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= 007094
(618 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 129 bits (325), Expect = 4e-30, Method: Compositional matrix adjust.
Identities = 99/342 (28%), Positives = 157/342 (45%), Gaps = 47/342 (13%)
Query: 35 SCYLNSVLQCLTYTPPLANFCLKLQHSSLCKQLTGDSALDAERKRECPFCILEKRIVRSL 94
+C+++S+LQCL + P + HS+ CK + D +C C L+K IV L
Sbjct: 150 TCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPD---------KCFSCALDK-IVHEL 199
Query: 95 SVDLTLDAPAK-------------IQSCLRIFAEHFKCGRQEDAHEFLRYVIDACHNT-C 140
L + + +C ++ Q+DAHEF +++I+ H +
Sbjct: 200 YGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQSYV 259
Query: 141 LRLKKLRRKXXXXXXXXXXXXXXXXXXXVVKEIFGGALQSQVKCLACGAES-NKVDEIMD 199
L L + +V +F G+L+S + C C S +D +D
Sbjct: 260 LDLPNAKE---------VSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLD 310
Query: 200 ISLDILNSCSLKEAMQKFFQPEVLDGNNKYKCDNCKKLVSARKQMSILQSPNILVIQLKR 259
+SLDI + L E + F + E L N Y C C A KQ+ I + P++LV+QLKR
Sbjct: 311 LSLDIKDKKKLYECLDSFHKKEQLKDFN-YHCGECNSTQDAIKQLGIHKLPSVLVLQLKR 369
Query: 260 FEGIFGG---KIDKAIAFEEVLVLSSFMCKASQDPQPE--------YKLFGTIVHSGFSP 308
FE + G K+D I F L + ++ +D E Y+L G + H G +
Sbjct: 370 FEHLLNGSNRKLDDFIEFPTYLNMKNYCSTKEKDKHSENGKVPDIIYELIGIVSHKG-TV 428
Query: 309 DSGHYYAYIKDAIGRWYCCNDSYVSVSTLQEVLSEKVYILFF 350
+ GHY A+ K + G+W+ NDS VS + +EVL E+ Y+LF+
Sbjct: 429 NEGHYIAFCKISGGQWFKFNDSMVSSISQEEVLKEQAYLLFY 470
>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 = 129 bits (325), Expect = 4e-30, Method: Compositional matrix adjust.
Identities = 99/342 (28%), Positives = 157/342 (45%), Gaps = 47/342 (13%)
Query: 35 SCYLNSVLQCLTYTPPLANFCLKLQHSSLCKQLTGDSALDAERKRECPFCILEKRIVRSL 94
+C+++S+LQCL + P + HS+ CK + D +C C L+K IV L
Sbjct: 150 TCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPD---------KCFSCALDK-IVHEL 199
Query: 95 SVDLTLDAPAK-------------IQSCLRIFAEHFKCGRQEDAHEFLRYVIDACHNT-C 140
L + + +C ++ Q+DAHEF +++I+ H +
Sbjct: 200 YGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQSYV 259
Query: 141 LRLKKLRRKXXXXXXXXXXXXXXXXXXXVVKEIFGGALQSQVKCLACGAES-NKVDEIMD 199
L L + +V +F G+L+S + C C S +D +D
Sbjct: 260 LDLPNAKE---------VSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLD 310
Query: 200 ISLDILNSCSLKEAMQKFFQPEVLDGNNKYKCDNCKKLVSARKQMSILQSPNILVIQLKR 259
+SLDI + L E + F + E L N Y C C A KQ+ I + P++LV+QLKR
Sbjct: 311 LSLDIKDKKKLYECLDSFHKKEQLKDFN-YHCGECNSTQDAIKQLGIHKLPSVLVLQLKR 369
Query: 260 FEGIFGG---KIDKAIAFEEVLVLSSFMCKASQDPQPE--------YKLFGTIVHSGFSP 308
FE + G K+D I F L + ++ +D E Y+L G + H G +
Sbjct: 370 FEHLLNGSNRKLDDFIEFPTYLNMKNYCSTKEKDKHSENGKVPDIIYELIGIVSHKG-TV 428
Query: 309 DSGHYYAYIKDAIGRWYCCNDSYVSVSTLQEVLSEKVYILFF 350
+ GHY A+ K + G+W+ NDS VS + +EVL E+ Y+LF+
Sbjct: 429 NEGHYIAFCKISGGQWFKFNDSMVSSISQEEVLKEQAYLLFY 470
>pdb|3M99|A Chain A, Structure Of The Ubp8-Sgf11-Sgf73-Sus1 Saga Dub Module
Length = 471
Score = 129 bits (324), Expect = 4e-30, Method: Compositional matrix adjust.
