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= 005687
(683 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 150 bits (378), Expect = 3e-36, Method: Compositional matrix adjust.
Identities = 116/335 (34%), Positives = 172/335 (51%), Gaps = 32/335 (9%)
Query: 108 AGLENLGNTCFINAILQCFTHTLPLVQALRSFDHPRPCDGATEGFCVICALRDHIELSL- 166
+GL N+GNTCF+++ILQC H ++ S H C + C CAL D I L
Sbjct: 142 SGLINMGNTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCAL-DKIVHELY 200
Query: 167 -------ASSGKVLSPRK-----LVDNLNYISSFFQRYQQEDAHEFLQCLLDRL-ESCCL 213
ASS + R+ L+ I+ Y Q+DAHEF Q +++++ +S L
Sbjct: 201 GALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQSYVL 260
Query: 214 D---SKTKDESLSSQGDNIVQRVFGGCLISKLQCCNCGSCSDT-YEPLIDLSLEIEDVGS 269
D +K + + Q + IV VF G L S + C C + S T +P +DLSL+I+D
Sbjct: 261 DLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIKDKKK 320
Query: 270 LGSALESFTKLEKIEDPETKFTCEKCKEQVSVEKQLMLDKVPSVAAFHLKRFK--TDGSY 327
L L+SF K E+++D + C +C KQL + K+PSV LKRF+ +GS
Sbjct: 321 LYECLDSFHKKEQLKD--FNYHCGECNSTQDAIKQLGIHKLPSVLVLQLKRFEHLLNGSN 378
Query: 328 VVKIDKHVEFPLELDLKPYTSG------GQNSDV-ELKYHLYAIVEHMGSSPTCGHYFSY 380
K+D +EFP L++K Y S +N V ++ Y L IV H G+ GHY ++
Sbjct: 379 R-KLDDFIEFPTYLNMKNYCSTKEKDKHSENGKVPDIIYELIGIVSHKGTVNE-GHYIAF 436
Query: 381 IRSSPDTWHRLNDSRVTRVEEEFVLSQDAYILFYA 415
+ S W + NDS V+ + +E VL + AY+LFY
Sbjct: 437 CKISGGQWFKFNDSMVSSISQEEVLKEQAYLLFYT 471
>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 = 147 bits (372), Expect = 2e-35, Method: Compositional matrix adjust.
Identities = 115/335 (34%), Positives = 172/335 (51%), Gaps = 32/335 (9%)
Query: 108 AGLENLGNTCFINAILQCFTHTLPLVQALRSFDHPRPCDGATEGFCVICALRDHIELSL- 166
+GL N+G+TCF+++ILQC H ++ S H C + C CAL D I L
Sbjct: 142 SGLINMGSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCAL-DKIVHELY 200
Query: 167 -------ASSGKVLSPRK-----LVDNLNYISSFFQRYQQEDAHEFLQCLLDRL-ESCCL 213
ASS + R+ L+ I+ Y Q+DAHEF Q +++++ +S L
Sbjct: 201 GALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQSYVL 260
Query: 214 D---SKTKDESLSSQGDNIVQRVFGGCLISKLQCCNCGSCSDT-YEPLIDLSLEIEDVGS 269
D +K + + Q + IV VF G L S + C C + S T +P +DLSL+I+D
Sbjct: 261 DLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIKDKKK 320
Query: 270 LGSALESFTKLEKIEDPETKFTCEKCKEQVSVEKQLMLDKVPSVAAFHLKRFK--TDGSY 327
L L+SF K E+++D + C +C KQL + K+PSV LKRF+ +GS
Sbjct: 321 LYECLDSFHKKEQLKD--FNYHCGECNSTQDAIKQLGIHKLPSVLVLQLKRFEHLLNGSN 378
Query: 328 VVKIDKHVEFPLELDLKPYTSG------GQNSDV-ELKYHLYAIVEHMGSSPTCGHYFSY 380
K+D +EFP L++K Y S +N V ++ Y L IV H G+ GHY ++
Sbjct: 379 R-KLDDFIEFPTYLNMKNYCSTKEKDKHSENGKVPDIIYELIGIVSHKGTVNE-GHYIAF 436
Query: 381 IRSSPDTWHRLNDSRVTRVEEEFVLSQDAYILFYA 415
+ S W + NDS V+ + +E VL + AY+LFY
Sbjct: 437 CKISGGQWFKFNDSMVSSISQEEVLKEQAYLLFYT 471
>pdb|3M99|A Chain A, Structure Of The Ubp8-Sgf11-Sgf73-Sus1 Saga Dub Module
Length = 471
Score = 147 bits (371), Expect = 2e-35, Method: Compositional matrix adjust.
