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= 002523
(912 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 = 219 bits (559), Expect = 4e-57, Method: Compositional matrix adjust.
Identities = 106/184 (57%), Positives = 129/184 (70%), Gaps = 1/184 (0%)
Query: 350 FMNSAIQCLAHTPEIVDYFLGD-YQKEINYENPLGLNGELALAFGDLLRKLWAPGGIPVA 408
FMNSA+QCL++T + DYFL D Y+ EIN +NPLG+ GE+A A+ +L++++W+ VA
Sbjct: 19 FMNSALQCLSNTAPLTDYFLKDEYEAEINRDNPLGMKGEIAEAYAELIKQMWSGRDAHVA 78
Query: 409 PRMFKLKLANFAPQFSGYNQHDSQEFLAFLLDGLHEDLNRVKCKPYLEAKDAXXXXXXXX 468
PRMFK ++ FAPQFSGY Q DSQE LAFLLDGLHEDLNRVK KPYLE KDA
Sbjct: 79 PRMFKTQVGRFAPQFSGYQQQDSQELLAFLLDGLHEDLNRVKKKPYLELKDANGRPDAVV 138
Query: 469 XXXYWRNHRARNDSIIVDLCQGQYRSMLVCPVCNKVSVTFDPLMYLSLPIPSTTMRTMTV 528
W NHR RNDS+IVD G ++S LVCP C KVSVTFDP YL+LP+P R M
Sbjct: 139 AKEAWENHRLRNDSVIVDTFHGLFKSTLVCPECAKVSVTFDPFCYLTLPLPLKKDRVMEG 198
Query: 529 TVLS 532
+L
Sbjct: 199 PMLQ 202
Score = 137 bits (346), Expect = 2e-32, Method: Compositional matrix adjust.
Identities = 66/116 (56%), Positives = 81/116 (69%), Gaps = 7/116 (6%)
Query: 787 SVSLYKCLEAFLKEEPLGPEDMWYCPRCKKHWQASKKLDLWRSPDILVIHLKRFSFSRYF 846
+V+L C+E F E LG D WYCP CKKH QA+KK DLW P ILV+HLKRFS++RY+
Sbjct: 210 TVALRDCIELFTTMETLGEHDPWYCPNCKKHQQATKKFDLWSLPKILVVHLKRFSYNRYW 269
Query: 847 KSKLDTYVDFPIDDLDLSNYVCCKNSQLSNR---YVLYAISNHYGGMGGGHYTAFV 899
+ KLDT V+FPI L++S +VC LS R Y L A+SNHYG MG GHYTA+
Sbjct: 270 RDKLDTVVEFPIRGLNMSEFVC----NLSARPYVYDLIAVSNHYGAMGVGHYTAYA 321
>pdb|3N3K|A Chain A, The Catalytic Domain Of Usp8 In Complex With A Usp8
Specific Inhibitor
Length = 396
Score = 152 bits (383), Expect = 1e-36, Method: Compositional matrix adjust.
Identities = 75/179 (41%), Positives = 109/179 (60%), Gaps = 1/179 (0%)
Query: 349 CFMNSAIQCLAHTPEIVDYFLGD-YQKEINYENPLGLNGELALAFGDLLRKLWAPGGIPV 407
C+MNS +QCL + P + DYF + YQ +IN N LG GE+A FG +++ LW +
Sbjct: 72 CYMNSILQCLCNAPHLADYFNRNCYQDDINRSNLLGHKGEVAEEFGIIMKALWTGQYRYI 131
Query: 408 APRMFKLKLANFAPQFSGYNQHDSQEFLAFLLDGLHEDLNRVKCKPYLEAKDAXXXXXXX 467
+P+ FK+ + QF+GY+Q DSQE L FL+DGLHEDLN+ + + ++
Sbjct: 132 SPKDFKITIGKINDQFAGYSQQDSQELLLFLMDGLHEDLNKADNRKRYKEENNDHLDDFK 191
Query: 468 XXXXYWRNHRARNDSIIVDLCQGQYRSMLVCPVCNKVSVTFDPLMYLSLPIPSTTMRTM 526
W+ H+ N+SIIV L QGQ++S + C C+K S TF+ MYLSLP+ ST+ T+
Sbjct: 192 AAEHAWQKHKQLNESIIVALFQGQFKSTVQCLTCHKKSRTFEAFMYLSLPLASTSKCTL 250
Score = 112 bits (280), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 54/123 (43%), Positives = 80/123 (65%), Gaps = 4/123 (3%)
Query: 779 LFTRMPPESVS---LYKCLEAFLKEEPLGPEDMWYCPRCKKHWQASKKLDLWRSPDILVI 835
++ +P S S L CL F KEE L + +YC C+ + KK+++W+ P +L++
Sbjct: 236 MYLSLPLASTSKCTLQDCLRLFSKEEKLTDNNRFYCSHCRARRDSLKKIEIWKLPPVLLV 295
Query: 836 HLKRFSFSRYFKSKLDTYVDFPIDDLDLSNYVCCKNSQLSNRYVLYAISNHYGGMGGGHY 895
HLKRFS+ +K KL T VDFP+++LDLS YV + L +Y L+++SNHYGG+ GGHY
Sbjct: 296 HLKRFSYDGRWKQKLQTSVDFPLENLDLSQYVIGPKNNLK-KYNLFSVSNHYGGLDGGHY 354
Query: 896 TAF 898
TA+
Sbjct: 355 TAY 357
>pdb|2GFO|A Chain A, Structure Of The Catalytic Domain Of Human Ubiquitin
Carboxyl-terminal Hydrolase 8
Length = 396
Score = 144 bits (364), Expect = 2e-34, Method: Compositional matrix adjust.
