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= psy1343
(337 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 96.7 bits (239), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 87/354 (24%), Positives = 148/354 (41%), Gaps = 49/354 (13%)
Query: 1 ALCHVTPLRDYFLREINYARVKRP-PGDSSFLLVQRFGELMRKLWNPRNFKSHVSPHEML 59
L + PL DYFL++ A + R P + + + EL++++W+ R+ +HV+P M
Sbjct: 26 CLSNTAPLTDYFLKDEYEAEINRDNPLGMKGEIAEAYAELIKQMWSGRD--AHVAP-RMF 82
Query: 60 QAVVLWSRKQFQFTEQSDPIDFLSWFLNTLHRALNGTKKKD-----------SSIVYKTF 108
+ V QF +Q D + L++ L+ LH LN KKK ++V K
Sbjct: 83 KTQVGRFAPQFSGYQQQDSQELLAFLLDGLHEDLNRVKKKPYLELKDANGRPDAVVAKEA 142
Query: 109 LGSMKVKTRKIPPVELEEKVRQRXXXXXXXXXXXXXSPFLYLTCDLPPPPLFKDEVLEN- 167
+ +++ + + PF YLT P PL KD V+E
Sbjct: 143 WENHRLRNDSVIVDTFHGLFKSTLVCPECAKVSVTFDPFCYLTL---PLPLKKDRVMEGP 199
Query: 168 -IIPQ------------VNLYTILTKFNNESEKEYKTYK--ENFLKRFEITSLPPYLILY 212
+ PQ + L+T + K + K+F++ SLP L+++
Sbjct: 200 MLQPQKKKKTTVALRDCIELFTTMETLGEHDPWYCPNCKKHQQATKKFDLWSLPKILVVH 259
Query: 213 VKRFTKNTFFVEKNPTIVNFPVKNVDFGDILTPEVKAKYESTMYDLVKAKYESTMYDLVA 272
+KRF+ N ++ +K T+V FP++ ++ + + Y +YDL+A
Sbjct: 260 LKRFSYNRYWRDKLDTVVEFPIRGLNMSEFVCNLSARPY---------------VYDLIA 304
Query: 273 NIVHDGEPSNGTYRVHLYHKGIGKWYEIQDLHVTDILPQMITLTEAYIQIYELR 326
H G G Y + +K GKWY D +V+ I AY+ Y+ R
Sbjct: 305 VSNHYGAMGVGHYTAYAKNKLNGKWYYFDDSNVSLASEDQIVTKAAYVLFYQRR 358
>pdb|2HD5|A Chain A, Usp2 In Complex With Ubiquitin
Length = 359
Score = 72.8 bits (177), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 81/346 (23%), Positives = 142/346 (41%), Gaps = 32/346 (9%)
Query: 1 ALCHVTPLRDYFLREINYARVKRPPGDSSFLLVQRFGELMRKLW--NPRNFKSHVSPHEM 58
L + LRDY L+ + Y R ++ LV+ F +L++ +W +P + VSP E
Sbjct: 27 CLSNTRELRDYCLQRL-YMRDLHHGSNAHTALVEEFAKLIQTIWTSSPNDV---VSPSEF 82
Query: 59 LQAVVLWSRKQFQFTEQSDPIDFLSWFLNTLHRALNGTKKKDSSIVYKTFLGSMKVKTRK 118
+ ++ + + +Q D +FL + L+ LH +N + S K R+
Sbjct: 83 KTQIQRYAPRFVGYNQQ-DAQEFLRFLLDGLHNEVNRVTLRPKSNPENLDHLPDDEKGRQ 141
Query: 119 IPPVELE-EKVRQRXXXXXXXXXXXXXSPFLYLTCDLPPPPLFKDEVLENIIPQVNLYTI 177
+ LE E R + Y + P + + P+V L
Sbjct: 142 MWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPIAKRGYPEVTLMDC 201
Query: 178 LTKFNNES-----EK---EYKTYKENFLKRFEITSLPPYLILYVKRFTKNTFFVEKNPTI 229
+ F E EK ++ +K+F I P L+L++KRF+++ K T
Sbjct: 202 MRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKILVLHLKRFSESRIRTSKLTTF 261
Query: 230 VNFPVKNVDFGDILTPEVKAKYESTMYDLVKAKYESTMYDLVANIVHDGEPSNGTYRVHL 289
VNFP++++D + + E+T + +Y+L A H G G Y +
Sbjct: 262 VNFPLRDLDLREFAS-------ENTNH---------AVYNLYAVSNHSGTTMGGHYTAYC 305
Query: 290 YHKGIGKWYEIQDLHVTDILPQMITLTEAYIQIYELRTTPSPTAMS 335
G G+W+ D VT + + ++AY+ YEL + PS A +
Sbjct: 306 RSPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFYELASPPSRMAAA 351
>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 = 72.0 bits (175), Expect = 5e-13, Method: Compositional matrix adjust.
