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= 017540
(369 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 120 bits (300), Expect = 2e-27, Method: Compositional matrix adjust.
Identities = 105/374 (28%), Positives = 152/374 (40%), Gaps = 57/374 (15%)
Query: 19 GERYFGLENFGNTCYCNSVLQALYFCVPFREQLL--DYYSNNKNLGDAEENLLTCLADLF 76
G + GL N GNTC+ N+VLQ L P R+ L D+ G A+E L AD+
Sbjct: 13 GSGHVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQE-LTEAFADVI 71
Query: 77 TQIRAQKKKTGVIAPKRFVQRLKKQNELFRSYMHQDAHEFLNFLLNELVDILXXXXXXXX 136
+ + P RF +K F Y QDA EFL L+ L
Sbjct: 72 GAL-WHPDSCEAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERL--------HLEI 122
Query: 137 XXXXXXXXXXTANGPTNGL---ANGVRKEPLVT--------W----------VHKNFQGI 175
ANGP + +EP ++ W + F G
Sbjct: 123 NRRGRRAPPILANGPVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQ 182
Query: 176 LTNETRCLRCETVTARDETFFDLSLDIEQNS------SITSCLKNFSSTETLNAEDKFFC 229
L + +C C + E F DLSL I + S+ C F+ E L +E+ C
Sbjct: 183 LKSCLKCQACGYRSTTFEVFCDLSLPIPKKGFAGGKVSLRDCFNLFTKEEELESENAPVC 242
Query: 230 DKCCSLQEAQKRMKIKKSPHTLVIHLKRFKYIEQLGRYKKLSYRVVFPLE-LKLSNTAED 288
D+C + K++ +++ P LV+HL RF G KK S V FPL+ L L + A D
Sbjct: 243 DRCRQKTRSTKKLTVQRFPRILVLHLNRFS--ASRGSIKKSSVGVDFPLQRLSLGDFASD 300
Query: 289 --ADIEYSLFAVVVHVGSGPNHGHYVSLVKSHNHWLFFDDENVEMIDESAVQTFFGSAQE 346
Y L+A+ H GS ++GHY +L + W ++D V + E+ V
Sbjct: 301 KAGSPVYQLYALCNHSGSV-HYGHYTALCRCQTGWHVYNDSRVSPVSENQVA-------- 351
Query: 347 YSSNTDHGYILFYE 360
+ GY+LFY+
Sbjct: 352 ----SSEGYVLFYQ 361
>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 = 119 bits (298), Expect = 3e-27, Method: Compositional matrix adjust.
Identities = 104/371 (28%), Positives = 151/371 (40%), Gaps = 57/371 (15%)
Query: 22 YFGLENFGNTCYCNSVLQALYFCVPFREQLL--DYYSNNKNLGDAEENLLTCLADLFTQI 79
+ GL N GNTC+ N+VLQ L P R+ L D+ G A+E L AD+ +
Sbjct: 22 HVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQE-LTEAFADVIGAL 80
Query: 80 RAQKKKTGVIAPKRFVQRLKKQNELFRSYMHQDAHEFLNFLLNELVDILXXXXXXXXXXX 139
+ P RF +K F Y QDA EFL L+ L
Sbjct: 81 -WHPDSCEAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERL--------HLEINRR 131
Query: 140 XXXXXXXTANGPTNGL---ANGVRKEPLVT--------W----------VHKNFQGILTN 178
ANGP + +EP ++ W + F G L +
Sbjct: 132 GRRAPPILANGPVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKS 191
Query: 179 ETRCLRCETVTARDETFFDLSLDIEQNS------SITSCLKNFSSTETLNAEDKFFCDKC 232
+C C + E F DLSL I + S+ C F+ E L +E+ CD+C
Sbjct: 192 CLKCQACGYRSTTFEVFCDLSLPIPKKGFAGGKVSLRDCFNLFTKEEELESENAPVCDRC 251
Query: 233 CSLQEAQKRMKIKKSPHTLVIHLKRFKYIEQLGRYKKLSYRVVFPLE-LKLSNTAED--A 289
+ K++ +++ P LV+HL RF G KK S V FPL+ L L + A D
Sbjct: 252 RQKTRSTKKLTVQRFPRILVLHLNRFS--ASRGSIKKSSVGVDFPLQRLSLGDFASDKAG 309
Query: 290 DIEYSLFAVVVHVGSGPNHGHYVSLVKSHNHWLFFDDENVEMIDESAVQTFFGSAQEYSS 349
Y L+A+ H GS ++GHY +L + W ++D V + E+ V
Sbjct: 310 SPVYQLYALCNHSGSV-HYGHYTALCRCQTGWHVYNDSRVSPVSENQVA----------- 357
Query: 350 NTDHGYILFYE 360
+ 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 = 118 bits (296), Expect = 4e-27, Method: Compositional matrix adjust.