Identities = 115/335 (34%), Positives = 172/335 (51%), Gaps = 32/335 (9%)
Query: 108 AGLENLGNTCFINAILQCFTHTLPLVQALRSFDHPRPCDGATEGFCVICALRDHIELSL- 166
+GL N+G+TCF+++ILQC H ++ S H C + C CAL D I L
Sbjct: 137 SGLINMGSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCAL-DKIVHELY 195
Query: 167 -------ASSGKVLSPRK-----LVDNLNYISSFFQRYQQEDAHEFLQCLLDRL-ESCCL 213
ASS + R+ L+ I+ Y Q+DAHEF Q +++++ +S L
Sbjct: 196 GALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQSYVL 255
Query: 214 D---SKTKDESLSSQGDNIVQRVFGGCLISKLQCCNCGSCSDT-YEPLIDLSLEIEDVGS 269
D +K + + Q + IV VF G L S + C C + S T +P +DLSL+I+D
Sbjct: 256 DLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIKDKKK 315
Query: 270 LGSALESFTKLEKIEDPETKFTCEKCKEQVSVEKQLMLDKVPSVAAFHLKRFK--TDGSY 327
L L+SF K E+++D + C +C KQL + K+PSV LKRF+ +GS
Sbjct: 316 LYECLDSFHKKEQLKD--FNYHCGECNSTQDAIKQLGIHKLPSVLVLQLKRFEHLLNGSN 373
Query: 328 VVKIDKHVEFPLELDLKPYTSG------GQNSDV-ELKYHLYAIVEHMGSSPTCGHYFSY 380
K+D +EFP L++K Y S +N V ++ Y L IV H G+ GHY ++
Sbjct: 374 R-KLDDFIEFPTYLNMKNYCSTKEKDKHSENGKVPDIIYELIGIVSHKGTVNE-GHYIAF 431
Query: 381 IRSSPDTWHRLNDSRVTRVEEEFVLSQDAYILFYA 415
+ S W + NDS V+ + +E VL + AY+LFY
Sbjct: 432 CKISGGQWFKFNDSMVSSISQEEVLKEQAYLLFYT 466
>pdb|2HD5|A Chain A, Usp2 In Complex With Ubiquitin
Length = 359
Score = 146 bits (369), Expect = 3e-35, Method: Compositional matrix adjust.
Identities = 118/341 (34%), Positives = 166/341 (48%), Gaps = 45/341 (13%)
Query: 108 AGLENLGNTCFINAILQCFTHTLPL----VQAL--RSFDHPRPCDGATEGFCVICALRDH 161
AGL NLGNTCF+N+ILQC ++T L +Q L R H G+ ++
Sbjct: 10 AGLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHH-----GSNAHTALVEEFAKL 64
Query: 162 IELSLASS-GKVLSPRKLVDNLNYISSFFQRYQQEDAHEFLQCLLDRLES----CCLDSK 216
I+ SS V+SP + + + F Y Q+DA EFL+ LLD L + L K
Sbjct: 65 IQTIWTSSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPK 124
Query: 217 TKDESLS----------------SQGDNIVQRVFGGCLISKLQCCNCGSCSDTYEPLIDL 260
+ E+L + D+ + +F G L S L C +CG CS ++P DL
Sbjct: 125 SNPENLDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDL 184
Query: 261 SLEIEDVG----SLGSALESFTKLEKIEDPETKFTCEKCKEQVSVEKQLMLDKVPSVAAF 316
SL I G +L + FTK E + D + K TC +C+ + K+ + + P +
Sbjct: 185 SLPIAKRGYPEVTLMDCMRLFTK-EDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKILVL 243
Query: 317 HLKRFKTDGSYVVKIDKHVEFPL-ELDLKPYTSGGQNSDVELKYHLYAIVEHMGSSPTCG 375
HLKRF K+ V FPL +LDL+ + S N V Y+LYA+ H G++ G
Sbjct: 244 HLKRFSESRIRTSKLTTFVNFPLRDLDLREFASENTNHAV---YNLYAVSNHSGTT-MGG 299
Query: 376 HYFSYIRSSPDT--WHRLNDSRVTRVEEEFVLSQDAYILFY 414
HY +Y R SP T WH NDS VT + V + DAY+LFY
Sbjct: 300 HYTAYCR-SPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFY 339
>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 = 146 bits (369), Expect = 4e-35, Method: Compositional matrix adjust.
Identities = 118/341 (34%), Positives = 166/341 (48%), Gaps = 45/341 (13%)
Query: 108 AGLENLGNTCFINAILQCFTHTLPL----VQAL--RSFDHPRPCDGATEGFCVICALRDH 161
AGL NLGNTCF+N+ILQC ++T L +Q L R H G+ ++
Sbjct: 29 AGLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHH-----GSNAHTALVEEFAKL 83
Query: 162 IELSLASS-GKVLSPRKLVDNLNYISSFFQRYQQEDAHEFLQCLLDRLES----CCLDSK 216
I+ SS V+SP + + + F Y Q+DA EFL+ LLD L + L K
Sbjct: 84 IQTIWTSSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPK 143
Query: 217 TKDESLS----------------SQGDNIVQRVFGGCLISKLQCCNCGSCSDTYEPLIDL 260
+ E+L + D+ + +F G L S L C +CG CS ++P DL
Sbjct: 144 SNPENLDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDL 203
Query: 261 SLEIEDVG----SLGSALESFTKLEKIEDPETKFTCEKCKEQVSVEKQLMLDKVPSVAAF 316
SL I G +L + FTK E + D + K TC +C+ + K+ + + P +
Sbjct: 204 SLPIAKRGYPEVTLMDCMRLFTK-EDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKILVL 262
Query: 317 HLKRFKTDGSYVVKIDKHVEFPL-ELDLKPYTSGGQNSDVELKYHLYAIVEHMGSSPTCG 375
HLKRF K+ V FPL +LDL+ + S N V Y+LYA+ H G++ G
Sbjct: 263 HLKRFSESRIRTSKLTTFVNFPLRDLDLREFASENTNHAV---YNLYAVSNHSGTT-MGG 318
Query: 376 HYFSYIRSSPDT--WHRLNDSRVTRVEEEFVLSQDAYILFY 414
HY +Y R SP T WH NDS VT + V + DAY+LFY
Sbjct: 319 HYTAYCR-SPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFY 358
>pdb|2IBI|A Chain A, Covalent Ubiquitin-Usp2 Complex
Length = 374
Score = 145 bits (366), Expect = 7e-35, Method: Compositional matrix adjust.