Identities = 78/341 (22%), Positives = 136/341 (39%), Gaps = 32/341 (9%)
Query: 1 ALCHVTPLRDYFLREINYARVKRPPGDSSFLLVQRFGELMRKLW--NPRNFKSHVSPHEM 58
L + LRDY L+ + Y R ++ LV+ F +L++ +W +P + VSP E
Sbjct: 46 CLSNTRELRDYCLQRL-YMRDLHHGSNAHTALVEEFAKLIQTIWTSSPNDV---VSPSEF 101
Query: 59 LQAVVLWSRKQFQFTEQSDPIDFLSWFLNTLHRALNGTKKKDSSIVYKTFLGSMKVKTRK 118
+ ++ + + +Q D +FL + L+ LH +N + S K R+
Sbjct: 102 KTQIQRYAPRFVGYNQQ-DAQEFLRFLLDGLHNEVNRVTLRPKSNPENLDHLPDDEKGRQ 160
Query: 119 IPPVELE-EKVRQRXXXXXXXXXXXXXSPFLYLTCDLPPPPLFKDEVLENIIPQVNLYTI 177
+ LE E R + Y + P + + P+V L
Sbjct: 161 MWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPIAKRGYPEVTLMDC 220
Query: 178 LTKFNNES-----EK---EYKTYKENFLKRFEITSLPPYLILYVKRFTKNTFFVEKNPTI 229
+ F E EK ++ +K+F I P L+L++KRF+++ K T
Sbjct: 221 MRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKILVLHLKRFSESRIRTSKLTTF 280
Query: 230 VNFPVKNVDFGDILTPEVKAKYESTMYDLVKAKYESTMYDLVANIVHDGEPSNGTYRVHL 289
VNFP++++D + + +Y+L A H G G Y +
Sbjct: 281 VNFPLRDLD----------------LREFASENTNHAVYNLYAVSNHSGTTMGGHYTAYC 324
Query: 290 YHKGIGKWYEIQDLHVTDILPQMITLTEAYIQIYELRTTPS 330
G G+W+ D VT + + ++AY+ YEL + PS
Sbjct: 325 RSPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFYELASPPS 365
>pdb|3NHE|A Chain A, High Resolution Structure (1.26a) Of Usp2a In Complex With
Ubiquitin
Length = 348
Score = 72.0 bits (175), Expect = 5e-13, Method: Compositional matrix adjust.
Identities = 80/341 (23%), Positives = 140/341 (41%), Gaps = 32/341 (9%)
Query: 1 ALCHVTPLRDYFLREINYARVKRPPGDSSFLLVQRFGELMRKLW--NPRNFKSHVSPHEM 58
L + LRDY L+ + Y R ++ LV+ F +L++ +W +P + VSP E
Sbjct: 27 CLSNTRELRDYCLQRL-YMRDLHHGSNAHTALVEEFAKLIQTIWTSSPNDV---VSPSEF 82
Query: 59 LQAVVLWSRKQFQFTEQSDPIDFLSWFLNTLHRALNGTKKKDSSIVYKTFLGSMKVKTRK 118
+ ++ + + +Q D +FL + L+ LH +N + S K R+
Sbjct: 83 KTQIQRYAPRFVGYNQQ-DAQEFLRFLLDGLHNEVNRVTLRPKSNPENLDHLPDDEKGRQ 141
Query: 119 IPPVELE-EKVRQRXXXXXXXXXXXXXSPFLYLTCDLPPPPLFKDEVLENIIPQVNLYTI 177
+ LE E R + Y + P + + P+V L
Sbjct: 142 MWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPIAKRGYPEVTLMDC 201
Query: 178 LTKFNNES-----EK---EYKTYKENFLKRFEITSLPPYLILYVKRFTKNTFFVEKNPTI 229
+ F E EK ++ +K+F I P L+L++KRF+++ K T
Sbjct: 202 MRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKILVLHLKRFSESRIRTSKLTTF 261
Query: 230 VNFPVKNVDFGDILTPEVKAKYESTMYDLVKAKYESTMYDLVANIVHDGEPSNGTYRVHL 289
VNFP++++D + + E+T + +Y+L A H G G Y +
Sbjct: 262 VNFPLRDLDLREFAS-------ENTNH---------AVYNLYAVSNHSGTTMGGHYTAYC 305
Query: 290 YHKGIGKWYEIQDLHVTDILPQMITLTEAYIQIYELRTTPS 330
G G+W+ D VT + + ++AY+ YEL + PS
Sbjct: 306 RSPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFYELASPPS 346
>pdb|2IBI|A Chain A, Covalent Ubiquitin-Usp2 Complex
Length = 374
Score = 71.6 bits (174), Expect = 5e-13, Method: Compositional matrix adjust.