Identities = 104/371 (28%), Positives = 151/371 (40%), Gaps = 57/371 (15%)
Query: 22 YFGLENFGNTCYCNSVLQALYFCVPFREQLL--DYYSNNKNLGDAEENLLTCLADLFTQI 79
+ GL N GNTC+ N+VLQ L P R+ L D+ G A+E L AD+ +
Sbjct: 3 HVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQE-LTEAFADVIGAL 61
Query: 80 RAQKKKTGVIAPKRFVQRLKKQNELFRSYMHQDAHEFLNFLLNELVDILXXXXXXXXXXX 139
+ P RF +K F Y QDA EFL L+ L
Sbjct: 62 -WHPDSCEAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERL--------HLEINRR 112
Query: 140 XXXXXXXTANGPTNGL---ANGVRKEPLVT--------W----------VHKNFQGILTN 178
ANGP + +EP ++ W + F G L +
Sbjct: 113 GRRAPPILANGPVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKS 172
Query: 179 ETRCLRCETVTARDETFFDLSLDIEQNS------SITSCLKNFSSTETLNAEDKFFCDKC 232
+C C + E F DLSL I + S+ C F+ E L +E+ CD+C
Sbjct: 173 CLKCQACGYRSTTFEVFCDLSLPIPKKGFAGGKVSLRDCFNLFTKEEELESENAPVCDRC 232
Query: 233 CSLQEAQKRMKIKKSPHTLVIHLKRFKYIEQLGRYKKLSYRVVFPLE-LKLSNTAED--A 289
+ K++ +++ P LV+HL RF G KK S V FPL+ L L + A D
Sbjct: 233 RQKTRSTKKLTVQRFPRILVLHLNRFS--ASRGSIKKSSVGVDFPLQRLSLGDFASDKAG 290
Query: 290 DIEYSLFAVVVHVGSGPNHGHYVSLVKSHNHWLFFDDENVEMIDESAVQTFFGSAQEYSS 349
Y L+A+ H GS ++GHY +L + W ++D V + E+ V
Sbjct: 291 SPVYQLYALCNHSGSV-HYGHYTALCRCQTGWHVYNDSRVSPVSENQVA----------- 338
Query: 350 NTDHGYILFYE 360
+ GY+LFY+
Sbjct: 339 -SSEGYVLFYQ 348
>pdb|3N3K|A Chain A, The Catalytic Domain Of Usp8 In Complex With A Usp8
Specific Inhibitor
Length = 396
Score = 117 bits (292), Expect = 1e-26, Method: Compositional matrix adjust.
Identities = 116/368 (31%), Positives = 163/368 (44%), Gaps = 53/368 (14%)
Query: 19 GERYFGLENFGNTCYCNSVLQALYFCVPFREQLLDYYSNN--------KNL----GDAEE 66
G GL N GNTCY NS+LQ C+ L DY++ N NL G+ E
Sbjct: 59 GPALTGLRNLGNTCYMNSILQ----CLCNAPHLADYFNRNCYQDDINRSNLLGHKGEVAE 114
Query: 67 NLLTCLADLFT-QIRAQKKKTGVIAPKRFVQRLKKQNELFRSYMHQDAHEFLNFLLNELV 125
+ L+T Q R I+PK F + K N+ F Y QD+ E L FL++ L
Sbjct: 115 EFGIIMKALWTGQYR-------YISPKDFKITIGKINDQFAGYSQQDSQELLLFLMDGLH 167
Query: 126 DILXXXXXXXXXXXXXXXXXXTANGPTNGLANGVR-KEPLVTWVHKNFQGILTNETRCLR 184
+ L + + E ++ + FQG + +CL
Sbjct: 168 EDLNKADNRKRYKEENNDHLDDFKAAEHAWQKHKQLNESIIVAL---FQGQFKSTVQCLT 224
Query: 185 CETVTARDETFFDLSLDIEQNSSIT--SCLKNFSSTETLNAEDKFFCDKCCSLQEAQKRM 242
C + E F LSL + S T CL+ FS E L ++F+C C + +++ K++
Sbjct: 225 CHKKSRTFEAFMYLSLPLASTSKCTLQDCLRLFSKEEKLTDNNRFYCSHCRARRDSLKKI 284
Query: 243 KIKKSPHTLVIHLKRFKYIEQLGRYK-KLSYRVVFPLE-LKLSN---TAEDADIEYSLFA 297
+I K P L++HLKRF Y GR+K KL V FPLE L LS ++ +Y+LF+
Sbjct: 285 EIWKLPPVLLVHLKRFSYD---GRWKQKLQTSVDFPLENLDLSQYVIGPKNNLKKYNLFS 341
Query: 298 VVVHVGSGPNHGHYVSLVK--SHNHWLFFDDENVEMIDESAVQTFFGSAQEYSSNTDHGY 355
V H G G + GHY + K + W FDD E+ D S +A Y
Sbjct: 342 VSNHYG-GLDGGHYTAYCKNAARQRWFKFDDH--EVSDISVSSVKSSAA----------Y 388
Query: 356 ILFYESLG 363
ILFY SLG
Sbjct: 389 ILFYTSLG 396
>pdb|2GFO|A Chain A, Structure Of The Catalytic Domain Of Human Ubiquitin
Carboxyl-terminal Hydrolase 8
Length = 396
Score = 114 bits (286), Expect = 6e-26, Method: Compositional matrix adjust.
