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= psy10711
(203 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 = 156 bits (394), Expect = 9e-39, Method: Compositional matrix adjust.
Identities = 88/214 (41%), Positives = 114/214 (53%), Gaps = 37/214 (17%)
Query: 11 IKIIFWTVGPGLTGLKNLGNTCYINSILQCLSNTSPLREYF-----VTEFKRSMTAAYSK 65
+ +F GP LTGL+NLGNTCY+NSILQCL N L +YF + RS +
Sbjct: 51 LNPVFGGSGPALTGLRNLGNTCYMNSILQCLCNAPHLADYFNRNCYQDDINRSNLLGHK- 109
Query: 66 TSGKLAEEFQLIFNMLWAGDSRYFSPQKFKVKHELVGKFKEEVGKMKRTFRGYEQQDSHE 125
G++AEEF +I LW G RY SP+ FK+ +GK+ F GY QQDS E
Sbjct: 110 --GEVAEEFGIIMKALWTGQYRYISPKDFKI----------TIGKINDQFAGYSQQDSQE 157
Query: 126 FLTILIDTLHEDLKES-------------------GEKSWGEFRKKNKSIISELFYGQLK 166
L L+D LHEDL ++ E +W + ++ N+SII LF GQ K
Sbjct: 158 LLLFLMDGLHEDLNKADNRKRYKEENNDHLDDFKAAEHAWQKHKQLNESIIVALFQGQFK 217
Query: 167 STVICCNCQETSSTFEVFSNVSLPLPSNDYCSLR 200
STV C C + S TFE F +SLPL S C+L+
Sbjct: 218 STVQCLTCHKKSRTFEAFMYLSLPLASTSKCTLQ 251
>pdb|2GFO|A Chain A, Structure Of The Catalytic Domain Of Human Ubiquitin
Carboxyl-terminal Hydrolase 8
Length = 396
Score = 153 bits (387), Expect = 5e-38, Method: Compositional matrix adjust.
Identities = 88/214 (41%), Positives = 112/214 (52%), Gaps = 37/214 (17%)
Query: 11 IKIIFWTVGPGLTGLKNLGNTCYINSILQCLSNTSPLREYF-----VTEFKRSMTAAYSK 65
+ +F GP LTGL+NLGNTCY NSILQCL N L +YF + RS +
Sbjct: 51 LNPVFGGSGPALTGLRNLGNTCYXNSILQCLCNAPHLADYFNRNCYQDDINRSNLLGHK- 109
Query: 66 TSGKLAEEFQLIFNMLWAGDSRYFSPQKFKVKHELVGKFKEEVGKMKRTFRGYEQQDSHE 125
G++AEEF +I LW G RY SP+ FK+ +GK+ F GY QQDS E
Sbjct: 110 --GEVAEEFGIIXKALWTGQYRYISPKDFKI----------TIGKINDQFAGYSQQDSQE 157
Query: 126 FLTILIDTLHEDLKES-------------------GEKSWGEFRKKNKSIISELFYGQLK 166
L L D LHEDL ++ E +W + ++ N+SII LF GQ K
Sbjct: 158 LLLFLXDGLHEDLNKADNRKRYKEENNDHLDDFKAAEHAWQKHKQLNESIIVALFQGQFK 217
Query: 167 STVICCNCQETSSTFEVFSNVSLPLPSNDYCSLR 200
STV C C + S TFE F +SLPL S C+L+
Sbjct: 218 STVQCLTCHKKSRTFEAFXYLSLPLASTSKCTLQ 251
>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 = 132 bits (333), Expect = 1e-31, Method: Compositional matrix adjust.
Identities = 72/199 (36%), Positives = 103/199 (51%), Gaps = 37/199 (18%)
Query: 18 VGPGLTGLKNLGNTCYINSILQCLSNTSPLREYFV-----TEFKRSMTAAYSKTSGKLAE 72
+ PGL GL NLGNT ++NS LQCLSNT+PL +YF+ E R G++AE
Sbjct: 4 IQPGLCGLGNLGNTXFMNSALQCLSNTAPLTDYFLKDEYEAEINRDNPLG---MKGEIAE 60
Query: 73 EFQLIFNMLWAGDSRYFSPQKFKVKHELVGKFKEEVGKMKRTFRGYEQQDSHEFLTILID 132
+ + +W+G + +P+ FK +VG+ F GY+QQDS E L L+D
Sbjct: 61 AYAELIKQMWSGRDAHVAPRMFKT----------QVGRFAPQFSGYQQQDSQELLAFLLD 110
Query: 133 TLHEDLKESGEK-------------------SWGEFRKKNKSIISELFYGQLKSTVICCN 173
LHEDL +K +W R +N S+I + F+G KST++C
Sbjct: 111 GLHEDLNRVKKKPYLELKDANGRPDAVVAKEAWENHRLRNDSVIVDTFHGLFKSTLVCPE 170
Query: 174 CQETSSTFEVFSNVSLPLP 192
C + S TF+ F ++LPLP
Sbjct: 171 CAKVSVTFDPFCYLTLPLP 189
>pdb|2HD5|A Chain A, Usp2 In Complex With Ubiquitin
Length = 359
Score = 117 bits (294), Expect = 3e-27, Method: Compositional matrix adjust.