Identities = 117/341 (34%), Positives = 165/341 (48%), Gaps = 45/341 (13%)
Query: 108 AGLENLGNTCFINAILQCFTHTLPL----VQAL--RSFDHPRPCDGATEGFCVICALRDH 161
AGL NLGNTCF+N+ILQC ++T L +Q L R H G+ ++
Sbjct: 36 AGLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHH-----GSNAHTALVEEFAKL 90
Query: 162 IELSLASS-GKVLSPRKLVDNLNYISSFFQRYQQEDAHEFLQCLLDRLES----CCLDSK 216
I+ SS V+SP + + + F Y Q+DA EFL+ LLD L + L K
Sbjct: 91 IQTIWTSSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPK 150
Query: 217 TKDESLS----------------SQGDNIVQRVFGGCLISKLQCCNCGSCSDTYEPLIDL 260
+ E+L + D+ + +F G L S L C +CG CS ++P DL
Sbjct: 151 SNPENLDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDL 210
Query: 261 SLEIEDVG----SLGSALESFTKLEKIEDPETKFTCEKCKEQVSVEKQLMLDKVPSVAAF 316
SL I G +L + FTK E + D + TC +C+ + K+ + + P +
Sbjct: 211 SLPIAKRGYPEVTLMDCMRLFTK-EDVLDGDAAPTCCRCRGRKRCIKKFSIQRFPKILVL 269
Query: 317 HLKRFKTDGSYVVKIDKHVEFPL-ELDLKPYTSGGQNSDVELKYHLYAIVEHMGSSPTCG 375
HLKRF K+ V FPL +LDL+ + S N V Y+LYA+ H G++ G
Sbjct: 270 HLKRFSESRIRTSKLTTFVNFPLRDLDLREFASENTNHAV---YNLYAVSNHSGTT-MGG 325
Query: 376 HYFSYIRSSPDT--WHRLNDSRVTRVEEEFVLSQDAYILFY 414
HY +Y R SP T WH NDS VT + V + DAY+LFY
Sbjct: 326 HYTAYCR-SPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFY 365
>pdb|3NHE|A Chain A, High Resolution Structure (1.26a) Of Usp2a In Complex With
Ubiquitin
Length = 348
Score = 143 bits (360), Expect = 3e-34, Method: Compositional matrix adjust.
Identities = 117/338 (34%), Positives = 162/338 (47%), Gaps = 39/338 (11%)
Query: 108 AGLENLGNTCFINAILQCFTHTLPL----VQALRSFDHPRPCDGATEGFCVICALRDHIE 163
AGL NLGNT F+N+ILQC ++T L +Q L D + T L I
Sbjct: 10 AGLRNLGNTXFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQTIW 69
Query: 164 LSLASSGKVLSPRKLVDNLNYISSFFQRYQQEDAHEFLQCLLDRLES----CCLDSKTKD 219
S S V+SP + + + F Y Q+DA EFL+ LLD L + L K+
Sbjct: 70 TS--SPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNP 127
Query: 220 ESLS----------------SQGDNIVQRVFGGCLISKLQCCNCGSCSDTYEPLIDLSLE 263
E+L + D+ + +F G L S L C +CG CS ++P DLSL
Sbjct: 128 ENLDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLP 187
Query: 264 IEDVG----SLGSALESFTKLEKIEDPETKFTCEKCKEQVSVEKQLMLDKVPSVAAFHLK 319
I G +L + FTK E + D + K TC +C+ + K+ + + P + HLK
Sbjct: 188 IAKRGYPEVTLMDCMRLFTK-EDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKILVLHLK 246
Query: 320 RFKTDGSYVVKIDKHVEFPL-ELDLKPYTSGGQNSDVELKYHLYAIVEHMGSSPTCGHYF 378
RF K+ V FPL +LDL+ + S N V Y+LYA+ H G++ GHY
Sbjct: 247 RFSESRIRTSKLTTFVNFPLRDLDLREFASENTNHAV---YNLYAVSNHSGTT-MGGHYT 302
Query: 379 SYIRSSPDT--WHRLNDSRVTRVEEEFVLSQDAYILFY 414
+Y R SP T WH NDS VT + V + DAY+LFY
Sbjct: 303 AYCR-SPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFY 339
>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 = 133 bits (334), Expect = 4e-31, Method: Compositional matrix adjust.
Identities = 110/355 (30%), Positives = 151/355 (42%), Gaps = 59/355 (16%)
Query: 108 AGLENLGNTCFINAILQCFTHTLPLVQAL--RSFDHPRPCDG----ATEGFCVICALRDH 161
GL NLGNTCF+NA+LQC + T PL R F P G TE F + H
Sbjct: 4 VGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQELTEAFADVIGALWH 63
Query: 162 IELSLASSGKVLSPRKLVDNLNYISSFFQRYQQEDAHEFLQCLLDRLESCCLDSKTKDES 221
+ S + ++P + F Y Q+DA EFL+ L++RL +
Sbjct: 64 PD-----SCEAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRAPP 118
Query: 222 LSSQG-----------------------------------DNIVQRVFGGCLISKLQCCN 246
+ + G D+ + +F G L S L+C
Sbjct: 119 ILANGPVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKCQA 178
Query: 247 CGSCSDTYEPLIDLSLEIEDVG------SLGSALESFTKLEKIEDPETKFTCEKCKEQVS 300
CG S T+E DLSL I G SL FTK E++E E C++C+++
Sbjct: 179 CGYRSTTFEVFCDLSLPIPKKGFAGGKVSLRDCFNLFTKEEELES-ENAPVCDRCRQKTR 237
Query: 301 VEKQLMLDKVPSVAAFHLKRFKTDGSYVVKIDKHVEFPLE-LDLKPYTSGGQNSDVELKY 359
K+L + + P + HL RF + K V+FPL+ L L + S S V Y
Sbjct: 238 STKKLTVQRFPRILVLHLNRFSASRGSIKKSSVGVDFPLQRLSLGDFASDKAGSPV---Y 294
Query: 360 HLYAIVEHMGSSPTCGHYFSYIRSSPDTWHRLNDSRVTRVEEEFVLSQDAYILFY 414
LYA+ H GS GHY + R WH NDSRV+ V E V S + Y+LFY
Sbjct: 295 QLYALCNHSGSVHY-GHYTALCRCQ-TGWHVYNDSRVSPVSENQVASSEGYVLFY 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 = 133 bits (334), Expect = 4e-31, Method: Compositional matrix adjust.