Identities = 76/341 (22%), Positives = 134/341 (39%), Gaps = 32/341 (9%)
Query: 1 ALCHVTPLRDYFLREINYARVKRPPGDSSFLLVQRFGELMRKLW--NPRNFKSHVSPHEM 58
L + LRDY L+ + Y R ++ LV+ F +L++ +W +P + VSP E
Sbjct: 53 CLSNTRELRDYCLQRL-YMRDLHHGSNAHTALVEEFAKLIQTIWTSSPNDV---VSPSEF 108
Query: 59 LQAVVLWSRKQFQFTEQSDPIDFLSWFLNTLHRALNGTKKKDSSIVYKTFLGSMKVKTRK 118
+ ++ + + +Q D +FL + L+ LH +N + S K R+
Sbjct: 109 KTQIQRYAPRFVGYNQQ-DAQEFLRFLLDGLHNEVNRVTLRPKSNPENLDHLPDDEKGRQ 167
Query: 119 IPPVELE-EKVRQRXXXXXXXXXXXXXSPFLYLTCDLPPPPLFKDEVLENIIPQVNLYTI 177
+ LE E R + Y + P + + P+V L
Sbjct: 168 MWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPIAKRGYPEVTLMDC 227
Query: 178 LTKFNNES--------EKEYKTYKENFLKRFEITSLPPYLILYVKRFTKNTFFVEKNPTI 229
+ F E ++ +K+F I P L+L++KRF+++ K T
Sbjct: 228 MRLFTKEDVLDGDAAPTCCRCRGRKRCIKKFSIQRFPKILVLHLKRFSESRIRTSKLTTF 287
Query: 230 VNFPVKNVDFGDILTPEVKAKYESTMYDLVKAKYESTMYDLVANIVHDGEPSNGTYRVHL 289
VNFP++++D + + +Y+L A H G G Y +
Sbjct: 288 VNFPLRDLD----------------LREFASENTNHAVYNLYAVSNHSGTTMGGHYTAYC 331
Query: 290 YHKGIGKWYEIQDLHVTDILPQMITLTEAYIQIYELRTTPS 330
G G+W+ D VT + + ++AY+ YEL + PS
Sbjct: 332 RSPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFYELASPPS 372
>pdb|3N3K|A Chain A, The Catalytic Domain Of Usp8 In Complex With A Usp8
Specific Inhibitor
Length = 396
Score = 57.0 bits (136), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 79/343 (23%), Positives = 137/343 (39%), Gaps = 50/343 (14%)
Query: 1 ALCHVTPLRDYFLR-----EINYARVKRPPGDSSFLLVQRFGELMRKLWNPRNFKSHVSP 55
LC+ L DYF R +IN + + G+ + + FG +M+ LW + ++SP
Sbjct: 80 CLCNAPHLADYFNRNCYQDDINRSNLLGHKGE----VAEEFGIIMKALWTGQ--YRYISP 133
Query: 56 HEMLQAVVLWSRKQFQFTEQSDPIDFLSWFLNTLHRALNGTKKKDSSIVYK----TFLGS 111
+ + + QF Q D + L + ++ LH LN K D+ YK L
Sbjct: 134 KD-FKITIGKINDQFAGYSQQDSQELLLFLMDGLHEDLN---KADNRKRYKEENNDHLDD 189
Query: 112 MKVK----------TRKIPPVELEEKVRQRXXXXXXXXXXXXXSPFLYLTCDLPPPPLFK 161
K I + + + F+YL+ LP K
Sbjct: 190 FKAAEHAWQKHKQLNESIIVALFQGQFKSTVQCLTCHKKSRTFEAFMYLS--LPLASTSK 247
Query: 162 DEVLENIIPQVNLYTILTKFNNESEKEYKTYKENFLKRFEITSLPPYLILYVKRFTKNTF 221
L++ + + LT NN + + + LK+ EI LPP L++++KRF+ +
Sbjct: 248 -CTLQDCLRLFSKEEKLTD-NNRFYCSHCRARRDSLKKIEIWKLPPVLLVHLKRFSYDGR 305
Query: 222 FVEKNPTIVNFPVKNVDFGD-ILTPEVKAKYESTMYDLVKAKYESTMYDLVANIVHDGEP 280
+ +K T V+FP++N+D ++ P+ K Y+L + H G
Sbjct: 306 WKQKLQTSVDFPLENLDLSQYVIGPKNNLK----------------KYNLFSVSNHYGGL 349
Query: 281 SNGTYRVHLYHKGIGKWYEIQDLHVTDILPQMITLTEAYIQIY 323
G Y + + +W++ D V+DI + + AYI Y
Sbjct: 350 DGGHYTAYCKNAARQRWFKFDDHEVSDISVSSVKSSAAYILFY 392
>pdb|2GFO|A Chain A, Structure Of The Catalytic Domain Of Human Ubiquitin
Carboxyl-terminal Hydrolase 8
Length = 396
Score = 51.6 bits (122), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 78/343 (22%), Positives = 134/343 (39%), Gaps = 50/343 (14%)
Query: 1 ALCHVTPLRDYFLR-----EINYARVKRPPGDSSFLLVQRFGELMRKLWNPRNFKSHVSP 55
