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= 001625
(1042 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2HD5|A Chain A, Usp2 In Complex With Ubiquitin
Length = 359
Score = 97.1 bits (240), Expect = 5e-20, Method: Compositional matrix adjust.
Identities = 65/184 (35%), Positives = 99/184 (53%), Gaps = 22/184 (11%)
Query: 231 GLANLGNTCFFNSVMQNLLAMSQLQDYFLNA----ELTFGP-LTIALKKLFA---ETKPE 282
GL NLGNTCF NS++Q L +L+DY L +L G AL + FA +T
Sbjct: 11 GLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQTIWT 70
Query: 283 TGLRNVINPRSFFGCICSKAPQFKGYQQHDSHELLRCLLDGLCSE--ELAFRKRNSPSEG 340
+ +V++P F I AP+F GY Q D+ E LR LLDGL +E + R +++P
Sbjct: 71 SSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPENL 130
Query: 341 NGISSNQG--PVFVDYV----------FGGQIASTVRCVECGHSSTVYEPFLDLSLPVPT 388
+ + ++ ++ Y+ F GQ+ S++ C +CG+ STV++PF DLSLP+
Sbjct: 131 DHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPIAK 190
Query: 389 KKAP 392
+ P
Sbjct: 191 RGYP 194
Score = 68.9 bits (167), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 48/126 (38%), Positives = 64/126 (50%), Gaps = 16/126 (12%)
Query: 916 KRVLINKAPPILTIHLKRFSQDARGRLSKLNGHVNFS-EIINLRPYMDPGCTDHDNYDYR 974
K+ I + P IL +HLKRFS+ +R R SKL VNF ++LR + T+H Y+
Sbjct: 230 KKFSIQRFPKILVLHLKRFSE-SRIRTSKLTTFVNFPLRDLDLREFASEN-TNHAVYN-- 285
Query: 975 LVGVVEHLGTMRGGHYVAYVRGGPKNKVKAKKESVGGVWYHASDVYVREVSLEEVLRCEA 1034
L V H GT GGHY AY R G W+ +D V +S +V +A
Sbjct: 286 LYAVSNHSGTTMGGHYTAYCRSPGT-----------GEWHTFNDSSVTPMSSSQVRTSDA 334
Query: 1035 YILFYE 1040
Y+LFYE
Sbjct: 335 YLLFYE 340
>pdb|2IBI|A Chain A, Covalent Ubiquitin-Usp2 Complex
Length = 374
Score = 96.7 bits (239), Expect = 6e-20, Method: Compositional matrix adjust.
Identities = 65/184 (35%), Positives = 99/184 (53%), Gaps = 22/184 (11%)
Query: 231 GLANLGNTCFFNSVMQNLLAMSQLQDYFLNA----ELTFGP-LTIALKKLFA---ETKPE 282
GL NLGNTCF NS++Q L +L+DY L +L G AL + FA +T
Sbjct: 37 GLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQTIWT 96
Query: 283 TGLRNVINPRSFFGCICSKAPQFKGYQQHDSHELLRCLLDGLCSE--ELAFRKRNSPSEG 340
+ +V++P F I AP+F GY Q D+ E LR LLDGL +E + R +++P
Sbjct: 97 SSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPENL 156
Query: 341 NGISSNQG--PVFVDYV----------FGGQIASTVRCVECGHSSTVYEPFLDLSLPVPT 388
+ + ++ ++ Y+ F GQ+ S++ C +CG+ STV++PF DLSLP+
Sbjct: 157 DHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPIAK 216
Query: 389 KKAP 392
+ P
Sbjct: 217 RGYP 220
Score = 68.6 bits (166), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 50/127 (39%), Positives = 66/127 (51%), Gaps = 18/127 (14%)
Query: 916 KRVLINKAPPILTIHLKRFSQDARGRLSKLNGHVNFS-EIINLRPYMDPGCTDHDNYDYR 974
K+ I + P IL +HLKRFS+ +R R SKL VNF ++LR + T+H Y+
Sbjct: 256 KKFSIQRFPKILVLHLKRFSE-SRIRTSKLTTFVNFPLRDLDLREFASEN-TNHAVYN-- 311
Query: 975 LVGVVEHLGTMRGGHYVAYVRGGPKNKVKAKKESVG-GVWYHASDVYVREVSLEEVLRCE 1033
L V H GT GGHY AY R S G G W+ +D V +S +V +
Sbjct: 312 LYAVSNHSGTTMGGHYTAYCR------------SPGTGEWHTFNDSSVTPMSSSQVRTSD 359
Query: 1034 AYILFYE 1040
AY+LFYE
Sbjct: 360 AYLLFYE 366
>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 = 96.7 bits (239), Expect = 6e-20, Method: Compositional matrix adjust.
Identities = 65/184 (35%), Positives = 99/184 (53%), Gaps = 22/184 (11%)
Query: 231 GLANLGNTCFFNSVMQNLLAMSQLQDYFLNA----ELTFGP-LTIALKKLFA---ETKPE 282
GL NLGNTCF NS++Q L +L+DY L +L G AL + FA +T
Sbjct: 30 GLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQTIWT 89
Query: 283 TGLRNVINPRSFFGCICSKAPQFKGYQQHDSHELLRCLLDGLCSE--ELAFRKRNSPSEG 340
+ +V++P F I AP+F GY Q D+ E LR LLDGL +E + R +++P
Sbjct: 90 SSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPENL 149
Query: 341 NGISSNQG--PVFVDYV----------FGGQIASTVRCVECGHSSTVYEPFLDLSLPVPT 388
+ + ++ ++ Y+ F GQ+ S++ C +CG+ STV++PF DLSLP+
Sbjct: 150 DHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPIAK 209
Query: 389 KKAP 392
+ P
Sbjct: 210 RGYP 213
Score = 68.6 bits (166), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 48/126 (38%), Positives = 64/126 (50%), Gaps = 16/126 (12%)
Query: 916 KRVLINKAPPILTIHLKRFSQDARGRLSKLNGHVNFS-EIINLRPYMDPGCTDHDNYDYR 974
K+ I + P IL +HLKRFS+ +R R SKL VNF ++LR + T+H Y+
Sbjct: 249 KKFSIQRFPKILVLHLKRFSE-SRIRTSKLTTFVNFPLRDLDLREFASEN-TNHAVYN-- 304
Query: 975 LVGVVEHLGTMRGGHYVAYVRGGPKNKVKAKKESVGGVWYHASDVYVREVSLEEVLRCEA 1034
L V H GT GGHY AY R G W+ +D V +S +V +A
Sbjct: 305 LYAVSNHSGTTMGGHYTAYCRSPGT-----------GEWHTFNDSSVTPMSSSQVRTSDA 353
Query: 1035 YILFYE 1040
Y+LFYE
Sbjct: 354 YLLFYE 359
>pdb|3NHE|A Chain A, High Resolution Structure (1.26a) Of Usp2a In Complex With
Ubiquitin
Length = 348
Score = 93.2 bits (230), Expect = 7e-19, Method: Compositional matrix adjust.