Identities = 99/342 (28%), Positives = 157/342 (45%), Gaps = 47/342 (13%)
Query: 35 SCYLNSVLQCLTYTPPLANFCLKLQHSSLCKQLTGDSALDAERKRECPFCILEKRIVRSL 94
+C+++S+LQCL + P + HS+ CK + D +C C L+K IV L
Sbjct: 145 TCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPD---------KCFSCALDK-IVHEL 194
Query: 95 SVDLTLDAPAK-------------IQSCLRIFAEHFKCGRQEDAHEFLRYVIDACHNT-C 140
L + + +C ++ Q+DAHEF +++I+ H +
Sbjct: 195 YGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQSYV 254
Query: 141 LRLKKLRRKXXXXXXXXXXXXXXXXXXXVVKEIFGGALQSQVKCLACGAES-NKVDEIMD 199
L L + +V +F G+L+S + C C S +D +D
Sbjct: 255 LDLPNAKE---------VSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLD 305
Query: 200 ISLDILNSCSLKEAMQKFFQPEVLDGNNKYKCDNCKKLVSARKQMSILQSPNILVIQLKR 259
+SLDI + L E + F + E L N Y C C A KQ+ I + P++LV+QLKR
Sbjct: 306 LSLDIKDKKKLYECLDSFHKKEQLKDFN-YHCGECNSTQDAIKQLGIHKLPSVLVLQLKR 364
Query: 260 FEGIFGG---KIDKAIAFEEVLVLSSFMCKASQDPQPE--------YKLFGTIVHSGFSP 308
FE + G K+D I F L + ++ +D E Y+L G + H G +
Sbjct: 365 FEHLLNGSNRKLDDFIEFPTYLNMKNYCSTKEKDKHSENGKVPDIIYELIGIVSHKG-TV 423
Query: 309 DSGHYYAYIKDAIGRWYCCNDSYVSVSTLQEVLSEKVYILFF 350
+ GHY A+ K + G+W+ NDS VS + +EVL E+ Y+LF+
Sbjct: 424 NEGHYIAFCKISGGQWFKFNDSMVSSISQEEVLKEQAYLLFY 465
>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 = 111 bits (278), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 96/333 (28%), Positives = 151/333 (45%), Gaps = 28/333 (8%)
Query: 35 SCYLNSVLQCLTYTPPLANFCL-KLQHSSLCKQLTGDSALDAERKRECPFCILEKRIVRS 93
+C++NS+LQCL+ T L ++CL +L L +AL E F L + I S
Sbjct: 37 TCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEE------FAKLIQTIWTS 90
Query: 94 LSVDLTLDAPAKIQSCLRIFAEHFKCGRQEDAHEFLRYVIDACHNTCLRL--------KK 145
D+ +P++ ++ ++ +A F Q+DA EFLR+++D HN R+ +
Sbjct: 91 SPNDVV--SPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPEN 148
Query: 146 LRRKXXXXXXXXXXXXXXXXXXXVVKEIFGGALQSQVKCLACGAESNKVDEIMDISLDIL 205
L + ++F G L+S + C CG S D D+SL I
Sbjct: 149 LDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPIA 208
Query: 206 N----SCSLKEAMQKFFQPEVLDGNNKYKCDNCKKLVSARKQMSILQSPNILVIQLKRFE 261
+L + M+ F + +VLDG+ K C C+ K+ SI + P ILV+ LKRF
Sbjct: 209 KRGYPEVTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKILVLHLKRFS 268
Query: 262 G--IFGGKIDKAIAFE-EVLVLSSFMCKASQDPQPEYKLFGTIVHSGFSPDSGHYYAYIK 318
I K+ + F L L F + + Y L+ HSG + GHY AY +
Sbjct: 269 ESRIRTSKLTTFVNFPLRDLDLREFASENTN--HAVYNLYAVSNHSG-TTMGGHYTAYCR 325
Query: 319 D-AIGRWYCCNDSYVSVSTLQEVLSEKVYILFF 350
G W+ NDS V+ + +V + Y+LF+
Sbjct: 326 SPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFY 358
>pdb|2HD5|A Chain A, Usp2 In Complex With Ubiquitin
Length = 359
Score = 110 bits (276), Expect = 2e-24, Method: Compositional matrix adjust.
Identities = 96/333 (28%), Positives = 151/333 (45%), Gaps = 28/333 (8%)
Query: 35 SCYLNSVLQCLTYTPPLANFCL-KLQHSSLCKQLTGDSALDAERKRECPFCILEKRIVRS 93
+C++NS+LQCL+ T L ++CL +L L +AL E F L + I S
Sbjct: 18 TCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEE------FAKLIQTIWTS 71
Query: 94 LSVDLTLDAPAKIQSCLRIFAEHFKCGRQEDAHEFLRYVIDACHNTCLRL--------KK 145
D+ +P++ ++ ++ +A F Q+DA EFLR+++D HN R+ +
Sbjct: 72 SPNDVV--SPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPEN 129
Query: 146 LRRKXXXXXXXXXXXXXXXXXXXVVKEIFGGALQSQVKCLACGAESNKVDEIMDISLDIL 205
L + ++F G L+S + C CG S D D+SL I
Sbjct: 130 LDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPIA 189
Query: 206 N----SCSLKEAMQKFFQPEVLDGNNKYKCDNCKKLVSARKQMSILQSPNILVIQLKRFE 261
+L + M+ F + +VLDG+ K C C+ K+ SI + P ILV+ LKRF
Sbjct: 190 KRGYPEVTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKILVLHLKRFS 249
Query: 262 G--IFGGKIDKAIAFE-EVLVLSSFMCKASQDPQPEYKLFGTIVHSGFSPDSGHYYAYIK 318
I K+ + F L L F + + Y L+ HSG + GHY AY +
Sbjct: 250 ESRIRTSKLTTFVNFPLRDLDLREFASENTN--HAVYNLYAVSNHSG-TTMGGHYTAYCR 306
Query: 319 D-AIGRWYCCNDSYVSVSTLQEVLSEKVYILFF 350
G W+ NDS V+ + +V + Y+LF+
Sbjct: 307 SPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFY 339
>pdb|2IBI|A Chain A, Covalent Ubiquitin-Usp2 Complex
Length = 374
Score = 110 bits (274), Expect = 3e-24, Method: Compositional matrix adjust.