Identities = 115/361 (31%), Positives = 161/361 (44%), Gaps = 39/361 (10%)
Query: 19 GERYFGLENFGNTCYCNSVLQALYFCVPFREQLLDYYSNNKNLGDA-EENLLTCLADLFT 77
G GL N GNTCY NS+LQ C+ L DY++ N D NLL ++
Sbjct: 59 GPALTGLRNLGNTCYXNSILQ----CLCNAPHLADYFNRNCYQDDINRSNLLGHKGEVAE 114
Query: 78 QIRAQKKK--TG---VIAPKRFVQRLKKQNELFRSYMHQDAHEFLNFLLNELVDILXXXX 132
+ K TG I+PK F + K N+ F Y QD+ E L FL + L + L
Sbjct: 115 EFGIIXKALWTGQYRYISPKDFKITIGKINDQFAGYSQQDSQELLLFLXDGLHEDLNKAD 174
Query: 133 XXXXXXXXXXXXXXTANGPTNGLANGVR-KEPLVTWVHKNFQGILTNETRCLRCETVTAR 191
+ + E ++ + FQG + +CL C +
Sbjct: 175 NRKRYKEENNDHLDDFKAAEHAWQKHKQLNESIIVAL---FQGQFKSTVQCLTCHKKSRT 231
Query: 192 DETFFDLSLDIEQNSSIT--SCLKNFSSTETLNAEDKFFCDKCCSLQEAQKRMKIKKSPH 249
E F LSL + S T CL+ FS E L ++F+C C + +++ K+++I K P
Sbjct: 232 FEAFXYLSLPLASTSKCTLQDCLRLFSKEEKLTDNNRFYCSHCRARRDSLKKIEIWKLPP 291
Query: 250 TLVIHLKRFKYIEQLGRYK-KLSYRVVFPLE-LKLSN---TAEDADIEYSLFAVVVHVGS 304
L++HLKRF Y GR+K KL V FPLE L LS ++ +Y+LF+V H G
Sbjct: 292 VLLVHLKRFSYD---GRWKQKLQTSVDFPLENLDLSQYVIGPKNNLKKYNLFSVSNHYG- 347
Query: 305 GPNHGHYVSLVK--SHNHWLFFDDENVEMIDESAVQTFFGSAQEYSSNTDHGYILFYESL 362
G + GHY + K + W FDD E+ D S +A YILFY SL
Sbjct: 348 GLDGGHYTAYCKNAARQRWFKFDDH--EVSDISVSSVKSSAA----------YILFYTSL 395
Query: 363 G 363
G
Sbjct: 396 G 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 = 108 bits (270), Expect = 5e-24, Method: Compositional matrix adjust.
Identities = 105/375 (28%), Positives = 158/375 (42%), Gaps = 69/375 (18%)
Query: 17 PEGERYFGLE---NFGNTCYCNSVLQAL----YFCVPFREQLLDYYSNNKNLGDAEENLL 69
P ER GL N GNTC+ +S+LQ L YF R + +SNN + + +
Sbjct: 133 PSMERRDGLSGLINMGNTCFMSSILQCLIHNPYF---IRHSMSQIHSNNCKV-RSPDKCF 188
Query: 70 TCLAD-----LFTQIRAQKKKTGVIAPKR---FVQRLK---KQNELFRSYMHQDAHEFLN 118
+C D L+ + ++ + + R F+ L K N+ Y QDAHEF
Sbjct: 189 SCALDKIVHELYGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQ 248
Query: 119 FLLNELVDILXXXXXXXXXXXXXXXXXXTANGPTNGLANGVRKEPLVTWVHKNFQGILTN 178
F++N++ N AN + E + VH F+G L +
Sbjct: 249 FIINQI---------------HQSYVLDLPNAKEVSRANNKQCECI---VHTVFEGSLES 290
Query: 179 ETRCLRCETVTARD-ETFFDLSLDIEQNSSITSCLKNFSSTETLNAEDKFFCDKCCSLQE 237
C C+ + + F DLSLDI+ + CL +F E L + + C +C S Q+
Sbjct: 291 SIVCPGCQNNSKTTIDPFLDLSLDIKDKKKLYECLDSFHKKEQL-KDFNYHCGECNSTQD 349
Query: 238 AQKRMKIKKSPHTLVIHLKRFKYIEQLGRYKKLSYRVVFPLELKLSN------------T 285
A K++ I K P LV+ LKRF+++ G +KL + FP L + N
Sbjct: 350 AIKQLGIHKLPSVLVLQLKRFEHLLN-GSNRKLDDFIEFPTYLNMKNYCSTKEKDKHSEN 408
Query: 286 AEDADIEYSLFAVVVHVGSGPNHGHYVSLVK-SHNHWLFFDDENVEMIDESAVQTFFGSA 344
+ DI Y L +V H G+ N GHY++ K S W F+D V I + V
Sbjct: 409 GKVPDIIYELIGIVSHKGT-VNEGHYIAFCKISGGQWFKFNDSMVSSISQEEVL------ 461
Query: 345 QEYSSNTDHGYILFY 359
+ Y+LFY
Sbjct: 462 ------KEQAYLLFY 470
>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 = 106 bits (265), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 104/375 (27%), Positives = 158/375 (42%), Gaps = 69/375 (18%)
Query: 17 PEGERYFGLE---NFGNTCYCNSVLQAL----YFCVPFREQLLDYYSNNKNLGDAEENLL 69
P ER GL N G+TC+ +S+LQ L YF R + +SNN + + +
Sbjct: 133 PSMERRDGLSGLINMGSTCFMSSILQCLIHNPYF---IRHSMSQIHSNNCKV-RSPDKCF 188
Query: 70 TCLAD-----LFTQIRAQKKKTGVIAPKR---FVQRLK---KQNELFRSYMHQDAHEFLN 118
+C D L+ + ++ + + R F+ L K N+ Y QDAHEF
Sbjct: 189 SCALDKIVHELYGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQ 248
Query: 119 FLLNELVDILXXXXXXXXXXXXXXXXXXTANGPTNGLANGVRKEPLVTWVHKNFQGILTN 178
F++N++ N AN + E + VH F+G L +
Sbjct: 249 FIINQI---------------HQSYVLDLPNAKEVSRANNKQCECI---VHTVFEGSLES 290
Query: 179 ETRCLRCETVTARD-ETFFDLSLDIEQNSSITSCLKNFSSTETLNAEDKFFCDKCCSLQE 237