Identities = 64/184 (34%), Positives = 98/184 (53%), Gaps = 22/184 (11%)
Query: 231 GLANLGNTCFFNSVMQNLLAMSQLQDYFLNA----ELTFGP-LTIALKKLFA---ETKPE 282
GL NLGNT F NS++Q L +L+DY L +L G AL + FA +T
Sbjct: 11 GLRNLGNTXFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQTIWT 70
Query: 283 TGLRNVINPRSFFGCICSKAPQFKGYQQHDSHELLRCLLDGLCSE--ELAFRKRNSPSEG 340
+ +V++P F I AP+F GY Q D+ E LR LLDGL +E + R +++P
Sbjct: 71 SSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPENL 130
Query: 341 NGISSNQG--PVFVDYV----------FGGQIASTVRCVECGHSSTVYEPFLDLSLPVPT 388
+ + ++ ++ Y+ F GQ+ S++ C +CG+ STV++PF DLSLP+
Sbjct: 131 DHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPIAK 190
Query: 389 KKAP 392
+ P
Sbjct: 191 RGYP 194
Score = 68.6 bits (166), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 48/126 (38%), Positives = 64/126 (50%), Gaps = 16/126 (12%)
Query: 916 KRVLINKAPPILTIHLKRFSQDARGRLSKLNGHVNFS-EIINLRPYMDPGCTDHDNYDYR 974
K+ I + P IL +HLKRFS+ +R R SKL VNF ++LR + T+H Y+
Sbjct: 230 KKFSIQRFPKILVLHLKRFSE-SRIRTSKLTTFVNFPLRDLDLREFASEN-TNHAVYN-- 285
Query: 975 LVGVVEHLGTMRGGHYVAYVRGGPKNKVKAKKESVGGVWYHASDVYVREVSLEEVLRCEA 1034
L V H GT GGHY AY R G W+ +D V +S +V +A
Sbjct: 286 LYAVSNHSGTTMGGHYTAYCRSPGT-----------GEWHTFNDSSVTPMSSSQVRTSDA 334
Query: 1035 YILFYE 1040
Y+LFYE
Sbjct: 335 YLLFYE 340
>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 = 85.9 bits (211), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 75/206 (36%), Positives = 93/206 (45%), Gaps = 36/206 (17%)
Query: 231 GLANLGNTCFFNSVMQNLLAMSQLQDYFLNAELTF-----GPLTIALKKLFAETKPE--- 282
GL NLGNT F NS +Q L + L DYFL E PL +K AE E
Sbjct: 10 GLGNLGNTXFMNSALQCLSNTAPLTDYFLKDEYEAEINRDNPL--GMKGEIAEAYAELIK 67
Query: 283 ---TGLRNVINPRSFFGCICSKAPQFKGYQQHDSHELLRCLLDGLCSEELAFRKRNSP-- 337
+G + PR F + APQF GYQQ DS ELL LLDGL E+L R + P
Sbjct: 68 QMWSGRDAHVAPRMFKTQVGRFAPQFSGYQQQDSQELLAFLLDGL-HEDLN-RVKKKPYL 125
Query: 338 --SEGNG----ISSNQG---------PVFVDYVFGGQIASTVRCVECGHSSTVYEPFLDL 382
+ NG + + + V VD F G ST+ C EC S ++PF L
Sbjct: 126 ELKDANGRPDAVVAKEAWENHRLRNDSVIVD-TFHGLFKSTLVCPECAKVSVTFDPFCYL 184
Query: 383 SLPVPTKK---APSKKTQPASRAKKT 405
+LP+P KK QP + K T
Sbjct: 185 TLPLPLKKDRVMEGPMLQPQKKKKTT 210
Score = 63.5 bits (153), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 50/143 (34%), Positives = 68/143 (47%), Gaps = 33/143 (23%)
Query: 909 KVKRDATKRVLINKAPPILTIHLKRFSQDARGRLSKLNGHVNF-------SEII-NL--R 958
K + ATK+ + P IL +HLKRFS + R KL+ V F SE + NL R
Sbjct: 238 KKHQQATKKFDLWSLPKILVVHLKRFSYNRYWR-DKLDTVVEFPIRGLNMSEFVCNLSAR 296
Query: 959 PYMDPGCTDHDNYDYRLVGVVEHLGTMRGGHYVAYVRGGPKNKVKAKKESVGGVWYHASD 1018
PY+ Y L+ V H G M GHY AY KNK+ K WY+ D
Sbjct: 297 PYV-----------YDLIAVSNHYGAMGVGHYTAYA----KNKLNGK-------WYYFDD 334
Query: 1019 VYVREVSLEEVLRCEAYILFYEK 1041
V S ++++ AY+LFY++
Sbjct: 335 SNVSLASEDQIVTKAAYVLFYQR 357
>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 = 79.7 bits (195), Expect = 7e-15, Method: Compositional matrix adjust.
