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= 004724
(733 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 = 149 bits (375), Expect = 7e-36, Method: Compositional matrix adjust.
Identities = 108/333 (32%), Positives = 166/333 (49%), Gaps = 35/333 (10%)
Query: 181 GLLNCGNSCFANVVLQCLTYTRPLVAYLLEKGHRKECG--RDDWCFLCEFQTHV------ 232
GL+N GN+CF + +LQCL + + + + + H C D CF C V
Sbjct: 143 GLINMGNTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHELYGA 202
Query: 233 ---EKASQSSHPFSPMS----ILSRLPNIGGNLGYGRQEDAHEFMRFAIDTM-QSICLDE 284
++AS SS + + +L+ I NL Q+DAHEF +F I+ + QS LD
Sbjct: 203 LNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQSYVLDL 262
Query: 285 FGGEKAVPPRSQETTLIQH-IFGGHLQSQVICSKC-NNISNQYENMMDLTVEIHGDAASL 342
++ +++ I H +F G L+S ++C C NN + +DL+++I D L
Sbjct: 263 PNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDI-KDKKKL 321
Query: 343 EECLDQFTAKEWLDGDNMYKCDGCNDYVKAWKRLTVRRAPNILTIALKRFQ---SGRFGK 399
ECLD F KE L N Y C CN A K+L + + P++L + LKRF+ +G K
Sbjct: 322 YECLDSFHKKEQLKDFN-YHCGECNSTQDAIKQLGIHKLPSVLVLQLKRFEHLLNGSNRK 380
Query: 400 LNKRVTFPETLDLSPY--------MSDGGDRTDV-YKLYAVVVHVDMLNASFFGHYICYV 450
L+ + FP L++ Y S+ G D+ Y+L +V H +N GHYI +
Sbjct: 381 LDDFIEFPTYLNMKNYCSTKEKDKHSENGKVPDIIYELIGIVSHKGTVNE---GHYIAFC 437
Query: 451 KDFRGHWYRVDDCKVTSVDLEEVLSQGAYMLLY 483
K G W++ +D V+S+ EEVL + AY+L Y
Sbjct: 438 KISGGQWFKFNDSMVSSISQEEVLKEQAYLLFY 470
>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 (370), Expect = 3e-35, Method: Compositional matrix adjust.
Identities = 107/333 (32%), Positives = 166/333 (49%), Gaps = 35/333 (10%)
Query: 181 GLLNCGNSCFANVVLQCLTYTRPLVAYLLEKGHRKECG--RDDWCFLCEFQTHV------ 232
GL+N G++CF + +LQCL + + + + + H C D CF C V
Sbjct: 143 GLINMGSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHELYGA 202
Query: 233 ---EKASQSSHPFSPMS----ILSRLPNIGGNLGYGRQEDAHEFMRFAIDTM-QSICLDE 284
++AS SS + + +L+ I NL Q+DAHEF +F I+ + QS LD
Sbjct: 203 LNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQSYVLDL 262
Query: 285 FGGEKAVPPRSQETTLIQH-IFGGHLQSQVICSKC-NNISNQYENMMDLTVEIHGDAASL 342
++ +++ I H +F G L+S ++C C NN + +DL+++I D L
Sbjct: 263 PNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDI-KDKKKL 321
Query: 343 EECLDQFTAKEWLDGDNMYKCDGCNDYVKAWKRLTVRRAPNILTIALKRFQ---SGRFGK 399
ECLD F KE L N Y C CN A K+L + + P++L + LKRF+ +G K
Sbjct: 322 YECLDSFHKKEQLKDFN-YHCGECNSTQDAIKQLGIHKLPSVLVLQLKRFEHLLNGSNRK 380
Query: 400 LNKRVTFPETLDLSPY--------MSDGGDRTDV-YKLYAVVVHVDMLNASFFGHYICYV 450
L+ + FP L++ Y S+ G D+ Y+L +V H +N GHYI +
Sbjct: 381 LDDFIEFPTYLNMKNYCSTKEKDKHSENGKVPDIIYELIGIVSHKGTVNE---GHYIAFC 437
Query: 451 KDFRGHWYRVDDCKVTSVDLEEVLSQGAYMLLY 483
K G W++ +D V+S+ EEVL + AY+L Y
Sbjct: 438 KISGGQWFKFNDSMVSSISQEEVLKEQAYLLFY 470
>pdb|3M99|A Chain A, Structure Of The Ubp8-Sgf11-Sgf73-Sus1 Saga Dub Module
Length = 471
Score = 147 bits (370), Expect = 3e-35, Method: Compositional matrix adjust.
