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= 008789
(553 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3M99|A Chain A, Structure Of The Ubp8-Sgf11-Sgf73-Sus1 Saga Dub Module
Length = 471
Score = 190 bits (482), Expect = 2e-48, Method: Compositional matrix adjust.
Identities = 122/364 (33%), Positives = 186/364 (51%), Gaps = 51/364 (14%)
Query: 178 GLRGLNNLGSTCFMNSVLQALLHAPPFRNYFLTGQRNHEVCRKRSSDRLCLLCDIYVFFS 237
GL GL N+GSTCFM+S+LQ L+H P F + ++ Q + C+ RS D+ C C +
Sbjct: 135 GLSGLINMGSTCFMSSILQCLIHNPYFIRHSMS-QIHSNNCKVRSPDK-CFSCALDKIVH 192
Query: 238 AVFSGDRTPYSPAQ------------LLYSWWQHSANLASYEQQDAHEFFISMLDGIHEN 285
++ T + + LL W+ + NLA Y QQDAHEF+ +++ IH++
Sbjct: 193 ELYGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQS 252
Query: 286 GVKARSPIKDTG-----ECHCVAHRVFSGQLRSDVTCMSCGYTS-TTYDPFMDISLNLDT 339
V K+ +C C+ H VF G L S + C C S TT DPF+D+SL
Sbjct: 253 YVLDLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLDLSL---- 308
Query: 340 GNCPSTDLANKSLKPSDNTYVSTLLGCLDLFTKPEKLGSDQKFFCENCQERQDSVKQMSI 399
D+ +K L CLD F K E+L D + C C QD++KQ+ I
Sbjct: 309 ------DIKDKK----------KLYECLDSFHKKEQL-KDFNYHCGECNSTQDAIKQLGI 351
Query: 400 KRLPLVLCLHIKRFEHFPVRRMSRKIDRYMQFPFCLDMNPYLSSSVVRNRFGNRMFAFEG 459
+LP VL L +KRFEH + +RK+D +++FP L+M Y S+ N G
Sbjct: 352 HKLPSVLVLQLKRFEHL-LNGSNRKLDDFIEFPTYLNMKNYCSTKEKDKHSEN------G 404
Query: 460 DELDTSTEFEIFAVVTHSGTLDSGHYVTYLHLK-DQWYKCDDAWITAVEEEVVRASQCYM 518
D +E+ +V+H GT++ GHY+ + + QW+K +D+ ++++ +E V Q Y+
Sbjct: 405 KVPDII--YELIGIVSHKGTVNEGHYIAFCKISGGQWFKFNDSMVSSISQEEVLKEQAYL 462
Query: 519 LFYA 522
LFY
Sbjct: 463 LFYT 466
>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 = 190 bits (482), Expect = 2e-48, Method: Compositional matrix adjust.
Identities = 122/364 (33%), Positives = 186/364 (51%), Gaps = 51/364 (14%)
Query: 178 GLRGLNNLGSTCFMNSVLQALLHAPPFRNYFLTGQRNHEVCRKRSSDRLCLLCDIYVFFS 237
GL GL N+GSTCFM+S+LQ L+H P F + ++ Q + C+ RS D+ C C +
Sbjct: 140 GLSGLINMGSTCFMSSILQCLIHNPYFIRHSMS-QIHSNNCKVRSPDK-CFSCALDKIVH 197
Query: 238 AVFSGDRTPYSPAQ------------LLYSWWQHSANLASYEQQDAHEFFISMLDGIHEN 285
++ T + + LL W+ + NLA Y QQDAHEF+ +++ IH++
Sbjct: 198 ELYGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQS 257
Query: 286 GVKARSPIKDTG-----ECHCVAHRVFSGQLRSDVTCMSCGYTS-TTYDPFMDISLNLDT 339
V K+ +C C+ H VF G L S + C C S TT DPF+D+SL
Sbjct: 258 YVLDLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLDLSL---- 313
Query: 340 GNCPSTDLANKSLKPSDNTYVSTLLGCLDLFTKPEKLGSDQKFFCENCQERQDSVKQMSI 399
D+ +K L CLD F K E+L D + C C QD++KQ+ I
Sbjct: 314 ------DIKDKK----------KLYECLDSFHKKEQL-KDFNYHCGECNSTQDAIKQLGI 356
Query: 400 KRLPLVLCLHIKRFEHFPVRRMSRKIDRYMQFPFCLDMNPYLSSSVVRNRFGNRMFAFEG 459
+LP VL L +KRFEH + +RK+D +++FP L+M Y S+ N G
Sbjct: 357 HKLPSVLVLQLKRFEHL-LNGSNRKLDDFIEFPTYLNMKNYCSTKEKDKHSEN------G 409
Query: 460 DELDTSTEFEIFAVVTHSGTLDSGHYVTYLHLK-DQWYKCDDAWITAVEEEVVRASQCYM 518
D +E+ +V+H GT++ GHY+ + + QW+K +D+ ++++ +E V Q Y+
Sbjct: 410 KVPDII--YELIGIVSHKGTVNEGHYIAFCKISGGQWFKFNDSMVSSISQEEVLKEQAYL 467
Query: 519 LFYA 522
LFY
Sbjct: 468 LFYT 471
>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 = 189 bits (479), Expect = 5e-48, Method: Compositional matrix adjust.