Identities = 44/135 (32%), Positives = 69/135 (51%), Gaps = 19/135 (14%)
Query: 912 RDATKRVLINKAPPILTIHLKRFSQDARGRLSKLNGHVNFSEIINLRPYMDPGCTDHDNY 971
+DA K++ I+K P +L + LKRF G KL+ + F +N++ Y D +
Sbjct: 348 QDAIKQLGIHKLPSVLVLQLKRFEHLLNGSNRKLDDFIEFPTYLNMKNYCSTKEKDKHSE 407
Query: 972 D-------YRLVGVVEHLGTMRGGHYVAYVRGGPKNKVKAKKESVGGVWYHASDVYVREV 1024
+ Y L+G+V H GT+ GHY+A+ + GG W+ +D V +
Sbjct: 408 NGKVPDIIYELIGIVSHKGTVNEGHYIAFCKIS------------GGQWFKFNDSMVSSI 455
Query: 1025 SLEEVLRCEAYILFY 1039
S EEVL+ +AY+LFY
Sbjct: 456 SQEEVLKEQAYLLFY 470
Score = 64.7 bits (156), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 75/308 (24%), Positives = 124/308 (40%), Gaps = 64/308 (20%)
Query: 102 VDSKAIWVCLGCGHYACGGVGLPTTPQSHVVRHARQTRHPLVIQWENPHLRWCFPCNTLI 161
++S A ++CL CG C SH + H++Q H I N L +CF C I
Sbjct: 57 INSGATFMCLQCGFCGCWN-------HSHFLSHSKQIGHIFGIN-SNNGLLFCFKCEDYI 108
Query: 162 PVEKTEENGENKDALSEVVKLIKGRSTEISSVDVEDAWFGSGNVNSEIKSESTVVSGSDL 221
N D +++ + + W ++ +++ V S
Sbjct: 109 G---------NIDLINDAI--------------LAKYW-------DDVCTKTMVPSMERR 138
Query: 222 DGNACYVVRGLANLGNTCFFNSVMQNLL--------AMSQLQDYFLNAELTFGPLTIALK 273
DG + GL N+G+TCF +S++Q L+ +MSQ+ + AL
Sbjct: 139 DG-----LSGLINMGSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALD 193
Query: 274 KLFAE------TKPETGLRNVINPRSFF----GCICSKAPQFKGYQQHDSHELLRCLLDG 323
K+ E TK + N ++ F C GY Q D+HE + +++
Sbjct: 194 KIVHELYGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQ 253
Query: 324 LCSEELAFRKRNSPSEGNGISSNQGPVFVDYVFGGQIASTVRCVEC-GHSSTVYEPFLDL 382
+ + N+ E + ++ Q V VF G + S++ C C +S T +PFLDL
Sbjct: 254 I-HQSYVLDLPNAK-EVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLDL 311
Query: 383 SLPVPTKK 390
SL + KK
Sbjct: 312 SLDIKDKK 319
>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 = 79.7 bits (195), Expect = 8e-15, Method: Compositional matrix adjust.
Identities = 44/135 (32%), Positives = 69/135 (51%), Gaps = 19/135 (14%)
Query: 912 RDATKRVLINKAPPILTIHLKRFSQDARGRLSKLNGHVNFSEIINLRPYMDPGCTDHDNY 971
+DA K++ I+K P +L + LKRF G KL+ + F +N++ Y D +
Sbjct: 348 QDAIKQLGIHKLPSVLVLQLKRFEHLLNGSNRKLDDFIEFPTYLNMKNYCSTKEKDKHSE 407
Query: 972 D-------YRLVGVVEHLGTMRGGHYVAYVRGGPKNKVKAKKESVGGVWYHASDVYVREV 1024
+ Y L+G+V H GT+ GHY+A+ + GG W+ +D V +
Sbjct: 408 NGKVPDIIYELIGIVSHKGTVNEGHYIAFCKIS------------GGQWFKFNDSMVSSI 455
Query: 1025 SLEEVLRCEAYILFY 1039
S EEVL+ +AY+LFY
Sbjct: 456 SQEEVLKEQAYLLFY 470
Score = 67.0 bits (162), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 76/308 (24%), Positives = 124/308 (40%), Gaps = 64/308 (20%)
Query: 102 VDSKAIWVCLGCGHYACGGVGLPTTPQSHVVRHARQTRHPLVIQWENPHLRWCFPCNTLI 161
++S A ++CL CG C SH + H++Q H I N L +CF C I
Sbjct: 57 INSGATFMCLQCGFCGCWN-------HSHFLSHSKQIGHIFGIN-SNNGLLFCFKCEDYI 108
Query: 162 PVEKTEENGENKDALSEVVKLIKGRSTEISSVDVEDAWFGSGNVNSEIKSESTVVSGSDL 221
N D +++ + + W ++ +++ V S
Sbjct: 109 G---------NIDLINDAI--------------LAKYW-------DDVCTKTMVPSMERR 138
Query: 222 DGNACYVVRGLANLGNTCFFNSVMQNLL--------AMSQLQDYFLNAELTFGPLTIALK 273
DG + GL N+GNTCF +S++Q L+ +MSQ+ + AL
Sbjct: 139 DG-----LSGLINMGNTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALD 193
Query: 274 KLFAE------TKPETGLRNVINPRSFF----GCICSKAPQFKGYQQHDSHELLRCLLDG 323
K+ E TK + N ++ F C GY Q D+HE + +++
Sbjct: 194 KIVHELYGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQ 253
Query: 324 LCSEELAFRKRNSPSEGNGISSNQGPVFVDYVFGGQIASTVRCVEC-GHSSTVYEPFLDL 382
+ + N+ E + ++ Q V VF G + S++ C C +S T +PFLDL
Sbjct: 254 I-HQSYVLDLPNAK-EVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLDL 311
Query: 383 SLPVPTKK 390
SL + KK
Sbjct: 312 SLDIKDKK 319
>pdb|3M99|A Chain A, Structure Of The Ubp8-Sgf11-Sgf73-Sus1 Saga Dub Module
Length = 471
Score = 79.7 bits (195), Expect = 8e-15, Method: Compositional matrix adjust.