Identities = 110/355 (30%), Positives = 151/355 (42%), Gaps = 59/355 (16%)
Query: 108 AGLENLGNTCFINAILQCFTHTLPLVQAL--RSFDHPRPCDG----ATEGFCVICALRDH 161
GL NLGNTCF+NA+LQC + T PL R F P G TE F + H
Sbjct: 23 VGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQELTEAFADVIGALWH 82
Query: 162 IELSLASSGKVLSPRKLVDNLNYISSFFQRYQQEDAHEFLQCLLDRLESCCLDSKTKDES 221
+ S + ++P + F Y Q+DA EFL+ L++RL +
Sbjct: 83 PD-----SCEAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRAPP 137
Query: 222 LSSQG-----------------------------------DNIVQRVFGGCLISKLQCCN 246
+ + G D+ + +F G L S L+C
Sbjct: 138 ILANGPVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKCQA 197
Query: 247 CGSCSDTYEPLIDLSLEIEDVG------SLGSALESFTKLEKIEDPETKFTCEKCKEQVS 300
CG S T+E DLSL I G SL FTK E++E E C++C+++
Sbjct: 198 CGYRSTTFEVFCDLSLPIPKKGFAGGKVSLRDCFNLFTKEEELES-ENAPVCDRCRQKTR 256
Query: 301 VEKQLMLDKVPSVAAFHLKRFKTDGSYVVKIDKHVEFPLE-LDLKPYTSGGQNSDVELKY 359
K+L + + P + HL RF + K V+FPL+ L L + S S V Y
Sbjct: 257 STKKLTVQRFPRILVLHLNRFSASRGSIKKSSVGVDFPLQRLSLGDFASDKAGSPV---Y 313
Query: 360 HLYAIVEHMGSSPTCGHYFSYIRSSPDTWHRLNDSRVTRVEEEFVLSQDAYILFY 414
LYA+ H GS GHY + R WH NDSRV+ V E V S + Y+LFY
Sbjct: 314 QLYALCNHSGSVHY-GHYTALCRCQ-TGWHVYNDSRVSPVSENQVASSEGYVLFY 366
>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 = 132 bits (332), Expect = 6e-31, Method: Compositional matrix adjust.
Identities = 110/355 (30%), Positives = 151/355 (42%), Gaps = 59/355 (16%)
Query: 108 AGLENLGNTCFINAILQCFTHTLPLVQAL--RSFDHPRPCDG----ATEGFCVICALRDH 161
GL NLGNTCF+NA+LQC + T PL R F P G TE F + H
Sbjct: 17 VGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQELTEAFADVIGALWH 76
Query: 162 IELSLASSGKVLSPRKLVDNLNYISSFFQRYQQEDAHEFLQCLLDRLESCCLDSKTKDES 221
+ S + ++P + F Y Q+DA EFL+ L++RL +
Sbjct: 77 PD-----SCEAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRAPP 131
Query: 222 LSSQG-----------------------------------DNIVQRVFGGCLISKLQCCN 246
+ + G D+ + +F G L S L+C
Sbjct: 132 ILANGPVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKCQA 191
Query: 247 CGSCSDTYEPLIDLSLEIEDVG------SLGSALESFTKLEKIEDPETKFTCEKCKEQVS 300
CG S T+E DLSL I G SL FTK E++E E C++C+++
Sbjct: 192 CGYRSTTFEVFCDLSLPIPKKGFAGGKVSLRDCFNLFTKEEELES-ENAPVCDRCRQKTR 250
Query: 301 VEKQLMLDKVPSVAAFHLKRFKTDGSYVVKIDKHVEFPLE-LDLKPYTSGGQNSDVELKY 359
K+L + + P + HL RF + K V+FPL+ L L + S S V Y
Sbjct: 251 STKKLTVQRFPRILVLHLNRFSASRGSIKKSSVGVDFPLQRLSLGDFASDKAGSPV---Y 307
Query: 360 HLYAIVEHMGSSPTCGHYFSYIRSSPDTWHRLNDSRVTRVEEEFVLSQDAYILFY 414
LYA+ H GS GHY + R WH NDSRV+ V E V S + Y+LFY
Sbjct: 308 QLYALCNHSGSVHY-GHYTALCRCQ-TGWHVYNDSRVSPVSENQVASSEGYVLFY 360
>pdb|3N3K|A Chain A, The Catalytic Domain Of Usp8 In Complex With A Usp8
Specific Inhibitor
Length = 396
Score = 118 bits (296), Expect = 1e-26, Method: Compositional matrix adjust.