Identities = 73/179 (40%), Positives = 105/179 (58%), Gaps = 1/179 (0%)
Query: 349 CFMNSAIQCLAHTPEIVDYFLGD-YQKEINYENPLGLNGELALAFGDLLRKLWAPGGIPV 407
C+ NS +QCL + P + DYF + YQ +IN N LG GE+A FG + + LW +
Sbjct: 72 CYXNSILQCLCNAPHLADYFNRNCYQDDINRSNLLGHKGEVAEEFGIIXKALWTGQYRYI 131
Query: 408 APRMFKLKLANFAPQFSGYNQHDSQEFLAFLLDGLHEDLNRVKCKPYLEAKDAXXXXXXX 467
+P+ FK+ + QF+GY+Q DSQE L FL DGLHEDLN+ + + ++
Sbjct: 132 SPKDFKITIGKINDQFAGYSQQDSQELLLFLXDGLHEDLNKADNRKRYKEENNDHLDDFK 191
Query: 468 XXXXYWRNHRARNDSIIVDLCQGQYRSMLVCPVCNKVSVTFDPLMYLSLPIPSTTMRTM 526
W+ H+ N+SIIV L QGQ++S + C C+K S TF+ YLSLP+ ST+ T+
Sbjct: 192 AAEHAWQKHKQLNESIIVALFQGQFKSTVQCLTCHKKSRTFEAFXYLSLPLASTSKCTL 250
Score = 111 bits (278), Expect = 2e-24, Method: Compositional matrix adjust.
Identities = 51/110 (46%), Positives = 75/110 (68%), Gaps = 1/110 (0%)
Query: 789 SLYKCLEAFLKEEPLGPEDMWYCPRCKKHWQASKKLDLWRSPDILVIHLKRFSFSRYFKS 848
+L CL F KEE L + +YC C+ + KK+++W+ P +L++HLKRFS+ +K
Sbjct: 249 TLQDCLRLFSKEEKLTDNNRFYCSHCRARRDSLKKIEIWKLPPVLLVHLKRFSYDGRWKQ 308
Query: 849 KLDTYVDFPIDDLDLSNYVCCKNSQLSNRYVLYAISNHYGGMGGGHYTAF 898
KL T VDFP+++LDLS YV + L +Y L+++SNHYGG+ GGHYTA+
Sbjct: 309 KLQTSVDFPLENLDLSQYVIGPKNNLK-KYNLFSVSNHYGGLDGGHYTAY 357
>pdb|2HD5|A Chain A, Usp2 In Complex With Ubiquitin
Length = 359
Score = 127 bits (320), Expect = 2e-29, Method: Compositional matrix adjust.