Identities = 44/135 (32%), Positives = 69/135 (51%), Gaps = 19/135 (14%)
Query: 912 RDATKRVLINKAPPILTIHLKRFSQDARGRLSKLNGHVNFSEIINLRPYMDPGCTDHDNY 971
+DA K++ I+K P +L + LKRF G KL+ + F +N++ Y D +
Sbjct: 343 QDAIKQLGIHKLPSVLVLQLKRFEHLLNGSNRKLDDFIEFPTYLNMKNYCSTKEKDKHSE 402
Query: 972 D-------YRLVGVVEHLGTMRGGHYVAYVRGGPKNKVKAKKESVGGVWYHASDVYVREV 1024
+ Y L+G+V H GT+ GHY+A+ + GG W+ +D V +
Sbjct: 403 NGKVPDIIYELIGIVSHKGTVNEGHYIAFCKIS------------GGQWFKFNDSMVSSI 450
Query: 1025 SLEEVLRCEAYILFY 1039
S EEVL+ +AY+LFY
Sbjct: 451 SQEEVLKEQAYLLFY 465
Score = 64.7 bits (156), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 75/308 (24%), Positives = 124/308 (40%), Gaps = 64/308 (20%)
Query: 102 VDSKAIWVCLGCGHYACGGVGLPTTPQSHVVRHARQTRHPLVIQWENPHLRWCFPCNTLI 161
++S A ++CL CG C SH + H++Q H I N L +CF C I
Sbjct: 52 INSGATFMCLQCGFCGCWN-------HSHFLSHSKQIGHIFGIN-SNNGLLFCFKCEDYI 103
Query: 162 PVEKTEENGENKDALSEVVKLIKGRSTEISSVDVEDAWFGSGNVNSEIKSESTVVSGSDL 221
N D +++ + + W ++ +++ V S
Sbjct: 104 G---------NIDLINDAI--------------LAKYW-------DDVCTKTMVPSMERR 133
Query: 222 DGNACYVVRGLANLGNTCFFNSVMQNLL--------AMSQLQDYFLNAELTFGPLTIALK 273
DG + GL N+G+TCF +S++Q L+ +MSQ+ + AL
Sbjct: 134 DG-----LSGLINMGSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALD 188
Query: 274 KLFAE------TKPETGLRNVINPRSFF----GCICSKAPQFKGYQQHDSHELLRCLLDG 323
K+ E TK + N ++ F C GY Q D+HE + +++
Sbjct: 189 KIVHELYGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQ 248
Query: 324 LCSEELAFRKRNSPSEGNGISSNQGPVFVDYVFGGQIASTVRCVEC-GHSSTVYEPFLDL 382
+ + N+ E + ++ Q V VF G + S++ C C +S T +PFLDL
Sbjct: 249 I-HQSYVLDLPNAK-EVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLDL 306
Query: 383 SLPVPTKK 390
SL + KK
Sbjct: 307 SLDIKDKK 314
>pdb|3N3K|A Chain A, The Catalytic Domain Of Usp8 In Complex With A Usp8
Specific Inhibitor
Length = 396
Score = 77.4 bits (189), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 68/212 (32%), Positives = 94/212 (44%), Gaps = 43/212 (20%)
Query: 207 SEIKSESTVVSGSDLDGNACYVVRGLANLGNTCFFNSVMQNLLAMSQLQDYF-------- 258
S+I++ + V GS G A + GL NLGNTC+ NS++Q L L DYF
Sbjct: 46 SQIRNLNPVFGGS---GPA---LTGLRNLGNTCYMNSILQCLCNAPHLADYFNRNCYQDD 99
Query: 259 LNAELTFG-------PLTIALKKLFAETKPETGLRNVINPRSFFGCICSKAPQFKGYQQH 311
+N G I +K L+ TG I+P+ F I QF GY Q
Sbjct: 100 INRSNLLGHKGEVAEEFGIIMKALW------TGQYRYISPKDFKITIGKINDQFAGYSQQ 153
Query: 312 DSHELLRCLLDGLCSEELA---FRKRNSPSEGNGISSNQGP------------VFVDYVF 356
DS ELL L+DGL E+L RKR + + + + +F
Sbjct: 154 DSQELLLFLMDGL-HEDLNKADNRKRYKEENNDHLDDFKAAEHAWQKHKQLNESIIVALF 212
Query: 357 GGQIASTVRCVECGHSSTVYEPFLDLSLPVPT 388
GQ STV+C+ C S +E F+ LSLP+ +
Sbjct: 213 QGQFKSTVQCLTCHKKSRTFEAFMYLSLPLAS 244
Score = 65.1 bits (157), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 45/135 (33%), Positives = 68/135 (50%), Gaps = 15/135 (11%)
Query: 909 KVKRDATKRVLINKAPPILTIHLKRFSQDARGRLSKLNGHVNFS-EIINLRPYMDPGCTD 967
+ +RD+ K++ I K PP+L +HLKRFS D R + KL V+F E ++L Y+ +
Sbjct: 275 RARRDSLKKIEIWKLPPVLLVHLKRFSYDGRWK-QKLQTSVDFPLENLDLSQYVIGPKNN 333
Query: 968 HDNYDYRLVGVVEHLGTMRGGHYVAYVRGGPKNKVKAKKESVGGVWYHASDVYVREVSLE 1027
Y+ L V H G + GGHY AY + + + W+ D V ++S+
Sbjct: 334 LKKYN--LFSVSNHYGGLDGGHYTAYCKNAARQR-----------WFKFDDHEVSDISVS 380
Query: 1028 EVLRCEAYILFYEKI 1042
V AYILFY +
Sbjct: 381 SVKSSAAYILFYTSL 395
>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 = 77.4 bits (189), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 59/197 (29%), Positives = 85/197 (43%), Gaps = 40/197 (20%)
Query: 231 GLANLGNTCFFNSVMQNLLAMSQLQDYFL----NAELTFGPLTIALKKLFAET-----KP 281
GL NLGNTCF N+V+Q L + L+D+ L E+ G L + FA+ P
Sbjct: 5 GLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQELTEAFADVIGALWHP 64
Query: 282 ETGLRNVINPRSFFGCICSKAPQFKGYQQHDSHELLRCLLDGLCSEELAFRKRNSPSEGN 341
++ +NP F P F GY Q D+ E L+ L++ L E +R P N
Sbjct: 65 DSC--EAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRAPPILAN 122
Query: 342 G---ISSNQGPVFVDY--------------------------VFGGQIASTVRCVECGHS 372
G +G ++ +F GQ+ S ++C CG+
Sbjct: 123 GPVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKCQACGYR 182