Identities = 100/344 (29%), Positives = 151/344 (43%), Gaps = 45/344 (13%)
Query: 109 GLENLGNTCFINAILQCFTHTLPLVQAL----------RSFDHPRPCDGATEGFCVICAL 158
GL NLGNTC++N+ILQC + L RS + A E ++ AL
Sbjct: 64 GLRNLGNTCYMNSILQCLCNAPHLADYFNRNCYQDDINRSNLLGHKGEVAEEFGIIMKAL 123
Query: 159 RDHIELSLASSGKVLSPRKLVDNLNYISSFFQRYQQEDAHEFLQCLLDRLESCCLDSKTK 218
+ +SP+ + I+ F Y Q+D+ E L L+D L + +
Sbjct: 124 -------WTGQYRYISPKDFKITIGKINDQFAGYSQQDSQELLLFLMDGLHEDLNKADNR 176
Query: 219 DESLSSQGDN--------------------IVQRVFGGCLISKLQCCNCGSCSDTYEPLI 258
D+ I+ +F G S +QC C S T+E +
Sbjct: 177 KRYKEENNDHLDDFKAAEHAWQKHKQLNESIIVALFQGQFKSTVQCLTCHKKSRTFEAFM 236
Query: 259 DLSLEIEDVG--SLGSALESFTKLEKIEDPETKFTCEKCKEQVSVEKQLMLDKVPSVAAF 316
LSL + +L L F+K EK+ D +F C C+ + K++ + K+P V
Sbjct: 237 YLSLPLASTSKCTLQDCLRLFSKEEKLTD-NNRFYCSHCRARRDSLKKIEIWKLPPVLLV 295
Query: 317 HLKRFKTDGSYVVKIDKHVEFPLE-LDLKPYTSGGQNSDVELKYHLYAIVEHMGSSPTCG 375
HLKRF DG + K+ V+FPLE LDL Y G +N+ KY+L+++ H G G
Sbjct: 296 HLKRFSYDGRWKQKLQTSVDFPLENLDLSQYVIGPKNN--LKKYNLFSVSNHYGGLDG-G 352
Query: 376 HYFSYIRSSP-DTWHRLNDSRVTRVEEEFVLSQDAYILFYAKQG 418
HY +Y +++ W + +D V+ + V S AYILFY G
Sbjct: 353 HYTAYCKNAARQRWFKFDDHEVSDISVSSVKSSAAYILFYTSLG 396
>pdb|2GFO|A Chain A, Structure Of The Catalytic Domain Of Human Ubiquitin
Carboxyl-terminal Hydrolase 8
Length = 396
Score = 113 bits (282), Expect = 4e-25, Method: Compositional matrix adjust.
Identities = 100/344 (29%), Positives = 147/344 (42%), Gaps = 45/344 (13%)
Query: 109 GLENLGNTCFINAILQCFTHTLPLVQAL----------RSFDHPRPCDGATEGFCVICAL 158
GL NLGNTC+ N+ILQC + L RS + A E + AL
Sbjct: 64 GLRNLGNTCYXNSILQCLCNAPHLADYFNRNCYQDDINRSNLLGHKGEVAEEFGIIXKAL 123
Query: 159 RDHIELSLASSGKVLSPRKLVDNLNYISSFFQRYQQEDAHEFLQCLLDRLESCCLDSKTK 218
+ +SP+ + I+ F Y Q+D+ E L L D L + +
Sbjct: 124 -------WTGQYRYISPKDFKITIGKINDQFAGYSQQDSQELLLFLXDGLHEDLNKADNR 176
Query: 219 DESLSSQGDN--------------------IVQRVFGGCLISKLQCCNCGSCSDTYEPLI 258
D+ I+ +F G S +QC C S T+E
Sbjct: 177 KRYKEENNDHLDDFKAAEHAWQKHKQLNESIIVALFQGQFKSTVQCLTCHKKSRTFEAFX 236
Query: 259 DLSLEIEDVG--SLGSALESFTKLEKIEDPETKFTCEKCKEQVSVEKQLMLDKVPSVAAF 316
LSL + +L L F+K EK+ D +F C C+ + K++ + K+P V
Sbjct: 237 YLSLPLASTSKCTLQDCLRLFSKEEKLTD-NNRFYCSHCRARRDSLKKIEIWKLPPVLLV 295
Query: 317 HLKRFKTDGSYVVKIDKHVEFPLE-LDLKPYTSGGQNSDVELKYHLYAIVEHMGSSPTCG 375
HLKRF DG + K+ V+FPLE LDL Y G +N+ KY+L+++ H G G
Sbjct: 296 HLKRFSYDGRWKQKLQTSVDFPLENLDLSQYVIGPKNN--LKKYNLFSVSNHYGGLDG-G 352
Query: 376 HYFSYIRSSP-DTWHRLNDSRVTRVEEEFVLSQDAYILFYAKQG 418
HY +Y +++ W + +D V+ + V S AYILFY G
Sbjct: 353 HYTAYCKNAARQRWFKFDDHEVSDISVSSVKSSAAYILFYTSLG 396
>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 = 110 bits (275), Expect = 3e-24, Method: Compositional matrix adjust.