Identities = 121/364 (33%), Positives = 186/364 (51%), Gaps = 51/364 (14%)
Query: 178 GLRGLNNLGSTCFMNSVLQALLHAPPFRNYFLTGQRNHEVCRKRSSDRLCLLCDIYVFFS 237
GL GL N+G+TCFM+S+LQ L+H P F + ++ Q + C+ RS D+ C C +
Sbjct: 140 GLSGLINMGNTCFMSSILQCLIHNPYFIRHSMS-QIHSNNCKVRSPDK-CFSCALDKIVH 197
Query: 238 AVFSGDRTPYSPAQ------------LLYSWWQHSANLASYEQQDAHEFFISMLDGIHEN 285
++ T + + LL W+ + NLA Y QQDAHEF+ +++ IH++
Sbjct: 198 ELYGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQS 257
Query: 286 GVKARSPIKDTG-----ECHCVAHRVFSGQLRSDVTCMSCGYTS-TTYDPFMDISLNLDT 339
V K+ +C C+ H VF G L S + C C S TT DPF+D+SL
Sbjct: 258 YVLDLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLDLSL---- 313
Query: 340 GNCPSTDLANKSLKPSDNTYVSTLLGCLDLFTKPEKLGSDQKFFCENCQERQDSVKQMSI 399
D+ +K L CLD F K E+L D + C C QD++KQ+ I
Sbjct: 314 ------DIKDKK----------KLYECLDSFHKKEQL-KDFNYHCGECNSTQDAIKQLGI 356
Query: 400 KRLPLVLCLHIKRFEHFPVRRMSRKIDRYMQFPFCLDMNPYLSSSVVRNRFGNRMFAFEG 459
+LP VL L +KRFEH + +RK+D +++FP L+M Y S+ N G
Sbjct: 357 HKLPSVLVLQLKRFEHL-LNGSNRKLDDFIEFPTYLNMKNYCSTKEKDKHSEN------G 409
Query: 460 DELDTSTEFEIFAVVTHSGTLDSGHYVTYLHLK-DQWYKCDDAWITAVEEEVVRASQCYM 518
D +E+ +V+H GT++ GHY+ + + QW+K +D+ ++++ +E V Q Y+
Sbjct: 410 KVPDII--YELIGIVSHKGTVNEGHYIAFCKISGGQWFKFNDSMVSSISQEEVLKEQAYL 467
Query: 519 LFYA 522
LFY
Sbjct: 468 LFYT 471
>pdb|3N3K|A Chain A, The Catalytic Domain Of Usp8 In Complex With A Usp8
Specific Inhibitor
Length = 396
Score = 147 bits (372), Expect = 1e-35, Method: Compositional matrix adjust.
Identities = 111/376 (29%), Positives = 176/376 (46%), Gaps = 74/376 (19%)
Query: 178 GLRGLNNLGSTCFMNSVLQALLHAPPFRNYFLTGQRNHEVCRKRSSDRLCLLC------- 230
L GL NLG+TC+MNS+LQ L +AP +YF RN C + +R LL
Sbjct: 61 ALTGLRNLGNTCYMNSILQCLCNAPHLADYF---NRN---CYQDDINRSNLLGHKGEVAE 114
Query: 231 DIYVFFSAVFSGDRTPYSPAQLLYSWWQHSANLASYEQQDAHEFFISMLDGIHENGVKA- 289
+ + A+++G SP + + + A Y QQD+ E + ++DG+HE+ KA
Sbjct: 115 EFGIIMKALWTGQYRYISPKDFKITIGKINDQFAGYSQQDSQELLLFLMDGLHEDLNKAD 174
Query: 290 -RSPIKDTGECH-------------------CVAHRVFSGQLRSDVTCMSCGYTSTTYDP 329
R K+ H + +F GQ +S V C++C S T++
Sbjct: 175 NRKRYKEENNDHLDDFKAAEHAWQKHKQLNESIIVALFQGQFKSTVQCLTCHKKSRTFEA 234
Query: 330 FMDISLNLDTGNCPSTDLANKSLKPSDNTYVSTLLGCLDLFTKPEKLGSDQKFFCENCQE 389
FM +SL P +T TL CL LF+K EKL + +F+C +C+
Sbjct: 235 FMYLSL------------------PLASTSKCTLQDCLRLFSKEEKLTDNNRFYCSHCRA 276
Query: 390 RQDSVKQMSIKRLPLVLCLHIKRFEHFPVRRMSRKIDRYMQFPF-CLDMNPYLSSSVVRN 448
R+DS+K++ I +LP VL +H+KRF + R +K+ + FP LD++ Y+
Sbjct: 277 RRDSLKKIEIWKLPPVLLVHLKRFSY--DGRWKQKLQTSVDFPLENLDLSQYVIGPK--- 331
Query: 449 RFGNRMFAFEGDELDTSTEFEIFAVVTHSGTLDSGHYVTYLH--LKDQWYKCDDAWITAV 506
+ ++ +F+V H G LD GHY Y + +W+K DD ++ +
Sbjct: 332 --------------NNLKKYNLFSVSNHYGGLDGGHYTAYCKNAARQRWFKFDDHEVSDI 377
Query: 507 EEEVVRASQCYMLFYA 522
V++S Y+LFY
Sbjct: 378 SVSSVKSSAAYILFYT 393
>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 = 142 bits (357), Expect = 6e-34, Method: Compositional matrix adjust.
Identities = 102/373 (27%), Positives = 164/373 (43%), Gaps = 47/373 (12%)
Query: 178 GLRGLNNLGSTCFMNSVLQALLHAPPFRNYFLTGQRNHEVCRKRSSDRLCLLCDIYV-FF 236
GL GL NLG+T FMNS LQ L + P +YFL + E+ R + + Y
Sbjct: 7 GLCGLGNLGNTXFMNSALQCLSNTAPLTDYFLKDEYEAEINRDNPLGMKGEIAEAYAELI 66
Query: 237 SAVFSGDRTPYSPAQLLYSWWQHSANLASYEQQDAHEFFISMLDGIHE--NGVKARSPI- 293
++SG +P + + + Y+QQD+ E +LDG+HE N VK + +
Sbjct: 67 KQMWSGRDAHVAPRMFKTQVGRFAPQFSGYQQQDSQELLAFLLDGLHEDLNRVKKKPYLE 126
Query: 294 -------------KDTGECH-----CVAHRVFSGQLRSDVTCMSCGYTSTTYDPFMDISL 335
K+ E H V F G +S + C C S T+DPF ++L
Sbjct: 127 LKDANGRPDAVVAKEAWENHRLRNDSVIVDTFHGLFKSTLVCPECAKVSVTFDPFCYLTL 186
Query: 336 NLDTGNCPSTDLANKSLKPSDNTYVSTLL-GCLDLFTKPEKLGSDQKFFCENCQERQDSV 394
L + L+P + L C++LFT E LG ++C NC++ Q +
Sbjct: 187 PLPLKK--DRVMEGPMLQPQKKKKTTVALRDCIELFTTMETLGEHDPWYCPNCKKHQQAT 244
Query: 395 KQMSIKRLPLVLCLHIKRFEHFPVRRMSRKIDRYMQFPF-CLDMNPYLSSSVVRNRFGNR 453
K+ + LP +L +H+KRF + R K+D ++FP L+M+ ++ + R
Sbjct: 245 KKFDLWSLPKILVVHLKRFSY--NRYWRDKLDTVVEFPIRGLNMSEFVCNLSARPYV--- 299
Query: 454 MFAFEGDELDTSTEFEIFAVVTHSGTLDSGHYVTYL--HLKDQWYKCDDAWITAVEEEVV 511
+++ AV H G + GHY Y L +WY DD+ ++ E+ +
Sbjct: 300 --------------YDLIAVSNHYGAMGVGHYTAYAKNKLNGKWYYFDDSNVSLASEDQI 345
Query: 512 RASQCYMLFYAQK 524
Y+LFY ++
Sbjct: 346 VTKAAYVLFYQRR 358
>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 = 142 bits (357), Expect = 7e-34, Method: Compositional matrix adjust.