Query: 373 STVYEPFLDLSLPVPTK 389
ST +E F DLSLP+P K
Sbjct: 183 STTFEVFCDLSLPIPKK 199
Score = 51.2 bits (121), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 55/214 (25%), Positives = 90/214 (42%), Gaps = 24/214 (11%)
Query: 830 EKGKMKINDAVEMQSRSSCLRDSCSQESITDQDEGSCSVDGATSSGYSAEKVYQSDSQLV 889
E+ KI D Q +S +C S T + S+ G++ KV D
Sbjct: 156 EREDSKIVDLFVGQLKSCLKCQACGYRSTTFEVFCDLSLP-IPKKGFAGGKVSLRD---- 210
Query: 890 AGNCESEESKVEEINSKIV---KVKRDATKRVLINKAPPILTIHLKRFSQDARGRLSKLN 946
N ++E ++E N+ + + K +TK++ + + P IL +HL RFS +RG + K +
Sbjct: 211 CFNLFTKEEELESENAPVCDRCRQKTRSTKKLTVQRFPRILVLHLNRFSA-SRGSIKKSS 269
Query: 947 GHVNFSEIINLRPYMDPGCTDHDNYDYRLVGVVEHLGTMRGGHYVAYVRGGPKNKVKAKK 1006
V+F + D + Y+L + H G++ GHY A R
Sbjct: 270 VGVDFP--LQRLSLGDFASDKAGSPVYQLYALCNHSGSVHYGHYTALCR----------- 316
Query: 1007 ESVGGVWYHASDVYVREVSLEEVLRCEAYILFYE 1040
W+ +D V VS +V E Y+LFY+
Sbjct: 317 --CQTGWHVYNDSRVSPVSENQVASSEGYVLFYQ 348
>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 = 77.4 bits (189), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 59/197 (29%), Positives = 85/197 (43%), Gaps = 40/197 (20%)
Query: 231 GLANLGNTCFFNSVMQNLLAMSQLQDYFL----NAELTFGPLTIALKKLFAET-----KP 281
GL NLGNTCF N+V+Q L + L+D+ L E+ G L + FA+ P
Sbjct: 18 GLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQELTEAFADVIGALWHP 77
Query: 282 ETGLRNVINPRSFFGCICSKAPQFKGYQQHDSHELLRCLLDGLCSEELAFRKRNSPSEGN 341
++ +NP F P F GY Q D+ E L+ L++ L E +R P N
Sbjct: 78 DSC--EAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRAPPILAN 135
Query: 342 G---ISSNQGPVFVDY--------------------------VFGGQIASTVRCVECGHS 372
G +G ++ +F GQ+ S ++C CG+
Sbjct: 136 GPVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKCQACGYR 195
Query: 373 STVYEPFLDLSLPVPTK 389
ST +E F DLSLP+P K
Sbjct: 196 STTFEVFCDLSLPIPKK 212
Score = 51.2 bits (121), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 55/214 (25%), Positives = 90/214 (42%), Gaps = 24/214 (11%)
Query: 830 EKGKMKINDAVEMQSRSSCLRDSCSQESITDQDEGSCSVDGATSSGYSAEKVYQSDSQLV 889
E+ KI D Q +S +C S T + S+ G++ KV D
Sbjct: 169 EREDSKIVDLFVGQLKSCLKCQACGYRSTTFEVFCDLSLP-IPKKGFAGGKVSLRD---- 223
Query: 890 AGNCESEESKVEEINSKIV---KVKRDATKRVLINKAPPILTIHLKRFSQDARGRLSKLN 946
N ++E ++E N+ + + K +TK++ + + P IL +HL RFS +RG + K +
Sbjct: 224 CFNLFTKEEELESENAPVCDRCRQKTRSTKKLTVQRFPRILVLHLNRFSA-SRGSIKKSS 282
Query: 947 GHVNFSEIINLRPYMDPGCTDHDNYDYRLVGVVEHLGTMRGGHYVAYVRGGPKNKVKAKK 1006
V+F + D + Y+L + H G++ GHY A R
Sbjct: 283 VGVDFP--LQRLSLGDFASDKAGSPVYQLYALCNHSGSVHYGHYTALCR----------- 329
Query: 1007 ESVGGVWYHASDVYVREVSLEEVLRCEAYILFYE 1040
W+ +D V VS +V E Y+LFY+
Sbjct: 330 --CQTGWHVYNDSRVSPVSENQVASSEGYVLFYQ 361
>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 = 77.4 bits (189), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 59/197 (29%), Positives = 85/197 (43%), Gaps = 40/197 (20%)
Query: 231 GLANLGNTCFFNSVMQNLLAMSQLQDYFL----NAELTFGPLTIALKKLFAET-----KP 281
GL NLGNTCF N+V+Q L + L+D+ L E+ G L + FA+ P
Sbjct: 24 GLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQELTEAFADVIGALWHP 83
Query: 282 ETGLRNVINPRSFFGCICSKAPQFKGYQQHDSHELLRCLLDGLCSEELAFRKRNSPSEGN 341
++ +NP F P F GY Q D+ E L+ L++ L E +R P N
Sbjct: 84 DSC--EAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRAPPILAN 141
Query: 342 G---ISSNQGPVFVDY--------------------------VFGGQIASTVRCVECGHS 372
G +G ++ +F GQ+ S ++C CG+
Sbjct: 142 GPVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKCQACGYR 201
Query: 373 STVYEPFLDLSLPVPTK 389
ST +E F DLSLP+P K
Sbjct: 202 STTFEVFCDLSLPIPKK 218
Score = 51.6 bits (122), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 55/214 (25%), Positives = 90/214 (42%), Gaps = 24/214 (11%)
Query: 830 EKGKMKINDAVEMQSRSSCLRDSCSQESITDQDEGSCSVDGATSSGYSAEKVYQSDSQLV 889
E+ KI D Q +S +C S T + S+ G++ KV D
Sbjct: 175 EREDSKIVDLFVGQLKSCLKCQACGYRSTTFEVFCDLSLP-IPKKGFAGGKVSLRD---- 229
Query: 890 AGNCESEESKVEEINSKIV---KVKRDATKRVLINKAPPILTIHLKRFSQDARGRLSKLN 946
N ++E ++E N+ + + K +TK++ + + P IL +HL RFS +RG + K +
Sbjct: 230 CFNLFTKEEELESENAPVCDRCRQKTRSTKKLTVQRFPRILVLHLNRFSA-SRGSIKKSS 288