C C+ + + F DLSLDI+ + CL +F E L + + C +C S Q+
Sbjct: 291 SIVCPGCQNNSKTTIDPFLDLSLDIKDKKKLYECLDSFHKKEQL-KDFNYHCGECNSTQD 349
Query: 238 AQKRMKIKKSPHTLVIHLKRFKYIEQLGRYKKLSYRVVFPLELKLSN------------T 285
A K++ I K P LV+ LKRF+++ G +KL + FP L + N
Sbjct: 350 AIKQLGIHKLPSVLVLQLKRFEHLLN-GSNRKLDDFIEFPTYLNMKNYCSTKEKDKHSEN 408
Query: 286 AEDADIEYSLFAVVVHVGSGPNHGHYVSLVK-SHNHWLFFDDENVEMIDESAVQTFFGSA 344
+ DI Y L +V H G+ N GHY++ K S W F+D V I + V
Sbjct: 409 GKVPDIIYELIGIVSHKGT-VNEGHYIAFCKISGGQWFKFNDSMVSSISQEEVL------ 461
Query: 345 QEYSSNTDHGYILFY 359
+ Y+LFY
Sbjct: 462 ------KEQAYLLFY 470
>pdb|3M99|A Chain A, Structure Of The Ubp8-Sgf11-Sgf73-Sus1 Saga Dub Module
Length = 471
Score = 106 bits (264), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 104/375 (27%), Positives = 158/375 (42%), Gaps = 69/375 (18%)
Query: 17 PEGERYFGLE---NFGNTCYCNSVLQAL----YFCVPFREQLLDYYSNNKNLGDAEENLL 69
P ER GL N G+TC+ +S+LQ L YF R + +SNN + + +
Sbjct: 128 PSMERRDGLSGLINMGSTCFMSSILQCLIHNPYF---IRHSMSQIHSNNCKV-RSPDKCF 183
Query: 70 TCLAD-----LFTQIRAQKKKTGVIAPKR---FVQRLK---KQNELFRSYMHQDAHEFLN 118
+C D L+ + ++ + + R F+ L K N+ Y QDAHEF
Sbjct: 184 SCALDKIVHELYGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQ 243
Query: 119 FLLNELVDILXXXXXXXXXXXXXXXXXXTANGPTNGLANGVRKEPLVTWVHKNFQGILTN 178
F++N++ N AN + E + VH F+G L +
Sbjct: 244 FIINQI---------------HQSYVLDLPNAKEVSRANNKQCECI---VHTVFEGSLES 285
Query: 179 ETRCLRCETVTARD-ETFFDLSLDIEQNSSITSCLKNFSSTETLNAEDKFFCDKCCSLQE 237
C C+ + + F DLSLDI+ + CL +F E L + + C +C S Q+
Sbjct: 286 SIVCPGCQNNSKTTIDPFLDLSLDIKDKKKLYECLDSFHKKEQL-KDFNYHCGECNSTQD 344
Query: 238 AQKRMKIKKSPHTLVIHLKRFKYIEQLGRYKKLSYRVVFPLELKLSN------------T 285
A K++ I K P LV+ LKRF+++ G +KL + FP L + N
Sbjct: 345 AIKQLGIHKLPSVLVLQLKRFEHLLN-GSNRKLDDFIEFPTYLNMKNYCSTKEKDKHSEN 403
Query: 286 AEDADIEYSLFAVVVHVGSGPNHGHYVSLVK-SHNHWLFFDDENVEMIDESAVQTFFGSA 344
+ DI Y L +V H G+ N GHY++ K S W F+D V I + V
Sbjct: 404 GKVPDIIYELIGIVSHKGT-VNEGHYIAFCKISGGQWFKFNDSMVSSISQEEVL------ 456
Query: 345 QEYSSNTDHGYILFY 359
+ Y+LFY
Sbjct: 457 ------KEQAYLLFY 465
>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 = 99.0 bits (245), Expect = 4e-21, Method: Compositional matrix adjust.
Identities = 96/369 (26%), Positives = 147/369 (39%), Gaps = 54/369 (14%)
Query: 24 GLENFGNTCYCNSVLQALYFCVPFREQLL-DYYS---NNKNLGDAEENLLTCLADLFTQI 79
GL N GNT + NS LQ L P + L D Y N N + + A+L Q+
Sbjct: 10 GLGNLGNTXFMNSALQCLSNTAPLTDYFLKDEYEAEINRDNPLGMKGEIAEAYAELIKQM 69
Query: 80 RAQKKKTGVIAPKRFVQRLKKQNELFRSYMHQDAHEFLNFLLNELVDILXXXXXXXXXXX 139
+ + +AP+ F ++ + F Y QD+ E L FLL+ L + L
Sbjct: 70 WS--GRDAHVAPRMFKTQVGRFAPQFSGYQQQDSQELLAFLLDGLHEDLNRVKKKPYLEL 127
Query: 140 XXXXXXXTANGPTNGLAN-GVRKEPLVTWVHKNFQGILTNETRCLRCETVTARDETFFDL 198
A N +R + ++ F G+ + C C V+ + F L
Sbjct: 128 KDANGRPDAVVAKEAWENHRLRNDSVIV---DTFHGLFKSTLVCPECAKVSVTFDPFCYL 184
Query: 199 SLDI-------------------EQNSSITSCLKNFSSTETLNAEDKFFCDKCCSLQEAQ 239
+L + + ++ C++ F++ ETL D ++C C Q+A
Sbjct: 185 TLPLPLKKDRVMEGPMLQPQKKKKTTVALRDCIELFTTMETLGEHDPWYCPNCKKHQQAT 244
Query: 240 KRMKIKKSPHTLVIHLKRFKYIEQLGRY--KKLSYRVVFPLE-LKLSNTAEDADIE---Y 293
K+ + P LV+HLKRF Y RY KL V FP+ L +S + Y
Sbjct: 245 KKFDLWSLPKILVVHLKRFSY----NRYWRDKLDTVVEFPIRGLNMSEFVCNLSARPYVY 300
Query: 294 SLFAVVVHVGSGPNHGHYVSLVKS--HNHWLFFDDENVEMIDESAVQTFFGSAQEYSSNT 351
L AV H G+ GHY + K+ + W +FDD NV + E + T
Sbjct: 301 DLIAVSNHYGAM-GVGHYTAYAKNKLNGKWYYFDDSNVSLASEDQIV------------T 347
Query: 352 DHGYILFYE 360
Y+LFY+
Sbjct: 348 KAAYVLFYQ 356
>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 = 95.1 bits (235), Expect = 5e-20, Method: Compositional matrix adjust.