Identities = 95/333 (28%), Positives = 150/333 (45%), Gaps = 28/333 (8%)
Query: 35 SCYLNSVLQCLTYTPPLANFCL-KLQHSSLCKQLTGDSALDAERKRECPFCILEKRIVRS 93
+C++NS+LQCL+ T L ++CL +L L +AL E F L + I S
Sbjct: 44 TCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEE------FAKLIQTIWTS 97
Query: 94 LSVDLTLDAPAKIQSCLRIFAEHFKCGRQEDAHEFLRYVIDACHNTCLRL--------KK 145
D+ +P++ ++ ++ +A F Q+DA EFLR+++D HN R+ +
Sbjct: 98 SPNDVV--SPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPEN 155
Query: 146 LRRKXXXXXXXXXXXXXXXXXXXVVKEIFGGALQSQVKCLACGAESNKVDEIMDISLDIL 205
L + ++F G L+S + C CG S D D+SL I
Sbjct: 156 LDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPIA 215
Query: 206 N----SCSLKEAMQKFFQPEVLDGNNKYKCDNCKKLVSARKQMSILQSPNILVIQLKRFE 261
+L + M+ F + +VLDG+ C C+ K+ SI + P ILV+ LKRF
Sbjct: 216 KRGYPEVTLMDCMRLFTKEDVLDGDAAPTCCRCRGRKRCIKKFSIQRFPKILVLHLKRFS 275
Query: 262 G--IFGGKIDKAIAFE-EVLVLSSFMCKASQDPQPEYKLFGTIVHSGFSPDSGHYYAYIK 318
I K+ + F L L F + + Y L+ HSG + GHY AY +
Sbjct: 276 ESRIRTSKLTTFVNFPLRDLDLREFASENTN--HAVYNLYAVSNHSG-TTMGGHYTAYCR 332
Query: 319 D-AIGRWYCCNDSYVSVSTLQEVLSEKVYILFF 350
G W+ NDS V+ + +V + Y+LF+
Sbjct: 333 SPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFY 365
>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 = 108 bits (270), Expect = 8e-24, Method: Compositional matrix adjust.
Identities = 87/349 (24%), Positives = 154/349 (44%), Gaps = 39/349 (11%)
Query: 35 SCYLNSVLQCLTYTPPLANFCLKLQHSSLCKQLTGDSALDAERKRECPFCILEKRIVRSL 94
+ ++NS LQCL+ T PL ++ LK ++ + ++ D+ L + + + L K++
Sbjct: 17 TXFMNSALQCLSNTAPLTDYFLKDEYEA---EINRDNPLGMKGEIAEAYAELIKQMWSGR 73
Query: 95 SVDLTLDAPAKIQSCLRIFAEHFKCGRQEDAHEFLRYVIDACHNTC--------LRLKKL 146
+ AP ++ + FA F +Q+D+ E L +++D H L LK
Sbjct: 74 DAHV---APRMFKTQVGRFAPQFSGYQQQDSQELLAFLLDGLHEDLNRVKKKPYLELKDA 130
Query: 147 RRKXXXXXXXXXXXXXXXXXXXVVKEIFGGALQSQVKCLACGAESNKVDEIMDISLDI-- 204
+ V+ + F G +S + C C S D ++L +
Sbjct: 131 NGRPDAVVAKEAWENHRLRNDSVIVDTFHGLFKSTLVCPECAKVSVTFDPFCYLTLPLPL 190
Query: 205 -----------------LNSCSLKEAMQKFFQPEVLDGNNKYKCDNCKKLVSARKQMSIL 247
+ +L++ ++ F E L ++ + C NCKK A K+ +
Sbjct: 191 KKDRVMEGPMLQPQKKKKTTVALRDCIELFTTMETLGEHDPWYCPNCKKHQQATKKFDLW 250
Query: 248 QSPNILVIQLKRF--EGIFGGKIDKAIAFE-EVLVLSSFMCKASQDPQPEYKLFGTIVHS 304
P ILV+ LKRF + K+D + F L +S F+C S P Y L H
Sbjct: 251 SLPKILVVHLKRFSYNRYWRDKLDTVVEFPIRGLNMSEFVCNLSARPY-VYDLIAVSNHY 309
Query: 305 GFSPDSGHYYAYIKDAI-GRWYCCNDSYVSVSTLQEVLSEKVYILFFIR 352
G + GHY AY K+ + G+WY +DS VS+++ +++++ Y+LF+ R
Sbjct: 310 G-AMGVGHYTAYAKNKLNGKWYYFDDSNVSLASEDQIVTKAAYVLFYQR 357
>pdb|3NHE|A Chain A, High Resolution Structure (1.26a) Of Usp2a In Complex With
Ubiquitin
Length = 348
Score = 107 bits (267), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 95/333 (28%), Positives = 150/333 (45%), Gaps = 28/333 (8%)
Query: 35 SCYLNSVLQCLTYTPPLANFCL-KLQHSSLCKQLTGDSALDAERKRECPFCILEKRIVRS 93
+ ++NS+LQCL+ T L ++CL +L L +AL E F L + I S
Sbjct: 18 TXFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEE------FAKLIQTIWTS 71
Query: 94 LSVDLTLDAPAKIQSCLRIFAEHFKCGRQEDAHEFLRYVIDACHNTCLRL--------KK 145
D+ +P++ ++ ++ +A F Q+DA EFLR+++D HN R+ +
Sbjct: 72 SPNDVV--SPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPEN 129
Query: 146 LRRKXXXXXXXXXXXXXXXXXXXVVKEIFGGALQSQVKCLACGAESNKVDEIMDISLDIL 205
L + ++F G L+S + C CG S D D+SL I
Sbjct: 130 LDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPIA 189