Identities = 72/175 (41%), Positives = 99/175 (56%), Gaps = 10/175 (5%)
Query: 349 CFMNSAIQCLAHTPEIVDYFLGD-YQKEINYENPLGLNGELALA--FGDLLRKLW--APG 403
CFMNS +QCL++T E+ DY L Y +++++ G N AL F L++ +W +P
Sbjct: 19 CFMNSILQCLSNTRELRDYCLQRLYMRDLHH----GSNAHTALVEEFAKLIQTIWTSSPN 74
Query: 404 GIPVAPRMFKLKLANFAPQFSGYNQHDSQEFLAFLLDGLHEDLNRVKCKPYLEAKDAXXX 463
+ V+P FK ++ +AP+F GYNQ D+QEFL FLLDGLH ++NRV +P ++
Sbjct: 75 DV-VSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPENLDHL 133
Query: 464 XXXXXXXXYWRNHRARNDSIIVDLCQGQYRSMLVCPVCNKVSVTFDPLMYLSLPI 518
WR + R DS I DL GQ +S L C C S FDP LSLPI
Sbjct: 134 PDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPI 188
Score = 82.8 bits (203), Expect = 8e-16, Method: Compositional matrix adjust.
Identities = 54/116 (46%), Positives = 71/116 (61%), Gaps = 7/116 (6%)
Query: 785 PESVSLYKCLEAFLKEEPLGPEDMWYCPRCKKHWQASKKLDLWRSPDILVIHLKRFSFSR 844
PE V+L C+ F KE+ L ++ C RC+ + KK + R P ILV+HLKRFS SR
Sbjct: 194 PE-VTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKILVLHLKRFSESR 252
Query: 845 YFKSKLDTYVDFPIDDLDLSNYVCCKNSQLSNR--YVLYAISNHYGGMGGGHYTAF 898
SKL T+V+FP+ DLDL + S+ +N Y LYA+SNH G GGHYTA+
Sbjct: 253 IRTSKLTTFVNFPLRDLDLREFA----SENTNHAVYNLYAVSNHSGTTMGGHYTAY 304
>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 = 127 bits (320), Expect = 2e-29, Method: Compositional matrix adjust.
Identities = 72/175 (41%), Positives = 99/175 (56%), Gaps = 10/175 (5%)
Query: 349 CFMNSAIQCLAHTPEIVDYFLGD-YQKEINYENPLGLNGELALA--FGDLLRKLW--APG 403
CFMNS +QCL++T E+ DY L Y +++++ G N AL F L++ +W +P
Sbjct: 38 CFMNSILQCLSNTRELRDYCLQRLYMRDLHH----GSNAHTALVEEFAKLIQTIWTSSPN 93
Query: 404 GIPVAPRMFKLKLANFAPQFSGYNQHDSQEFLAFLLDGLHEDLNRVKCKPYLEAKDAXXX 463
+ V+P FK ++ +AP+F GYNQ D+QEFL FLLDGLH ++NRV +P ++
Sbjct: 94 DV-VSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPENLDHL 152
Query: 464 XXXXXXXXYWRNHRARNDSIIVDLCQGQYRSMLVCPVCNKVSVTFDPLMYLSLPI 518
WR + R DS I DL GQ +S L C C S FDP LSLPI
Sbjct: 153 PDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPI 207
Score = 82.8 bits (203), Expect = 8e-16, Method: Compositional matrix adjust.
Identities = 55/126 (43%), Positives = 73/126 (57%), Gaps = 7/126 (5%)
Query: 785 PESVSLYKCLEAFLKEEPLGPEDMWYCPRCKKHWQASKKLDLWRSPDILVIHLKRFSFSR 844
PE V+L C+ F KE+ L ++ C RC+ + KK + R P ILV+HLKRFS SR
Sbjct: 213 PE-VTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKILVLHLKRFSESR 271
Query: 845 YFKSKLDTYVDFPIDDLDLSNYVCCKNSQLSNR--YVLYAISNHYGGMGGGHYTAFVDVS 902
SKL T+V+FP+ DLDL + S+ +N Y LYA+SNH G GGHYTA+
Sbjct: 272 IRTSKLTTFVNFPLRDLDLREFA----SENTNHAVYNLYAVSNHSGTTMGGHYTAYCRSP 327
Query: 903 CVYSFH 908
+H
Sbjct: 328 GTGEWH 333
>pdb|2IBI|A Chain A, Covalent Ubiquitin-Usp2 Complex
Length = 374
Score = 127 bits (319), Expect = 3e-29, Method: Compositional matrix adjust.