Identities = 96/348 (27%), Positives = 149/348 (42%), Gaps = 29/348 (8%)
Query: 24 GLENFGNTCYCNSVLQALYFCVPFREQLLD--YYSNNKNLGDAEENLLTCLADLFTQIRA 81
GL N GNTC+ NS+LQ L R+ L Y + + +A L+ A L I
Sbjct: 30 GLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQTIWT 89
Query: 82 QKKKTGVIAPKRFVQRLKKQNELFRSYMHQDAHEFLNFLLNELVDILXXXXXXXXXXXXX 141
V++P F ++++ F Y QDA EFL FLL+ L + +
Sbjct: 90 SSPN-DVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPEN 148
Query: 142 XXXXXTANGPTNGLANGVRKEPLVTWVHKNFQGILTNETRCLRCETVTARDETFFDLSLD 201
+ +E + + F G L + C C + + F+DLSL
Sbjct: 149 LDHLPDDEKGRQMWRKYLERED--SRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLP 206
Query: 202 IEQNS----SITSCLKNFSSTETLNAEDKFFCDKCCSLQEAQKRMKIKKSPHTLVIHLKR 257
I + ++ C++ F+ + L+ ++K C +C + K+ I++ P LV+HLKR
Sbjct: 207 IAKRGYPEVTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKILVLHLKR 266
Query: 258 FKYIEQLGRYKKLSYRVVFPL-ELKLSNTAEDAD--IEYSLFAVVVHVGSGPNHGHYVSL 314
F E R KL+ V FPL +L L A + Y+L+AV H G+ GHY +
Sbjct: 267 FS--ESRIRTSKLTTFVNFPLRDLDLREFASENTNHAVYNLYAVSNHSGTTMG-GHYTAY 323
Query: 315 VKSH--NHWLFFDDENVEMIDESAVQTFFGSAQEYSSNTDHGYILFYE 360
+S W F+D +V + S V+ T Y+LFYE
Sbjct: 324 CRSPGTGEWHTFNDSSVTPMSSSQVR------------TSDAYLLFYE 359
>pdb|2HD5|A Chain A, Usp2 In Complex With Ubiquitin
Length = 359
Score = 95.1 bits (235), Expect = 5e-20, Method: Compositional matrix adjust.
Identities = 96/348 (27%), Positives = 149/348 (42%), Gaps = 29/348 (8%)
Query: 24 GLENFGNTCYCNSVLQALYFCVPFREQLLD--YYSNNKNLGDAEENLLTCLADLFTQIRA 81
GL N GNTC+ NS+LQ L R+ L Y + + +A L+ A L I
Sbjct: 11 GLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQTIWT 70
Query: 82 QKKKTGVIAPKRFVQRLKKQNELFRSYMHQDAHEFLNFLLNELVDILXXXXXXXXXXXXX 141
V++P F ++++ F Y QDA EFL FLL+ L + +
Sbjct: 71 SSPN-DVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPEN 129
Query: 142 XXXXXTANGPTNGLANGVRKEPLVTWVHKNFQGILTNETRCLRCETVTARDETFFDLSLD 201
+ +E + + F G L + C C + + F+DLSL
Sbjct: 130 LDHLPDDEKGRQMWRKYLERED--SRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLP 187
Query: 202 IEQNS----SITSCLKNFSSTETLNAEDKFFCDKCCSLQEAQKRMKIKKSPHTLVIHLKR 257
I + ++ C++ F+ + L+ ++K C +C + K+ I++ P LV+HLKR
Sbjct: 188 IAKRGYPEVTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKILVLHLKR 247
Query: 258 FKYIEQLGRYKKLSYRVVFPL-ELKLSNTAEDAD--IEYSLFAVVVHVGSGPNHGHYVSL 314
F E R KL+ V FPL +L L A + Y+L+AV H G+ GHY +
Sbjct: 248 FS--ESRIRTSKLTTFVNFPLRDLDLREFASENTNHAVYNLYAVSNHSGTTMG-GHYTAY 304
Query: 315 VKSH--NHWLFFDDENVEMIDESAVQTFFGSAQEYSSNTDHGYILFYE 360
+S W F+D +V + S V+ T Y+LFYE
Sbjct: 305 CRSPGTGEWHTFNDSSVTPMSSSQVR------------TSDAYLLFYE 340
>pdb|2IBI|A Chain A, Covalent Ubiquitin-Usp2 Complex
Length = 374
Score = 92.0 bits (227), Expect = 4e-19, Method: Compositional matrix adjust.