Identities = 96/376 (25%), Positives = 156/376 (41%), Gaps = 80/376 (21%)
Query: 109 GLENLGNTCFINAILQCFTHTLPLV--------QALRSFDHPRPCDGATEGFCVICALRD 160
GL NLGNT F+N+ LQC ++T PL +A + D+P G + A +
Sbjct: 10 GLGNLGNTXFMNSALQCLSNTAPLTDYFLKDEYEAEINRDNPLGMKGE-----IAEAYAE 64
Query: 161 HIELSLASSGKVLSPRKLVDNLNYISSFFQRYQQEDAHEFLQCLLDRLESCCLDSKTKD- 219
I+ + ++PR + + F YQQ+D+ E L LLD L K K
Sbjct: 65 LIKQMWSGRDAHVAPRMFKTQVGRFAPQFSGYQQQDSQELLAFLLDGLHEDLNRVKKKPY 124
Query: 220 -------------------ESLSSQGDNIVQRVFGGCLISKLQCCNCGSCSDTYEPLIDL 260
E+ + D+++ F G S L C C S T++P L
Sbjct: 125 LELKDANGRPDAVVAKEAWENHRLRNDSVIVDTFHGLFKSTLVCPECAKVSVTFDPFCYL 184
Query: 261 SLEI-------------------EDVGSLGSALESFTKLEKI--EDPETKFTCEKCKEQV 299
+L + + +L +E FT +E + DP + C CK+
Sbjct: 185 TLPLPLKKDRVMEGPMLQPQKKKKTTVALRDCIELFTTMETLGEHDP---WYCPNCKKHQ 241
Query: 300 SVEKQLMLDKVPSVAAFHLKRFKTDGSYVVKIDKHVEFPLE----------LDLKPYTSG 349
K+ L +P + HLKRF + + K+D VEFP+ L +PY
Sbjct: 242 QATKKFDLWSLPKILVVHLKRFSYNRYWRDKLDTVVEFPIRGLNMSEFVCNLSARPYV-- 299
Query: 350 GQNSDVELKYHLYAIVEHMGSSPTCGHYFSYIRSSPD-TWHRLNDSRVTRVEEEFVLSQD 408
Y L A+ H G+ GHY +Y ++ + W+ +DS V+ E+ ++++
Sbjct: 300 ---------YDLIAVSNHYGAM-GVGHYTAYAKNKLNGKWYYFDDSNVSLASEDQIVTKA 349
Query: 409 AYILFYAKQGTEWVSS 424
AY+LFY ++ E+ +
Sbjct: 350 AYVLFYQRRDDEFYKT 365
>pdb|2F1Z|A Chain A, Crystal Structure Of Hausp
pdb|2F1Z|B Chain B, Crystal Structure Of Hausp
Length = 522
Score = 83.2 bits (204), Expect = 4e-16, Method: Compositional matrix adjust.
Identities = 88/345 (25%), Positives = 149/345 (43%), Gaps = 41/345 (11%)
Query: 102 KPTGVGAGLENLGNTCFINAILQCFTHTLPLVQALRSFDHPRPCDGATEGFCVICALRDH 161
K TG GL+N G TC++N++LQ TL LR + P +G V AL+
Sbjct: 171 KHTGY-VGLKNQGATCYMNSLLQ----TLFFTNQLRKAVYMMPTEGDDSSKSVPLALQ-R 224
Query: 162 IELSLASSGKVLSPRKLVDNLNYISSFFQRYQQEDAHEFLQCLLDRLESCCLDSKTKDES 221
+ L S K + +KL + + + + Q D E + LLD +E +K K
Sbjct: 225 VFYELQHSDKPVGTKKLTKSFGWET--LDSFMQHDVQELCRVLLDNVE-----NKMKGTC 277
Query: 222 LSSQGDNIVQRVFGGCLISKLQCCNCGSCSDTYEPLIDLSLEIEDVGSLGSALESFTKLE 281
+ + + ++F G ++S +QC SD E D+ L I+ ++ + + +E
Sbjct: 278 V----EGTIPKLFRGKMVSYIQCKEVDYRSDRREDYYDIQLSIKGKKNIFESFVDYVAVE 333
Query: 282 KIEDPETKFTCEKCKEQVSVEKQLMLDKVPSVAAFHLKRFKTD--GSYVVKIDKHVEFPL 339
++ D + K+ + Q EK + +P V L RF D +KI+ EFP
Sbjct: 334 QL-DGDNKYDAGEHGLQ-EAEKGVKFLTLPPVLHLQLMRFMYDPQTDQNIKINDRFEFPE 391
Query: 340 ELDLKPYTSGGQNSDVELKYHLYAIVEHMGSSPTCGHYFSYIRSSPD-TWHRLNDSRVTR 398
+L L + D Y L+A++ H G + GHY Y+ D W + +D V+R
Sbjct: 392 QLPLDEFLQKTDPKD-PANYILHAVLVHSGDN-HGGHYVVYLNPKGDGKWCKFDDDVVSR 449
Query: 399 VEEEFVLSQ---------------DAYILFYAKQGTEWVSSLLEA 428
+E + +AY+L Y ++ +S +L+A
Sbjct: 450 CTKEEAIEHNYGGHDDDLSVRHCTNAYMLVYIRESK--LSEVLQA 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 = 81.6 bits (200), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 88/345 (25%), Positives = 149/345 (43%), Gaps = 41/345 (11%)
Query: 102 KPTGVGAGLENLGNTCFINAILQCFTHTLPLVQALRSFDHPRPCDGATEGFCVICALRDH 161
K TG GL+N G TC++N++LQ TL LR + P +G V AL+
Sbjct: 2 KHTGY-VGLKNQGATCYMNSLLQ----TLFFTNQLRKAVYMMPTEGDDSSKSVPLALQ-R 55
Query: 162 IELSLASSGKVLSPRKLVDNLNYISSFFQRYQQEDAHEFLQCLLDRLESCCLDSKTKDES 221
+ L S K + +KL + + + + Q D E + LLD +E +K K
Sbjct: 56 VFYELQHSDKPVGTKKLTKSFGWET--LDSFMQHDVQELCRVLLDNVE-----NKMKGTC 108
Query: 222 LSSQGDNIVQRVFGGCLISKLQCCNCGSCSDTYEPLIDLSLEIEDVGSLGSALESFTKLE 281