Identities = 107/333 (32%), Positives = 166/333 (49%), Gaps = 35/333 (10%)
Query: 181 GLLNCGNSCFANVVLQCLTYTRPLVAYLLEKGHRKECG--RDDWCFLCEFQTHV------ 232
GL+N G++CF + +LQCL + + + + + H C D CF C V
Sbjct: 138 GLINMGSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHELYGA 197
Query: 233 ---EKASQSSHPFSPMS----ILSRLPNIGGNLGYGRQEDAHEFMRFAIDTM-QSICLDE 284
++AS SS + + +L+ I NL Q+DAHEF +F I+ + QS LD
Sbjct: 198 LNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQSYVLDL 257
Query: 285 FGGEKAVPPRSQETTLIQH-IFGGHLQSQVICSKC-NNISNQYENMMDLTVEIHGDAASL 342
++ +++ I H +F G L+S ++C C NN + +DL+++I D L
Sbjct: 258 PNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDI-KDKKKL 316
Query: 343 EECLDQFTAKEWLDGDNMYKCDGCNDYVKAWKRLTVRRAPNILTIALKRFQ---SGRFGK 399
ECLD F KE L N Y C CN A K+L + + P++L + LKRF+ +G K
Sbjct: 317 YECLDSFHKKEQLKDFN-YHCGECNSTQDAIKQLGIHKLPSVLVLQLKRFEHLLNGSNRK 375
Query: 400 LNKRVTFPETLDLSPY--------MSDGGDRTDV-YKLYAVVVHVDMLNASFFGHYICYV 450
L+ + FP L++ Y S+ G D+ Y+L +V H +N GHYI +
Sbjct: 376 LDDFIEFPTYLNMKNYCSTKEKDKHSENGKVPDIIYELIGIVSHKGTVNE---GHYIAFC 432
Query: 451 KDFRGHWYRVDDCKVTSVDLEEVLSQGAYMLLY 483
K G W++ +D V+S+ EEVL + AY+L Y
Sbjct: 433 KISGGQWFKFNDSMVSSISQEEVLKEQAYLLFY 465
>pdb|2IBI|A Chain A, Covalent Ubiquitin-Usp2 Complex
Length = 374
Score = 120 bits (302), Expect = 2e-27, Method: Compositional matrix adjust.
Identities = 99/338 (29%), Positives = 153/338 (45%), Gaps = 34/338 (10%)
Query: 180 CGLLNCGNSCFANVVLQCLTYTRPLVAYLLEKGHRKEC--GRDDWCFLCEFQTHVEKASQ 237
GL N GN+CF N +LQCL+ TR L Y L++ + ++ G + L E + +
Sbjct: 36 AGLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQTIW 95
Query: 238 SSHP---FSPMSILSRLPNIGGNLGYGRQEDAHEFMRFAIDTMQS----ICL-------- 282
+S P SP +++ Q+DA EF+RF +D + + + L
Sbjct: 96 TSSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPEN 155
Query: 283 ------DEFGGEKAVPPRSQETTLIQHIFGGHLQSQVICSKCNNISNQYENMMDLTVEIH 336
DE G + +E + I +F G L+S + C+ C S ++ DL++ I
Sbjct: 156 LDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPIA 215
Query: 337 GDA---ASLEECLDQFTAKEWLDGDNMYKCDGCNDYVKAWKRLTVRRAPNILTIALKRFQ 393
+L +C+ FT ++ LDGD C C + K+ +++R P IL + LKRF
Sbjct: 216 KRGYPEVTLMDCMRLFTKEDVLDGDAAPTCCRCRGRKRCIKKFSIQRFPKILVLHLKRFS 275
Query: 394 SGRF--GKLNKRVTFP-ETLDLSPYMSDGGDRTDVYKLYAVVVHVDMLNASFFGHYICYV 450
R KL V FP LDL + S+ + VY LYAV H + GHY Y
Sbjct: 276 ESRIRTSKLTTFVNFPLRDLDLREFASENTNHA-VYNLYAVSNHS---GTTMGGHYTAYC 331
Query: 451 KD-FRGHWYRVDDCKVTSVDLEEVLSQGAYMLLYNRVS 487
+ G W+ +D VT + +V + AY+L Y S
Sbjct: 332 RSPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFYELAS 369
>pdb|2HD5|A Chain A, Usp2 In Complex With Ubiquitin
Length = 359
Score = 120 bits (302), Expect = 2e-27, Method: Compositional matrix adjust.
Identities = 99/338 (29%), Positives = 153/338 (45%), Gaps = 34/338 (10%)
Query: 180 CGLLNCGNSCFANVVLQCLTYTRPLVAYLLEKGHRKEC--GRDDWCFLCEFQTHVEKASQ 237
GL N GN+CF N +LQCL+ TR L Y L++ + ++ G + L E + +
Sbjct: 10 AGLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQTIW 69
Query: 238 SSHP---FSPMSILSRLPNIGGNLGYGRQEDAHEFMRFAIDTMQS----ICL-------- 282
+S P SP +++ Q+DA EF+RF +D + + + L
Sbjct: 70 TSSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPEN 129
Query: 283 ------DEFGGEKAVPPRSQETTLIQHIFGGHLQSQVICSKCNNISNQYENMMDLTVEIH 336
DE G + +E + I +F G L+S + C+ C S ++ DL++ I
Sbjct: 130 LDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPIA 189
Query: 337 GDA---ASLEECLDQFTAKEWLDGDNMYKCDGCNDYVKAWKRLTVRRAPNILTIALKRFQ 393
+L +C+ FT ++ LDGD C C + K+ +++R P IL + LKRF
Sbjct: 190 KRGYPEVTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKILVLHLKRFS 249
Query: 394 SGRF--GKLNKRVTFP-ETLDLSPYMSDGGDRTDVYKLYAVVVHVDMLNASFFGHYICYV 450
R KL V FP LDL + S+ + VY LYAV H + GHY Y
Sbjct: 250 ESRIRTSKLTTFVNFPLRDLDLREFASENTNHA-VYNLYAVSNHS---GTTMGGHYTAYC 305
Query: 451 KD-FRGHWYRVDDCKVTSVDLEEVLSQGAYMLLYNRVS 487
+ G W+ +D VT + +V + AY+L Y S
Sbjct: 306 RSPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFYELAS 343
>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 = 120 bits (301), Expect = 3e-27, Method: Compositional matrix adjust.