Query: 206 N----SCSLKEAMQKFFQPEVLDGNNKYKCDNCKKLVSARKQMSILQSPNILVIQLKRFE 261
+L + M+ F + +VLDG+ K C C+ K+ SI + P ILV+ LKRF
Sbjct: 190 KRGYPEVTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKILVLHLKRFS 249
Query: 262 G--IFGGKIDKAIAFE-EVLVLSSFMCKASQDPQPEYKLFGTIVHSGFSPDSGHYYAYIK 318
I K+ + F L L F + + Y L+ HSG + GHY AY +
Sbjct: 250 ESRIRTSKLTTFVNFPLRDLDLREFASENTN--HAVYNLYAVSNHSG-TTMGGHYTAYCR 306
Query: 319 D-AIGRWYCCNDSYVSVSTLQEVLSEKVYILFF 350
G W+ NDS V+ + +V + Y+LF+
Sbjct: 307 SPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFY 339
>pdb|3N3K|A Chain A, The Catalytic Domain Of Usp8 In Complex With A Usp8
Specific Inhibitor
Length = 396
Score = 100 bits (250), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 87/332 (26%), Positives = 151/332 (45%), Gaps = 26/332 (7%)
Query: 35 SCYLNSVLQCLTYTPPLANFCLK--LQHSSLCKQLTGDSALDAERKRECPFCILEKRIVR 92
+CY+NS+LQCL P LA++ + Q L G AE F I+ K +
Sbjct: 71 TCYMNSILQCLCNAPHLADYFNRNCYQDDINRSNLLGHKGEVAEE-----FGIIMKAL-- 123
Query: 93 SLSVDLTLDAPAKIQSCLRIFAEHFKCGRQEDAHEFLRYVIDACHNTCLRLKKLRRKXXX 152
+ +P + + + F Q+D+ E L +++D H + +R
Sbjct: 124 -WTGQYRYISPKDFKITIGKINDQFAGYSQQDSQELLLFLMDGLHEDLNKADNRKRYKEE 182
Query: 153 X--------XXXXXXXXXXXXXXXVVKEIFGGALQSQVKCLACGAESNKVDEIMDISLDI 204
++ +F G +S V+CL C +S + M +SL +
Sbjct: 183 NNDHLDDFKAAEHAWQKHKQLNESIIVALFQGQFKSTVQCLTCHKKSRTFEAFMYLSLPL 242
Query: 205 LNS--CSLKEAMQKFFQPEVLDGNNKYKCDNCKKLVSARKQMSILQSPNILVIQLKRF-- 260
++ C+L++ ++ F + E L NN++ C +C+ + K++ I + P +L++ LKRF
Sbjct: 243 ASTSKCTLQDCLRLFSKEEKLTDNNRFYCSHCRARRDSLKKIEIWKLPPVLLVHLKRFSY 302
Query: 261 EGIFGGKIDKAIAFE-EVLVLSSFMCKASQDPQPEYKLFGTIVHSGFSPDSGHYYAYIKD 319
+G + K+ ++ F E L LS ++ ++ +Y LF H G D GHY AY K+
Sbjct: 303 DGRWKQKLQTSVDFPLENLDLSQYVI-GPKNNLKKYNLFSVSNHYG-GLDGGHYTAYCKN 360
Query: 320 AI-GRWYCCNDSYVSVSTLQEVLSEKVYILFF 350
A RW+ +D VS ++ V S YILF+
Sbjct: 361 AARQRWFKFDDHEVSDISVSSVKSSAAYILFY 392
>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 = 99.4 bits (246), Expect = 5e-21, Method: Compositional matrix adjust.
Identities = 90/360 (25%), Positives = 156/360 (43%), Gaps = 54/360 (15%)
Query: 35 SCYLNSVLQCLTYTPPLANFCLKLQHSSLCKQLTGDSALDAERKRECPFCILEKRIVRSL 94
+C+LN+VLQCL+ T PL +FCL+ +++ G R +E + ++ +L
Sbjct: 31 TCFLNAVLQCLSSTRPLRDFCLR---RDFRQEVPGGG-----RAQELTEAFAD--VIGAL 80
Query: 95 SVDLTLDA--PAKIQSCLRIFAEHFKCGRQEDAHEFLRYVIDACHNTCLRLKKLRRKXXX 152
+ +A P + ++ + + F Q+DA EFL+ +++ H L + + R+
Sbjct: 81 WHPDSCEAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLH---LEINRRGRRAPP 137
Query: 153 XXXXXXXXXXXXXXXXVVKE--------------------------IFGGALQSQVKCLA 186
+++E +F G L+S +KC A
Sbjct: 138 ILANGPVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKCQA 197
Query: 187 CGAESNKVDEIMDISLDIL------NSCSLKEAMQKFFQPEVLDGNNKYKCDNCKKLVSA 240
CG S + D+SL I SL++ F + E L+ N CD C++ +
Sbjct: 198 CGYRSTTFEVFCDLSLPIPKKGFAGGKVSLRDCFNLFTKEEELESENAPVCDRCRQKTRS 257
Query: 241 RKQMSILQSPNILVIQLKRFEGIFGGKIDKAIAFE---EVLVLSSFMCKASQDPQPEYKL 297
K++++ + P ILV+ L RF G ++ + + L L F + + P Y+L
Sbjct: 258 TKKLTVQRFPRILVLHLNRFSASRGSIKKSSVGVDFPLQRLSLGDF--ASDKAGSPVYQL 315
Query: 298 FGTIVHSGFSPDSGHYYAYIKDAIGRWYCCNDSYVSVSTLQEVLSEKVYILFFIRANQRP 357
+ HSG S GHY A + G W+ NDS VS + +V S + Y+LF+ + P
Sbjct: 316 YALCNHSG-SVHYGHYTALCRCQTG-WHVYNDSRVSPVSENQVASSEGYVLFYQLMQEPP 373
>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 = 99.0 bits (245), Expect = 6e-21, Method: Compositional matrix adjust.