+ + + ++F G ++S +QC SD E D+ L I+ ++ + + +E
Sbjct: 109 V----EGTIPKLFRGKMVSYIQCKEVDYRSDRREDYYDIQLSIKGKKNIFESFVDYVAVE 164
Query: 282 KIEDPETKFTCEKCKEQVSVEKQLMLDKVPSVAAFHLKRFKTD--GSYVVKIDKHVEFPL 339
++ D + K+ + Q EK + +P V L RF D +KI+ EFP
Sbjct: 165 QL-DGDNKYDAGEHGLQ-EAEKGVKFLTLPPVLHLQLMRFMYDPQTDQNIKINDRFEFPE 222
Query: 340 ELDLKPYTSGGQNSDVELKYHLYAIVEHMGSSPTCGHYFSYIRSSPD-TWHRLNDSRVTR 398
+L L + D Y L+A++ H G + GHY Y+ D W + +D V+R
Sbjct: 223 QLPLDEFLQKTDPKD-PANYILHAVLVHSGDN-HGGHYVVYLNPKGDGKWCKFDDDVVSR 280
Query: 399 VEEEFVLSQ---------------DAYILFYAKQGTEWVSSLLEA 428
+E + +AY+L Y ++ +S +L+A
Sbjct: 281 CTKEEAIEHNYGGHDDDLSVRHCTNAYMLVYIRESK--LSEVLQA 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 = 79.7 bits (195), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 81/304 (26%), Positives = 132/304 (43%), Gaps = 24/304 (7%)
Query: 102 KPTGVGAGLENLGNTCFINAILQCFTHTLPLVQALRSFDHPRPCDGATEGFCVICALRDH 161
K TG GL+N G TC+ N++LQ TL LR + P +G V AL+
Sbjct: 2 KHTGY-VGLKNQGATCYXNSLLQ----TLFFTNQLRKAVYXXPTEGDDSSKSVPLALQ-R 55
Query: 162 IELSLASSGKVLSPRKLVDNLNYISSFFQRYQQEDAHEFLQCLLDRLESCCLDSKTKDES 221
+ L S K + +KL + + + + Q D E + LLD +E+ K +
Sbjct: 56 VFYELQHSDKPVGTKKLTKSFGWET--LDSFXQHDVQELCRVLLDNVEN-------KXKG 106
Query: 222 LSSQGDNIVQRVFGGCLISKLQCCNCGSCSDTYEPLIDLSLEIEDVGSLGSALESFTKLE 281
+G + ++F G +S +QC SD E D+ L I+ ++ + + +E
Sbjct: 107 TCVEG--TIPKLFRGKXVSYIQCKEVDYRSDRREDYYDIQLSIKGKKNIFESFVDYVAVE 164
Query: 282 KIEDPETKFTCEKCKEQVSVEKQLMLDKVPSVAAFHLKRFKTD--GSYVVKIDKHVEFPL 339
++ D + K+ + Q EK + +P V L RF D +KI+ EFP
Sbjct: 165 QL-DGDNKYDAGEHGLQ-EAEKGVKFLTLPPVLHLQLXRFXYDPQTDQNIKINDRFEFPE 222
Query: 340 ELDLKPYTSGGQNSDVELKYHLYAIVEHMGSSPTCGHYFSYIRSSPD-TWHRLNDSRVTR 398
+L L + D Y L+A++ H G + GHY Y+ D W + +D V+R
Sbjct: 223 QLPLDEFLQKTDPKD-PANYILHAVLVHSGDN-HGGHYVVYLNPKGDGKWCKFDDDVVSR 280
Query: 399 VEEE 402
+E
Sbjct: 281 CTKE 284
>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 = 68.6 bits (166), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 97/398 (24%), Positives = 166/398 (41%), Gaps = 87/398 (21%)
Query: 109 GLENLGNTCFINAILQCFTHTLPLVQALRSFDHPRPCDG-ATEGFCVICALRDHIELSLA 167
GL NLGNTC++NA +QC L AL+ + G + ALRD + S+
Sbjct: 16 GLTNLGNTCYMNATVQCIRSVPELKDALKRYAGALRASGEMASAQYITAALRDLFD-SMD 74
Query: 168 SSGKVLSPRKLVDNLNYISSFFQ------RYQQEDAHE----FLQCLLDRLESCCLDSKT 217
+ + P L+ L+ F +Y Q+DA+E ++ L +LE+ DS
Sbjct: 75 KTSSSIPPIILLQFLHMAFPQFAEKGEQGQYLQQDANECWIQMMRVLQQKLEAIEDDSVK 134
Query: 218 KDESLS------SQGDNIVQRVFGGCLISKLQCCNC--GSCSDTYEPLIDLSLEI-EDVG 268
+ +S S S+ +++ + FG + ++C + E + LS I ++V
Sbjct: 135 ETDSSSASAATPSKKKSLIDQFFGVEFETTMKCTESEEEEVTKGKENQLQLSCFINQEVK 194
Query: 269 SLGSALESFTKLEKIEDPETKFTCEKCKEQVSVEKQLMLDKVPSVAAFHLKRF--KTDGS 326
L + L KL ++++ TK + + + + K + ++P+ + RF K S
Sbjct: 195 YLFTGL----KL-RLQEEITKQSPTLQRNALYI-KSSKISRLPAYLTIQMVRFFYKEKES 248
Query: 327 YVVKIDKHVEFPLELDL-----------------------------KPYTSGGQNS-DVE 356
K+ K V+FPL LD+ +P TS ++S E
Sbjct: 249 VNAKVLKDVKFPLMLDMYELCTPELQEKMVSFRSKFKDLEDKKVNQQPNTSDKKSSPQKE 308
Query: 357 LKYH-----------------LYAIVEHMGSSPTCGHYFSYIRSSPDTWHRLNDSRVTRV 399
+KY L A++ H G S + GHY S+++ D W + +D +V+ V
Sbjct: 309 VKYEPFSFADDIGSNNCGYYDLQAVLTHQGRSSSSGHYVSWVKRKQDEWIKFDDDKVSIV 368
Query: 400 EEEFVLSQD-------AYILFYAKQGTEWVSSLLEAES 430
E +L AY+L Y + E ++E ES
Sbjct: 369 TPEDILRLSGGGDWHIAYVLLYGPRRVE----IMEEES 402