Identities = 68/195 (34%), Positives = 96/195 (49%), Gaps = 28/195 (14%)
Query: 21 GLTGLKNLGNTCYINSILQCLSNTSPLREYFVTEFKRSMTAAYSKTSGKLAEEFQLIFNM 80
GL GL+NLGNTC++NSILQCLSNT LR+Y + S L EEF +
Sbjct: 8 GLAGLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQT 67
Query: 81 LWAGDSRYFSPQKFKVKHELVGKFKEEVGKMKRTFRGYEQQDSHEFLTILIDTLHEDLK- 139
+W SP E FK ++ + F GY QQD+ EFL L+D LH ++
Sbjct: 68 IWTS-----SPNDVVSPSE----FKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNR 118
Query: 140 ------------------ESGEKSWGEFRKKNKSIISELFYGQLKSTVICCNCQETSSTF 181
E G + W ++ ++ S I +LF GQLKS++ C +C S+ F
Sbjct: 119 VTLRPKSNPENLDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVF 178
Query: 182 EVFSNVSLPLPSNDY 196
+ F ++SLP+ Y
Sbjct: 179 DPFWDLSLPIAKRGY 193
>pdb|2IBI|A Chain A, Covalent Ubiquitin-Usp2 Complex
Length = 374
Score = 117 bits (294), Expect = 4e-27, Method: Compositional matrix adjust.
Identities = 68/195 (34%), Positives = 96/195 (49%), Gaps = 28/195 (14%)
Query: 21 GLTGLKNLGNTCYINSILQCLSNTSPLREYFVTEFKRSMTAAYSKTSGKLAEEFQLIFNM 80
GL GL+NLGNTC++NSILQCLSNT LR+Y + S L EEF +
Sbjct: 34 GLAGLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQT 93
Query: 81 LWAGDSRYFSPQKFKVKHELVGKFKEEVGKMKRTFRGYEQQDSHEFLTILIDTLHEDLK- 139
+W SP E FK ++ + F GY QQD+ EFL L+D LH ++
Sbjct: 94 IWTS-----SPNDVVSPSE----FKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNR 144
Query: 140 ------------------ESGEKSWGEFRKKNKSIISELFYGQLKSTVICCNCQETSSTF 181
E G + W ++ ++ S I +LF GQLKS++ C +C S+ F
Sbjct: 145 VTLRPKSNPENLDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVF 204
Query: 182 EVFSNVSLPLPSNDY 196
+ F ++SLP+ Y
Sbjct: 205 DPFWDLSLPIAKRGY 219
>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 = 117 bits (293), Expect = 4e-27, Method: Compositional matrix adjust.
Identities = 68/195 (34%), Positives = 96/195 (49%), Gaps = 28/195 (14%)
Query: 21 GLTGLKNLGNTCYINSILQCLSNTSPLREYFVTEFKRSMTAAYSKTSGKLAEEFQLIFNM 80
GL GL+NLGNTC++NSILQCLSNT LR+Y + S L EEF +
Sbjct: 27 GLAGLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQT 86
Query: 81 LWAGDSRYFSPQKFKVKHELVGKFKEEVGKMKRTFRGYEQQDSHEFLTILIDTLHEDLK- 139
+W SP E FK ++ + F GY QQD+ EFL L+D LH ++
Sbjct: 87 IWTS-----SPNDVVSPSE----FKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNR 137
Query: 140 ------------------ESGEKSWGEFRKKNKSIISELFYGQLKSTVICCNCQETSSTF 181
E G + W ++ ++ S I +LF GQLKS++ C +C S+ F
Sbjct: 138 VTLRPKSNPENLDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVF 197
Query: 182 EVFSNVSLPLPSNDY 196
+ F ++SLP+ Y
Sbjct: 198 DPFWDLSLPIAKRGY 212
>pdb|3NHE|A Chain A, High Resolution Structure (1.26a) Of Usp2a In Complex With
Ubiquitin
Length = 348
Score = 113 bits (283), Expect = 7e-26, Method: Compositional matrix adjust.