Identities = 117/384 (30%), Positives = 172/384 (44%), Gaps = 64/384 (16%)
Query: 163 LVSMRDLRAKSCYPLGLRGLNNLGSTCFMNSVLQALLHAPPFRNYFLTGQRNHEVCRKRS 222
LV + +KS GL GL NLG+TCFMNS+LQ L + R+Y L ++ S
Sbjct: 14 LVPRGSMNSKSAQ--GLAGLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDL-HHGS 70
Query: 223 SDRLCLLCDIYVFFSAVF-SGDRTPYSPAQLLYSWWQHSANLASYEQQDAHEFFISMLDG 281
+ L+ + ++ S SP++ +++ Y QQDA EF +LDG
Sbjct: 71 NAHTALVEEFAKLIQTIWTSSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDG 130
Query: 282 IHE--NGVKARS----------PIKDTGECHCVAH---------RVFSGQLRSDVTCMSC 320
+H N V R P + G + +F GQL+S +TC C
Sbjct: 131 LHNEVNRVTLRPKSNPENLDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDC 190
Query: 321 GYTSTTYDPFMDISLNLDTGNCPSTDLANKSLKPSDNTYVSTLLGCLDLFTKPEKLGSDQ 380
GY ST +DPF D+SL + P TL+ C+ LFTK + L D+
Sbjct: 191 GYCSTVFDPFWDLSLPIAKRGYPEV----------------TLMDCMRLFTKEDVLDGDE 234
Query: 381 KFFCENCQERQDSVKQMSIKRLPLVLCLHIKRFEHFPVRRMSRKIDRYMQFPFC-LDMNP 439
K C C+ R+ +K+ SI+R P +L LH+KRF +R + K+ ++ FP LD+
Sbjct: 235 KPTCCRCRGRKRCIKKFSIQRFPKILVLHLKRFSESRIR--TSKLTTFVNFPLRDLDL-- 290
Query: 440 YLSSSVVRNRFGNRMFAFEGDELDTSTEFEIFAVVTHSGTLDSGHYVTYLHL--KDQWYK 497
R FA E + ++AV HSGT GHY Y +W+
Sbjct: 291 -------------REFASEN---TNHAVYNLYAVSNHSGTTMGGHYTAYCRSPGTGEWHT 334
Query: 498 CDDAWITAVEEEVVRASQCYMLFY 521
+D+ +T + VR S Y+LFY
Sbjct: 335 FNDSSVTPMSSSQVRTSDAYLLFY 358
>pdb|2HD5|A Chain A, Usp2 In Complex With Ubiquitin
Length = 359
Score = 142 bits (357), Expect = 7e-34, Method: Compositional matrix adjust.
Identities = 113/369 (30%), Positives = 166/369 (44%), Gaps = 62/369 (16%)
Query: 178 GLRGLNNLGSTCFMNSVLQALLHAPPFRNYFLTGQRNHEVCRKRSSDRLCLLCDIYVFFS 237
GL GL NLG+TCFMNS+LQ L + R+Y L ++ S+ L+ +
Sbjct: 8 GLAGLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDL-HHGSNAHTALVEEFAKLIQ 66
Query: 238 AVF-SGDRTPYSPAQLLYSWWQHSANLASYEQQDAHEFFISMLDGIHE--NGVKARS--- 291
++ S SP++ +++ Y QQDA EF +LDG+H N V R
Sbjct: 67 TIWTSSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSN 126
Query: 292 -------PIKDTGECHCVAH---------RVFSGQLRSDVTCMSCGYTSTTYDPFMDISL 335
P + G + +F GQL+S +TC CGY ST +DPF D+SL
Sbjct: 127 PENLDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSL 186
Query: 336 NLDTGNCPSTDLANKSLKPSDNTYVSTLLGCLDLFTKPEKLGSDQKFFCENCQERQDSVK 395
+ P TL+ C+ LFTK + L D+K C C+ R+ +K
Sbjct: 187 PIAKRGYPEV----------------TLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRCIK 230
Query: 396 QMSIKRLPLVLCLHIKRFEHFPVRRMSRKIDRYMQFPFC-LDMNPYLSSSVVRNRFGNRM 454
+ SI+R P +L LH+KRF +R + K+ ++ FP LD+ R
Sbjct: 231 KFSIQRFPKILVLHLKRFSESRIR--TSKLTTFVNFPLRDLDL---------------RE 273
Query: 455 FAFEGDELDTSTEFEIFAVVTHSGTLDSGHYVTYLHL--KDQWYKCDDAWITAVEEEVVR 512
FA E + ++AV HSGT GHY Y +W+ +D+ +T + VR
Sbjct: 274 FASEN---TNHAVYNLYAVSNHSGTTMGGHYTAYCRSPGTGEWHTFNDSSVTPMSSSQVR 330
Query: 513 ASQCYMLFY 521
S Y+LFY
Sbjct: 331 TSDAYLLFY 339
>pdb|2GFO|A Chain A, Structure Of The Catalytic Domain Of Human Ubiquitin
Carboxyl-terminal Hydrolase 8
Length = 396
Score = 140 bits (354), Expect = 1e-33, Method: Compositional matrix adjust.