Identities = 99/338 (29%), Positives = 153/338 (45%), Gaps = 34/338 (10%)
Query: 180 CGLLNCGNSCFANVVLQCLTYTRPLVAYLLEKGHRKEC--GRDDWCFLCEFQTHVEKASQ 237
GL N GN+CF N +LQCL+ TR L Y L++ + ++ G + L E + +
Sbjct: 29 AGLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQTIW 88
Query: 238 SSHP---FSPMSILSRLPNIGGNLGYGRQEDAHEFMRFAIDTMQS----ICL-------- 282
+S P SP +++ Q+DA EF+RF +D + + + L
Sbjct: 89 TSSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPEN 148
Query: 283 ------DEFGGEKAVPPRSQETTLIQHIFGGHLQSQVICSKCNNISNQYENMMDLTVEIH 336
DE G + +E + I +F G L+S + C+ C S ++ DL++ I
Sbjct: 149 LDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPIA 208
Query: 337 GDA---ASLEECLDQFTAKEWLDGDNMYKCDGCNDYVKAWKRLTVRRAPNILTIALKRFQ 393
+L +C+ FT ++ LDGD C C + K+ +++R P IL + LKRF
Sbjct: 209 KRGYPEVTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKILVLHLKRFS 268
Query: 394 SGRF--GKLNKRVTFP-ETLDLSPYMSDGGDRTDVYKLYAVVVHVDMLNASFFGHYICYV 450
R KL V FP LDL + S+ + VY LYAV H + GHY Y
Sbjct: 269 ESRIRTSKLTTFVNFPLRDLDLREFASENTNHA-VYNLYAVSNHS---GTTMGGHYTAYC 324
Query: 451 KD-FRGHWYRVDDCKVTSVDLEEVLSQGAYMLLYNRVS 487
+ G W+ +D VT + +V + AY+L Y S
Sbjct: 325 RSPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFYELAS 362
>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 = 118 bits (295), Expect = 1e-26, Method: Compositional matrix adjust.
Identities = 105/362 (29%), Positives = 158/362 (43%), Gaps = 58/362 (16%)
Query: 181 GLLNCGNSCFANVVLQCLTYTRPLVAYLLEKGHRKEC---GRDDWCFLCEFQTHVEKA-- 235
GL N GN+CF N VLQCL+ TRPL + L + R+E GR L E V A
Sbjct: 18 GLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQE--LTEAFADVIGALW 75
Query: 236 -SQSSHPFSPMSILSRLPNIGGNLGYGRQEDAHEFMRFAIDTMQSICLDEFG-------- 286
S +P + + Q+DA EF++ ++ + + ++ G
Sbjct: 76 HPDSCEAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLH-LEINRRGRRAPPILA 134
Query: 287 -GEKAVPPR-------------------------SQETTLIQHIFGGHLQSQVICSKCNN 320
G PPR +E + I +F G L+S + C C
Sbjct: 135 NGPVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKCQACGY 194
Query: 321 ISNQYENMMDLTVEI-----HGDAASLEECLDQFTAKEWLDGDNMYKCDGCNDYVKAWKR 375
S +E DL++ I G SL +C + FT +E L+ +N CD C ++ K+
Sbjct: 195 RSTTFEVFCDLSLPIPKKGFAGGKVSLRDCFNLFTKEEELESENAPVCDRCRQKTRSTKK 254
Query: 376 LTVRRAPNILTIALKRFQSGRFGKLNKR---VTFP-ETLDLSPYMSDGGDRTDVYKLYAV 431
LTV+R P IL + L RF + R G + K V FP + L L + SD + VY+LYA+
Sbjct: 255 LTVQRFPRILVLHLNRFSASR-GSIKKSSVGVDFPLQRLSLGDFASDKAG-SPVYQLYAL 312
Query: 432 VVHVDMLNASFFGHYICYVKDFRGHWYRVDDCKVTSVDLEEVLSQGAYMLLYNRVSARPS 491
H ++ +GHY + G W+ +D +V+ V +V S Y+L Y + P
Sbjct: 313 CNHSGSVH---YGHYTALCRCQTG-WHVYNDSRVSPVSENQVASSEGYVLFYQLMQEPPR 368
Query: 492 YL 493
L
Sbjct: 369 CL 370
>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 = 118 bits (295), Expect = 1e-26, Method: Compositional matrix adjust.
