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= 025024
(259 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 = 67.4 bits (163), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 64/230 (27%), Positives = 93/230 (40%), Gaps = 30/230 (13%)
Query: 19 GERYFGLENFGNTCYCNSVLQALYFCVPFREQLLDYYS--------NNKNL----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 CETVTARDETFFDLSLDIEQNS--SITSCLKNFSSTETLNAEDKFFCDKC 232
C + E F LSL + S ++ CL+ FS E L ++F+C C
Sbjct: 225 CHKKSRTFEAFMYLSLPLASTSKCTLQDCLRLFSKEEKLTDNNRFYCSHC 274
>pdb|2GFO|A Chain A, Structure Of The Catalytic Domain Of Human Ubiquitin
Carboxyl-terminal Hydrolase 8
Length = 396
Score = 64.7 bits (156), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 64/223 (28%), Positives = 90/223 (40%), Gaps = 16/223 (7%)
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--SCLKNFSSTETLNAEDKFFCDKC 232
E F LSL + S T CL+ FS E L ++F+C C
Sbjct: 232 FEAFXYLSLPLASTSKCTLQDCLRLFSKEEKLTDNNRFYCSHC 274
>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 = 64.7 bits (156), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 65/243 (26%), Positives = 90/243 (37%), Gaps = 39/243 (16%)
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 DKC 232
D+C
Sbjct: 243 DRC 245
>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 = 63.5 bits (153), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 66/246 (26%), Positives = 91/246 (36%), Gaps = 40/246 (16%)
Query: 17 PEGER-YFGLENFGNTCYCNSVLQALYFCVPFREQLL--DYYSNNKNLGDAEENLLTCLA 73
P G + GL N GNTC+ N+VLQ L P R+ L D+ G A+E L A
Sbjct: 16 PRGSSGHVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQE-LTEAFA 74
Query: 74 DLFTQIRAQKKKTGVIAPKRFVQRLKKQNELFRSYMHQDAHEFLNFLLNELVDILXXXXX 133
D+ + + P RF +K F Y QDA EFL L+ L
Sbjct: 75 DVIGAL-WHPDSCEAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERL--------H 125
Query: 134 XXXXXXXXXXXXXTANGPTNGL---ANGVRKEPLVT--------W----------VHKNF 172
ANGP + +EP ++ W + F
Sbjct: 126 LEINRRGRRAPPILANGPVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLF 185
Query: 173 QGILTNETRCLRCETVTARDETFFDLSLDIEQNS------SITSCLKNFSSTETLNAEDK 226
G L + +C C + E F DLSL I + S+ C F+ E L +E+
Sbjct: 186 VGQLKSCLKCQACGYRSTTFEVFCDLSLPIPKKGFAGGKVSLRDCFNLFTKEEELESENA 245
Query: 227 FFCDKC 232
CD+C
Sbjct: 246 PVCDRC 251
>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 = 63.5 bits (153), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 64/240 (26%), Positives = 89/240 (37%), Gaps = 39/240 (16%)
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
>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 = 57.8 bits (138), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 62/235 (26%), Positives = 96/235 (40%), Gaps = 42/235 (17%)
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-ETFFDLSLDIEQNSSITSCLKNFSSTETLNAEDKFFCDKC 232
C C+ + + F DLSLDI+ + CL +F E L + + C +C
Sbjct: 291 SIVCPGCQNNSKTTIDPFLDLSLDIKDKKKLYECLDSFHKKEQL-KDFNYHCGEC 344
>pdb|3M99|A Chain A, Structure Of The Ubp8-Sgf11-Sgf73-Sus1 Saga Dub Module
Length = 471
Score = 55.8 bits (133), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 61/235 (25%), Positives = 96/235 (40%), Gaps = 42/235 (17%)
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-ETFFDLSLDIEQNSSITSCLKNFSSTETLNAEDKFFCDKC 232
C C+ + + F DLSLDI+ + CL +F E L + + C +C
Sbjct: 286 SIVCPGCQNNSKTTIDPFLDLSLDIKDKKKLYECLDSFHKKEQL-KDFNYHCGEC 339
>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 = 55.8 bits (133), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 61/235 (25%), Positives = 96/235 (40%), Gaps = 42/235 (17%)
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-ETFFDLSLDIEQNSSITSCLKNFSSTETLNAEDKFFCDKC 232
C C+ + + F DLSLDI+ + CL +F E L + + C +C
Sbjct: 291 SIVCPGCQNNSKTTIDPFLDLSLDIKDKKKLYECLDSFHKKEQL-KDFNYHCGEC 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 = 55.1 bits (131), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 51/209 (24%), Positives = 85/209 (40%), Gaps = 9/209 (4%)
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----SITSCLKNFSSTETLNAEDK 226
I + ++ C++ F+ + L+ ++K
Sbjct: 207 IAKRGYPEVTLMDCMRLFTKEDVLDGDEK 235
>pdb|2HD5|A Chain A, Usp2 In Complex With Ubiquitin
Length = 359
Score = 54.7 bits (130), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 51/209 (24%), Positives = 85/209 (40%), Gaps = 9/209 (4%)
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----SITSCLKNFSSTETLNAEDK 226
I + ++ C++ F+ + L+ ++K
Sbjct: 188 IAKRGYPEVTLMDCMRLFTKEDVLDGDEK 216
>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 = 53.1 bits (126), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 53/233 (22%), Positives = 88/233 (37%), Gaps = 29/233 (12%)