Identities = 72/175 (41%), Positives = 99/175 (56%), Gaps = 10/175 (5%)
Query: 349 CFMNSAIQCLAHTPEIVDYFLGD-YQKEINYENPLGLNGELALA--FGDLLRKLW--APG 403
CFMNS +QCL++T E+ DY L Y +++++ G N AL F L++ +W +P
Sbjct: 45 CFMNSILQCLSNTRELRDYCLQRLYMRDLHH----GSNAHTALVEEFAKLIQTIWTSSPN 100
Query: 404 GIPVAPRMFKLKLANFAPQFSGYNQHDSQEFLAFLLDGLHEDLNRVKCKPYLEAKDAXXX 463
+ V+P FK ++ +AP+F GYNQ D+QEFL FLLDGLH ++NRV +P ++
Sbjct: 101 DV-VSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPENLDHL 159
Query: 464 XXXXXXXXYWRNHRARNDSIIVDLCQGQYRSMLVCPVCNKVSVTFDPLMYLSLPI 518
WR + R DS I DL GQ +S L C C S FDP LSLPI
Sbjct: 160 PDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPI 214
Score = 81.6 bits (200), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 55/126 (43%), Positives = 72/126 (57%), Gaps = 7/126 (5%)
Query: 785 PESVSLYKCLEAFLKEEPLGPEDMWYCPRCKKHWQASKKLDLWRSPDILVIHLKRFSFSR 844
PE V+L C+ F KE+ L + C RC+ + KK + R P ILV+HLKRFS SR
Sbjct: 220 PE-VTLMDCMRLFTKEDVLDGDAAPTCCRCRGRKRCIKKFSIQRFPKILVLHLKRFSESR 278
Query: 845 YFKSKLDTYVDFPIDDLDLSNYVCCKNSQLSNR--YVLYAISNHYGGMGGGHYTAFVDVS 902
SKL T+V+FP+ DLDL + S+ +N Y LYA+SNH G GGHYTA+
Sbjct: 279 IRTSKLTTFVNFPLRDLDLREFA----SENTNHAVYNLYAVSNHSGTTMGGHYTAYCRSP 334
Query: 903 CVYSFH 908
+H
Sbjct: 335 GTGEWH 340
>pdb|3NHE|A Chain A, High Resolution Structure (1.26a) Of Usp2a In Complex With
Ubiquitin
Length = 348
Score = 124 bits (311), Expect = 2e-28, Method: Compositional matrix adjust.
Identities = 71/174 (40%), Positives = 98/174 (56%), Gaps = 10/174 (5%)
Query: 350 FMNSAIQCLAHTPEIVDYFLGD-YQKEINYENPLGLNGELALA--FGDLLRKLW--APGG 404
FMNS +QCL++T E+ DY L Y +++++ G N AL F L++ +W +P
Sbjct: 20 FMNSILQCLSNTRELRDYCLQRLYMRDLHH----GSNAHTALVEEFAKLIQTIWTSSPND 75
Query: 405 IPVAPRMFKLKLANFAPQFSGYNQHDSQEFLAFLLDGLHEDLNRVKCKPYLEAKDAXXXX 464
+ V+P FK ++ +AP+F GYNQ D+QEFL FLLDGLH ++NRV +P ++
Sbjct: 76 V-VSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPENLDHLP 134
Query: 465 XXXXXXXYWRNHRARNDSIIVDLCQGQYRSMLVCPVCNKVSVTFDPLMYLSLPI 518
WR + R DS I DL GQ +S L C C S FDP LSLPI
Sbjct: 135 DDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPI 188
Score = 82.8 bits (203), Expect = 8e-16, Method: Compositional matrix adjust.