Identities = 104/359 (28%), Positives = 157/359 (43%), Gaps = 58/359 (16%)
Query: 181 GLLNCGNSCFANVVLQCLTYTRPLVAYLLEKGHRKEC---GRDDWCFLCEFQTHVEKA-- 235
GL N GN+CF N VLQCL+ TRPL + L + R+E GR L E V A
Sbjct: 5 GLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQE--LTEAFADVIGALW 62
Query: 236 -SQSSHPFSPMSILSRLPNIGGNLGYGRQEDAHEFMRFAIDTMQSICLDEFG-------- 286
S +P + + Q+DA EF++ ++ + + ++ G
Sbjct: 63 HPDSCEAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLH-LEINRRGRRAPPILA 121
Query: 287 -GEKAVPPR-------------------------SQETTLIQHIFGGHLQSQVICSKCNN 320
G PPR +E + I +F G L+S + C C
Sbjct: 122 NGPVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKCQACGY 181
Query: 321 ISNQYENMMDLTVEI-----HGDAASLEECLDQFTAKEWLDGDNMYKCDGCNDYVKAWKR 375
S +E DL++ I G SL +C + FT +E L+ +N CD C ++ K+
Sbjct: 182 RSTTFEVFCDLSLPIPKKGFAGGKVSLRDCFNLFTKEEELESENAPVCDRCRQKTRSTKK 241
Query: 376 LTVRRAPNILTIALKRFQSGRFGKLNKR---VTFP-ETLDLSPYMSDGGDRTDVYKLYAV 431
LTV+R P IL + L RF + R G + K V FP + L L + SD + VY+LYA+
Sbjct: 242 LTVQRFPRILVLHLNRFSASR-GSIKKSSVGVDFPLQRLSLGDFASDKAG-SPVYQLYAL 299
Query: 432 VVHVDMLNASFFGHYICYVKDFRGHWYRVDDCKVTSVDLEEVLSQGAYMLLYNRVSARP 490
H ++ +GHY + G W+ +D +V+ V +V S Y+L Y + P
Sbjct: 300 CNHSGSVH---YGHYTALCRCQTG-WHVYNDSRVSPVSENQVASSEGYVLFYQLMQEPP 354
>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 = 117 bits (294), Expect = 2e-26, Method: Compositional matrix adjust.
Identities = 105/363 (28%), Positives = 163/363 (44%), Gaps = 66/363 (18%)
Query: 181 GLLNCGNSCFANVVLQCLTYTRPLVAYLLEKGHRKEC---GRDDWCFLCEFQTHVEKA-- 235
GL N GN+CF N VLQCL+ TRPL + L + R+E GR L E V A
Sbjct: 24 GLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQE--LTEAFADVIGALW 81
Query: 236 ----SQSSHPFSPMSILSR-LPNIGGNLGYGRQEDAHEFMRFAIDTMQSICLDEFG---- 286
++ +P ++ + +P+ G Q+DA EF++ ++ + + ++ G
Sbjct: 82 HPDSCEAVNPTRFRAVFQKYVPSFSGY----SQQDAQEFLKLLMERLH-LEINRRGRRAP 136
Query: 287 -----GEKAVPPR-------------------------SQETTLIQHIFGGHLQSQVICS 316
G PPR +E + I +F G L+S + C
Sbjct: 137 PILANGPVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKCQ 196
Query: 317 KCNNISNQYENMMDLTVEI-----HGDAASLEECLDQFTAKEWLDGDNMYKCDGCNDYVK 371
C S +E DL++ I G SL +C + FT +E L+ +N CD C +
Sbjct: 197 ACGYRSTTFEVFCDLSLPIPKKGFAGGKVSLRDCFNLFTKEEELESENAPVCDRCRQKTR 256
Query: 372 AWKRLTVRRAPNILTIALKRFQSGRFGKLNKR---VTFP-ETLDLSPYMSDGGDRTDVYK 427
+ K+LTV+R P IL + L RF + R G + K V FP + L L + SD + VY+
Sbjct: 257 STKKLTVQRFPRILVLHLNRFSASR-GSIKKSSVGVDFPLQRLSLGDFASDKAG-SPVYQ 314
Query: 428 LYAVVVHVDMLNASFFGHYICYVKDFRGHWYRVDDCKVTSVDLEEVLSQGAYMLLYNRVS 487
LYA+ H ++ +GHY + G W+ +D +V+ V +V S Y+L Y +
Sbjct: 315 LYALCNHSGSVH---YGHYTALCRCQTG-WHVYNDSRVSPVSENQVASSEGYVLFYQLMQ 370
Query: 488 ARP 490
P
Sbjct: 371 EPP 373
>pdb|3NHE|A Chain A, High Resolution Structure (1.26a) Of Usp2a In Complex With
Ubiquitin
Length = 348
Score = 117 bits (292), Expect = 3e-26, Method: Compositional matrix adjust.