Identities = 67/195 (34%), Positives = 95/195 (48%), Gaps = 28/195 (14%)
Query: 21 GLTGLKNLGNTCYINSILQCLSNTSPLREYFVTEFKRSMTAAYSKTSGKLAEEFQLIFNM 80
GL GL+NLGNT ++NSILQCLSNT LR+Y + S L EEF +
Sbjct: 8 GLAGLRNLGNTXFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQT 67
Query: 81 LWAGDSRYFSPQKFKVKHELVGKFKEEVGKMKRTFRGYEQQDSHEFLTILIDTLHEDLK- 139
+W SP E FK ++ + F GY QQD+ EFL L+D LH ++
Sbjct: 68 IWTS-----SPNDVVSPSE----FKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNR 118
Query: 140 ------------------ESGEKSWGEFRKKNKSIISELFYGQLKSTVICCNCQETSSTF 181
E G + W ++ ++ S I +LF GQLKS++ C +C S+ F
Sbjct: 119 VTLRPKSNPENLDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVF 178
Query: 182 EVFSNVSLPLPSNDY 196
+ F ++SLP+ Y
Sbjct: 179 DPFWDLSLPIAKRGY 193
>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 = 112 bits (281), Expect = 1e-25, Method: Compositional matrix adjust.
Identities = 68/221 (30%), Positives = 105/221 (47%), Gaps = 46/221 (20%)
Query: 18 VGPGLTGLKNLGNTCYINSILQCLSNTSPLREYFVTEFKRSMTAAYSKTSGKLAEEFQLI 77
+G G GL+NLGNTC++N++LQCLS+T PLR++ + R + +L E F +
Sbjct: 12 LGSGHVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQ-ELTEAFADV 70
Query: 78 FNMLWAGDS-RYFSPQKFKVKHELVGKFKEEVGKMKRTFRGYEQQDSHEFLTILIDTLHE 136
LW DS +P +F+ + K +F GY QQD+ EFL +L++ LH
Sbjct: 71 IGALWHPDSCEAVNPTRFRAVFQ----------KYVPSFSGYSQQDAQEFLKLLMERLHL 120
Query: 137 DLKESGEKS----------------------------------WGEFRKKNKSIISELFY 162
++ G ++ W + ++ S I +LF
Sbjct: 121 EINRRGRRAPPILANGPVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFV 180
Query: 163 GQLKSTVICCNCQETSSTFEVFSNVSLPLPSNDYCSLRVSF 203
GQLKS + C C S+TFEVF ++SLP+P + +VS
Sbjct: 181 GQLKSCLKCQACGYRSTTFEVFCDLSLPIPKKGFAGGKVSL 221
>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 = 110 bits (276), Expect = 4e-25, Method: Compositional matrix adjust.
Identities = 67/218 (30%), Positives = 103/218 (47%), Gaps = 46/218 (21%)
Query: 21 GLTGLKNLGNTCYINSILQCLSNTSPLREYFVTEFKRSMTAAYSKTSGKLAEEFQLIFNM 80
G GL+NLGNTC++N++LQCLS+T PLR++ + R + +L E F +
Sbjct: 21 GHVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQ-ELTEAFADVIGA 79
Query: 81 LWAGDS-RYFSPQKFKVKHELVGKFKEEVGKMKRTFRGYEQQDSHEFLTILIDTLHEDLK 139
LW DS +P +F+ + K +F GY QQD+ EFL +L++ LH ++
Sbjct: 80 LWHPDSCEAVNPTRFRAVFQ----------KYVPSFSGYSQQDAQEFLKLLMERLHLEIN 129
Query: 140 ESGEKS----------------------------------WGEFRKKNKSIISELFYGQL 165
G ++ W + ++ S I +LF GQL
Sbjct: 130 RRGRRAPPILANGPVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQL 189
Query: 166 KSTVICCNCQETSSTFEVFSNVSLPLPSNDYCSLRVSF 203
KS + C C S+TFEVF ++SLP+P + +VS
Sbjct: 190 KSCLKCQACGYRSTTFEVFCDLSLPIPKKGFAGGKVSL 227
>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 = 110 bits (275), Expect = 5e-25, Method: Compositional matrix adjust.