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 XXXXXXXTANGPTNGLANG-VRKEPLVTWVHKNFQGILTNETRCLRCETVTARDETFFDL 198
A N +R + ++ F G+ + C C V+ + F L
Sbjct: 128 KDANGRPDAVVAKEAWENHRLRNDSVIV---DTFHGLFKSTLVCPECAKVSVTFDPFCYL 184
Query: 199 SLDI-------------------EQNSSITSCLKNFSSTETLNAEDKFFCDKC 232
+L + + ++ C++ F++ ETL D ++C C
Sbjct: 185 TLPLPLKKDRVMEGPMLQPQKKKKTTVALRDCIELFTTMETLGEHDPWYCPNC 237
>pdb|2IBI|A Chain A, Covalent Ubiquitin-Usp2 Complex
Length = 374
Score = 52.8 bits (125), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 35/103 (33%), Positives = 49/103 (47%), Gaps = 3/103 (2%)
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 QKKKTGVIAPKRFVQRLKKQNELFRSYMHQDAHEFLNFLLNEL 124
V++P F ++++ F Y QDA EFL FLL+ L
Sbjct: 97 SSPND-VVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGL 138
>pdb|3NHE|A Chain A, High Resolution Structure (1.26a) Of Usp2a In Complex With
Ubiquitin
Length = 348
Score = 50.8 bits (120), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 50/209 (23%), Positives = 84/209 (40%), Gaps = 9/209 (4%)
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----SITSCLKNFSSTETLNAEDK 226
I + ++ C++ F+ + L+ ++K
Sbjct: 188 IAKRGYPEVTLMDCMRLFTKEDVLDGDEK 216
>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 = 49.3 bits (116), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 43/206 (20%), Positives = 83/206 (40%), Gaps = 39/206 (18%)
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--ETLDSFMQHDVQELCRVLL-------------------- 97
Query: 142 XXXXXTANGPTNGLANGVRKEPLVTWVHKNFQGILTNETRCLRCETVTARDETFFDLSLD 201
+ + N ++ + + K F+G + + +C + + R E ++D+ L
Sbjct: 98 -----------DNVENKMKGTCVEGTIPKLFRGKMVSYIQCKEVDYRSDRREDYYDIQLS 146
Query: 202 IEQNSSITSCLKNFSSTETLNAEDKF 227
I+ +I ++ + E L+ ++K+
Sbjct: 147 IKGKKNIFESFVDYVAVEQLDGDNKY 172
>pdb|2F1Z|A Chain A, Crystal Structure Of Hausp
pdb|2F1Z|B Chain B, Crystal Structure Of Hausp
Length = 522
Score = 48.5 bits (114), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 43/206 (20%), Positives = 83/206 (40%), Gaps = 39/206 (18%)
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--ETLDSFMQHDVQELCRVLL-------------------- 266
Query: 142 XXXXXTANGPTNGLANGVRKEPLVTWVHKNFQGILTNETRCLRCETVTARDETFFDLSLD 201
+ + N ++ + + K F+G + + +C + + R E ++D+ L
Sbjct: 267 -----------DNVENKMKGTCVEGTIPKLFRGKMVSYIQCKEVDYRSDRREDYYDIQLS 315
Query: 202 IEQNSSITSCLKNFSSTETLNAEDKF 227
I+ +I ++ + E L+ ++K+
Sbjct: 316 IKGKKNIFESFVDYVAVEQLDGDNKY 341
>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
Length = 854
Score = 45.8 bits (107), Expect = 2e-05, Method: Composition-based stats.
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
>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 = 44.7 bits (104), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 42/206 (20%), Positives = 80/206 (38%), Gaps = 39/206 (18%)
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--ETLDSFXQHDVQELCRVLL-------------------- 97
Query: 142 XXXXXTANGPTNGLANGVRKEPLVTWVHKNFQGILTNETRCLRCETVTARDETFFDLSLD 201
+ + N + + + K F+G + +C + + R E ++D+ L
Sbjct: 98 -----------DNVENKXKGTCVEGTIPKLFRGKXVSYIQCKEVDYRSDRREDYYDIQLS 146
Query: 202 IEQNSSITSCLKNFSSTETLNAEDKF 227
I+ +I ++ + E L+ ++K+
Sbjct: 147 IKGKKNIFESFVDYVAVEQLDGDNKY 172
>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 = 38.9 bits (89), Expect = 0.003, 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 = 34.7 bits (78), Expect = 0.057, 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 = 29.6 bits (65), Expect = 1.9, 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|1JFI|B Chain B, Crystal Structure Of The Nc2-Tbp-Dna Ternary Complex
Length = 179
Score = 27.3 bits (59), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 25/57 (43%)
Query: 24 GLENFGNTCYCNSVLQALYFCVPFREQLLDYYSNNKNLGDAEENLLTCLADLFTQIR 80
LE+ G Y + V + L C + S +NLG EE LL +LF + R
Sbjct: 77 ALESLGFGSYISEVKEVLQECKTVALKRRKASSRLENLGIPEEELLRQQQELFAKAR 133
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
0.323 0.137 0.416
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,901,458
Number of Sequences: 62578
Number of extensions: 251540
Number of successful extensions: 600
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 550
Number of HSP's gapped (non-prelim): 35
length of query: 259
length of database: 14,973,337
effective HSP length: 97
effective length of query: 162
effective length of database: 8,903,271
effective search space: 1442329902
effective search space used: 1442329902
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 50 (23.9 bits)