Query: 947 GHVNFSEIINLRPYMDPGCTDHDNYDYRLVGVVEHLGTMRGGHYVAYVRGGPKNKVKAKK 1006
V+F + D + Y+L + H G++ GHY A R
Sbjct: 289 VGVDFP--LQRLSLGDFASDKAGSPVYQLYALCNHSGSVHYGHYTALCR----------- 335
Query: 1007 ESVGGVWYHASDVYVREVSLEEVLRCEAYILFYE 1040
W+ +D V VS +V E Y+LFY+
Sbjct: 336 --CQTGWHVYNDSRVSPVSENQVASSEGYVLFYQ 367
>pdb|2GFO|A Chain A, Structure Of The Catalytic Domain Of Human Ubiquitin
Carboxyl-terminal Hydrolase 8
Length = 396
Score = 72.4 bits (176), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 68/212 (32%), Positives = 91/212 (42%), Gaps = 43/212 (20%)
Query: 207 SEIKSESTVVSGSDLDGNACYVVRGLANLGNTCFFNSVMQNLLAMSQLQDYF-------- 258
S+I++ + V GS G A + GL NLGNTC+ NS++Q L L DYF
Sbjct: 46 SQIRNLNPVFGGS---GPA---LTGLRNLGNTCYXNSILQCLCNAPHLADYFNRNCYQDD 99
Query: 259 LNAELTFG-------PLTIALKKLFAETKPETGLRNVINPRSFFGCICSKAPQFKGYQQH 311
+N G I K L+ TG I+P+ F I QF GY Q
Sbjct: 100 INRSNLLGHKGEVAEEFGIIXKALW------TGQYRYISPKDFKITIGKINDQFAGYSQQ 153
Query: 312 DSHELLRCLLDGLCSEELA---FRKRNSPSEGNGISSNQGP------------VFVDYVF 356
DS ELL L DGL E+L RKR + + + + +F
Sbjct: 154 DSQELLLFLXDGL-HEDLNKADNRKRYKEENNDHLDDFKAAEHAWQKHKQLNESIIVALF 212
Query: 357 GGQIASTVRCVECGHSSTVYEPFLDLSLPVPT 388
GQ STV+C+ C S +E F LSLP+ +
Sbjct: 213 QGQFKSTVQCLTCHKKSRTFEAFXYLSLPLAS 244
Score = 65.1 bits (157), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 45/135 (33%), Positives = 68/135 (50%), Gaps = 15/135 (11%)
Query: 909 KVKRDATKRVLINKAPPILTIHLKRFSQDARGRLSKLNGHVNFS-EIINLRPYMDPGCTD 967
+ +RD+ K++ I K PP+L +HLKRFS D R + KL V+F E ++L Y+ +
Sbjct: 275 RARRDSLKKIEIWKLPPVLLVHLKRFSYDGRWK-QKLQTSVDFPLENLDLSQYVIGPKNN 333
Query: 968 HDNYDYRLVGVVEHLGTMRGGHYVAYVRGGPKNKVKAKKESVGGVWYHASDVYVREVSLE 1027
Y+ L V H G + GGHY AY + + + W+ D V ++S+
Sbjct: 334 LKKYN--LFSVSNHYGGLDGGHYTAYCKNAARQR-----------WFKFDDHEVSDISVS 380
Query: 1028 EVLRCEAYILFYEKI 1042
V AYILFY +
Sbjct: 381 SVKSSAAYILFYTSL 395
>pdb|2F1Z|A Chain A, Crystal Structure Of Hausp
pdb|2F1Z|B Chain B, Crystal Structure Of Hausp
Length = 522
Score = 50.4 bits (119), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 48/201 (23%), Positives = 81/201 (40%), Gaps = 24/201 (11%)
Query: 194 DVEDAWFGSGNVNSEIKSESTVVSGSDLDGNACYVVRGLANLGNTCFFNSVMQNLLAMSQ 253
D E + V E+ ++ G D GL N G TC+ NS++Q L +Q
Sbjct: 140 DPEKGFIDDDKVTFEVFVQADAPHGVAWDSKKHTGYVGLKNQGATCYMNSLLQTLFFTNQ 199
Query: 254 LQD--YFLNAEL--TFGPLTIALKKLFAETKPETGLRNVINPRSFFGCICSKAPQFKGYQ 309
L+ Y + E + + +AL+++F E + FG +
Sbjct: 200 LRKAVYMMPTEGDDSSKSVPLALQRVFYELQHSDKPVGTKKLTKSFGW-----ETLDSFM 254
Query: 310 QHDSHELLRCLLDGLCSEELAFRKRNSPSEGNGISSNQGPVFVDYVFGGQIASTVRCVEC 369
QHD EL R LLD + + + + + EG + +F G++ S ++C E
Sbjct: 255 QHDVQELCRVLLDNVEN-----KMKGTCVEGT----------IPKLFRGKMVSYIQCKEV 299
Query: 370 GHSSTVYEPFLDLSLPVPTKK 390
+ S E + D+ L + KK
Sbjct: 300 DYRSDRREDYYDIQLSIKGKK 320
Score = 43.5 bits (101), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 45/151 (29%), Positives = 64/151 (42%), Gaps = 37/151 (24%)
Query: 912 RDATKRVLINKAPPILTIHLKRFSQDARGRLS-KLNGHVNFSEIINLRPYM---DPGCTD 967
++A K V PP+L + L RF D + + K+N F E + L ++ DP
Sbjct: 349 QEAEKGVKFLTLPPVLHLQLMRFMYDPQTDQNIKINDRFEFPEQLPLDEFLQKTDPK--- 405
Query: 968 HDNYDYRLVGVVEHLGTMRGGHYVAYV--RGGPK------------NKVKAKKESVGGVW 1013
D +Y L V+ H G GGHYV Y+ +G K K +A + + GG
Sbjct: 406 -DPANYILHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGG-- 462
Query: 1014 YHASD------------VYVREVSLEEVLRC 1032
H D VY+RE L EVL+
Sbjct: 463 -HDDDLSVRHCTNAYMLVYIRESKLSEVLQA 492
>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 = 48.9 bits (115), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 42/164 (25%), Positives = 71/164 (43%), Gaps = 24/164 (14%)
Query: 231 GLANLGNTCFFNSVMQNLLAMSQLQD--YFLNAEL--TFGPLTIALKKLFAETKPETGLR 286
GL N G TC+ NS++Q L +QL+ Y + E + + +AL+++F E +
Sbjct: 8 GLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPTEGDDSSKSVPLALQRVFYELQHSDKPV 67
Query: 287 NVINPRSFFGCICSKAPQFKGYQQHDSHELLRCLLDGLCSEELAFRKRNSPSEGNGISSN 346
FG + QHD EL R LLD + + + + + EG
Sbjct: 68 GTKKLTKSFGW-----ETLDSFMQHDVQELCRVLLDNVEN-----KMKGTCVEGT----- 112
Query: 347 QGPVFVDYVFGGQIASTVRCVECGHSSTVYEPFLDLSLPVPTKK 390