Identities = 67/218 (30%), Positives = 103/218 (47%), Gaps = 46/218 (21%)
Query: 21 GLTGLKNLGNTCYINSILQCLSNTSPLREYFVTEFKRSMTAAYSKTSGKLAEEFQLIFNM 80
G GL+NLGNTC++N++LQCLS+T PLR++ + R + +L E F +
Sbjct: 2 GHVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQ-ELTEAFADVIGA 60
Query: 81 LWAGDS-RYFSPQKFKVKHELVGKFKEEVGKMKRTFRGYEQQDSHEFLTILIDTLHEDLK 139
LW DS +P +F+ + K +F GY QQD+ EFL +L++ LH ++
Sbjct: 61 LWHPDSCEAVNPTRFRAVFQ----------KYVPSFSGYSQQDAQEFLKLLMERLHLEIN 110
Query: 140 ESGEKS----------------------------------WGEFRKKNKSIISELFYGQL 165
G ++ W + ++ S I +LF GQL
Sbjct: 111 RRGRRAPPILANGPVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQL 170
Query: 166 KSTVICCNCQETSSTFEVFSNVSLPLPSNDYCSLRVSF 203
KS + C C S+TFEVF ++SLP+P + +VS
Sbjct: 171 KSCLKCQACGYRSTTFEVFCDLSLPIPKKGFAGGKVSL 208
>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 = 74.7 bits (182), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 53/182 (29%), Positives = 91/182 (50%), Gaps = 17/182 (9%)
Query: 21 GLTGLKNLGNTCYINSILQCLSNTSPLREYFVTEFK------RSMTAAYSKTSGKLAEEF 74
GL+GL N+GNTC+++SILQCL + + +++ RS +S K+ E
Sbjct: 140 GLSGLINMGNTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHEL 199
Query: 75 QLIFNMLWAGDSRYFSPQKFKVKHELVGKFKEEVGKMKRTFRGYEQQDSHEFLTILIDTL 134
N A S + ++ + L + K+ + GY QQD+HEF +I+ +
Sbjct: 200 YGALNTKQASSSSTSTNRQTGFIYLLTCAW-----KINQNLAGYSQQDAHEFWQFIINQI 254
Query: 135 HE----DLKESGEKSWGEFRKKNKSIISELFYGQLKSTVICCNCQETS-STFEVFSNVSL 189
H+ DL + E S K+ + I+ +F G L+S+++C CQ S +T + F ++SL
Sbjct: 255 HQSYVLDLPNAKEVSRAN-NKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLDLSL 313
Query: 190 PL 191
+
Sbjct: 314 DI 315
>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 = 72.8 bits (177), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 52/182 (28%), Positives = 91/182 (50%), Gaps = 17/182 (9%)
Query: 21 GLTGLKNLGNTCYINSILQCLSNTSPLREYFVTEFK------RSMTAAYSKTSGKLAEEF 74
GL+GL N+G+TC+++SILQCL + + +++ RS +S K+ E
Sbjct: 140 GLSGLINMGSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHEL 199
Query: 75 QLIFNMLWAGDSRYFSPQKFKVKHELVGKFKEEVGKMKRTFRGYEQQDSHEFLTILIDTL 134
N A S + ++ + L + K+ + GY QQD+HEF +I+ +
Sbjct: 200 YGALNTKQASSSSTSTNRQTGFIYLLTCAW-----KINQNLAGYSQQDAHEFWQFIINQI 254
Query: 135 HE----DLKESGEKSWGEFRKKNKSIISELFYGQLKSTVICCNCQETS-STFEVFSNVSL 189
H+ DL + E S K+ + I+ +F G L+S+++C CQ S +T + F ++SL
Sbjct: 255 HQSYVLDLPNAKEVSRAN-NKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLDLSL 313
Query: 190 PL 191
+
Sbjct: 314 DI 315
>pdb|3M99|A Chain A, Structure Of The Ubp8-Sgf11-Sgf73-Sus1 Saga Dub Module
Length = 471
Score = 72.4 bits (176), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 52/182 (28%), Positives = 91/182 (50%), Gaps = 17/182 (9%)
Query: 21 GLTGLKNLGNTCYINSILQCLSNTSPLREYFVTEFK------RSMTAAYSKTSGKLAEEF 74
GL+GL N+G+TC+++SILQCL + + +++ RS +S K+ E
Sbjct: 135 GLSGLINMGSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHEL 194
Query: 75 QLIFNMLWAGDSRYFSPQKFKVKHELVGKFKEEVGKMKRTFRGYEQQDSHEFLTILIDTL 134
N A S + ++ + L + K+ + GY QQD+HEF +I+ +
Sbjct: 195 YGALNTKQASSSSTSTNRQTGFIYLLTCAW-----KINQNLAGYSQQDAHEFWQFIINQI 249
Query: 135 HE----DLKESGEKSWGEFRKKNKSIISELFYGQLKSTVICCNCQETS-STFEVFSNVSL 189
H+ DL + E S K+ + I+ +F G L+S+++C CQ S +T + F ++SL
Sbjct: 250 HQSYVLDLPNAKEVSRAN-NKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLDLSL 308
Query: 190 PL 191
+
Sbjct: 309 DI 310
>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
Length = 854
Score = 57.8 bits (138), Expect = 5e-09, Method: Composition-based stats.