Identities = 95/348 (27%), Positives = 147/348 (42%), Gaps = 29/348 (8%)
Query: 24 GLENFGNTCYCNSVLQALYFCVPFREQLLD--YYSNNKNLGDAEENLLTCLADLFTQIRA 81
GL N GNTC+ NS+LQ L R+ L Y + + +A L+ A L I
Sbjct: 37 GLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQTIWT 96
Query: 82 QKKKTGVIAPKRFVQRLKKQNELFRSYMHQDAHEFLNFLLNELVDILXXXXXXXXXXXXX 141
V++P F ++++ F Y QDA EFL FLL+ L + +
Sbjct: 97 SSPN-DVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPEN 155
Query: 142 XXXXXTANGPTNGLANGVRKEPLVTWVHKNFQGILTNETRCLRCETVTARDETFFDLSLD 201
+ +E + + F G L + C C + + F+DLSL
Sbjct: 156 LDHLPDDEKGRQMWRKYLERED--SRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLP 213
Query: 202 IEQNS----SITSCLKNFSSTETLNAEDKFFCDKCCSLQEAQKRMKIKKSPHTLVIHLKR 257
I + ++ C++ F+ + L+ + C +C + K+ I++ P LV+HLKR
Sbjct: 214 IAKRGYPEVTLMDCMRLFTKEDVLDGDAAPTCCRCRGRKRCIKKFSIQRFPKILVLHLKR 273
Query: 258 FKYIEQLGRYKKLSYRVVFPL-ELKLSNTAEDAD--IEYSLFAVVVHVGSGPNHGHYVSL 314
F E R KL+ V FPL +L L A + Y+L+AV H G+ GHY +
Sbjct: 274 FS--ESRIRTSKLTTFVNFPLRDLDLREFASENTNHAVYNLYAVSNHSGTTMG-GHYTAY 330
Query: 315 VKSH--NHWLFFDDENVEMIDESAVQTFFGSAQEYSSNTDHGYILFYE 360
+S W F+D +V + S V+ T Y+LFYE
Sbjct: 331 CRSPGTGEWHTFNDSSVTPMSSSQVR------------TSDAYLLFYE 366
>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 = 92.0 bits (227), Expect = 5e-19, Method: Compositional matrix adjust.
Identities = 90/348 (25%), Positives = 150/348 (43%), Gaps = 52/348 (14%)
Query: 22 YFGLENFGNTCYCNSVLQALYFCVPFREQLLDYYSNNKNLGDAEENLLTCLADLFTQIRA 81
Y GL+N G TCY NS+LQ L+F R+ + Y D+ +++ L +F +++
Sbjct: 6 YVGLKNQGATCYMNSLLQTLFFTNQLRKAV---YMMPTEGDDSSKSVPLALQRVFYELQH 62
Query: 82 QKKKTGVIAPKRFVQRLKKQNELFRSYMHQDAHEFLNFLLNELVDILXXXXXXXXXXXXX 141
K G K+ + E S+M D E LL+
Sbjct: 63 SDKPVGT---KKLTKSFGW--ETLDSFMQHDVQELCRVLLD------------------- 98
Query: 142 XXXXXTANGPTNGLANGVRKEPLVTWVHKNFQGILTNETRCLRCETVTARDETFFDLSLD 201
+ N ++ + + K F+G + + +C + + R E ++D+ L
Sbjct: 99 ------------NVENKMKGTCVEGTIPKLFRGKMVSYIQCKEVDYRSDRREDYYDIQLS 146
Query: 202 IEQNSSITSCLKNFSSTETLNAEDKFFCDKCCSLQEAQKRMKIKKSPHTLVIHLKRFKYI 261
I+ +I ++ + E L+ ++K+ + LQEA+K +K P L + L RF Y
Sbjct: 147 IKGKKNIFESFVDYVAVEQLDGDNKYDAGEH-GLQEAEKGVKFLTLPPVLHLQLMRFMYD 205
Query: 262 EQLGRYKKLSYRVVFPLELKLSNTAEDADIE----YSLFAVVVHVGSGPNH-GHYVSLV- 315
Q + K++ R FP +L L + D + Y L AV+VH SG NH GHYV +
Sbjct: 206 PQTDQNIKINDRFEFPEQLPLDEFLQKTDPKDPANYILHAVLVH--SGDNHGGHYVVYLN 263
Query: 316 -KSHNHWLFFDDENVEM-IDESAVQTFFGSAQEYSS--NTDHGYILFY 359
K W FDD+ V E A++ +G + S + + Y+L Y
Sbjct: 264 PKGDGKWCKFDDDVVSRCTKEEAIEHNYGGHDDDLSVRHCTNAYMLVY 311
>pdb|2F1Z|A Chain A, Crystal Structure Of Hausp
pdb|2F1Z|B Chain B, Crystal Structure Of Hausp
Length = 522
Score = 91.7 bits (226), Expect = 7e-19, Method: Compositional matrix adjust.