LC+ L DYF R +IN + + G+ + + FG + + LW + ++SP
Sbjct: 80 CLCNAPHLADYFNRNCYQDDINRSNLLGHKGE----VAEEFGIIXKALWTGQ--YRYISP 133
Query: 56 HEMLQAVVLWSRKQFQFTEQSDPIDFLSWFLNTLHRALNGTKKKDSSIVYK----TFLGS 111
+ + + QF Q D + L + + LH LN K D+ YK L
Sbjct: 134 KD-FKITIGKINDQFAGYSQQDSQELLLFLXDGLHEDLN---KADNRKRYKEENNDHLDD 189
Query: 112 MKVK----------TRKIPPVELEEKVRQRXXXXXXXXXXXXXSPFLYLTCDLPPPPLFK 161
K I + + + F YL+ LP K
Sbjct: 190 FKAAEHAWQKHKQLNESIIVALFQGQFKSTVQCLTCHKKSRTFEAFXYLS--LPLASTSK 247
Query: 162 DEVLENIIPQVNLYTILTKFNNESEKEYKTYKENFLKRFEITSLPPYLILYVKRFTKNTF 221
L++ + + LT NN + + + LK+ EI LPP L++++KRF+ +
Sbjct: 248 -CTLQDCLRLFSKEEKLTD-NNRFYCSHCRARRDSLKKIEIWKLPPVLLVHLKRFSYDGR 305
Query: 222 FVEKNPTIVNFPVKNVDFGD-ILTPEVKAKYESTMYDLVKAKYESTMYDLVANIVHDGEP 280
+ +K T V+FP++N+D ++ P+ K Y+L + H G
Sbjct: 306 WKQKLQTSVDFPLENLDLSQYVIGPKNNLK----------------KYNLFSVSNHYGGL 349
Query: 281 SNGTYRVHLYHKGIGKWYEIQDLHVTDILPQMITLTEAYIQIY 323
G Y + + +W++ D V+DI + + AYI Y
Sbjct: 350 DGGHYTAYCKNAARQRWFKFDDHEVSDISVSSVKSSAAYILFY 392
>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 = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 38/167 (22%), Positives = 64/167 (38%), Gaps = 26/167 (15%)
Query: 171 QVNLYTILTKFNNESEKEYKTY--------KENFLKRFEITSLPPYLILYVKRFTKNTFF 222
+V+L F E E E + K K+ + P L+L++ RF+ +
Sbjct: 205 KVSLRDCFNLFTKEEELESENAPVCDRCRQKTRSTKKLTVQRFPRILVLHLNRFSASRGS 264
Query: 223 VEKNPTIVNFPVKNVDFGDILTPEVKAKYESTMYDLVKAKYESTMYDLVANIVHDGEPSN 282
++K+ V+FP++ + GD + K S +Y L A H G
Sbjct: 265 IKKSSVGVDFPLQRLSLGDFASD----------------KAGSPVYQLYALCNHSGSVHY 308
Query: 283 GTYRVHLYHKGIGKWYEIQDLHVTDILPQMITLTEAYIQIYELRTTP 329
G Y L G W+ D V+ + + +E Y+ Y+L P
Sbjct: 309 GHY-TALCRCQTG-WHVYNDSRVSPVSENQVASSEGYVLFYQLMQEP 353
>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 = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 38/167 (22%), Positives = 64/167 (38%), Gaps = 26/167 (15%)
Query: 171 QVNLYTILTKFNNESEKEYKTY--------KENFLKRFEITSLPPYLILYVKRFTKNTFF 222
+V+L F E E E + K K+ + P L+L++ RF+ +
Sbjct: 218 KVSLRDCFNLFTKEEELESENAPVCDRCRQKTRSTKKLTVQRFPRILVLHLNRFSASRGS 277
Query: 223 VEKNPTIVNFPVKNVDFGDILTPEVKAKYESTMYDLVKAKYESTMYDLVANIVHDGEPSN 282
++K+ V+FP++ + GD + K S +Y L A H G
Sbjct: 278 IKKSSVGVDFPLQRLSLGDFASD----------------KAGSPVYQLYALCNHSGSVHY 321
Query: 283 GTYRVHLYHKGIGKWYEIQDLHVTDILPQMITLTEAYIQIYELRTTP 329
G Y L G W+ D V+ + + +E Y+ Y+L P
Sbjct: 322 GHY-TALCRCQTG-WHVYNDSRVSPVSENQVASSEGYVLFYQLMQEP 366
>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 = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 38/167 (22%), Positives = 64/167 (38%), Gaps = 26/167 (15%)
Query: 171 QVNLYTILTKFNNESEKEYKTY--------KENFLKRFEITSLPPYLILYVKRFTKNTFF 222
+V+L F E E E + K K+ + P L+L++ RF+ +
Sbjct: 224 KVSLRDCFNLFTKEEELESENAPVCDRCRQKTRSTKKLTVQRFPRILVLHLNRFSASRGS 283