Identities = 90/360 (25%), Positives = 156/360 (43%), Gaps = 54/360 (15%)
Query: 35 SCYLNSVLQCLTYTPPLANFCLKLQHSSLCKQLTGDSALDAERKRECPFCILEKRIVRSL 94
+C+LN+VLQCL+ T PL +FCL+ +++ G R +E + ++ +L
Sbjct: 12 TCFLNAVLQCLSSTRPLRDFCLR---RDFRQEVPGGG-----RAQELTEAFAD--VIGAL 61
Query: 95 SVDLTLDA--PAKIQSCLRIFAEHFKCGRQEDAHEFLRYVIDACHNTCLRLKKLRRKXXX 152
+ +A P + ++ + + F Q+DA EFL+ +++ H L + + R+
Sbjct: 62 WHPDSCEAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLH---LEINRRGRRAPP 118
Query: 153 XXXXXXXXXXXXXXXXVVKE--------------------------IFGGALQSQVKCLA 186
+++E +F G L+S +KC A
Sbjct: 119 ILANGPVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKCQA 178
Query: 187 CGAESNKVDEIMDISLDIL------NSCSLKEAMQKFFQPEVLDGNNKYKCDNCKKLVSA 240
CG S + D+SL I SL++ F + E L+ N CD C++ +
Sbjct: 179 CGYRSTTFEVFCDLSLPIPKKGFAGGKVSLRDCFNLFTKEEELESENAPVCDRCRQKTRS 238
Query: 241 RKQMSILQSPNILVIQLKRFEGIFGGKIDKAIAFE---EVLVLSSFMCKASQDPQPEYKL 297
K++++ + P ILV+ L RF G ++ + + L L F + + P Y+L
Sbjct: 239 TKKLTVQRFPRILVLHLNRFSASRGSIKKSSVGVDFPLQRLSLGDFA--SDKAGSPVYQL 296
Query: 298 FGTIVHSGFSPDSGHYYAYIKDAIGRWYCCNDSYVSVSTLQEVLSEKVYILFFIRANQRP 357
+ HSG S GHY A + G W+ NDS VS + +V S + Y+LF+ + P
Sbjct: 297 YALCNHSG-SVHYGHYTALCRCQTG-WHVYNDSRVSPVSENQVASSEGYVLFYQLMQEPP 354
>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 = 98.6 bits (244), Expect = 9e-21, Method: Compositional matrix adjust.
Identities = 90/360 (25%), Positives = 156/360 (43%), Gaps = 54/360 (15%)
Query: 35 SCYLNSVLQCLTYTPPLANFCLKLQHSSLCKQLTGDSALDAERKRECPFCILEKRIVRSL 94
+C+LN+VLQCL+ T PL +FCL+ +++ G R +E + ++ +L
Sbjct: 25 TCFLNAVLQCLSSTRPLRDFCLR---RDFRQEVPGGG-----RAQELTEAFAD--VIGAL 74
Query: 95 SVDLTLDA--PAKIQSCLRIFAEHFKCGRQEDAHEFLRYVIDACHNTCLRLKKLRRKXXX 152
+ +A P + ++ + + F Q+DA EFL+ +++ H L + + R+
Sbjct: 75 WHPDSCEAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLH---LEINRRGRRAPP 131
Query: 153 XXXXXXXXXXXXXXXXVVKE--------------------------IFGGALQSQVKCLA 186
+++E +F G L+S +KC A
Sbjct: 132 ILANGPVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKCQA 191
Query: 187 CGAESNKVDEIMDISLDIL------NSCSLKEAMQKFFQPEVLDGNNKYKCDNCKKLVSA 240
CG S + D+SL I SL++ F + E L+ N CD C++ +
Sbjct: 192 CGYRSTTFEVFCDLSLPIPKKGFAGGKVSLRDCFNLFTKEEELESENAPVCDRCRQKTRS 251
Query: 241 RKQMSILQSPNILVIQLKRFEGIFGGKIDKAIAFE---EVLVLSSFMCKASQDPQPEYKL 297
K++++ + P ILV+ L RF G ++ + + L L F + + P Y+L
Sbjct: 252 TKKLTVQRFPRILVLHLNRFSASRGSIKKSSVGVDFPLQRLSLGDF--ASDKAGSPVYQL 309
Query: 298 FGTIVHSGFSPDSGHYYAYIKDAIGRWYCCNDSYVSVSTLQEVLSEKVYILFFIRANQRP 357
+ HSG S GHY A + G W+ NDS VS + +V S + Y+LF+ + P
Sbjct: 310 YALCNHSG-SVHYGHYTALCRCQTG-WHVYNDSRVSPVSENQVASSEGYVLFYQLMQEPP 367
>pdb|2GFO|A Chain A, Structure Of The Catalytic Domain Of Human Ubiquitin
Carboxyl-terminal Hydrolase 8
Length = 396
Score = 96.3 bits (238), Expect = 5e-20, Method: Compositional matrix adjust.