+ +F G++ S ++C E + S E + D+ L + KK
Sbjct: 113 -----IPKLFRGKMVSYIQCKEVDYRSDRREDYYDIQLSIKGKK 151
Score = 42.0 bits (97), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 45/151 (29%), Positives = 64/151 (42%), Gaps = 37/151 (24%)
Query: 912 RDATKRVLINKAPPILTIHLKRFSQDARGRLS-KLNGHVNFSEIINLRPYM---DPGCTD 967
++A K V PP+L + L RF D + + K+N F E + L ++ DP
Sbjct: 180 QEAEKGVKFLTLPPVLHLQLMRFMYDPQTDQNIKINDRFEFPEQLPLDEFLQKTDPK--- 236
Query: 968 HDNYDYRLVGVVEHLGTMRGGHYVAYV--RGGPK------------NKVKAKKESVGGVW 1013
D +Y L V+ H G GGHYV Y+ +G K K +A + + GG
Sbjct: 237 -DPANYILHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGG-- 293
Query: 1014 YHASD------------VYVREVSLEEVLRC 1032
H D VY+RE L EVL+
Sbjct: 294 -HDDDLSVRHCTNAYMLVYIRESKLSEVLQA 323
>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 = 45.8 bits (107), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 40/164 (24%), Positives = 68/164 (41%), Gaps = 24/164 (14%)
Query: 231 GLANLGNTCFFNSVMQNLLAMSQLQDYFL----NAELTFGPLTIALKKLFAETKPETGLR 286
GL N G TC+ NS++Q L +QL+ + + + +AL+++F E +
Sbjct: 8 GLKNQGATCYXNSLLQTLFFTNQLRKAVYXXPTEGDDSSKSVPLALQRVFYELQHSDKPV 67
Query: 287 NVINPRSFFGCICSKAPQFKGYQQHDSHELLRCLLDGLCSEELAFRKRNSPSEGNGISSN 346
FG + QHD EL R LLD + + + + + EG
Sbjct: 68 GTKKLTKSFGW-----ETLDSFXQHDVQELCRVLLDNVEN-----KXKGTCVEGT----- 112
Query: 347 QGPVFVDYVFGGQIASTVRCVECGHSSTVYEPFLDLSLPVPTKK 390
+ +F G+ S ++C E + S E + D+ L + KK
Sbjct: 113 -----IPKLFRGKXVSYIQCKEVDYRSDRREDYYDIQLSIKGKK 151
Score = 42.7 bits (99), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 45/151 (29%), Positives = 64/151 (42%), Gaps = 37/151 (24%)
Query: 912 RDATKRVLINKAPPILTIHLKRFSQDARGRLS-KLNGHVNFSEIINLRPYM---DPGCTD 967
++A K V PP+L + L RF D + + K+N F E + L ++ DP
Sbjct: 180 QEAEKGVKFLTLPPVLHLQLXRFXYDPQTDQNIKINDRFEFPEQLPLDEFLQKTDPK--- 236
Query: 968 HDNYDYRLVGVVEHLGTMRGGHYVAYV--RGGPK------------NKVKAKKESVGGVW 1013
D +Y L V+ H G GGHYV Y+ +G K K +A + + GG
Sbjct: 237 -DPANYILHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGG-- 293
Query: 1014 YHASD------------VYVREVSLEEVLRC 1032
H D VY+RE L EVL+
Sbjct: 294 -HDDDLSVRHCTNAYXLVYIRESKLSEVLQA 323
>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
Length = 854
Score = 42.0 bits (97), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 71/324 (21%), Positives = 126/324 (38%), Gaps = 74/324 (22%)
Query: 107 IWVCLGCGHYACGGVGLPTTP-QSHVVRHARQTRHPLVIQWENPHLRWCFPCNTLIP--- 162
+W+ L G CG + +H V H R+T +PL ++ T+ P
Sbjct: 227 LWLNLTDGSILCGRRYFDGSGGNNHAVEHYRETGYPLAVK-----------LGTITPDGA 275
Query: 163 -VEKTEENGENKD-ALSEV-----VKLIKGRSTEISSVDVEDAWFGSGNVNSEI-KSEST 214
V +E+ D +L+E + ++K + T+ + ++E ++N I + E
Sbjct: 276 DVYSYDEDDMVLDPSLAEHLSHFGIDMLKMQKTDKTMTELEI------DMNQRIGEWELI 329
Query: 215 VVSGSDLDGNACYVVRGLANLGNTCFFNSVMQNLLAMSQLQDYFLNA-ELTF--GP---- 267
SG L G+ NLGN+C+ NSV+Q L ++ Q +++ E F P
Sbjct: 330 QESGVPLKPLFGPGYTGIRNLGNSCYLNSVVQVLFSIPDFQRKYVDKLEKIFQNAPTDPT 389
Query: 268 --LTIALKKL--------FAETKPETG----------LRNVINPRSFFGCICSKAPQFKG 307
+ + KL +++ PE+G +++ I PR F I P+F
Sbjct: 390 QDFSTQVAKLGHGLLSGEYSKPVPESGDGERVPEQKEVQDGIAPRMFKALIGKGHPEFST 449
Query: 308 YQQHDSHELLRCLLDGLCSEELAFRKRNSPSEGNGISSNQGPVFVDYVFGGQIASTVRCV 367
+Q D+ E L++ + E R +P+E VF + ++C+
Sbjct: 450 NRQQDAQEFFLHLINMV---ERNCRSSENPNE---------------VFRFLVEEKIKCL 491
Query: 368 ECGHSSTVYEPFLDLSLPVPTKKA 391
+ LPVP A
Sbjct: 492 ATEKVKYTQRVDYIMQLPVPMDAA 515
>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 = 41.2 bits (95), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 42/157 (26%), Positives = 70/157 (44%), Gaps = 22/157 (14%)
Query: 231 GLANLGNTCFFNSVMQNLLAMSQLQD---YFLNAELTFGPL------TIALKKLFAETKP 281
GL NLGNTC+ N+ +Q + ++ +L+D + A G + T AL+ LF
Sbjct: 16 GLTNLGNTCYMNATVQCIRSVPELKDALKRYAGALRASGEMASAQYITAALRDLFDSMDK 75
Query: 282 ETGLRNVINPRSFFGCICSKAPQF--KG----YQQHDSHE----LLRCLLDGLCSEELAF 331
+ + I P + PQF KG Y Q D++E ++R L L + E
Sbjct: 76 TS---SSIPPIILLQFLHMAFPQFAEKGEQGQYLQQDANECWIQMMRVLQQKLEAIEDDS 132
Query: 332 RKRNSPSEGNGISSNQGPVFVDYVFGGQIASTVRCVE 368
K S + + ++ +D FG + +T++C E