Identities = 43/184 (23%), Positives = 85/184 (46%), Gaps = 23/184 (12%)
Query: 19 GPGLTGLKNLGNTCYINSILQCLSNTSPLREYFVTEFKRSMTAAYSKTSGKLAEEFQLIF 78
GPG TG++NLGN+CY+NS++Q L + + +V + ++ A + + + + +
Sbjct: 341 GPGYTGIRNLGNSCYLNSVVQVLFSIPDFQRKYVDKLEKIFQNAPTDPTQDFSTQVAKLG 400
Query: 79 NMLWAGD-SRYFS--------PQKFKVKHELVGK-FKEEVGKMKRTFRGYEQQDSHEFLT 128
+ L +G+ S+ P++ +V+ + + FK +GK F QQD+ EF
Sbjct: 401 HGLLSGEYSKPVPESGDGERVPEQKEVQDGIAPRMFKALIGKGHPEFSTNRQQDAQEFFL 460
Query: 129 ILIDTLHEDLKESGEKSWGEFRKKNKSIISELFYGQLKSTVICCNCQETSSTFEVFSNVS 188
LI+ + + + S +E+F ++ + C ++ T V +
Sbjct: 461 HLINMVERNCRSSENP-------------NEVFRFLVEEKIKCLATEKVKYTQRVDYIMQ 507
Query: 189 LPLP 192
LP+P
Sbjct: 508 LPVP 511
>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 = 40.8 bits (94), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 40/169 (23%), Positives = 75/169 (44%), Gaps = 20/169 (11%)
Query: 24 GLKNLGNTCYINSILQCLSNTSPLREYFVTEFKRSMTAAYSKTSGK-LAEEFQLIFNMLW 82
GL NLGNTCY+N+ +QC+ + L++ + + ++ A+ S + + + +F+ +
Sbjct: 16 GLTNLGNTCYMNATVQCIRSVPELKDA-LKRYAGALRASGEMASAQYITAALRDLFDSMD 74
Query: 83 AGDSRYFSPQKFKVKHELVGKFKE--EVGKMKRTFRGYEQQDSHEFLTILIDTLHEDLKE 140
S + H +F E E G+ Y QQD++E ++ L + L+
Sbjct: 75 KTSSSIPPIILLQFLHMAFPQFAEKGEQGQ-------YLQQDANECWIQMMRVLQQKLEA 127
Query: 141 SGEKSWGEFR---------KKNKSIISELFYGQLKSTVICCNCQETSST 180
+ S E K KS+I + F + ++T+ C +E T
Sbjct: 128 IEDDSVKETDSSSASAATPSKKKSLIDQFFGVEFETTMKCTESEEEEVT 176
>pdb|2F1Z|A Chain A, Crystal Structure Of Hausp
pdb|2F1Z|B Chain B, Crystal Structure Of Hausp
Length = 522
Score = 40.4 bits (93), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 44/171 (25%), Positives = 67/171 (39%), Gaps = 28/171 (16%)
Query: 21 GLTGLKNLGNTCYINSILQCLSNTSPLREYFVTEFKRSMTAAYSKTSGKLAEEFQLIFNM 80
G GLKN G TCY+NS+LQ L T+ LR+ M +S + Q +F
Sbjct: 174 GYVGLKNQGATCYMNSLLQTLFFTNQLRKAVYM-----MPTEGDDSSKSVPLALQRVFYE 228
Query: 81 LWAGDSRYFSPQKFKVKHELVGKFKEEVGKMKRTFRGYEQQDSHEFLTILIDTLHEDLKE 140
L D P K +L F E T + Q D E +L+D + +K
Sbjct: 229 LQHSD----KPVGTK---KLTKSFGWE------TLDSFMQHDVQELCRVLLDNVENKMKG 275
Query: 141 SGEKSWGEFRKKNKSIISELFYGQLKSTVICCNCQETSSTFEVFSNVSLPL 191
+ + I +LF G++ S + C S E + ++ L +
Sbjct: 276 TCV----------EGTIPKLFRGKMVSYIQCKEVDYRSDRREDYYDIQLSI 316
>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 = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 44/171 (25%), Positives = 67/171 (39%), Gaps = 28/171 (16%)
Query: 21 GLTGLKNLGNTCYINSILQCLSNTSPLREYFVTEFKRSMTAAYSKTSGKLAEEFQLIFNM 80
G GLKN G TCY+NS+LQ L T+ LR+ M +S + Q +F
Sbjct: 5 GYVGLKNQGATCYMNSLLQTLFFTNQLRKAVYM-----MPTEGDDSSKSVPLALQRVFYE 59
Query: 81 LWAGDSRYFSPQKFKVKHELVGKFKEEVGKMKRTFRGYEQQDSHEFLTILIDTLHEDLKE 140
L D P K +L F E T + Q D E +L+D + +K
Sbjct: 60 LQHSD----KPVGTK---KLTKSFGWE------TLDSFMQHDVQELCRVLLDNVENKMKG 106
Query: 141 SGEKSWGEFRKKNKSIISELFYGQLKSTVICCNCQETSSTFEVFSNVSLPL 191
+ + I +LF G++ S + C S E + ++ L +
Sbjct: 107 TCV----------EGTIPKLFRGKMVSYIQCKEVDYRSDRREDYYDIQLSI 147
>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 = 36.2 bits (82), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 48/171 (28%), Positives = 65/171 (38%), Gaps = 28/171 (16%)
Query: 21 GLTGLKNLGNTCYINSILQCLSNTSPLREYFVTEFKRSMTAAYSKTSGKLAEEFQLIFNM 80
G GLKN G TCY NS+LQ L T+ LR+ + S S LA Q +F
Sbjct: 5 GYVGLKNQGATCYXNSLLQTLFFTNQLRKAV---YXXPTEGDDSSKSVPLA--LQRVFYE 59