Identities = 86/332 (25%), Positives = 148/332 (44%), Gaps = 26/332 (7%)
Query: 35 SCYLNSVLQCLTYTPPLANFCLK--LQHSSLCKQLTGDSALDAERKRECPFCILEKRIVR 92
+CY NS+LQCL P LA++ + Q L G AE F I+ K +
Sbjct: 71 TCYXNSILQCLCNAPHLADYFNRNCYQDDINRSNLLGHKGEVAEE-----FGIIXKAL-- 123
Query: 93 SLSVDLTLDAPAKIQSCLRIFAEHFKCGRQEDAHEFLRYVIDACHNTCLRLKKLRRKXXX 152
+ +P + + + F Q+D+ E L ++ D H + +R
Sbjct: 124 -WTGQYRYISPKDFKITIGKINDQFAGYSQQDSQELLLFLXDGLHEDLNKADNRKRYKEE 182
Query: 153 X--------XXXXXXXXXXXXXXXVVKEIFGGALQSQVKCLACGAESNKVDEIMDISLDI 204
++ +F G +S V+CL C +S + +SL +
Sbjct: 183 NNDHLDDFKAAEHAWQKHKQLNESIIVALFQGQFKSTVQCLTCHKKSRTFEAFXYLSLPL 242
Query: 205 LNS--CSLKEAMQKFFQPEVLDGNNKYKCDNCKKLVSARKQMSILQSPNILVIQLKRF-- 260
++ C+L++ ++ F + E L NN++ C +C+ + K++ I + P +L++ LKRF
Sbjct: 243 ASTSKCTLQDCLRLFSKEEKLTDNNRFYCSHCRARRDSLKKIEIWKLPPVLLVHLKRFSY 302
Query: 261 EGIFGGKIDKAIAFE-EVLVLSSFMCKASQDPQPEYKLFGTIVHSGFSPDSGHYYAYIKD 319
+G + K+ ++ F E L LS ++ ++ +Y LF H G D GHY AY K+
Sbjct: 303 DGRWKQKLQTSVDFPLENLDLSQYVI-GPKNNLKKYNLFSVSNHYG-GLDGGHYTAYCKN 360
Query: 320 AI-GRWYCCNDSYVSVSTLQEVLSEKVYILFF 350
A RW+ +D VS ++ V S YILF+
Sbjct: 361 AARQRWFKFDDHEVSDISVSSVKSSAAYILFY 392
>pdb|2F1Z|A Chain A, Crystal Structure Of Hausp
pdb|2F1Z|B Chain B, Crystal Structure Of Hausp
Length = 522
Score = 73.9 bits (180), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 78/317 (24%), Positives = 122/317 (38%), Gaps = 54/317 (17%)
Query: 35 SCYLNSVLQCLTYTPPLANFCLKLQHSSLCKQLTGDSALDAERKRECPFCILEKRIVRSL 94
+CY+NS+LQ L +T +L+ + GD + + P + +R+ L
Sbjct: 184 TCYMNSLLQTLFFTN-------QLRKAVYMMPTEGDDS-----SKSVPLAL--QRVFYEL 229
Query: 95 SVDLTLDAPAKIQSCLRIFA-EHFKCGRQEDAHEFLRYVIDACHN----TCLRLKKLRRK 149
D P + + F E Q D E R ++D N TC+
Sbjct: 230 Q---HSDKPVGTKKLTKSFGWETLDSFMQHDVQELCRVLLDNVENKMKGTCVE------- 279
Query: 150 XXXXXXXXXXXXXXXXXXXVVKEIFGGALQSQVKCLACGAESNKVDEIMDISLDILNSCS 209
+ ++F G + S ++C S++ ++ DI L I +
Sbjct: 280 ------------------GTIPKLFRGKMVSYIQCKEVDYRSDRREDYYDIQLSIKGKKN 321
Query: 210 LKEAMQKFFQPEVLDGNNKYKCDNCKKLVSARKQMSILQSPNILVIQLKRF----EGIFG 265
+ E+ + E LDG+NKY L A K + L P +L +QL RF +
Sbjct: 322 IFESFVDYVAVEQLDGDNKYDAGE-HGLQEAEKGVKFLTLPPVLHLQLMRFMYDPQTDQN 380
Query: 266 GKIDKAIAFEEVLVLSSFMCKASQDPQPEYKLFGTIVHSGFSPDSGHYYAYIK-DAIGRW 324
KI+ F E L L F+ K Y L +VHSG GHY Y+ G+W
Sbjct: 381 IKINDRFEFPEQLPLDEFLQKTDPKDPANYILHAVLVHSG-DNHGGHYVVYLNPKGDGKW 439
Query: 325 YCCNDSYVSVSTLQEVL 341
+D VS T +E +
Sbjct: 440 CKFDDDVVSRCTKEEAI 456
>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 = 73.6 bits (179), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 78/318 (24%), Positives = 122/318 (38%), Gaps = 54/318 (16%)
Query: 35 SCYLNSVLQCLTYTPPLANFCLKLQHSSLCKQLTGDSALDAERKRECPFCILEKRIVRSL 94
+CY+NS+LQ L +T +L+ + GD + + P + +R+ L
Sbjct: 15 TCYMNSLLQTLFFTN-------QLRKAVYMMPTEGDDS-----SKSVPLAL--QRVFYEL 60
Query: 95 SVDLTLDAPAKIQSCLRIFA-EHFKCGRQEDAHEFLRYVIDACHN----TCLRLKKLRRK 149
D P + + F E Q D E R ++D N TC+
Sbjct: 61 Q---HSDKPVGTKKLTKSFGWETLDSFMQHDVQELCRVLLDNVENKMKGTCVE------- 110
Query: 150 XXXXXXXXXXXXXXXXXXXVVKEIFGGALQSQVKCLACGAESNKVDEIMDISLDILNSCS 209
+ ++F G + S ++C S++ ++ DI L I +