Query: 223 VEKNPTIVNFPVKNVDFGDILTPEVKAKYESTMYDLVKAKYESTMYDLVANIVHDGEPSN 282
++K+ V+FP++ + GD + K S +Y L A H G
Sbjct: 284 IKKSSVGVDFPLQRLSLGDFASD----------------KAGSPVYQLYALCNHSGSVHY 327
Query: 283 GTYRVHLYHKGIGKWYEIQDLHVTDILPQMITLTEAYIQIYELRTTP 329
G Y L G W+ D V+ + + +E Y+ Y+L P
Sbjct: 328 GHY-TALCRCQTG-WHVYNDSRVSPVSENQVASSEGYVLFYQLMQEP 372
>pdb|3M99|A Chain A, Structure Of The Ubp8-Sgf11-Sgf73-Sus1 Saga Dub Module
Length = 471
Score = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 70/348 (20%), Positives = 125/348 (35%), Gaps = 71/348 (20%)
Query: 11 YFLREI------NYARVKRPPGDSSFLLVQRFGELMRKLWNPRNFKSHVSPHEMLQAVVL 64
YF+R N +V+ P S L + EL L + S S + + L
Sbjct: 160 YFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHELYGALNTKQASSSSTSTNRQTGFIYL 219
Query: 65 ----WSRKQ-FQFTEQSDPIDFLSWFLNTLHRAL-----------NGTKKKDSSIVYKTF 108
W Q Q D +F + +N +H++ K+ IV+ F
Sbjct: 220 LTCAWKINQNLAGYSQQDAHEFWQFIINQIHQSYVLDLPNAKEVSRANNKQCECIVHTVF 279
Query: 109 LGSMKVKTRKIPPVELEEKVRQRXXXXXXXXXXXXXSPFLYLTCDLPPPPLFKDEVLENI 168
GS++ + P + K PFL L+ D+
Sbjct: 280 EGSLE-SSIVCPGCQNNSKT--------------TIDPFLDLSLDIKDKK---------- 314
Query: 169 IPQVNLYTILTKFNNESE-KEYKTY------KENFLKRFEITSLPPYLILYVKRFTKNTF 221
LY L F+ + + K++ + ++ +K+ I LP L+L +KRF
Sbjct: 315 ----KLYECLDSFHKKEQLKDFNYHCGECNSTQDAIKQLGIHKLPSVLVLQLKRFEH--L 368
Query: 222 FVEKNPTI---VNFPVKNVDFGDILTPEVKAKYESTMYDLVKAKYESTMYDLVANIVHDG 278
N + + FP ++ + + + K K+ K +Y+L+ + H G
Sbjct: 369 LNGSNRKLDDFIEFPTY-LNMKNYCSTKEKDKHSEN------GKVPDIIYELIGIVSHKG 421
Query: 279 EPSNGTYRVHLYHKGIGKWYEIQDLHVTDILPQMITLTEAYIQIYELR 326
+ G Y G G+W++ D V+ I + + +AY+ Y +R
Sbjct: 422 TVNEGHYIAFCKISG-GQWFKFNDSMVSSISQEEVLKEQAYLLFYTIR 468
>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 = 38.1 bits (87), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 70/348 (20%), Positives = 125/348 (35%), Gaps = 71/348 (20%)
Query: 11 YFLREI------NYARVKRPPGDSSFLLVQRFGELMRKLWNPRNFKSHVSPHEMLQAVVL 64
YF+R N +V+ P S L + EL L + S S + + L
Sbjct: 165 YFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHELYGALNTKQASSSSTSTNRQTGFIYL 224
Query: 65 ----WSRKQ-FQFTEQSDPIDFLSWFLNTLHRAL-----------NGTKKKDSSIVYKTF 108
W Q Q D +F + +N +H++ K+ IV+ F
Sbjct: 225 LTCAWKINQNLAGYSQQDAHEFWQFIINQIHQSYVLDLPNAKEVSRANNKQCECIVHTVF 284
Query: 109 LGSMKVKTRKIPPVELEEKVRQRXXXXXXXXXXXXXSPFLYLTCDLPPPPLFKDEVLENI 168
GS++ + P + K PFL L+ D+
Sbjct: 285 EGSLE-SSIVCPGCQNNSKT--------------TIDPFLDLSLDIKDKK---------- 319
Query: 169 IPQVNLYTILTKFNNESE-KEYKTY------KENFLKRFEITSLPPYLILYVKRFTKNTF 221
LY L F+ + + K++ + ++ +K+ I LP L+L +KRF
Sbjct: 320 ----KLYECLDSFHKKEQLKDFNYHCGECNSTQDAIKQLGIHKLPSVLVLQLKRFEH--L 373
Query: 222 FVEKNPTI---VNFPVKNVDFGDILTPEVKAKYESTMYDLVKAKYESTMYDLVANIVHDG 278
N + + FP ++ + + + K K+ K +Y+L+ + H G
Sbjct: 374 LNGSNRKLDDFIEFPTY-LNMKNYCSTKEKDKHSEN------GKVPDIIYELIGIVSHKG 426