Query: 81 LWAGDSRYFSPQKFKVKHELVGKFKEEVGKMKRTFRGYEQQDSHEFLTILIDTLHEDLKE 140
L D P K +L F E T + Q D E +L+D + K
Sbjct: 60 LQHSD----KPVGTK---KLTKSFGWE------TLDSFXQHDVQELCRVLLDNVEN--KX 104
Query: 141 SGEKSWGEFRKKNKSIISELFYGQLKSTVICCNCQETSSTFEVFSNVSLPL 191
G G I +LF G+ S + C S E + ++ L +
Sbjct: 105 KGTCVEG--------TIPKLFRGKXVSYIQCKEVDYRSDRREDYYDIQLSI 147
>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 = 35.8 bits (81), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 14/30 (46%), Positives = 19/30 (63%)
Query: 24 GLKNLGNTCYINSILQCLSNTSPLREYFVT 53
G KN GNTCY+N+ LQ L + LR+ +
Sbjct: 26 GFKNXGNTCYLNATLQALYRVNDLRDXILN 55
>pdb|1H0H|A Chain A, Tungsten Containing Formate Dehydrogenase From
Desulfovibrio Gigas
pdb|1H0H|K Chain K, Tungsten Containing Formate Dehydrogenase From
Desulfovibrio Gigas
Length = 977
Score = 31.6 bits (70), Expect = 0.30, Method: Composition-based stats.
Identities = 22/79 (27%), Positives = 33/79 (41%), Gaps = 8/79 (10%)
Query: 51 FVTEFKRSMTAAYSKTSGKLAEEFQLIFNMLWAGDSRYFSPQK-------FKVKHELVGK 103
+ E + + +KT GKLA + W D +F P K F +K VG
Sbjct: 608 LIVELAKRVQKLLAKTPGKLAAPVTKLKTDYWVNDHGHFDPHKIAKLINGFALKDFKVGD 667
Query: 104 FKEEVGKMKRTFRGYEQQD 122
+ + G+ TF G+ Q D
Sbjct: 668 VEYKAGQQIATF-GHLQAD 685
>pdb|1CC1|L Chain L, Crystal Structure Of A Reduced, Active Form Of The
Ni-Fe-Se Hydrogenase From Desulfomicrobium Baculatum
Length = 498
Score = 29.3 bits (64), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 30/69 (43%), Gaps = 6/69 (8%)
Query: 53 TEFKRSMTAAYSKTSGKLAEEFQLIFNMLWAGDSRYFSPQKFKVKHELVG------KFKE 106
TE R Y K K E +Q++ LW + R Q+ ++ L+G K
Sbjct: 421 TEAPRGALLHYLKIKDKKIENYQIVSATLWNANPRDDMGQRGPIEEALIGVPVPDIKNPV 480
Query: 107 EVGKMKRTF 115
VG++ R++
Sbjct: 481 NVGRLVRSY 489
>pdb|3UQH|A Chain A, Crystal Strcuture Of Aba Receptor Pyl10 (Apo)
pdb|3UQH|B Chain B, Crystal Strcuture Of Aba Receptor Pyl10 (Apo)
pdb|3R6P|A Chain A, Crystal Structure Of Abscisic Acid-Bound Pyl10
Length = 191
Score = 28.5 bits (62), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 35/76 (46%), Gaps = 4/76 (5%)
Query: 64 SKTSGKLAEEFQLIFNMLWAGDSRYFSPQKFK--VKHELVGKFKEEVGKMKRTF--RGYE 119
S+ S L + + +++W+ R+ PQK+K + +V K EVG ++ G
Sbjct: 25 SQCSSTLVKHIKAPLHLVWSIVRRFDEPQKYKPFISRCVVQGKKLEVGSVREVDLKSGLP 84
Query: 120 QQDSHEFLTILIDTLH 135
S E L IL D H
Sbjct: 85 ATKSTEVLEILDDNEH 100
>pdb|3RT2|A Chain A, Crystal Structure Of Apo-Pyl10
Length = 183
Score = 28.5 bits (62), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 35/76 (46%), Gaps = 4/76 (5%)
Query: 64 SKTSGKLAEEFQLIFNMLWAGDSRYFSPQKFK--VKHELVGKFKEEVGKMKRTF--RGYE 119
S+ S L + + +++W+ R+ PQK+K + +V K EVG ++ G
Sbjct: 25 SQCSSTLVKHIKAPLHLVWSIVRRFDEPQKYKPFISRCVVQGKKLEVGSVREVDLKSGLP 84
Query: 120 QQDSHEFLTILIDTLH 135
S E L IL D H
Sbjct: 85 ATKSTEVLEILDDNEH 100
>pdb|3RT0|C Chain C, Crystal Structure Of Pyl10-Hab1 Complex In The Absence Of
Abscisic Acid (Aba)
pdb|3RT0|D Chain D, Crystal Structure Of Pyl10-Hab1 Complex In The Absence Of
Abscisic Acid (Aba)
Length = 183
Score = 28.1 bits (61), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 35/76 (46%), Gaps = 4/76 (5%)
Query: 64 SKTSGKLAEEFQLIFNMLWAGDSRYFSPQKFK--VKHELVGKFKEEVGKMKRTF--RGYE 119
S+ S L + + +++W+ R+ PQK+K + +V K EVG ++ G
Sbjct: 25 SQCSSTLVKHIKAPLHLVWSIVRRFDEPQKYKPFISRCVVQGKKLEVGSVREVDLKSGLP 84
Query: 120 QQDSHEFLTILIDTLH 135