>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 = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 31/50 (62%), Gaps = 2/50 (4%)
Query: 359 YHLYAIVEHMGSSPTCGHYFSYIRSSPD--TWHRLNDSRVTRVEEEFVLS 406
Y+L ++ H G++ GHY ++IR D W++ ND +V+ VE+E + S
Sbjct: 346 YNLIGVITHQGANSESGHYQAFIRDELDENKWYKFNDDKVSVVEKEKIES 395
>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
Length = 854
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/60 (38%), Positives = 32/60 (53%), Gaps = 5/60 (8%)
Query: 358 KYHLYAIVEHMGSSPTCGHYFSYIRSSPDTWHRLNDSRVTRVEEEFVLSQD-AYILFYAK 416
KY L+A + HMG+S CGHY +I+ W ND +V E+ +D YI FY +
Sbjct: 796 KYQLFAFISHMGTSTMCGHYVCHIKKE-GRWVIYNDQKVCASEKP---PKDLGYIYFYQR 851
>pdb|2XSJ|C Chain C, Structure Of Desulforubidin From Desulfomicrobium
Norvegicum
pdb|2XSJ|F Chain F, Structure Of Desulforubidin From Desulfomicrobium
Norvegicum
Length = 105
Score = 29.6 bits (65), Expect = 5.6, Method: Composition-based stats.
Identities = 16/60 (26%), Positives = 35/60 (58%), Gaps = 5/60 (8%)
Query: 401 EEFVLSQDAYILFYAKQGTEWVSSLLEAESIGMNADISNSSPKSVLDNVENDYTSRSGVA 460
+ F + +D ++L + G EW + E+E I ++I+ + + +LD ++ DY ++G+A
Sbjct: 9 KSFEIDEDGFLLKFEDWGPEWAEYVKESEGI---SEITEAH-QQILDFLQ-DYYKKNGIA 63
>pdb|2V4J|C Chain C, The Crystal Structure Of Desulfovibrio Vulgaris
Dissimilatory Sulfite Reductase Bound To Dsrc Provides
Novel Insights Into The Mechanism Of Sulfate Respiration
pdb|2V4J|F Chain F, The Crystal Structure Of Desulfovibrio Vulgaris
Dissimilatory Sulfite Reductase Bound To Dsrc Provides
Novel Insights Into The Mechanism Of Sulfate Respiration
Length = 105
Score = 29.6 bits (65), Expect = 5.8, Method: Composition-based stats.
Identities = 20/67 (29%), Positives = 37/67 (55%), Gaps = 5/67 (7%)
Query: 394 SRVTRVEEEFVLSQDAYILFYAKQGTEWVSSLLEAESIGMNADISNSSPKSVLDNVENDY 453
+ VT + F + +D ++L + EWV + E+E I +DIS K ++D ++ DY
Sbjct: 2 AEVTYKGKSFEVDEDGFLLRFDDWCPEWVEYVKESEGI---SDISPDHQK-IIDFLQ-DY 56
Query: 454 TSRSGVA 460
++G+A
Sbjct: 57 YKKNGIA 63
>pdb|3LSQ|A Chain A, Trypanosoma Brucei Seryl-Trna Synthetase
pdb|3LSQ|B Chain B, Trypanosoma Brucei Seryl-Trna Synthetase
pdb|3LSS|A Chain A, Trypanosoma Brucei Seryl-Trna Synthetase In Complex With
Atp
pdb|3LSS|B Chain B, Trypanosoma Brucei Seryl-Trna Synthetase In Complex With
Atp
Length = 484
Score = 29.3 bits (64), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 35/81 (43%), Gaps = 5/81 (6%)
Query: 608 CKTQLERNGKDLERQEAVRCIKKTMTGERYMKLMAAVND-----VSLNRKRRLKSSPCKR 662
C QL++ KDL Q A + E KLM V + V + + ++ +
Sbjct: 105 CVLQLKQLSKDLSDQVAGLAKEAQQLEEERDKLMLNVGNILHESVPIAQDEETGNTVVRT 164
Query: 663 FSPTRARRKHNHGSVMRRVAI 683
F T R K NH S+M R+ +
Sbjct: 165 FGNTTKRAKLNHVSIMERLGM 185
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.316 0.132 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,195,998
Number of Sequences: 62578
Number of extensions: 838778
Number of successful extensions: 1737
Number of sequences better than 100.0: 31
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 1657
Number of HSP's gapped (non-prelim): 40
length of query: 683
length of database: 14,973,337
effective HSP length: 105
effective length of query: 578
effective length of database: 8,402,647
effective search space: 4856729966
effective search space used: 4856729966
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)