Identities = 90/348 (25%), Positives = 150/348 (43%), Gaps = 52/348 (14%)
Query: 22 YFGLENFGNTCYCNSVLQALYFCVPFREQLLDYYSNNKNLGDAEENLLTCLADLFTQIRA 81
Y GL+N G TCY NS+LQ L+F R+ + Y D+ +++ L +F +++
Sbjct: 175 YVGLKNQGATCYMNSLLQTLFFTNQLRKAV---YMMPTEGDDSSKSVPLALQRVFYELQH 231
Query: 82 QKKKTGVIAPKRFVQRLKKQNELFRSYMHQDAHEFLNFLLNELVDILXXXXXXXXXXXXX 141
K G K+ + E S+M D E LL+
Sbjct: 232 SDKPVGT---KKLTKSFGW--ETLDSFMQHDVQELCRVLLD------------------- 267
Query: 142 XXXXXTANGPTNGLANGVRKEPLVTWVHKNFQGILTNETRCLRCETVTARDETFFDLSLD 201
+ N ++ + + K F+G + + +C + + R E ++D+ L
Sbjct: 268 ------------NVENKMKGTCVEGTIPKLFRGKMVSYIQCKEVDYRSDRREDYYDIQLS 315
Query: 202 IEQNSSITSCLKNFSSTETLNAEDKFFCDKCCSLQEAQKRMKIKKSPHTLVIHLKRFKYI 261
I+ +I ++ + E L+ ++K+ + LQEA+K +K P L + L RF Y
Sbjct: 316 IKGKKNIFESFVDYVAVEQLDGDNKYDAGEH-GLQEAEKGVKFLTLPPVLHLQLMRFMYD 374
Query: 262 EQLGRYKKLSYRVVFPLELKLSNTAEDADIE----YSLFAVVVHVGSGPNH-GHYVSLV- 315
Q + K++ R FP +L L + D + Y L AV+VH SG NH GHYV +
Sbjct: 375 PQTDQNIKINDRFEFPEQLPLDEFLQKTDPKDPANYILHAVLVH--SGDNHGGHYVVYLN 432
Query: 316 -KSHNHWLFFDDENVEM-IDESAVQTFFGSAQEYSS--NTDHGYILFY 359
K W FDD+ V E A++ +G + S + + Y+L Y
Sbjct: 433 PKGDGKWCKFDDDVVSRCTKEEAIEHNYGGHDDDLSVRHCTNAYMLVY 480
>pdb|3NHE|A Chain A, High Resolution Structure (1.26a) Of Usp2a In Complex With
Ubiquitin
Length = 348
Score = 90.9 bits (224), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 95/348 (27%), Positives = 148/348 (42%), Gaps = 29/348 (8%)
Query: 24 GLENFGNTCYCNSVLQALYFCVPFREQLLD--YYSNNKNLGDAEENLLTCLADLFTQIRA 81
GL N GNT + NS+LQ L R+ L Y + + +A L+ A L I
Sbjct: 11 GLRNLGNTXFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQTIWT 70
Query: 82 QKKKTGVIAPKRFVQRLKKQNELFRSYMHQDAHEFLNFLLNELVDILXXXXXXXXXXXXX 141
V++P F ++++ F Y QDA EFL FLL+ L + +
Sbjct: 71 SSPN-DVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPEN 129
Query: 142 XXXXXTANGPTNGLANGVRKEPLVTWVHKNFQGILTNETRCLRCETVTARDETFFDLSLD 201
+ +E + + F G L + C C + + F+DLSL
Sbjct: 130 LDHLPDDEKGRQMWRKYLERED--SRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLP 187
Query: 202 IEQNS----SITSCLKNFSSTETLNAEDKFFCDKCCSLQEAQKRMKIKKSPHTLVIHLKR 257
I + ++ C++ F+ + L+ ++K C +C + K+ I++ P LV+HLKR
Sbjct: 188 IAKRGYPEVTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKILVLHLKR 247
Query: 258 FKYIEQLGRYKKLSYRVVFPL-ELKLSNTAEDAD--IEYSLFAVVVHVGSGPNHGHYVSL 314
F E R KL+ V FPL +L L A + Y+L+AV H G+ GHY +
Sbjct: 248 FS--ESRIRTSKLTTFVNFPLRDLDLREFASENTNHAVYNLYAVSNHSGTTMG-GHYTAY 304
Query: 315 VKSH--NHWLFFDDENVEMIDESAVQTFFGSAQEYSSNTDHGYILFYE 360
+S W F+D +V + S V+ T Y+LFYE
Sbjct: 305 CRSPGTGEWHTFNDSSVTPMSSSQVR------------TSDAYLLFYE 340
>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 = 88.2 bits (217), Expect = 7e-18, Method: Compositional matrix adjust.
Identities = 85/330 (25%), Positives = 139/330 (42%), Gaps = 50/330 (15%)
Query: 22 YFGLENFGNTCYCNSVLQALYFCVPFREQLLDYYSNNKNLGDAEENLLTCLADLFTQIRA 81
Y GL+N G TCY NS+LQ L+F R+ + Y D+ +++ L +F +++
Sbjct: 6 YVGLKNQGATCYXNSLLQTLFFTNQLRKAV---YXXPTEGDDSSKSVPLALQRVFYELQH 62
Query: 82 QKKKTGVIAPKRFVQRLKKQNELFRSYMHQDAHEFLNFLLNELVDILXXXXXXXXXXXXX 141
K G K+ + E S+ D E LL+
Sbjct: 63 SDKPVGT---KKLTKSFGW--ETLDSFXQHDVQELCRVLLD------------------- 98
Query: 142 XXXXXTANGPTNGLANGVRKEPLVTWVHKNFQGILTNETRCLRCETVTARDETFFDLSLD 201
+ N + + + K F+G + +C + + R E ++D+ L
Sbjct: 99 ------------NVENKXKGTCVEGTIPKLFRGKXVSYIQCKEVDYRSDRREDYYDIQLS 146
Query: 202 IEQNSSITSCLKNFSSTETLNAEDKFFCDKCCSLQEAQKRMKIKKSPHTLVIHLKRFKYI 261
I+ +I ++ + E L+ ++K+ + LQEA+K +K P L + L RF Y
Sbjct: 147 IKGKKNIFESFVDYVAVEQLDGDNKYDAGEH-GLQEAEKGVKFLTLPPVLHLQLXRFXYD 205
Query: 262 EQLGRYKKLSYRVVFPLELKLSNTAEDADIE----YSLFAVVVHVGSGPNH-GHYVSLV- 315
Q + K++ R FP +L L + D + Y L AV+VH SG NH GHYV +
Sbjct: 206 PQTDQNIKINDRFEFPEQLPLDEFLQKTDPKDPANYILHAVLVH--SGDNHGGHYVVYLN 263
Query: 316 -KSHNHWLFFDDENVEM-IDESAVQTFFGS 343
K W FDD+ V E A++ +G
Sbjct: 264 PKGDGKWCKFDDDVVSRCTKEEAIEHNYGG 293
>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
Length = 854