Identities = 98/338 (28%), Positives = 152/338 (44%), Gaps = 34/338 (10%)
Query: 180 CGLLNCGNSCFANVVLQCLTYTRPLVAYLLEKGHRKEC--GRDDWCFLCEFQTHVEKASQ 237
GL N GN+ F N +LQCL+ TR L Y L++ + ++ G + L E + +
Sbjct: 10 AGLRNLGNTXFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQTIW 69
Query: 238 SSHP---FSPMSILSRLPNIGGNLGYGRQEDAHEFMRFAIDTMQS----ICL-------- 282
+S P SP +++ Q+DA EF+RF +D + + + L
Sbjct: 70 TSSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPEN 129
Query: 283 ------DEFGGEKAVPPRSQETTLIQHIFGGHLQSQVICSKCNNISNQYENMMDLTVEIH 336
DE G + +E + I +F G L+S + C+ C S ++ DL++ I
Sbjct: 130 LDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPIA 189
Query: 337 GDA---ASLEECLDQFTAKEWLDGDNMYKCDGCNDYVKAWKRLTVRRAPNILTIALKRFQ 393
+L +C+ FT ++ LDGD C C + K+ +++R P IL + LKRF
Sbjct: 190 KRGYPEVTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKILVLHLKRFS 249
Query: 394 SGRF--GKLNKRVTFP-ETLDLSPYMSDGGDRTDVYKLYAVVVHVDMLNASFFGHYICYV 450
R KL V FP LDL + S+ + VY LYAV H + GHY Y
Sbjct: 250 ESRIRTSKLTTFVNFPLRDLDLREFASENTNHA-VYNLYAVSNHS---GTTMGGHYTAYC 305
Query: 451 KD-FRGHWYRVDDCKVTSVDLEEVLSQGAYMLLYNRVS 487
+ G W+ +D VT + +V + AY+L Y S
Sbjct: 306 RSPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFYELAS 343
>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 = 113 bits (283), Expect = 3e-25, Method: Compositional matrix adjust.
Identities = 93/358 (25%), Positives = 151/358 (42%), Gaps = 51/358 (14%)
Query: 174 KPGFAPCGLLNCGNSCFANVVLQCLTYTRPLVAYLLEKGHRKECGRDDWCFL----CEFQ 229
+PG CGL N GN+ F N LQCL+ T PL Y L+ + E RD+ + E
Sbjct: 5 QPGL--CGLGNLGNTXFMNSALQCLSNTAPLTDYFLKDEYEAEINRDNPLGMKGEIAEAY 62
Query: 230 THVEKASQSSHP--FSPMSILSRLPNIGGNLGYGRQEDAHEFMRFAIDTMQS-------- 279
+ K S +P +++ +Q+D+ E + F +D +
Sbjct: 63 AELIKQMWSGRDAHVAPRMFKTQVGRFAPQFSGYQQQDSQELLAFLLDGLHEDLNRVKKK 122
Query: 280 ---ICLDEFGGEKAVPP-------RSQETTLIQHIFGGHLQSQVICSKCNNISNQYENMM 329
D G AV R + ++I F G +S ++C +C +S ++
Sbjct: 123 PYLELKDANGRPDAVVAKEAWENHRLRNDSVIVDTFHGLFKSTLVCPECAKVSVTFDPFC 182
Query: 330 DLTVEI------------------HGDAASLEECLDQFTAKEWLDGDNMYKCDGCNDYVK 371
LT+ + +L +C++ FT E L + + C C + +
Sbjct: 183 YLTLPLPLKKDRVMEGPMLQPQKKKKTTVALRDCIELFTTMETLGEHDPWYCPNCKKHQQ 242
Query: 372 AWKRLTVRRAPNILTIALKRFQSGRF--GKLNKRVTFP-ETLDLSPYMSDGGDRTDVYKL 428
A K+ + P IL + LKRF R+ KL+ V FP L++S ++ + R VY L
Sbjct: 243 ATKKFDLWSLPKILVVHLKRFSYNRYWRDKLDTVVEFPIRGLNMSEFVCNLSARPYVYDL 302
Query: 429 YAVVVHVDMLNASFFGHYICYVKD-FRGHWYRVDDCKVTSVDLEEVLSQGAYMLLYNR 485
AV H + GHY Y K+ G WY DD V+ ++++++ AY+L Y R
Sbjct: 303 IAVSNHYGAMGV---GHYTAYAKNKLNGKWYYFDDSNVSLASEDQIVTKAAYVLFYQR 357
>pdb|3N3K|A Chain A, The Catalytic Domain Of Usp8 In Complex With A Usp8
Specific Inhibitor
Length = 396
Score = 104 bits (259), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 93/337 (27%), Positives = 149/337 (44%), Gaps = 32/337 (9%)
Query: 176 GFAPCGLLNCGNSCFANVVLQCLTYTRPLVAYLLEKGHRKECGRDDWC-----FLCEFQT 230
G A GL N GN+C+ N +LQCL L Y ++ + R + EF
Sbjct: 59 GPALTGLRNLGNTCYMNSILQCLCNAPHLADYFNRNCYQDDINRSNLLGHKGEVAEEFGI 118
Query: 231 HVEKASQSSHPF-SPMSILSRLPNIGGNLGYGRQEDAHEFMRFAIDTMQSIC-------- 281
++ + + SP + I Q+D+ E + F +D +
Sbjct: 119 IMKALWTGQYRYISPKDFKITIGKINDQFAGYSQQDSQELLLFLMDGLHEDLNKADNRKR 178
Query: 282 --------LDEF-GGEKAVPPRSQ-ETTLIQHIFGGHLQSQVICSKCNNISNQYENMMDL 331
LD+F E A Q ++I +F G +S V C C+ S +E M L
Sbjct: 179 YKEENNDHLDDFKAAEHAWQKHKQLNESIIVALFQGQFKSTVQCLTCHKKSRTFEAFMYL 238