Identities = 109/376 (28%), Positives = 173/376 (46%), Gaps = 74/376 (19%)
Query: 178 GLRGLNNLGSTCFMNSVLQALLHAPPFRNYFLTGQRNHEVCRKRSSDRLCLLC------- 230
L GL NLG+TC+ NS+LQ L +AP +YF RN C + +R LL
Sbjct: 61 ALTGLRNLGNTCYXNSILQCLCNAPHLADYF---NRN---CYQDDINRSNLLGHKGEVAE 114
Query: 231 DIYVFFSAVFSGDRTPYSPAQLLYSWWQHSANLASYEQQDAHEFFISMLDGIHENGVKA- 289
+ + A+++G SP + + + A Y QQD+ E + + DG+HE+ KA
Sbjct: 115 EFGIIXKALWTGQYRYISPKDFKITIGKINDQFAGYSQQDSQELLLFLXDGLHEDLNKAD 174
Query: 290 -RSPIKDTGECH-------------------CVAHRVFSGQLRSDVTCMSCGYTSTTYDP 329
R K+ H + +F GQ +S V C++C S T++
Sbjct: 175 NRKRYKEENNDHLDDFKAAEHAWQKHKQLNESIIVALFQGQFKSTVQCLTCHKKSRTFEA 234
Query: 330 FMDISLNLDTGNCPSTDLANKSLKPSDNTYVSTLLGCLDLFTKPEKLGSDQKFFCENCQE 389
F +SL P +T TL CL LF+K EKL + +F+C +C+
Sbjct: 235 FXYLSL------------------PLASTSKCTLQDCLRLFSKEEKLTDNNRFYCSHCRA 276
Query: 390 RQDSVKQMSIKRLPLVLCLHIKRFEHFPVRRMSRKIDRYMQFPF-CLDMNPYLSSSVVRN 448
R+DS+K++ I +LP VL +H+KRF + R +K+ + FP LD++ Y+
Sbjct: 277 RRDSLKKIEIWKLPPVLLVHLKRFSY--DGRWKQKLQTSVDFPLENLDLSQYVIGPK--- 331
Query: 449 RFGNRMFAFEGDELDTSTEFEIFAVVTHSGTLDSGHYVTYLH--LKDQWYKCDDAWITAV 506
+ ++ +F+V H G LD GHY Y + +W+K DD ++ +
Sbjct: 332 --------------NNLKKYNLFSVSNHYGGLDGGHYTAYCKNAARQRWFKFDDHEVSDI 377
Query: 507 EEEVVRASQCYMLFYA 522
V++S Y+LFY
Sbjct: 378 SVSSVKSSAAYILFYT 393
>pdb|2IBI|A Chain A, Covalent Ubiquitin-Usp2 Complex
Length = 374
Score = 139 bits (349), Expect = 5e-33, Method: Compositional matrix adjust.
Identities = 114/370 (30%), Positives = 163/370 (44%), Gaps = 64/370 (17%)
Query: 178 GLRGLNNLGSTCFMNSVLQALLHAPPFRNYFLTGQRNHEVCRKRSSDRLCLLCDIYVFFS 237
GL GL NLG+TCFMNS+LQ L + R+Y L QR + S+ L + +
Sbjct: 34 GLAGLRNLGNTCFMNSILQCLSNTRELRDYCL--QRLYMRDLHHGSNAHTALVEEFAKLI 91
Query: 238 AVF--SGDRTPYSPAQLLYSWWQHSANLASYEQQDAHEFFISMLDGIHE--NGVKARS-- 291
S SP++ +++ Y QQDA EF +LDG+H N V R
Sbjct: 92 QTIWTSSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKS 151
Query: 292 --------PIKDTGECHCVAH---------RVFSGQLRSDVTCMSCGYTSTTYDPFMDIS 334
P + G + +F GQL+S +TC CGY ST +DPF D+S
Sbjct: 152 NPENLDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLS 211
Query: 335 LNLDTGNCPSTDLANKSLKPSDNTYVSTLLGCLDLFTKPEKLGSDQKFFCENCQERQDSV 394
L + P TL+ C+ LFTK + L D C C+ R+ +
Sbjct: 212 LPIAKRGYPEV----------------TLMDCMRLFTKEDVLDGDAAPTCCRCRGRKRCI 255
Query: 395 KQMSIKRLPLVLCLHIKRFEHFPVRRMSRKIDRYMQFPFC-LDMNPYLSSSVVRNRFGNR 453
K+ SI+R P +L LH+KRF +R + K+ ++ FP LD+ R
Sbjct: 256 KKFSIQRFPKILVLHLKRFSESRIR--TSKLTTFVNFPLRDLDL---------------R 298
Query: 454 MFAFEGDELDTSTEFEIFAVVTHSGTLDSGHYVTYLHL--KDQWYKCDDAWITAVEEEVV 511
FA E + ++AV HSGT GHY Y +W+ +D+ +T + V
Sbjct: 299 EFASEN---TNHAVYNLYAVSNHSGTTMGGHYTAYCRSPGTGEWHTFNDSSVTPMSSSQV 355
Query: 512 RASQCYMLFY 521
R S Y+LFY
Sbjct: 356 RTSDAYLLFY 365
>pdb|3NHE|A Chain A, High Resolution Structure (1.26a) Of Usp2a In Complex With
Ubiquitin
Length = 348
Score = 138 bits (348), Expect = 8e-33, Method: Compositional matrix adjust.