Query: 279 EPSNGTYRVHLYHKGIGKWYEIQDLHVTDILPQMITLTEAYIQIYELR 326
+ G Y G G+W++ D V+ I + + +AY+ Y +R
Sbjct: 427 TVNEGHYIAFCKISG-GQWFKFNDSMVSSISQEEVLKEQAYLLFYTIR 473
>pdb|3MHH|A Chain A, Structure Of The Saga Ubp8SGF11SUS1SGF73 DUB MODULE
pdb|3MHS|A Chain A, Structure Of The Saga Ubp8SGF11SUS1SGF73 DUB MODULE BOUND
Ubiquitin Aldehyde
pdb|4FJC|A Chain A, Structure Of The Saga Ubp8SGF11(1-72, Delta-Znf)SUS1SGF73
DUB Module
pdb|4FJC|E Chain E, Structure Of The Saga Ubp8SGF11(1-72, Delta-Znf)SUS1SGF73
DUB Module
Length = 476
Score = 38.1 bits (87), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 70/348 (20%), Positives = 125/348 (35%), Gaps = 71/348 (20%)
Query: 11 YFLREI------NYARVKRPPGDSSFLLVQRFGELMRKLWNPRNFKSHVSPHEMLQAVVL 64
YF+R N +V+ P S L + EL L + S S + + L
Sbjct: 165 YFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHELYGALNTKQASSSSTSTNRQTGFIYL 224
Query: 65 ----WSRKQ-FQFTEQSDPIDFLSWFLNTLHRAL-----------NGTKKKDSSIVYKTF 108
W Q Q D +F + +N +H++ K+ IV+ F
Sbjct: 225 LTCAWKINQNLAGYSQQDAHEFWQFIINQIHQSYVLDLPNAKEVSRANNKQCECIVHTVF 284
Query: 109 LGSMKVKTRKIPPVELEEKVRQRXXXXXXXXXXXXXSPFLYLTCDLPPPPLFKDEVLENI 168
GS++ + P + K PFL L+ D+
Sbjct: 285 EGSLE-SSIVCPGCQNNSKT--------------TIDPFLDLSLDIKDKK---------- 319
Query: 169 IPQVNLYTILTKFNNESE-KEYKTY------KENFLKRFEITSLPPYLILYVKRFTKNTF 221
LY L F+ + + K++ + ++ +K+ I LP L+L +KRF
Sbjct: 320 ----KLYECLDSFHKKEQLKDFNYHCGECNSTQDAIKQLGIHKLPSVLVLQLKRFEH--L 373
Query: 222 FVEKNPTI---VNFPVKNVDFGDILTPEVKAKYESTMYDLVKAKYESTMYDLVANIVHDG 278
N + + FP ++ + + + K K+ K +Y+L+ + H G
Sbjct: 374 LNGSNRKLDDFIEFPTY-LNMKNYCSTKEKDKHSEN------GKVPDIIYELIGIVSHKG 426
Query: 279 EPSNGTYRVHLYHKGIGKWYEIQDLHVTDILPQMITLTEAYIQIYELR 326
+ G Y G G+W++ D V+ I + + +AY+ Y +R
Sbjct: 427 TVNEGHYIAFCKISG-GQWFKFNDSMVSSISQEEVLKEQAYLLFYTIR 473
>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 = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 46/183 (25%), Positives = 75/183 (40%), Gaps = 48/183 (26%)
Query: 174 LYTILT-KFNNESEKEYKTYKEN--FLKRFEITSLPPYLILYVKRFTKNTFFVEK---NP 227
L+T L + E K+ T + N ++K +I+ LP YL + + RF F+ EK N
Sbjct: 196 LFTGLKLRLQEEITKQSPTLQRNALYIKSSKISRLPAYLTIQMVRF----FYKEKESVNA 251
Query: 228 TI---VNFPVKNVDFGDILTPEVKAK---YESTMYDLV-------------------KAK 262
+ V FP+ +D ++ TPE++ K + S DL + K
Sbjct: 252 KVLKDVKFPLM-LDMYELCTPELQEKMVSFRSKFKDLEDKKVNQQPNTSDKKSSPQKEVK 310
Query: 263 YE------------STMYDLVANIVHDGEPSNGTYRVHLYHKGIGKWYEIQDLHVTDILP 310
YE YDL A + H G S+ + V + +W + D V+ + P
Sbjct: 311 YEPFSFADDIGSNNCGYYDLQAVLTHQGRSSSSGHYVSWVKRKQDEWIKFDDDKVSIVTP 370
Query: 311 QMI 313
+ I
Sbjct: 371 EDI 373
>pdb|3B1C|A Chain A, Crystal Structure Of Betac-S Lyase From Streptococcus
Anginosus: Internal Aldimine Form
pdb|3B1C|B Chain B, Crystal Structure Of Betac-S Lyase From Streptococcus
Anginosus: Internal Aldimine Form
pdb|3B1C|C Chain C, Crystal Structure Of Betac-S Lyase From Streptococcus