Sbjct: 111 ------------------GTIPKLFRGKMVSYIQCKEVDYRSDRREDYYDIQLSIKGKKN 152
Query: 210 LKEAMQKFFQPEVLDGNNKYKCDNCKKLVSARKQMSILQSPNILVIQLKRF----EGIFG 265
+ E+ + E LDG+NKY L A K + L P +L +QL RF +
Sbjct: 153 IFESFVDYVAVEQLDGDNKYDAGE-HGLQEAEKGVKFLTLPPVLHLQLMRFMYDPQTDQN 211
Query: 266 GKIDKAIAFEEVLVLSSFMCKASQDPQPEYKLFGTIVHSGFSPDSGHYYAYIK-DAIGRW 324
KI+ F E L L F+ K Y L +VHSG GHY Y+ G+W
Sbjct: 212 IKINDRFEFPEQLPLDEFLQKTDPKDPANYILHAVLVHSG-DNHGGHYVVYLNPKGDGKW 270
Query: 325 YCCNDSYVSVSTLQEVLS 342
+D VS T +E +
Sbjct: 271 CKFDDDVVSRCTKEEAIE 288
>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 = 71.2 bits (173), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 78/318 (24%), Positives = 120/318 (37%), Gaps = 54/318 (16%)
Query: 35 SCYLNSVLQCLTYTPPLANFCLKLQHSSLCKQLTGDSALDAERKRECPFCILEKRIVRSL 94
+CY NS+LQ L +T +L+ + GD + + P + +R+ L
Sbjct: 15 TCYXNSLLQTLFFTN-------QLRKAVYXXPTEGDDS-----SKSVPLAL--QRVFYEL 60
Query: 95 SVDLTLDAPAKIQSCLRIFA-EHFKCGRQEDAHEFLRYVIDACHN----TCLRLKKLRRK 149
D P + + F E Q D E R ++D N TC+
Sbjct: 61 Q---HSDKPVGTKKLTKSFGWETLDSFXQHDVQELCRVLLDNVENKXKGTCVE------- 110
Query: 150 XXXXXXXXXXXXXXXXXXXVVKEIFGGALQSQVKCLACGAESNKVDEIMDISLDILNSCS 209
+ ++F G S ++C S++ ++ DI L I +
Sbjct: 111 ------------------GTIPKLFRGKXVSYIQCKEVDYRSDRREDYYDIQLSIKGKKN 152
Query: 210 LKEAMQKFFQPEVLDGNNKYKCDNCKKLVSARKQMSILQSPNILVIQLKRF----EGIFG 265
+ E+ + E LDG+NKY L A K + L P +L +QL RF +
Sbjct: 153 IFESFVDYVAVEQLDGDNKYDAGE-HGLQEAEKGVKFLTLPPVLHLQLXRFXYDPQTDQN 211
Query: 266 GKIDKAIAFEEVLVLSSFMCKASQDPQPEYKLFGTIVHSGFSPDSGHYYAYIK-DAIGRW 324
KI+ F E L L F+ K Y L +VHSG GHY Y+ G+W
Sbjct: 212 IKINDRFEFPEQLPLDEFLQKTDPKDPANYILHAVLVHSG-DNHGGHYVVYLNPKGDGKW 270
Query: 325 YCCNDSYVSVSTLQEVLS 342
+D VS T +E +
Sbjct: 271 CKFDDDVVSRCTKEEAIE 288
>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 = 47.4 bits (111), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/56 (39%), Positives = 33/56 (58%), Gaps = 2/56 (3%)
Query: 289 QDPQPEYKLFGTIVHSGFSPDSGHYYAYIKDAI--GRWYCCNDSYVSVSTLQEVLS 342
++P Y L G I H G + +SGHY A+I+D + +WY ND VSV +++ S
Sbjct: 340 ENPSCVYNLIGVITHQGANSESGHYQAFIRDELDENKWYKFNDDKVSVVEKEKIES 395
>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 = 37.7 bits (86), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 25/47 (53%)
Query: 295 YKLFGTIVHSGFSPDSGHYYAYIKDAIGRWYCCNDSYVSVSTLQEVL 341
Y L + H G S SGHY +++K W +D VS+ T +++L
Sbjct: 328 YDLQAVLTHQGRSSSSGHYVSWVKRKQDEWIKFDDDKVSIVTPEDIL 374
>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
Length = 854
Score = 37.4 bits (85), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 29/58 (50%), Gaps = 3/58 (5%)
Query: 295 YKLFGTIVHSGFSPDSGHYYAYIKDAIGRWYCCNDSYVSVSTLQEVLSEKVYILFFIR 352
Y+LF I H G S GHY +IK GRW ND V S ++ + YI F+ R
Sbjct: 797 YQLFAFISHMGTSTMCGHYVCHIKKE-GRWVIYNDQKVCAS--EKPPKDLGYIYFYQR 851
Score = 33.5 bits (75), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 62/298 (20%), Positives = 103/298 (34%), Gaps = 78/298 (26%)
Query: 35 SCYLNSVLQCLTYTPPLAN-FCLKLQH----------SSLCKQLT--GDSALDAERKREC 81
SCYLNSV+Q L P + KL+ Q+ G L E +
Sbjct: 353 SCYLNSVVQVLFSIPDFQRKYVDKLEKIFQNAPTDPTQDFSTQVAKLGHGLLSGEYSKPV 412