Identities = 114/370 (30%), Positives = 164/370 (44%), Gaps = 64/370 (17%)
Query: 178 GLRGLNNLGSTCFMNSVLQALLHAPPFRNYFLTGQRNHEVCRKRSSDRLCLLCDIYVFFS 237
GL GL NLG+T FMNS+LQ L + R+Y L QR + S+ L + +
Sbjct: 8 GLAGLRNLGNTXFMNSILQCLSNTRELRDYCL--QRLYMRDLHHGSNAHTALVEEFAKLI 65
Query: 238 AVF--SGDRTPYSPAQLLYSWWQHSANLASYEQQDAHEFFISMLDGIHE--NGVKARS-- 291
S SP++ +++ Y QQDA EF +LDG+H N V R
Sbjct: 66 QTIWTSSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKS 125
Query: 292 --------PIKDTGECHCVAH---------RVFSGQLRSDVTCMSCGYTSTTYDPFMDIS 334
P + G + +F GQL+S +TC CGY ST +DPF D+S
Sbjct: 126 NPENLDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLS 185
Query: 335 LNLDTGNCPSTDLANKSLKPSDNTYVSTLLGCLDLFTKPEKLGSDQKFFCENCQERQDSV 394
L + P TL+ C+ LFTK + L D+K C C+ R+ +
Sbjct: 186 LPIAKRGYPEV----------------TLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRCI 229
Query: 395 KQMSIKRLPLVLCLHIKRFEHFPVRRMSRKIDRYMQFPFC-LDMNPYLSSSVVRNRFGNR 453
K+ SI+R P +L LH+KRF +R + K+ ++ FP LD+ R
Sbjct: 230 KKFSIQRFPKILVLHLKRFSESRIR--TSKLTTFVNFPLRDLDL---------------R 272
Query: 454 MFAFEGDELDTSTEFEIFAVVTHSGTLDSGHYVTYLHL--KDQWYKCDDAWITAVEEEVV 511
FA E + ++AV HSGT GHY Y +W+ +D+ +T + V
Sbjct: 273 EFASEN---TNHAVYNLYAVSNHSGTTMGGHYTAYCRSPGTGEWHTFNDSSVTPMSSSQV 329
Query: 512 RASQCYMLFY 521
R S Y+LFY
Sbjct: 330 RTSDAYLLFY 339
>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 = 125 bits (314), Expect = 7e-29, Method: Compositional matrix adjust.
Identities = 101/383 (26%), Positives = 169/383 (44%), Gaps = 76/383 (19%)
Query: 178 GLRGLNNLGSTCFMNSVLQALLHAPPFRNYFLTGQRNHEV-CRKRSSDRLCLLCDIYVFF 236
G GL NLG+TCF+N+VLQ L P R++ L EV R+ + D+
Sbjct: 15 GHVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQELTEAFADV---I 71
Query: 237 SAVFSGDR-TPYSPAQLLYSWWQHSANLASYEQQDAHEFFISMLDGIH----ENGVKARS 291
A++ D +P + + ++ + + Y QQDA EF +++ +H G +A
Sbjct: 72 GALWHPDSCEAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRA-P 130
Query: 292 PIKDTGECHCVAHR---------------------------------VFSGQLRSDVTCM 318
PI G R +F GQL+S + C
Sbjct: 131 PILANGPVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKCQ 190
Query: 319 SCGYTSTTYDPFMDISLNLDTGNCPSTDLANKSLKPSDNTYVSTLLGCLDLFTKPEKLGS 378
+CGY STT++ F D+SL + P A + +L C +LFTK E+L S
Sbjct: 191 ACGYRSTTFEVFCDLSLPI-----PKKGFAGGKV---------SLRDCFNLFTKEEELES 236
Query: 379 DQKFFCENCQERQDSVKQMSIKRLPLVLCLHIKRFEHFPVRRMSRKIDRYMQFPFCLDMN 438
+ C+ C+++ S K+++++R P +L LH+ RF R +K + FP
Sbjct: 237 ENAPVCDRCRQKTRSTKKLTVQRFPRILVLHLNRFS--ASRGSIKKSSVGVDFP------ 288
Query: 439 PYLSSSVVRNRFGNRMFAFEGDELDTSTEFEIFAVVTHSGTLDSGHYVTYLHLKDQWYKC 498
+ R G+ F D+ + ++++A+ HSG++ GHY + W+
Sbjct: 289 ------LQRLSLGD----FASDKAGSPV-YQLYALCNHSGSVHYGHYTALCRCQTGWHVY 337
Query: 499 DDAWITAVEEEVVRASQCYMLFY 521
+D+ ++ V E V +S+ Y+LFY
Sbjct: 338 NDSRVSPVSENQVASSEGYVLFY 360
>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 = 125 bits (314), Expect = 7e-29, Method: Compositional matrix adjust.
Identities = 101/383 (26%), Positives = 169/383 (44%), Gaps = 76/383 (19%)
Query: 178 GLRGLNNLGSTCFMNSVLQALLHAPPFRNYFLTGQRNHEV-CRKRSSDRLCLLCDIYVFF 236
G GL NLG+TCF+N+VLQ L P R++ L EV R+ + D+
Sbjct: 2 GHVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQELTEAFADV---I 58
Query: 237 SAVFSGDR-TPYSPAQLLYSWWQHSANLASYEQQDAHEFFISMLDGIH----ENGVKARS 291
A++ D +P + + ++ + + Y QQDA EF +++ +H G +A
Sbjct: 59 GALWHPDSCEAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRA-P 117
Query: 292 PIKDTGECHCVAHR---------------------------------VFSGQLRSDVTCM 318
PI G R +F GQL+S + C
Sbjct: 118 PILANGPVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKCQ 177
Query: 319 SCGYTSTTYDPFMDISLNLDTGNCPSTDLANKSLKPSDNTYVSTLLGCLDLFTKPEKLGS 378
+CGY STT++ F D+SL + P A + +L C +LFTK E+L S
Sbjct: 178 ACGYRSTTFEVFCDLSLPI-----PKKGFAGGKV---------SLRDCFNLFTKEEELES 223
Query: 379 DQKFFCENCQERQDSVKQMSIKRLPLVLCLHIKRFEHFPVRRMSRKIDRYMQFPFCLDMN 438
+ C+ C+++ S K+++++R P +L LH+ RF R +K + FP
Sbjct: 224 ENAPVCDRCRQKTRSTKKLTVQRFPRILVLHLNRFS--ASRGSIKKSSVGVDFP------ 275
Query: 439 PYLSSSVVRNRFGNRMFAFEGDELDTSTEFEIFAVVTHSGTLDSGHYVTYLHLKDQWYKC 498
+ R G+ F D+ + ++++A+ HSG++ GHY + W+
Sbjct: 276 ------LQRLSLGD----FASDKAGSPV-YQLYALCNHSGSVHYGHYTALCRCQTGWHVY 324
Query: 499 DDAWITAVEEEVVRASQCYMLFY 521
+D+ ++ V E V +S+ Y+LFY
Sbjct: 325 NDSRVSPVSENQVASSEGYVLFY 347
>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 = 125 bits (313), Expect = 8e-29, Method: Compositional matrix adjust.