Anginosus: Internal Aldimine Form
pdb|3B1C|D Chain D, Crystal Structure Of Betac-S Lyase From Streptococcus
Anginosus: Internal Aldimine Form
pdb|3B1D|A Chain A, Crystal Structure Of Betac-S Lyase From Streptococcus
Anginosus In Complex With L-Serine: External Aldimine
Form
pdb|3B1D|B Chain B, Crystal Structure Of Betac-S Lyase From Streptococcus
Anginosus In Complex With L-Serine: External Aldimine
Form
pdb|3B1D|C Chain C, Crystal Structure Of Betac-S Lyase From Streptococcus
Anginosus In Complex With L-Serine: External Aldimine
Form
pdb|3B1D|D Chain D, Crystal Structure Of Betac-S Lyase From Streptococcus
Anginosus In Complex With L-Serine: External Aldimine
Form
pdb|3B1E|A Chain A, Crystal Structure Of Betac-S Lyase From Streptococcus
Anginosus In Complex With L-Serine: Alpha-Aminoacrylate
Form
pdb|3B1E|B Chain B, Crystal Structure Of Betac-S Lyase From Streptococcus
Anginosus In Complex With L-Serine: Alpha-Aminoacrylate
Form
pdb|3B1E|C Chain C, Crystal Structure Of Betac-S Lyase From Streptococcus
Anginosus In Complex With L-Serine: Alpha-Aminoacrylate
Form
pdb|3B1E|D Chain D, Crystal Structure Of Betac-S Lyase From Streptococcus
Anginosus In Complex With L-Serine: Alpha-Aminoacrylate
Form
Length = 392
Score = 33.1 bits (74), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 45/192 (23%), Positives = 81/192 (42%), Gaps = 21/192 (10%)
Query: 57 EMLQAVVLWSRKQFQFTEQSDPIDFLSWFLNTLHRALNGTKKKDSSI-----VYKTFLGS 111
E+LQAV+ W + + Q++ + I F+ + + A+ K+ ++ VY F S
Sbjct: 70 ELLQAVLDWEKSEHQYSFDKEDIVFVEGVVPAISIAIQAFTKEGEAVLINSPVYPPFARS 129
Query: 112 MKVKTRKIPPVEL-EEKVRQRXXXXXXXXXXXXXSPFLYLTCD--LPPPPLFKDEVLEN- 167
+++ RK+ L EE + LYL C+ P +++ EVLE
Sbjct: 130 VRLNNRKLVSNSLKEENGLFQIDFEQLENDIVENDVKLYLLCNPHNPGGRVWEREVLEQI 189
Query: 168 ---------IIPQVNLYTILTKFNNESEKEYKTYKENFLKRFEITSLPPYLILYVKRFTK 218
I+ ++ LT F +E + T +F K F + L + TK
Sbjct: 190 GHLCQKHHVILVSDEIHQDLTLFGHE-HVSFNTVSPDF-KDFALV-LSSATKTFNIAGTK 246
Query: 219 NTFFVEKNPTIV 230
N++ + +NPT+
Sbjct: 247 NSYAIIENPTLC 258
>pdb|2F1Z|A Chain A, Crystal Structure Of Hausp
pdb|2F1Z|B Chain B, Crystal Structure Of Hausp
Length = 522
Score = 32.3 bits (72), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 20/35 (57%)
Query: 268 YDLVANIVHDGEPSNGTYRVHLYHKGIGKWYEIQD 302
Y L A +VH G+ G Y V+L KG GKW + D
Sbjct: 410 YILHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFDD 444
>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 = 32.3 bits (72), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 20/35 (57%)
Query: 268 YDLVANIVHDGEPSNGTYRVHLYHKGIGKWYEIQD 302
Y L A +VH G+ G Y V+L KG GKW + D
Sbjct: 241 YILHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFDD 275
>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 = 32.0 bits (71), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 20/35 (57%)