Identities = 54/116 (46%), Positives = 71/116 (61%), Gaps = 7/116 (6%)
Query: 785 PESVSLYKCLEAFLKEEPLGPEDMWYCPRCKKHWQASKKLDLWRSPDILVIHLKRFSFSR 844
PE V+L C+ F KE+ L ++ C RC+ + KK + R P ILV+HLKRFS SR
Sbjct: 194 PE-VTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKILVLHLKRFSESR 252
Query: 845 YFKSKLDTYVDFPIDDLDLSNYVCCKNSQLSNR--YVLYAISNHYGGMGGGHYTAF 898
SKL T+V+FP+ DLDL + S+ +N Y LYA+SNH G GGHYTA+
Sbjct: 253 IRTSKLTTFVNFPLRDLDLREFA----SENTNHAVYNLYAVSNHSGTTMGGHYTAY 304
>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 = 97.8 bits (242), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 65/199 (32%), Positives = 91/199 (45%), Gaps = 20/199 (10%)
Query: 349 CFMNSAIQCLAHTPEIVDYFLGDYQKEINYENPLGLNG-ELALAFGDLLRKLWAPGGI-P 406
CF+N+ +QCL+ T + D+ L +++ E P G EL AF D++ LW P
Sbjct: 13 CFLNAVLQCLSSTRPLRDFCL---RRDFRQEVPGGGRAQELTEAFADVIGALWHPDSCEA 69
Query: 407 VAPRMFKLKLANFAPQFSGYNQHDSQEFLAFLLDGLHEDLNR--VKCKPYLEAKDAXXXX 464
V P F+ + P FSGY+Q D+QEFL L++ LH ++NR + P L
Sbjct: 70 VNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRAPPILANGPVPSPP 129
Query: 465 XXX-------------XXXXYWRNHRARNDSIIVDLCQGQYRSMLVCPVCNKVSVTFDPL 511
W+ + R DS IVDL GQ +S L C C S TF+
Sbjct: 130 RRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKCQACGYRSTTFEVF 189
Query: 512 MYLSLPIPSTTMRTMTVTV 530
LSLPIP V++
Sbjct: 190 CDLSLPIPKKGFAGGKVSL 208
Score = 86.7 bits (213), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 51/122 (41%), Positives = 66/122 (54%), Gaps = 4/122 (3%)
Query: 788 VSLYKCLEAFLKEEPLGPEDMWYCPRCKKHWQASKKLDLWRSPDILVIHLKRFSFSRYFK 847
VSL C F KEE L E+ C RC++ +++KKL + R P ILV+HL RFS SR
Sbjct: 206 VSLRDCFNLFTKEEELESENAPVCDRCRQKTRSTKKLTVQRFPRILVLHLNRFSASRGSI 265
Query: 848 SKLDTYVDFPIDDLDLSNYVCCKNSQLSNRYVLYAISNHYGGMGGGHYTAFVDVSCVYSF 907
K VDFP+ L L ++ K S Y LYA+ NH G + GHYTA C +
Sbjct: 266 KKSSVGVDFPLQRLSLGDFASDKAG--SPVYQLYALCNHSGSVHYGHYTAL--CRCQTGW 321
Query: 908 HI 909
H+
Sbjct: 322 HV 323
>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 = 97.8 bits (242), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 65/199 (32%), Positives = 92/199 (46%), Gaps = 20/199 (10%)
Query: 349 CFMNSAIQCLAHTPEIVDYFLGDYQKEINYENPLGLNG-ELALAFGDLLRKLWAPGGI-P 406
CF+N+ +QCL+ T + D+ L +++ E P G EL AF D++ LW P
Sbjct: 26 CFLNAVLQCLSSTRPLRDFCL---RRDFRQEVPGGGRAQELTEAFADVIGALWHPDSCEA 82
Query: 407 VAPRMFKLKLANFAPQFSGYNQHDSQEFLAFLLDGLHEDLNR--VKCKPYLEAK------ 458
V P F+ + P FSGY+Q D+QEFL L++ LH ++NR + P L
Sbjct: 83 VNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRAPPILANGPVPSPP 142
Query: 459 -------DAXXXXXXXXXXXYWRNHRARNDSIIVDLCQGQYRSMLVCPVCNKVSVTFDPL 511
+ W+ + R DS IVDL GQ +S L C C S TF+
Sbjct: 143 RRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKCQACGYRSTTFEVF 202
Query: 512 MYLSLPIPSTTMRTMTVTV 530
LSLPIP V++
Sbjct: 203 CDLSLPIPKKGFAGGKVSL 221
Score = 86.7 bits (213), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 51/122 (41%), Positives = 66/122 (54%), Gaps = 4/122 (3%)
Query: 788 VSLYKCLEAFLKEEPLGPEDMWYCPRCKKHWQASKKLDLWRSPDILVIHLKRFSFSRYFK 847
VSL C F KEE L E+ C RC++ +++KKL + R P ILV+HL RFS SR
Sbjct: 219 VSLRDCFNLFTKEEELESENAPVCDRCRQKTRSTKKLTVQRFPRILVLHLNRFSASRGSI 278