Identities = 101/383 (26%), Positives = 169/383 (44%), Gaps = 76/383 (19%)
Query: 178 GLRGLNNLGSTCFMNSVLQALLHAPPFRNYFLTGQRNHEV-CRKRSSDRLCLLCDIYVFF 236
G GL NLG+TCF+N+VLQ L P R++ L EV R+ + D+
Sbjct: 21 GHVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQELTEAFADV---I 77
Query: 237 SAVFSGDR-TPYSPAQLLYSWWQHSANLASYEQQDAHEFFISMLDGIH----ENGVKARS 291
A++ D +P + + ++ + + Y QQDA EF +++ +H G +A
Sbjct: 78 GALWHPDSCEAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRA-P 136
Query: 292 PIKDTGECHCVAHR---------------------------------VFSGQLRSDVTCM 318
PI G R +F GQL+S + C
Sbjct: 137 PILANGPVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKCQ 196
Query: 319 SCGYTSTTYDPFMDISLNLDTGNCPSTDLANKSLKPSDNTYVSTLLGCLDLFTKPEKLGS 378
+CGY STT++ F D+SL + P A + +L C +LFTK E+L S
Sbjct: 197 ACGYRSTTFEVFCDLSLPI-----PKKGFAGGKV---------SLRDCFNLFTKEEELES 242
Query: 379 DQKFFCENCQERQDSVKQMSIKRLPLVLCLHIKRFEHFPVRRMSRKIDRYMQFPFCLDMN 438
+ C+ C+++ S K+++++R P +L LH+ RF R +K + FP
Sbjct: 243 ENAPVCDRCRQKTRSTKKLTVQRFPRILVLHLNRFSA--SRGSIKKSSVGVDFP------ 294
Query: 439 PYLSSSVVRNRFGNRMFAFEGDELDTSTEFEIFAVVTHSGTLDSGHYVTYLHLKDQWYKC 498
+ R G+ F D+ + ++++A+ HSG++ GHY + W+
Sbjct: 295 ------LQRLSLGD----FASDKAGSPV-YQLYALCNHSGSVHYGHYTALCRCQTGWHVY 343
Query: 499 DDAWITAVEEEVVRASQCYMLFY 521
+D+ ++ V E V +S+ Y+LFY
Sbjct: 344 NDSRVSPVSENQVASSEGYVLFY 366
>pdb|1NBF|A Chain A, Crystal Structure Of A Ubp-Family Deubiquitinating Enzyme
In Isolation And In Complex With Ubiquitin Aldehyde
pdb|1NBF|B Chain B, Crystal Structure Of A Ubp-Family Deubiquitinating Enzyme
In Isolation And In Complex With Ubiquitin Aldehyde
pdb|1NBF|E Chain E, Crystal Structure Of A Ubp-Family Deubiquitinating Enzyme
In Isolation And In Complex With Ubiquitin Aldehyde
Length = 353
Score = 74.7 bits (182), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 89/344 (25%), Positives = 140/344 (40%), Gaps = 69/344 (20%)
Query: 178 GLRGLNNLGSTCFMNSVLQALLHAPPFRN--YFLTGQRNHEVCRKRSSDRLCLLCDIYVF 235
G GL N G+TC+MNS+LQ L R Y + + + S + L VF
Sbjct: 5 GYVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPTEGD-------DSSKSVPLALQRVF 57
Query: 236 FSAVFSGDRTPYSPAQLLYSW-WQHSANLASYEQQDAHEFFISMLDGIHENGVKARSPIK 294
+ S P +L S+ W+ L S+ Q D E +LD + EN +K
Sbjct: 58 YELQHSD--KPVGTKKLTKSFGWE---TLDSFMQHDVQELCRVLLDNV-ENKMK------ 105
Query: 295 DTGEC-HCVAHRVFSGQLRSDVTCMSCGYTSTTYDPFMDISLNLDTGNCPSTDLANKSLK 353
G C ++F G++ S + C Y S + + DI L S+K
Sbjct: 106 --GTCVEGTIPKLFRGKMVSYIQCKEVDYRSDRREDYYDIQL---------------SIK 148
Query: 354 PSDNTYVSTLLGCLDLFTKPEKLGSDQKFFC--ENCQERQDSVKQMSIKRLPLVLCLHIK 411
N + S + + E+L D K+ QE + VK ++ LP VL L +
Sbjct: 149 GKKNIFESFV-----DYVAVEQLDGDNKYDAGEHGLQEAEKGVKFLT---LPPVLHLQLM 200
Query: 412 RFEHFPVRRMSRKIDRYMQFPFCLDMNPYLSSSVVRNRFGNRMFAFEGDELDTSTEFEIF 471
RF + P + KI+ +FP L ++ +L + ++ + +
Sbjct: 201 RFMYDPQTDQNIKINDRFEFPEQLPLDEFLQKTDPKD----------------PANYILH 244
Query: 472 AVVTHSGTLDSGHYVTYLHLK--DQWYKCDDAWITA-VEEEVVR 512
AV+ HSG GHYV YL+ K +W K DD ++ +EE +
Sbjct: 245 AVLVHSGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIE 288
>pdb|2F1Z|A Chain A, Crystal Structure Of Hausp
pdb|2F1Z|B Chain B, Crystal Structure Of Hausp
Length = 522
Score = 72.4 bits (176), Expect = 6e-13, Method: Compositional matrix adjust.