Query: 268 YDLVANIVHDGEPSNGTYRVHLYHKGIGKWYEIQD 302
Y L A +VH G+ G Y V+L KG GKW + D
Sbjct: 241 YILHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFDD 275
>pdb|2H29|A Chain A, Crystal Structure Of Nicotinic Acid Mononucleotide
Adenylyltransferase From Staphylococcus Aureus: Product
Bound Form 1
pdb|2H29|B Chain B, Crystal Structure Of Nicotinic Acid Mononucleotide
Adenylyltransferase From Staphylococcus Aureus: Product
Bound Form 1
Length = 189
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 21/39 (53%)
Query: 223 VEKNPTIVNFPVKNVDFGDILTPEVKAKYESTMYDLVKA 261
V+ T++ + + FGDI E+K +S YD +KA
Sbjct: 53 VQHRLTMIQMIIDELGFGDICDDEIKRGGQSYTYDTIKA 91
>pdb|2H2A|A Chain A, Crystal Structure Of Nicotinic Acid Mononucleotide
Adenylyltransferase From Staphylococcus Aureus: Product
Bound Form 2
pdb|2H2A|B Chain B, Crystal Structure Of Nicotinic Acid Mononucleotide
Adenylyltransferase From Staphylococcus Aureus: Product
Bound Form 2
Length = 189
Score = 29.6 bits (65), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 21/39 (53%)
Query: 223 VEKNPTIVNFPVKNVDFGDILTPEVKAKYESTMYDLVKA 261
V+ T++ + + FGDI E+K +S YD +KA
Sbjct: 53 VQHRLTMIQMIIDELGFGDIXDDEIKRGGQSYTYDTIKA 91
>pdb|3DWL|D Chain D, Crystal Structure Of Fission Yeast Arp2/3 Complex Lacking
The Arp2 Subunit
pdb|3DWL|I Chain I, Crystal Structure Of Fission Yeast Arp2/3 Complex Lacking
The Arp2 Subunit
Length = 317
Score = 28.5 bits (62), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 30/67 (44%), Gaps = 5/67 (7%)
Query: 63 VLWSRKQFQFTEQS--DPIDFLSWFLNTLHRALNGTKKKDSSIVYKTFLGSMKVKTRKIP 120
VL+ R FT Q+ D I + F NTLH + +K + K KV R P
Sbjct: 244 VLFER---HFTPQNREDCISHIQVFRNTLHFHIKASKAYMHQRMRKRVADFQKVLNRAKP 300
Query: 121 PVELEEK 127
VELE K
Sbjct: 301 DVELERK 307
>pdb|1OH1|A Chain A, Solution Structure Of Staphostatin A Form Staphylococcus
Aureus Confirms The Discovery Of A Novel Class Of
Cysteine Proteinase Inhibitors
Length = 109
Score = 28.1 bits (61), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 21/34 (61%)
Query: 76 SDPIDFLSWFLNTLHRALNGTKKKDSSIVYKTFL 109
SD D++ ++NT H+ L K +SSIV + F+
Sbjct: 48 SDDSDYICKYINTEHKQLTLYNKNNSSIVIEIFI 81
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 0.137 0.413
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,201,826
Number of Sequences: 62578
Number of extensions: 420807
Number of successful extensions: 824
Number of sequences better than 100.0: 26
Number of HSP's better than 100.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 790
Number of HSP's gapped (non-prelim): 26
length of query: 337
length of database: 14,973,337
effective HSP length: 99
effective length of query: 238
effective length of database: 8,778,115
effective search space: 2089191370
effective search space used: 2089191370
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)