Query: 332 TVEIHGDAA-SLEECLDQFTAKEWLDGDNMYKCDGCNDYVKAWKRLTVRRAPNILTIALK 390
++ + + +L++CL F+ +E L +N + C C + K++ + + P +L + LK
Sbjct: 239 SLPLASTSKCTLQDCLRLFSKEEKLTDNNRFYCSHCRARRDSLKKIEIWKLPPVLLVHLK 298
Query: 391 RFQ-SGRFG-KLNKRVTFP-ETLDLSPYMSDGGDRTDVYKLYAVVVHVDMLNASFFGHYI 447
RF GR+ KL V FP E LDLS Y+ + Y L++V H L+ GHY
Sbjct: 299 RFSYDGRWKQKLQTSVDFPLENLDLSQYVIGPKNNLKKYNLFSVSNHYGGLDG---GHYT 355
Query: 448 CYVKD-FRGHWYRVDDCKVTSVDLEEVLSQGAYMLLY 483
Y K+ R W++ DD +V+ + + V S AY+L Y
Sbjct: 356 AYCKNAARQRWFKFDDHEVSDISVSSVKSSAAYILFY 392
>pdb|2GFO|A Chain A, Structure Of The Catalytic Domain Of Human Ubiquitin
Carboxyl-terminal Hydrolase 8
Length = 396
Score = 100 bits (249), Expect = 3e-21, Method: Compositional matrix adjust.
Identities = 92/337 (27%), Positives = 146/337 (43%), Gaps = 32/337 (9%)
Query: 176 GFAPCGLLNCGNSCFANVVLQCLTYTRPLVAYLLEKGHRKECGRDDWC-----FLCEFQT 230
G A GL N GN+C+ N +LQCL L Y ++ + R + EF
Sbjct: 59 GPALTGLRNLGNTCYXNSILQCLCNAPHLADYFNRNCYQDDINRSNLLGHKGEVAEEFGI 118
Query: 231 HVEKASQSSHPF-SPMSILSRLPNIGGNLGYGRQEDAHEFMRFAIDTMQSIC-------- 281
+ + + SP + I Q+D+ E + F D +
Sbjct: 119 IXKALWTGQYRYISPKDFKITIGKINDQFAGYSQQDSQELLLFLXDGLHEDLNKADNRKR 178
Query: 282 --------LDEF-GGEKAVPPRSQ-ETTLIQHIFGGHLQSQVICSKCNNISNQYENMMDL 331
LD+F E A Q ++I +F G +S V C C+ S +E L
Sbjct: 179 YKEENNDHLDDFKAAEHAWQKHKQLNESIIVALFQGQFKSTVQCLTCHKKSRTFEAFXYL 238
Query: 332 TVEIHGDAA-SLEECLDQFTAKEWLDGDNMYKCDGCNDYVKAWKRLTVRRAPNILTIALK 390
++ + + +L++CL F+ +E L +N + C C + K++ + + P +L + LK
Sbjct: 239 SLPLASTSKCTLQDCLRLFSKEEKLTDNNRFYCSHCRARRDSLKKIEIWKLPPVLLVHLK 298
Query: 391 RFQ-SGRFG-KLNKRVTFP-ETLDLSPYMSDGGDRTDVYKLYAVVVHVDMLNASFFGHYI 447
RF GR+ KL V FP E LDLS Y+ + Y L++V H L+ GHY
Sbjct: 299 RFSYDGRWKQKLQTSVDFPLENLDLSQYVIGPKNNLKKYNLFSVSNHYGGLDG---GHYT 355
Query: 448 CYVKD-FRGHWYRVDDCKVTSVDLEEVLSQGAYMLLY 483
Y K+ R W++ DD +V+ + + V S AY+L Y
Sbjct: 356 AYCKNAARQRWFKFDDHEVSDISVSSVKSSAAYILFY 392
>pdb|2F1Z|A Chain A, Crystal Structure Of Hausp
pdb|2F1Z|B Chain B, Crystal Structure Of Hausp
Length = 522
Score = 77.8 bits (190), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 95/349 (27%), Positives = 143/349 (40%), Gaps = 64/349 (18%)
Query: 172 WD-KPGFAPCGLLNCGNSCFANVVLQCLTYTRPL--VAYLLEKGHRKECGRDDWCFLCEF 228
WD K GL N G +C+ N +LQ L +T L Y++ G D
Sbjct: 167 WDSKKHTGYVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPTE-----GDD-------- 213
Query: 229 QTHVEKASQSSHPFSPMSILSRLPNIGGNLGYGR------QEDAHEFMRFAIDTMQSICL 282
S S P + + L + +G + E FM+ + + + L
Sbjct: 214 -------SSKSVPLALQRVFYELQHSDKPVGTKKLTKSFGWETLDSFMQHDVQELCRVLL 266
Query: 283 DEFGGEKAVPPRSQETTLIQHIFGGHLQSQVICSKCNNISNQYENMMDLTVEIHGDAASL 342
D E + E T I +F G + S + C + + S++ E+ D+ + I G
Sbjct: 267 DNV--ENKMKGTCVEGT-IPKLFRGKMVSYIQCKEVDYRSDRREDYYDIQLSIKGKKNIF 323
Query: 343 EECLDQFTAKEWLDGDNMYKC--DGCNDYVKAWKRLTVRRAPNILTIALKRF----QSGR 396
E +D + A E LDGDN Y G + K K LT+ P +L + L RF Q+ +
Sbjct: 324 ESFVD-YVAVEQLDGDNKYDAGEHGLQEAEKGVKFLTL---PPVLHLQLMRFMYDPQTDQ 379
Query: 397 FGKLNKRVTFPETLDLSPYM--SDGGDRTDVYKLYAVVVHVDMLNASFFGHYICYVK-DF 453
K+N R FPE L L ++ +D D + Y L+AV+VH + GHY+ Y+
Sbjct: 380 NIKINDRFEFPEQLPLDEFLQKTDPKDPAN-YILHAVLVHS---GDNHGGHYVVYLNPKG 435
Query: 454 RGHWYRVDDCKVTSVDLEEVLSQ---------------GAYMLLYNRVS 487
G W + DD V+ EE + AYML+Y R S
Sbjct: 436 DGKWCKFDDDVVSRCTKEEAIEHNYGGHDDDLSVRHCTNAYMLVYIRES 484
>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 = 75.9 bits (185), Expect = 8e-14, Method: Compositional matrix adjust.