Identities = 91/346 (26%), Positives = 139/346 (40%), Gaps = 73/346 (21%)
Query: 178 GLRGLNNLGSTCFMNSVLQALLHAPPFRNYFLTGQRNHEV----CRKRSSDRLCLLCDIY 233
G GL N G+TC+MNS+LQ L F T Q V S + L
Sbjct: 174 GYVGLKNQGATCYMNSLLQTL---------FFTNQLRKAVYMMPTEGDDSSKSVPLALQR 224
Query: 234 VFFSAVFSGDRTPYSPAQLLYSW-WQHSANLASYEQQDAHEFFISMLDGIHENGVKARSP 292
VF+ S P +L S+ W+ L S+ Q D E +LD + EN +K
Sbjct: 225 VFYELQHSD--KPVGTKKLTKSFGWE---TLDSFMQHDVQELCRVLLDNV-ENKMK---- 274
Query: 293 IKDTGEC-HCVAHRVFSGQLRSDVTCMSCGYTSTTYDPFMDISLNLDTGNCPSTDLANKS 351
G C ++F G++ S + C Y S + + DI L S
Sbjct: 275 ----GTCVEGTIPKLFRGKMVSYIQCKEVDYRSDRREDYYDIQL---------------S 315
Query: 352 LKPSDNTYVSTLLGCLDLFTKPEKLGSDQKFFC--ENCQERQDSVKQMSIKRLPLVLCLH 409
+K N + S + + E+L D K+ QE + VK ++ LP VL L
Sbjct: 316 IKGKKNIFESFV-----DYVAVEQLDGDNKYDAGEHGLQEAEKGVKFLT---LPPVLHLQ 367
Query: 410 IKRFEHFPVRRMSRKIDRYMQFPFCLDMNPYLSSSVVRNRFGNRMFAFEGDELDTSTEFE 469
+ RF + P + KI+ +FP L ++ +L + ++ +
Sbjct: 368 LMRFMYDPQTDQNIKINDRFEFPEQLPLDEFLQKTDPKD----------------PANYI 411
Query: 470 IFAVVTHSGTLDSGHYVTYLHLK--DQWYKCDDAWITA-VEEEVVR 512
+ AV+ HSG GHYV YL+ K +W K DD ++ +EE +
Sbjct: 412 LHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIE 457
>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 = 72.0 bits (175), Expect = 9e-13, Method: Compositional matrix adjust.
Identities = 90/346 (26%), Positives = 136/346 (39%), Gaps = 73/346 (21%)
Query: 178 GLRGLNNLGSTCFMNSVLQALLHAPPFRNYFLTGQRNHEV----CRKRSSDRLCLLCDIY 233
G GL N G+TC+ NS+LQ L F T Q V S + L
Sbjct: 5 GYVGLKNQGATCYXNSLLQTL---------FFTNQLRKAVYXXPTEGDDSSKSVPLALQR 55
Query: 234 VFFSAVFSGDRTPYSPAQLLYSW-WQHSANLASYEQQDAHEFFISMLDGIHENGVKARSP 292
VF+ S P +L S+ W+ L S+ Q D E +LD + EN
Sbjct: 56 VFYELQHSD--KPVGTKKLTKSFGWE---TLDSFXQHDVQELCRVLLDNV-EN------- 102
Query: 293 IKDTGEC-HCVAHRVFSGQLRSDVTCMSCGYTSTTYDPFMDISLNLDTGNCPSTDLANKS 351
K G C ++F G+ S + C Y S + + DI L S
Sbjct: 103 -KXKGTCVEGTIPKLFRGKXVSYIQCKEVDYRSDRREDYYDIQL---------------S 146
Query: 352 LKPSDNTYVSTLLGCLDLFTKPEKLGSDQKFFC--ENCQERQDSVKQMSIKRLPLVLCLH 409
+K N + S + + E+L D K+ QE + VK ++ LP VL L
Sbjct: 147 IKGKKNIFESFV-----DYVAVEQLDGDNKYDAGEHGLQEAEKGVKFLT---LPPVLHLQ 198
Query: 410 IKRFEHFPVRRMSRKIDRYMQFPFCLDMNPYLSSSVVRNRFGNRMFAFEGDELDTSTEFE 469
+ RF + P + KI+ +FP L ++ +L + ++ +
Sbjct: 199 LXRFXYDPQTDQNIKINDRFEFPEQLPLDEFLQKTDPKD----------------PANYI 242
Query: 470 IFAVVTHSGTLDSGHYVTYLHLK--DQWYKCDDAWITA-VEEEVVR 512
+ AV+ HSG GHYV YL+ K +W K DD ++ +EE +
Sbjct: 243 LHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIE 288
>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 = 56.2 bits (134), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 91/404 (22%), Positives = 157/404 (38%), Gaps = 90/404 (22%)
Query: 181 GLNNLGSTCFMNSVLQALLHAPPFRNYFLTGQRNHEVCRKRSSDRLCLLCDIYVFFSAVF 240
GL NLG+TC+MN+ +Q + P ++ R+S + I +F
Sbjct: 16 GLTNLGNTCYMNATVQCIRSVPELKDAL-----KRYAGALRASGEMASAQYITAALRDLF 70
Query: 241 -SGDRTPYS--PAQLL------YSWWQHSANLASYEQQDAHEFFISM-------LDGIHE 284
S D+T S P LL + + Y QQDA+E +I M L+ I +
Sbjct: 71 DSMDKTSSSIPPIILLQFLHMAFPQFAEKGEQGQYLQQDANECWIQMMRVLQQKLEAIED 130
Query: 285 NGVKARSPIKDT----GECHCVAHRVFSGQLRSDVTCMSCGYTSTTYDPFMDISLNLDTG 340
+ VK + + + + F + + + C T + L+
Sbjct: 131 DSVKETDSSSASAATPSKKKSLIDQFFGVEFETTMKCTESEEEEVTKGKENQLQLS---- 186
Query: 341 NCPSTDLANKSLKPSDNTYVSTLLGCLDLFTKPEKLGSDQKFFCENCQERQDSVKQMSIK 400
C N+ +K Y+ T L +L + Q +K I
Sbjct: 187 -C----FINQEVK-----YLFTGLKL--------RLQEEITKQSPTLQRNALYIKSSKIS 228
Query: 401 RLPLVLCLHIKRFEHFPVRRMSRKIDRYMQFPFCLDM----NPYLSSSVV--RNRFGN-- 452
RLP L + + RF + ++ K+ + ++FP LDM P L +V R++F +
Sbjct: 229 RLPAYLTIQMVRFFYKEKESVNAKVLKDVKFPLMLDMYELCTPELQEKMVSFRSKFKDLE 288
Query: 453 -----------------------RMFAFEGDELDTST--EFEIFAVVTHSG-TLDSGHYV 486
F+F D++ ++ +++ AV+TH G + SGHYV
Sbjct: 289 DKKVNQQPNTSDKKSSPQKEVKYEPFSF-ADDIGSNNCGYYDLQAVLTHQGRSSSSGHYV 347