Query: 848 SKLDTYVDFPIDDLDLSNYVCCKNSQLSNRYVLYAISNHYGGMGGGHYTAFVDVSCVYSF 907
K VDFP+ L L ++ K S Y LYA+ NH G + GHYTA C +
Sbjct: 279 KKSSVGVDFPLQRLSLGDFASDKAG--SPVYQLYALCNHSGSVHYGHYTAL--CRCQTGW 334
Query: 908 HI 909
H+
Sbjct: 335 HV 336
>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 = 97.8 bits (242), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 65/199 (32%), Positives = 91/199 (45%), Gaps = 20/199 (10%)
Query: 349 CFMNSAIQCLAHTPEIVDYFLGDYQKEINYENPLGLNG-ELALAFGDLLRKLWAPGGI-P 406
CF+N+ +QCL+ T + D+ L +++ E P G EL AF D++ LW P
Sbjct: 32 CFLNAVLQCLSSTRPLRDFCL---RRDFRQEVPGGGRAQELTEAFADVIGALWHPDSCEA 88
Query: 407 VAPRMFKLKLANFAPQFSGYNQHDSQEFLAFLLDGLHEDLNR--VKCKPYLEAKDAXXXX 464
V P F+ + P FSGY+Q D+QEFL L++ LH ++NR + P L
Sbjct: 89 VNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRAPPILANGPVPSPP 148
Query: 465 XXX-------------XXXXYWRNHRARNDSIIVDLCQGQYRSMLVCPVCNKVSVTFDPL 511
W+ + R DS IVDL GQ +S L C C S TF+
Sbjct: 149 RRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKCQACGYRSTTFEVF 208
Query: 512 MYLSLPIPSTTMRTMTVTV 530
LSLPIP V++
Sbjct: 209 CDLSLPIPKKGFAGGKVSL 227
Score = 86.7 bits (213), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 51/122 (41%), Positives = 66/122 (54%), Gaps = 4/122 (3%)
Query: 788 VSLYKCLEAFLKEEPLGPEDMWYCPRCKKHWQASKKLDLWRSPDILVIHLKRFSFSRYFK 847
VSL C F KEE L E+ C RC++ +++KKL + R P ILV+HL RFS SR
Sbjct: 225 VSLRDCFNLFTKEEELESENAPVCDRCRQKTRSTKKLTVQRFPRILVLHLNRFSASRGSI 284
Query: 848 SKLDTYVDFPIDDLDLSNYVCCKNSQLSNRYVLYAISNHYGGMGGGHYTAFVDVSCVYSF 907
K VDFP+ L L ++ K S Y LYA+ NH G + GHYTA C +
Sbjct: 285 KKSSVGVDFPLQRLSLGDFASDKAG--SPVYQLYALCNHSGSVHYGHYTAL--CRCQTGW 340
Query: 908 HI 909
H+
Sbjct: 341 HV 342
>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 = 60.1 bits (144), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 40/122 (32%), Positives = 61/122 (50%), Gaps = 11/122 (9%)
Query: 790 LYKCLEAFLKEEPLGPEDMWYCPRCKKHWQASKKLDLWRSPDILVIHLKRFS-FSRYFKS 848
LY+CL++F K+E L + ++C C A K+L + + P +LV+ LKRF
Sbjct: 321 LYECLDSFHKKEQLKDFN-YHCGECNSTQDAIKQLGIHKLPSVLVLQLKRFEHLLNGSNR 379
Query: 849 KLDTYVDFPIDDLDLSNYVCCKNSQLSNR--------YVLYAISNHYGGMGGGHYTAFVD 900
KLD +++FP L++ NY K + Y L I +H G + GHY AF
Sbjct: 380 KLDDFIEFPT-YLNMKNYCSTKEKDKHSENGKVPDIIYELIGIVSHKGTVNEGHYIAFCK 438
Query: 901 VS 902
+S
Sbjct: 439 IS 440
Score = 47.8 bits (112), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 45/185 (24%), Positives = 74/185 (40%), Gaps = 35/185 (18%)
Query: 349 CFMNSAIQCLAHTPEIVDYFLGDYQKEINYEN----------PLGLNGELALAFGDLLRK 398
CFM+S +QCL H P YF+ +I+ N L+ + +G L K
Sbjct: 151 CFMSSILQCLIHNP----YFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHELYGALNTK 206
Query: 399 LWAPGGIPVAPRMFKLKLANFA----PQFSGYNQHDSQEFLAFLLDGLHEDLNRVKCKPY 454
+ + + L A +GY+Q D+ EF F+++ +H+
Sbjct: 207 QASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQSY-------V 259
Query: 455 LEAKDAXXXXXXXXXXXYWRNHRARNDSIIVDLCQGQYRSMLVCPVC-NKVSVTFDPLMY 513
L+ +A R + + + I+ + +G S +VCP C N T DP +
Sbjct: 260 LDLPNAKEVS---------RANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLD 310
Query: 514 LSLPI 518