Sbjct: 133 VKETDSSSASAATPSKKKSLIDQFFGVEFETTMKCTE 169
>pdb|2I50|A Chain A, Solution Structure Of Ubp-M Znf-Ubp Domain
Length = 126
Score = 38.9 bits (89), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 28/127 (22%), Positives = 55/127 (43%), Gaps = 22/127 (17%)
Query: 50 CPHLDKGIDSDKISVKIGSSDPIRCEDCR--EGVGDRRXXXXXXXXXXXXXSSLVDSKAI 107
C H+ KG++ + + + + C+DC+ V D+ + ++
Sbjct: 7 CRHIRKGLEQGNLKKALVNVEWNICQDCKTDNKVKDKAEEETE------------EKPSV 54
Query: 108 WVCLGCGHYACGGVGLPTTPQSHVVRHA---RQTRHPLVIQWENPHLRWCFPCNTLIPVE 164
W+CL CGH CG + + H ++H R H LV+ +N + WC+ C+ +
Sbjct: 55 WLCLKCGHQGCG----RNSQEQHALKHYLTPRSEPHCLVLSLDNWSV-WCYVCDNEVQYC 109
Query: 165 KTEENGE 171
+ + G+
Sbjct: 110 SSNQLGQ 116
>pdb|2IDA|A Chain A, Solution Nmr Structure Of Protein Rpa1320 From
Rhodopseudomonas Palustris. Northeast Structural
Genomics Consortium Target Rpt3; Ontario Center For
Structural Proteomics Target Rp1313
Length = 102
Score = 36.2 bits (82), Expect = 0.11, Method: Composition-based stats.
Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 5/48 (10%)
Query: 109 VCLGCGHYACGGVGLPTTPQSHVVRHARQTRHPLVIQWENPH-LRWCF 155
+C CGH C +P H RH T HP++ ++ P WC+
Sbjct: 36 ICRTCGHVGC----CDDSPHKHATRHFHATGHPIIEGYDPPEGWGWCY 79
>pdb|1VJV|A Chain A, Crystal Structure Of Ubiquitin Carboxyl-terminal Hydrolase
6 (yfr010w) From Saccharomyces Cerevisiae At 1.74 A
Resolution
Length = 415
Score = 35.0 bits (79), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 29/111 (26%), Positives = 44/111 (39%), Gaps = 22/111 (19%)
Query: 231 GLANLGNTCFFNSVMQNLLAMSQLQDYFLNAELTFG-------------PLTIALKKLFA 277
G N GNTC+ N+ +Q L ++ L+D LN + G + I K+ F
Sbjct: 26 GFKNXGNTCYLNATLQALYRVNDLRDXILNYNPSQGVSNSGAQDEEIHKQIVIEXKRCF- 84
Query: 278 ETKPETGLRNVINPRSFFGCICSKAPQFK-------GYQQHDSHELLRCLL 321
E ++V+ P + PQF Y+Q D+ EL L
Sbjct: 85 ENLQNKSFKSVL-PVVLLNTLRKCYPQFAERDSQGGFYKQQDAEELFTQLF 134
>pdb|3GV4|A Chain A, Crystal Structure Of Human Hdac6 Zinc Finger Domain And
Ubiquitin C-Terminal Peptide Rlrgg
pdb|3PHD|A Chain A, Crystal Structure Of Human Hdac6 In Complex With Ubiquitin
pdb|3PHD|B Chain B, Crystal Structure Of Human Hdac6 In Complex With Ubiquitin
pdb|3PHD|C Chain C, Crystal Structure Of Human Hdac6 In Complex With Ubiquitin
pdb|3PHD|D Chain D, Crystal Structure Of Human Hdac6 In Complex With Ubiquitin
Length = 107
Score = 34.7 bits (78), Expect = 0.27, Method: Composition-based stats.
Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 6/54 (11%)
Query: 108 WVCLGCGHYACGGVGLPTTPQSHVVRHARQTRHPLVIQWENPHLRWCFPCNTLI 161
WVCL C CG H+++H + HPLV+ + + WC+ C +
Sbjct: 35 WVCLSCYQVYCG-----RYINGHMLQHHGNSGHPLVLSYIDLS-AWCYYCQAYV 82
>pdb|3C5K|A Chain A, Crystal Structure Of Human Hdac6 Zinc Finger Domain
Length = 109
Score = 34.7 bits (78), Expect = 0.30, Method: Composition-based stats.
Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 6/54 (11%)
Query: 108 WVCLGCGHYACGGVGLPTTPQSHVVRHARQTRHPLVIQWENPHLRWCFPCNTLI 161
WVCL C CG H+++H + HPLV+ + + WC+ C +
Sbjct: 37 WVCLSCYQVYCG-----RYINGHMLQHHGNSGHPLVLSYIDLS-AWCYYCQAYV 84
>pdb|3J21|II Chain i, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 83
Score = 32.7 bits (73), Expect = 1.0, Method: Composition-based stats.
Identities = 14/30 (46%), Positives = 14/30 (46%)
Query: 104 SKAIWVCLGCGHYACGGVGLPTTPQSHVVR 133
S IW C CG GG LP TP VR
Sbjct: 50 STGIWQCQKCGATFAGGAYLPVTPAGKAVR 79
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
0.313 0.132 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 28,994,386
Number of Sequences: 62578
Number of extensions: 1174720
Number of successful extensions: 2474
Number of sequences better than 100.0: 33
Number of HSP's better than 100.0 without gapping: 24
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 2371
Number of HSP's gapped (non-prelim): 56
length of query: 1042
length of database: 14,973,337
effective HSP length: 109
effective length of query: 933
effective length of database: 8,152,335
effective search space: 7606128555
effective search space used: 7606128555
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 57 (26.6 bits)