjct: 5 GYVGLKNQGATCYXNSLLQTLFFTNQLRKAV 35
>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 = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 37/67 (55%), Gaps = 4/67 (5%)
Query: 312 YDLCAVSNHIGKTALYGHYTAYCRREGTGRWYLYDD---TVVSPVDAQTVESAEAEHGAY 368
YDL AV H G+++ GHY ++ +R+ W +DD ++V+P D + H AY
Sbjct: 328 YDLQAVLTHQGRSSSSGHYVSWVKRK-QDEWIKFDDDKVSIVTPEDILRLSGGGDWHIAY 386
Query: 369 ILVYQRR 375
+L+Y R
Sbjct: 387 VLLYGPR 393
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 20/28 (71%)
Query: 7 GIANAGNTCYINSVLQCLSNTPAFRNVL 34
G+ N GNTCY+N+ +QC+ + P ++ L
Sbjct: 16 GLTNLGNTCYMNATVQCIRSVPELKDAL 43
>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 = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 33/66 (50%), Gaps = 4/66 (6%)
Query: 312 YDLCAVSNHIGKTALYGHYTAYCRRE-GTGRWYLYDDTVVSPVDAQTVESAEA---EHGA 367
Y+L V H G + GHY A+ R E +WY ++D VS V+ + +ES A
Sbjct: 346 YNLIGVITHQGANSESGHYQAFIRDELDENKWYKFNDDKVSVVEKEKIESLAGGGESDSA 405
Query: 368 YILVYQ 373
IL Y+
Sbjct: 406 LILXYK 411
Score = 35.4 bits (80), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 14/30 (46%), Positives = 18/30 (60%)
Query: 7 GIANAGNTCYINSVLQCLSNTPAFRNVLLN 36
G N GNTCY+N+ LQ L R+ +LN
Sbjct: 26 GFKNXGNTCYLNATLQALYRVNDLRDXILN 55
>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
Length = 854
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/29 (55%), Positives = 21/29 (72%)
Query: 3 PGLNGIANAGNTCYINSVLQCLSNTPAFR 31
PG GI N GN+CY+NSV+Q L + P F+
Sbjct: 342 PGYTGIRNLGNSCYLNSVVQVLFSIPDFQ 370
Score = 37.0 bits (84), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 32/63 (50%), Gaps = 8/63 (12%)
Query: 312 YDLCAVSNHIGKTALYGHYTAYCRREGTGRWYLYDDTVVSPVDAQTVESAEAEHGAYILV 371
Y L A +H+G + + GHY + ++E GRW +Y+D V E + G YI
Sbjct: 797 YQLFAFISHMGTSTMCGHYVCHIKKE--GRWVIYNDQKVC-----ASEKPPKDLG-YIYF 848
Query: 372 YQR 374
YQR
Sbjct: 849 YQR 851
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 0.414
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,162,586
Number of Sequences: 62578
Number of extensions: 448904
Number of successful extensions: 1039
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 21
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 929
Number of HSP's gapped (non-prelim): 55
length of query: 375
length of database: 14,973,337
effective HSP length: 100
effective length of query: 275
effective length of database: 8,715,537
effective search space: 2396772675
effective search space used: 2396772675
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: 52 (24.6 bits)