LSL I
Sbjct: 311 LSLDI 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 = 60.1 bits (144), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 40/122 (32%), Positives = 61/122 (50%), Gaps = 11/122 (9%)
Query: 790 LYKCLEAFLKEEPLGPEDMWYCPRCKKHWQASKKLDLWRSPDILVIHLKRFS-FSRYFKS 848
LY+CL++F K+E L + ++C C A K+L + + P +LV+ LKRF
Sbjct: 321 LYECLDSFHKKEQLKDFN-YHCGECNSTQDAIKQLGIHKLPSVLVLQLKRFEHLLNGSNR 379
Query: 849 KLDTYVDFPIDDLDLSNYVCCKNSQLSNR--------YVLYAISNHYGGMGGGHYTAFVD 900
KLD +++FP L++ NY K + Y L I +H G + GHY AF
Sbjct: 380 KLDDFIEFPT-YLNMKNYCSTKEKDKHSENGKVPDIIYELIGIVSHKGTVNEGHYIAFCK 438
Query: 901 VS 902
+S
Sbjct: 439 IS 440
Score = 47.8 bits (112), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 45/185 (24%), Positives = 74/185 (40%), Gaps = 35/185 (18%)
Query: 349 CFMNSAIQCLAHTPEIVDYFLGDYQKEINYEN----------PLGLNGELALAFGDLLRK 398
CFM+S +QCL H P YF+ +I+ N L+ + +G L K
Sbjct: 151 CFMSSILQCLIHNP----YFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHELYGALNTK 206
Query: 399 LWAPGGIPVAPRMFKLKLANFA----PQFSGYNQHDSQEFLAFLLDGLHEDLNRVKCKPY 454
+ + + L A +GY+Q D+ EF F+++ +H+
Sbjct: 207 QASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQSY-------V 259
Query: 455 LEAKDAXXXXXXXXXXXYWRNHRARNDSIIVDLCQGQYRSMLVCPVC-NKVSVTFDPLMY 513
L+ +A R + + + I+ + +G S +VCP C N T DP +
Sbjct: 260 LDLPNAKEVS---------RANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLD 310
Query: 514 LSLPI 518
LSL I
Sbjct: 311 LSLDI 315
>pdb|3M99|A Chain A, Structure Of The Ubp8-Sgf11-Sgf73-Sus1 Saga Dub Module
Length = 471
Score = 59.7 bits (143), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 40/122 (32%), Positives = 61/122 (50%), Gaps = 11/122 (9%)
Query: 790 LYKCLEAFLKEEPLGPEDMWYCPRCKKHWQASKKLDLWRSPDILVIHLKRFS-FSRYFKS 848
LY+CL++F K+E L + ++C C A K+L + + P +LV+ LKRF
Sbjct: 316 LYECLDSFHKKEQLKDFN-YHCGECNSTQDAIKQLGIHKLPSVLVLQLKRFEHLLNGSNR 374
Query: 849 KLDTYVDFPIDDLDLSNYVCCKNSQLSNR--------YVLYAISNHYGGMGGGHYTAFVD 900
KLD +++FP L++ NY K + Y L I +H G + GHY AF
Sbjct: 375 KLDDFIEFPT-YLNMKNYCSTKEKDKHSENGKVPDIIYELIGIVSHKGTVNEGHYIAFCK 433
Query: 901 VS 902
+S
Sbjct: 434 IS 435
Score = 47.8 bits (112), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 45/185 (24%), Positives = 74/185 (40%), Gaps = 35/185 (18%)
Query: 349 CFMNSAIQCLAHTPEIVDYFLGDYQKEINYEN----------PLGLNGELALAFGDLLRK 398
CFM+S +QCL H P YF+ +I+ N L+ + +G L K
Sbjct: 146 CFMSSILQCLIHNP----YFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHELYGALNTK 201
Query: 399 LWAPGGIPVAPRMFKLKLANFA----PQFSGYNQHDSQEFLAFLLDGLHEDLNRVKCKPY 454
+ + + L A +GY+Q D+ EF F+++ +H+
Sbjct: 202 QASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQSY-------V 254
Query: 455 LEAKDAXXXXXXXXXXXYWRNHRARNDSIIVDLCQGQYRSMLVCPVC-NKVSVTFDPLMY 513
L+ +A R + + + I+ + +G S +VCP C N T DP +
Sbjct: 255 LDLPNAKEVS---------RANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLD 305
Query: 514 LSLPI 518
LSL I
Sbjct: 306 LSLDI 310
>pdb|4ECN|A Chain A, Crystal Structure Of A Leucine-Rich Repeat Protein
(Bt_0210) From Bacteroides Thetaiotaomicron Vpi-5482 At
2.80 A Resolution
Length = 876