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 35/126 (27%), Positives = 54/126 (42%), Gaps = 24/126 (19%)
Query: 19 GERYFGLENFGNTCYCNSVLQALYFCVPFREQLLD----YYSNNKNLGDAEENLLTCLAD 74
G Y G+ N GN+CY NSV+Q L+ F+ + +D + N D ++ T +A
Sbjct: 341 GPGYTGIRNLGNSCYLNSVVQVLFSIPDFQRKYVDKLEKIFQNAPT--DPTQDFSTQVAK 398
Query: 75 LF------------------TQIRAQKKKTGVIAPKRFVQRLKKQNELFRSYMHQDAHEF 116
L ++ QK+ IAP+ F + K + F + QDA EF
Sbjct: 399 LGHGLLSGEYSKPVPESGDGERVPEQKEVQDGIAPRMFKALIGKGHPEFSTNRQQDAQEF 458
Query: 117 LNFLLN 122
L+N
Sbjct: 459 FLHLIN 464
Score = 41.6 bits (96), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 37/85 (43%), Gaps = 14/85 (16%)
Query: 280 LKLSNTAEDADIEYSLFAVVVHVGSGPNHGHYVSLVKSHNHWLFFDDENVEMIDESAVQT 339
+ + D +Y LFA + H+G+ GHYV +K W+ ++D+ V
Sbjct: 784 VPVGPKVRDGPGKYQLFAFISHMGTSTMCGHYVCHIKKEGRWVIYNDQKV---------- 833
Query: 340 FFGSAQEYSSNTDHGYILFYESLGA 364
A E D GYI FY+ + +
Sbjct: 834 ---CASEKPPK-DLGYIYFYQRVAS 854
>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 = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 24/95 (25%), Positives = 45/95 (47%), Gaps = 11/95 (11%)
Query: 272 YRVVFPLELKLSNTAEDADIEYSLFAVVVHVGSGPNHGHYVSLVK---SHNHWLFFDDEN 328
Y+ FP L+ E+ Y+L V+ H G+ GHY + ++ N W F+D+
Sbjct: 328 YKKHFPPNLE---KGENPSCVYNLIGVITHQGANSESGHYQAFIRDELDENKWYKFNDDK 384
Query: 329 VEMIDESAVQTFFGSAQEYSSNTDHGYILFYESLG 363
V ++++ +++ G + +D IL Y+ G
Sbjct: 385 VSVVEKEKIESLAGGGE-----SDSALILXYKGFG 414
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 16/31 (51%), Positives = 21/31 (67%)
Query: 24 GLENFGNTCYCNSVLQALYFCVPFREQLLDY 54
G +N GNTCY N+ LQALY R+ +L+Y
Sbjct: 26 GFKNXGNTCYLNATLQALYRVNDLRDXILNY 56
>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 = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 33/68 (48%), Gaps = 6/68 (8%)
Query: 293 YSLFAVVVHVGSGPNHGHYVSLVK-SHNHWLFFDDENVEMIDESAVQTFFGSAQEYSSNT 351
Y L AV+ H G + GHYVS VK + W+ FDD+ V ++ + G + +
Sbjct: 328 YDLQAVLTHQGRSSSSGHYVSWVKRKQDEWIKFDDDKVSIVTPEDILRLSGGGDWHIA-- 385
Query: 352 DHGYILFY 359
Y+L Y
Sbjct: 386 ---YVLLY 390
Score = 35.0 bits (79), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 28/100 (28%), Positives = 43/100 (43%), Gaps = 11/100 (11%)
Query: 24 GLENFGNTCYCNSVLQALYFCVPFREQLLDYYSNNKNLGD--AEENLLTCLADLFTQIRA 81
GL N GNTCY N+ +Q + ++ L Y + G+ + + + L DLF +
Sbjct: 16 GLTNLGNTCYMNATVQCIRSVPELKDALKRYAGALRASGEMASAQYITAALRDLFDSM-- 73
Query: 82 QKKKTGVIAPKRFVQRLKKQNELFR------SYMHQDAHE 115
K + I P +Q L F Y+ QDA+E
Sbjct: 74 -DKTSSSIPPIILLQFLHMAFPQFAEKGEQGQYLQQDANE 112
>pdb|2O3J|A Chain A, Structure Of Caenorhabditis Elegans Udp-Glucose
Dehydrogenase
pdb|2O3J|B Chain B, Structure Of Caenorhabditis Elegans Udp-Glucose
Dehydrogenase
pdb|2O3J|C Chain C, Structure Of Caenorhabditis Elegans Udp-Glucose
Dehydrogenase
Length = 481
Score = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 21/86 (24%), Positives = 38/86 (44%), Gaps = 4/86 (4%)
Query: 2 GAAGSKLEKALGDQFPEGERYFGLE-NFGNTCYCNSVLQALYFCVPFR-EQLLDYYSNNK 59
GA S++ A+G G ++ FG +C+ VL +Y C Q+ DY+
Sbjct: 252 GAEISEVAHAVGYDTRIGSKFLQASVGFGGSCFQKDVLSLVYLCESLNLPQVADYWQGVI 311
Query: 60 NLGDAEENLLT--CLADLFTQIRAQK 83
N+ + + +A+LF + +K
Sbjct: 312 NINNWQRRRFADKIIAELFNTVTDKK 337
>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 = 28.5 bits (62), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 20/44 (45%)
Query: 308 HGHYVSLVKSHNHWLFFDDENVEMIDESAVQTFFGSAQEYSSNT 351
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
0.320 0.135 0.401
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,384,261
Number of Sequences: 62578
Number of extensions: 404588
Number of successful extensions: 1045
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 22
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 966
Number of HSP's gapped (non-prelim): 43
length of query: 369
length of database: 14,973,337
effective HSP length: 100
effective length of query: 269
effective length of database: 8,715,537
effective search space: 2344479453
effective search space used: 2344479453
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)