S E L IL D H
Sbjct: 85 ATKSTEVLEILDDNEH 100
>pdb|3L1G|A Chain A, Human Alphab Crystallin
Length = 96
Score = 27.3 bits (59), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 8/44 (18%)
Query: 85 DSRYFSPQKFKVKHELVGKFKEEVGKMKRTFRGYEQQDSHEFLT 128
D ++FSP++ KVK ++G E GK + E+QD H F++
Sbjct: 14 DVKHFSPEELKVK--VLGDVIEVHGKHE------ERQDEHGFIS 49
>pdb|2Y1Z|A Chain A, Human Alphab Crystallin Acd R120g
pdb|2Y1Z|B Chain B, Human Alphab Crystallin Acd R120g
Length = 94
Score = 26.9 bits (58), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 8/44 (18%)
Query: 85 DSRYFSPQKFKVKHELVGKFKEEVGKMKRTFRGYEQQDSHEFLT 128
D ++FSP++ KVK ++G E GK + E+QD H F++
Sbjct: 17 DVKHFSPEELKVK--VLGDVIEVHGKHE------ERQDEHGFIS 52
>pdb|2WJ7|A Chain A, Human Alphab Crystallin
pdb|2WJ7|B Chain B, Human Alphab Crystallin
pdb|2WJ7|C Chain C, Human Alphab Crystallin
pdb|2WJ7|D Chain D, Human Alphab Crystallin
pdb|2WJ7|E Chain E, Human Alphab Crystallin
Length = 94
Score = 26.9 bits (58), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 8/44 (18%)
Query: 85 DSRYFSPQKFKVKHELVGKFKEEVGKMKRTFRGYEQQDSHEFLT 128
D ++FSP++ KVK ++G E GK + E+QD H F++
Sbjct: 17 DVKHFSPEELKVK--VLGDVIEVHGKHE------ERQDEHGFIS 52
>pdb|2Y22|A Chain A, Human Alphab-Crystallin Domain (Residues 67-157)
pdb|2Y22|B Chain B, Human Alphab-Crystallin Domain (Residues 67-157)
pdb|2Y22|C Chain C, Human Alphab-Crystallin Domain (Residues 67-157)
pdb|2Y22|D Chain D, Human Alphab-Crystallin Domain (Residues 67-157)
pdb|2Y22|E Chain E, Human Alphab-Crystallin Domain (Residues 67-157)
pdb|2Y22|F Chain F, Human Alphab-Crystallin Domain (Residues 67-157)
Length = 94
Score = 26.9 bits (58), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 8/44 (18%)
Query: 85 DSRYFSPQKFKVKHELVGKFKEEVGKMKRTFRGYEQQDSHEFLT 128
D ++FSP++ KVK ++G E GK + E+QD H F++
Sbjct: 17 DVKHFSPEELKVK--VLGDVIEVHGKHE------ERQDEHGFIS 52
>pdb|2Y1Y|A Chain A, Human Alphab Crystallin Acd(Residues 71-157)
Length = 90
Score = 26.9 bits (58), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 8/44 (18%)
Query: 85 DSRYFSPQKFKVKHELVGKFKEEVGKMKRTFRGYEQQDSHEFLT 128
D ++FSP++ KVK ++G E GK + E+QD H F++
Sbjct: 13 DVKHFSPEELKVK--VLGDVIEVHGKHE------ERQDEHGFIS 48
>pdb|2KLR|A Chain A, Solid-State Nmr Structure Of The Alpha-Crystallin Domain
In Alphab- Crystallin Oligomers
pdb|2KLR|B Chain B, Solid-State Nmr Structure Of The Alpha-Crystallin Domain
In Alphab- Crystallin Oligomers
pdb|2YGD|A Chain A, Molecular Architectures Of The 24meric Eye Lens Chaperone
Alphab-Crystallin Elucidated By A Triple Hybrid Approach
pdb|2YGD|B Chain B, Molecular Architectures Of The 24meric Eye Lens Chaperone
Alphab-Crystallin Elucidated By A Triple Hybrid Approach
pdb|2YGD|C Chain C, Molecular Architectures Of The 24meric Eye Lens Chaperone
Alphab-Crystallin Elucidated By A Triple Hybrid Approach
pdb|2YGD|D Chain D, Molecular Architectures Of The 24meric Eye Lens Chaperone
Alphab-Crystallin Elucidated By A Triple Hybrid Approach
pdb|2YGD|E Chain E, Molecular Architectures Of The 24meric Eye Lens Chaperone
Alphab-Crystallin Elucidated By A Triple Hybrid Approach
pdb|2YGD|F Chain F, Molecular Architectures Of The 24meric Eye Lens Chaperone
Alphab-Crystallin Elucidated By A Triple Hybrid Approach
pdb|2YGD|G Chain G, Molecular Architectures Of The 24meric Eye Lens Chaperone