Score = 38.5 bits (88), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 33/71 (46%)
Query: 355 IQCLAHTPEIVDYFLGDYQKEINYENPLGLNGELALAFGDLLRKLWAPGGIPVAPRMFKL 414
+Q LA T +IV Y+L D E+ P G + EL + G LL K +P FKL
Sbjct: 78 LQLLAGTYKIVGYYLYDGLDEVLLAGPAGDDNELTVVSGGLLEKALTVDAVPHGTVTFKL 137
Query: 415 KLANFAPQFSG 425
+ + +G
Sbjct: 138 SKEGISTRAAG 148
>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
Length = 854
Score = 36.6 bits (83), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 15/34 (44%), Positives = 21/34 (61%)
Query: 407 VAPRMFKLKLANFAPQFSGYNQHDSQEFLAFLLD 440
+APRMFK + P+FS Q D+QEF L++
Sbjct: 431 IAPRMFKALIGKGHPEFSTNRQQDAQEFFLHLIN 464
Score = 34.7 bits (78), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 38/79 (48%), Gaps = 5/79 (6%)
Query: 788 VSLYKCLEAFLKEEPLGPEDMWYCPRCKKHWQASKKLDLWRSPDILVIHLKRFSFS-RYF 846
V CLEA+ E + +D W K A K PD LVI +K+F+F +
Sbjct: 546 VPFSSCLEAYGAPEQV--DDFWSTALQAKSV-AVKTTRFASFPDYLVIQIKKFTFGLDWV 602
Query: 847 KSKLDTYVDFPIDDLDLSN 865
KLD ++ P ++LD+S
Sbjct: 603 PKKLDVSIEMP-EELDISQ 620
>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 = 33.5 bits (75), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 40/84 (47%), Gaps = 3/84 (3%)
Query: 819 QASKKLDLWRSPDILVIHLKRFSFSRYFKS--KLDTYVDFPIDDLDLSNYVCCKNSQLSN 876
+A K + P +L + L RF + K++ +FP + L L ++ + +
Sbjct: 181 EAEKGVKFLTLPPVLHLQLXRFXYDPQTDQNIKINDRFEFP-EQLPLDEFLQKTDPKDPA 239
Query: 877 RYVLYAISNHYGGMGGGHYTAFVD 900
Y+L+A+ H G GGHY +++
Sbjct: 240 NYILHAVLVHSGDNHGGHYVVYLN 263
>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 = 33.1 bits (74), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 40/84 (47%), Gaps = 3/84 (3%)
Query: 819 QASKKLDLWRSPDILVIHLKRFSFSRYFKS--KLDTYVDFPIDDLDLSNYVCCKNSQLSN 876
+A K + P +L + L RF + K++ +FP + L L ++ + +
Sbjct: 181 EAEKGVKFLTLPPVLHLQLMRFMYDPQTDQNIKINDRFEFP-EQLPLDEFLQKTDPKDPA 239
Query: 877 RYVLYAISNHYGGMGGGHYTAFVD 900
Y+L+A+ H G GGHY +++
Sbjct: 240 NYILHAVLVHSGDNHGGHYVVYLN 263
>pdb|2F1Z|A Chain A, Crystal Structure Of Hausp
pdb|2F1Z|B Chain B, Crystal Structure Of Hausp
Length = 522
Score = 33.1 bits (74), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 40/84 (47%), Gaps = 3/84 (3%)
Query: 819 QASKKLDLWRSPDILVIHLKRFSFSRYFKS--KLDTYVDFPIDDLDLSNYVCCKNSQLSN 876
+A K + P +L + L RF + K++ +FP + L L ++ + +
Sbjct: 350 EAEKGVKFLTLPPVLHLQLMRFMYDPQTDQNIKINDRFEFP-EQLPLDEFLQKTDPKDPA 408
Query: 877 RYVLYAISNHYGGMGGGHYTAFVD 900
Y+L+A+ H G GGHY +++
Sbjct: 409 NYILHAVLVHSGDNHGGHYVVYLN 432
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 0.414
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 26,662,835
Number of Sequences: 62578
Number of extensions: 1122263
Number of successful extensions: 2767
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 22
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 2681
Number of HSP's gapped (non-prelim): 51
length of query: 912
length of database: 14,973,337
effective HSP length: 108
effective length of query: 804
effective length of database: 8,214,913
effective search space: 6604790052
effective search space used: 6604790052
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: 56 (26.2 bits)