Query: 82 PFCILEKRIVRSLSVDLTLDAPAKIQSCLRIFAEHFKCGRQEDAHEFLRYVIDACHNTCL 141
P +R+ V + AP ++ + F RQ+DA EF ++I+ C
Sbjct: 413 PESGDGERVPEQKEVQDGI-APRMFKALIGKGHPEFSTNRQQDAQEFFLHLINMVERNCR 471
Query: 142 RLKKLRRKXXXXXXXXXXXXXXXXXXXVVKEIFGGALQSQVKCLACG--AESNKVDEIMD 199
+ E+F ++ ++KCLA + +VD IM
Sbjct: 472 SSEN------------------------PNEVFRFLVEEKIKCLATEKVKYTQRVDYIMQ 507
Query: 200 ISLDI-----------LNSCSLKEAMQKFFQPEVLDGNNKYKCDNCKKLVSARKQMSILQ 248
+ + + + +K PE++ + +C + A +Q+
Sbjct: 508 LPVPMDAALNKEELLEYEEKKRQAEEEKMALPELVRAQVPFS--SCLEAYGAPEQVDDFW 565
Query: 249 S------------------PNILVIQLKRFEGIFG-----GKIDKAIAFEEVLVLSSF 283
S P+ LVIQ+K+F FG K+D +I E L +S
Sbjct: 566 STALQAKSVAVKTTRFASFPDYLVIQIKKF--TFGLDWVPKKLDVSIEMPEELDISQL 621
>pdb|2W31|A Chain A, Globin Domain Of Geobacter Sulfurreducens Globin-Coupled
Sensor
pdb|2W31|B Chain B, Globin Domain Of Geobacter Sulfurreducens Globin-Coupled
Sensor
Length = 162
Score = 31.2 bits (69), Expect = 2.0, Method: Composition-based stats.
Identities = 12/25 (48%), Positives = 21/25 (84%)
Query: 194 VDEIMDISLDILNSCSLKEAMQKFF 218
V++I+DI+LDI+++ +E M+KFF
Sbjct: 135 VEKILDINLDIMSASYREEEMRKFF 159
>pdb|3EPS|A Chain A, The Crystal Structure Of Isocitrate Dehydrogenase
KinasePHOSPHATASE From E. Coli
pdb|3EPS|B Chain B, The Crystal Structure Of Isocitrate Dehydrogenase
KinasePHOSPHATASE From E. Coli
Length = 578
Score = 29.6 bits (65), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 20/34 (58%)
Query: 104 AKIQSCLRIFAEHFKCGRQEDAHEFLRYVIDACH 137
A +++C ++ EH + GR D EF +V++ H
Sbjct: 351 AHVRACYQLVKEHDRVGRMADTQEFENFVLEKRH 384
>pdb|3LC6|A Chain A, The Alternative Conformation Structure Of Isocitrate
Dehydrogenase Kinase/phosphatase From E. Coli
pdb|3LC6|B Chain B, The Alternative Conformation Structure Of Isocitrate
Dehydrogenase Kinase/phosphatase From E. Coli
pdb|3LCB|A Chain A, The Crystal Structure Of Isocitrate Dehydrogenase
KinasePHOSPHATASE In Complex With Its Substrate,
Isocitrate Dehydrogenase, From Escherichia Coli.
pdb|3LCB|B Chain B, The Crystal Structure Of Isocitrate Dehydrogenase
KinasePHOSPHATASE In Complex With Its Substrate,
Isocitrate Dehydrogenase, From Escherichia Coli
Length = 578
Score = 29.6 bits (65), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 20/34 (58%)
Query: 104 AKIQSCLRIFAEHFKCGRQEDAHEFLRYVIDACH 137
A +++C ++ EH + GR D EF +V++ H
Sbjct: 351 AHVRACYQLVKEHDRVGRMADTQEFENFVLEKRH 384
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.316 0.131 0.385
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,655,970
Number of Sequences: 62578
Number of extensions: 640028
Number of successful extensions: 1373
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 21
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1292
Number of HSP's gapped (non-prelim): 42
length of query: 618
length of database: 14,973,337
effective HSP length: 105
effective length of query: 513
effective length of database: 8,402,647
effective search space: 4310557911
effective search space used: 4310557911
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (25.4 bits)