Identities = 92/340 (27%), Positives = 140/340 (41%), Gaps = 63/340 (18%)
Query: 180 CGLLNCGNSCFANVVLQCLTYTRPL--VAYLLEKGHRKECGRDDWCFLCEFQTHVEKASQ 237
GL N G +C+ N +LQ L +T L Y++ G D S
Sbjct: 7 VGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPTE-----GDD---------------SS 46
Query: 238 SSHPFSPMSILSRLPNIGGNLGYGRQ------EDAHEFMRFAIDTMQSICLDEFGGEKAV 291
S P + + L + +G + E FM+ + + + LD E +
Sbjct: 47 KSVPLALQRVFYELQHSDKPVGTKKLTKSFGWETLDSFMQHDVQELCRVLLDNV--ENKM 104
Query: 292 PPRSQETTLIQHIFGGHLQSQVICSKCNNISNQYENMMDLTVEIHGDAASLEECLDQFTA 351
E T I +F G + S + C + + S++ E+ D+ + I G E +D + A
Sbjct: 105 KGTCVEGT-IPKLFRGKMVSYIQCKEVDYRSDRREDYYDIQLSIKGKKNIFESFVD-YVA 162
Query: 352 KEWLDGDNMYKC--DGCNDYVKAWKRLTVRRAPNILTIALKRF----QSGRFGKLNKRVT 405
E LDGDN Y G + K K LT+ P +L + L RF Q+ + K+N R
Sbjct: 163 VEQLDGDNKYDAGEHGLQEAEKGVKFLTL---PPVLHLQLMRFMYDPQTDQNIKINDRFE 219
Query: 406 FPETLDLSPYM--SDGGDRTDVYKLYAVVVHVDMLNASFFGHYICYVK-DFRGHWYRVDD 462
FPE L L ++ +D D + Y L+AV+VH + GHY+ Y+ G W + DD
Sbjct: 220 FPEQLPLDEFLQKTDPKDPAN-YILHAVLVHS---GDNHGGHYVVYLNPKGDGKWCKFDD 275
Query: 463 CKVTSVDLEEVLSQ---------------GAYMLLYNRVS 487
V+ EE + AYML+Y R S
Sbjct: 276 DVVSRCTKEEAIEHNYGGHDDDLSVRHCTNAYMLVYIRES 315
>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 = 69.7 bits (169), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 89/350 (25%), Positives = 137/350 (39%), Gaps = 83/350 (23%)
Query: 180 CGLLNCGNSCFANVVLQCLTYTRPLVAYLLEKGHRKECGRDDWCFLCEFQTHVEKASQSS 239
GL N G +C+ N +LQ L +T L + + DD S S
Sbjct: 7 VGLKNQGATCYXNSLLQTLFFTNQLRKAV----YXXPTEGDD--------------SSKS 48
Query: 240 HPFSPMSILSRLPNIGGNLGYGR--------------QEDAHEFMRFAIDTMQS----IC 281
P + + L + +G + Q D E R +D +++ C
Sbjct: 49 VPLALQRVFYELQHSDKPVGTKKLTKSFGWETLDSFXQHDVQELCRVLLDNVENKXKGTC 108
Query: 282 LDEFGGEKAVPPRSQETTLIQHIFGGHLQSQVICSKCNNISNQYENMMDLTVEIHGDAAS 341
+ E +P +F G S + C + + S++ E+ D+ + I G
Sbjct: 109 V-----EGTIPK----------LFRGKXVSYIQCKEVDYRSDRREDYYDIQLSIKGKKNI 153
Query: 342 LEECLDQFTAKEWLDGDNMYKC--DGCNDYVKAWKRLTVRRAPNILTIALKRF----QSG 395
E +D + A E LDGDN Y G + K K LT+ P +L + L RF Q+
Sbjct: 154 FESFVD-YVAVEQLDGDNKYDAGEHGLQEAEKGVKFLTL---PPVLHLQLXRFXYDPQTD 209
Query: 396 RFGKLNKRVTFPETLDLSPYM--SDGGDRTDVYKLYAVVVHVDMLNASFFGHYICYVK-D 452
+ K+N R FPE L L ++ +D D + Y L+AV+VH + GHY+ Y+
Sbjct: 210 QNIKINDRFEFPEQLPLDEFLQKTDPKDPAN-YILHAVLVHS---GDNHGGHYVVYLNPK 265
Query: 453 FRGHWYRVDDCKVTSVDLEEVLSQ---------------GAYMLLYNRVS 487
G W + DD V+ EE + AY L+Y R S