Alphab-Crystallin Elucidated By A Triple Hybrid Approach
pdb|2YGD|H Chain H, Molecular Architectures Of The 24meric Eye Lens Chaperone
Alphab-Crystallin Elucidated By A Triple Hybrid Approach
pdb|2YGD|I Chain I, Molecular Architectures Of The 24meric Eye Lens Chaperone
Alphab-Crystallin Elucidated By A Triple Hybrid Approach
pdb|2YGD|J Chain J, Molecular Architectures Of The 24meric Eye Lens Chaperone
Alphab-Crystallin Elucidated By A Triple Hybrid Approach
pdb|2YGD|K Chain K, Molecular Architectures Of The 24meric Eye Lens Chaperone
Alphab-Crystallin Elucidated By A Triple Hybrid Approach
pdb|2YGD|L Chain L, Molecular Architectures Of The 24meric Eye Lens Chaperone
Alphab-Crystallin Elucidated By A Triple Hybrid Approach
pdb|2YGD|M Chain M, Molecular Architectures Of The 24meric Eye Lens Chaperone
Alphab-Crystallin Elucidated By A Triple Hybrid Approach
pdb|2YGD|N Chain N, Molecular Architectures Of The 24meric Eye Lens Chaperone
Alphab-Crystallin Elucidated By A Triple Hybrid Approach
pdb|2YGD|O Chain O, Molecular Architectures Of The 24meric Eye Lens Chaperone
Alphab-Crystallin Elucidated By A Triple Hybrid Approach
pdb|2YGD|P Chain P, Molecular Architectures Of The 24meric Eye Lens Chaperone
Alphab-Crystallin Elucidated By A Triple Hybrid Approach
pdb|2YGD|Q Chain Q, Molecular Architectures Of The 24meric Eye Lens Chaperone
Alphab-Crystallin Elucidated By A Triple Hybrid Approach
pdb|2YGD|R Chain R, Molecular Architectures Of The 24meric Eye Lens Chaperone
Alphab-Crystallin Elucidated By A Triple Hybrid Approach
pdb|2YGD|S Chain S, Molecular Architectures Of The 24meric Eye Lens Chaperone
Alphab-Crystallin Elucidated By A Triple Hybrid Approach
pdb|2YGD|T Chain T, Molecular Architectures Of The 24meric Eye Lens Chaperone
Alphab-Crystallin Elucidated By A Triple Hybrid Approach
pdb|2YGD|U Chain U, Molecular Architectures Of The 24meric Eye Lens Chaperone
Alphab-Crystallin Elucidated By A Triple Hybrid Approach
pdb|2YGD|V Chain V, Molecular Architectures Of The 24meric Eye Lens Chaperone
Alphab-Crystallin Elucidated By A Triple Hybrid Approach
pdb|2YGD|W Chain W, Molecular Architectures Of The 24meric Eye Lens Chaperone
Alphab-Crystallin Elucidated By A Triple Hybrid Approach
pdb|2YGD|X Chain X, Molecular Architectures Of The 24meric Eye Lens Chaperone
Alphab-Crystallin Elucidated By A Triple Hybrid Approach
Length = 175
Score = 26.9 bits (58), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 8/44 (18%)
Query: 85 DSRYFSPQKFKVKHELVGKFKEEVGKMKRTFRGYEQQDSHEFLT 128
D ++FSP++ KVK ++G E GK + E+QD H F++
Sbjct: 80 DVKHFSPEELKVK--VLGDVIEVHGKHE------ERQDEHGFIS 115
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
0.321 0.136 0.408
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,818,981
Number of Sequences: 62578
Number of extensions: 227369
Number of successful extensions: 601
Number of sequences better than 100.0: 33
Number of HSP's better than 100.0 without gapping: 21
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 550
Number of HSP's gapped (non-prelim): 36
length of query: 203
length of database: 14,973,337
effective HSP length: 94
effective length of query: 109
effective length of database: 9,091,005
effective search space: 990919545
effective search space used: 990919545
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 49 (23.5 bits)