Query: 487 TYLHLK-DQWYKCDDAWITAVE-EEVVRASQ------CYMLFYA 522
+++ K D+W K DD ++ V E+++R S Y+L Y
Sbjct: 348 SWVKRKQDEWIKFDDDKVSIVTPEDILRLSGGGDWHIAYVLLYG 391
>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
Length = 854
Score = 56.2 bits (134), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 79/398 (19%), Positives = 158/398 (39%), Gaps = 83/398 (20%)
Query: 88 ENGHDIAVDI-----ERSELYCVLCCDQVYDPDFDKIVMLKHLMDLPRSGNGVDVSAGRR 142
E G+ +AV + + +++Y D V DP + +HL S G+D+ +
Sbjct: 258 ETGYPLAVKLGTITPDGADVYSYDEDDMVLDPS-----LAEHL-----SHFGIDM---LK 304
Query: 143 SSKRRRLCSALELDLKK---TKQLVSMRDLRAKSCYPLGLRGLNNLGSTCFMNSVLQALL 199
K + + LE+D+ + +L+ + K + G G+ NLG++C++NSV+Q L
Sbjct: 305 MQKTDKTMTELEIDMNQRIGEWELIQESGVPLKPLFGPGYTGIRNLGNSCYLNSVVQVLF 364
Query: 200 HAPPFRNYFLTGQRNHEVCRKRSSD-------RLCLLCDIYVFFSAVFS--------GDR 244
P F+ ++ + ++ + +D ++ L + S +S G+R
Sbjct: 365 SIPDFQRKYV--DKLEKIFQNAPTDPTQDFSTQVAKLG--HGLLSGEYSKPVPESGDGER 420
Query: 245 TP--------YSPAQLLYSWWQHSANLASYEQQDAHEFFISMLDGIHENGVKARSPIKDT 296
P +P + ++ QQDA EFF+ +++ + N + +P
Sbjct: 421 VPEQKEVQDGIAPRMFKALIGKGHPEFSTNRQQDAQEFFLHLINMVERNCRSSENP---- 476
Query: 297 GECHCVAHRVFSGQLRSDVTCMSCGYTSTT--YDPFMDISLNLDTG-------------- 340
+ VF + + C++ T D M + + +D
Sbjct: 477 -------NEVFRFLVEEKIKCLATEKVKYTQRVDYIMQLPVPMDAALNKEELLEYEEKKR 529
Query: 341 NCPSTDLANKSLKPSDNTYVSTLLGCLDLFTKPEKLGSDQKFFCENCQERQDSVKQMSIK 400
+A L + + S CL+ + PE++ F+ Q + +VK
Sbjct: 530 QAEEEKMALPELVRAQVPFSS----CLEAYGAPEQV---DDFWSTALQAKSVAVKTTRFA 582
Query: 401 RLPLVLCLHIKRFEHFPVRRMSRKIDRYMQFPFCLDMN 438
P L + IK+F F + + +K+D ++ P LD++
Sbjct: 583 SFPDYLVIQIKKF-TFGLDWVPKKLDVSIEMPEELDIS 619
Score = 30.0 bits (66), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 27/47 (57%), Gaps = 1/47 (2%)
Query: 463 DTSTEFEIFAVVTHSGTLDS-GHYVTYLHLKDQWYKCDDAWITAVEE 508
D ++++FA ++H GT GHYV ++ + +W +D + A E+
Sbjct: 792 DGPGKYQLFAFISHMGTSTMCGHYVCHIKKEGRWVIYNDQKVCASEK 838
>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 = 36.6 bits (83), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 60/281 (21%), Positives = 99/281 (35%), Gaps = 63/281 (22%)
Query: 181 GLNNLGSTCFMNSVLQALLHAPPFRNYFLTGQRNHEVCRKRSSDRLC---LLCDIYVFFS 237
G N G+TC++N+ LQAL R+ L + V + D ++ + F
Sbjct: 26 GFKNXGNTCYLNATLQALYRVNDLRDXILNYNPSQGVSNSGAQDEEIHKQIVIEXKRCFE 85
Query: 238 AVFSGDRTPYSPAQLLYS-------WWQHSANLASYEQQDAHEFFISML--------DGI 282
+ + P LL + + + + Y+QQDA E F + D
Sbjct: 86 NLQNKSFKSVLPVVLLNTLRKCYPQFAERDSQGGFYKQQDAEELFTQLFHSXSIVFGDKF 145
Query: 283 HEN-GVKARSPIKDTGECHCVAHRVFSGQLRSDVTCMSCGYTSTTYDPFMDISLNLDTGN 341
E+ ++ ++ IKDT + + V + S + C G T+ + ++
Sbjct: 146 SEDFRIQFKTTIKDTANDNDIT--VKENESDSKLQCHISGTTNFXRNGLLE--------- 194
Query: 342 CPSTDLANKSLKPSDNTYVSTLLGCLDLFTKPEKLGSDQKFFCENCQERQDSVKQMSIKR 401
L K K SD L G +++ +K I R
Sbjct: 195 ----GLNEKIEKRSD------LTGANSIYSVEKK-----------------------ISR 221
Query: 402 LPLVLCLHIKRFEHFPVRRMSRKIDRYMQFPFCLDMNPYLS 442
LP L + RF KI R + FPF LD+ L+
Sbjct: 222 LPKFLTVQYVRFFWKRSTNKKSKILRKVVFPFQLDVADXLT 262
Score = 35.4 bits (80), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 30/50 (60%), Gaps = 4/50 (8%)
Query: 468 FEIFAVVTHSGT-LDSGHYVTYLHLK---DQWYKCDDAWITAVEEEVVRA 513
+ + V+TH G +SGHY ++ + ++WYK +D ++ VE+E + +
Sbjct: 346 YNLIGVITHQGANSESGHYQAFIRDELDENKWYKFNDDKVSVVEKEKIES 395
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
0.324 0.137 0.434
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,014,788
Number of Sequences: 62578
Number of extensions: 632197
Number of successful extensions: 1538
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 1436
Number of HSP's gapped (non-prelim): 31
length of query: 553
length of database: 14,973,337
effective HSP length: 104
effective length of query: 449
effective length of database: 8,465,225
effective search space: 3800886025
effective search space used: 3800886025
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 54 (25.4 bits)