Sbjct: 266 GDGKWCKFDDDVVSRCTKEEAIEHNYGGHDDDLSVRHCTNAYXLVYIRES 315
>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 = 60.5 bits (145), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 91/386 (23%), Positives = 141/386 (36%), Gaps = 90/386 (23%)
Query: 179 PCGLLNCGNSCFANVVLQCLTYTRPLVAYL------LEKGHRKECGRDDWCFLCEFQTHV 232
PCGL N GN+C+ N +QC+ L L L + L + +
Sbjct: 14 PCGLTNLGNTCYMNATVQCIRSVPELKDALKRYAGALRASGEMASAQYITAALRDLFDSM 73
Query: 233 EKASQSSHPFSPMSILSR-LPNIG--GNLGYGRQEDAHE----FMRFAIDTMQSI----- 280
+K S S P + L P G G Q+DA+E MR +++I
Sbjct: 74 DKTSSSIPPIILLQFLHMAFPQFAEKGEQGQYLQQDANECWIQMMRVLQQKLEAIEDDSV 133
Query: 281 -CLDEFGGEKAVPPRSQETTLIQHIFGGHLQSQVICSKC--NNISNQYENMMDLTVEIHG 337
D A P S++ +LI FG ++ + C++ ++ EN + L+ I+
Sbjct: 134 KETDSSSASAATP--SKKKSLIDQFFGVEFETTMKCTESEEEEVTKGKENQLQLSCFINQ 191
Query: 338 DAASLEECLDQFTAKEWLDGDNMYKCDGCNDYVKAWKRLTVRRAPNILTIALKRF----Q 393
+ L L +E + + Y+K+ K + R P LTI + RF +
Sbjct: 192 EVKYLFTGLKLRLQEEITKQSPTLQRNAL--YIKSSK---ISRLPAYLTIQMVRFFYKEK 246
Query: 394 SGRFGKLNKRVTFPETLDL-----------------------------SPYMSD------ 418
K+ K V FP LD+ P SD
Sbjct: 247 ESVNAKVLKDVKFPLMLDMYELCTPELQEKMVSFRSKFKDLEDKKVNQQPNTSDKKSSPQ 306
Query: 419 --------------GGDRTDVYKLYAVVVHVDMLNASFFGHYICYVKDFRGHWYRVDDCK 464
G + Y L AV+ H ++S GHY+ +VK + W + DD K
Sbjct: 307 KEVKYEPFSFADDIGSNNCGYYDLQAVLTHQGRSSSS--GHYVSWVKRKQDEWIKFDDDK 364
Query: 465 VTSVDLEEVLSQG-------AYMLLY 483
V+ V E++L AY+LLY
Sbjct: 365 VSIVTPEDILRLSGGGDWHIAYVLLY 390
>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
Length = 854
Score = 39.7 bits (91), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 43/81 (53%), Gaps = 8/81 (9%)
Query: 408 ETLDLSPYMSDGGDRTDVYKLYAVVVHVDMLNASFFGHYICYVKDFRGHWYRVDDCKVTS 467
E++ + P + DG + Y+L+A + H M ++ GHY+C++K G W +D KV +
Sbjct: 782 ESVPVGPKVRDGPGK---YQLFAFISH--MGTSTMCGHYVCHIKK-EGRWVIYNDQKVCA 835
Query: 468 VDLEEVLSQGAYMLLYNRVSA 488
E+ Y+ Y RV++
Sbjct: 836 S--EKPPKDLGYIYFYQRVAS 854
>pdb|3OXF|A Chain A, Human Lysine Methyltransferase Smyd3 In Complex With
Adohcy (Form I)
pdb|3OXF|B Chain B, Human Lysine Methyltransferase Smyd3 In Complex With
Adohcy (Form I)
Length = 436
Score = 39.3 bits (90), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 22/35 (62%), Gaps = 1/35 (2%)
Query: 77 GNPGSKKCSRCKSVRYCSSKCQTSHWQSGHKRKCK 111
G +CS+C+ +YCS+KCQ W HKR+CK
Sbjct: 55 GKEKLMRCSQCRVAKYCSAKCQKKAW-PDHKRECK 88
>pdb|3RU0|A Chain A, Cocrystal Structure Of Human Smyd3 With Inhibitor
Sinefungin Bound
pdb|3RU0|B Chain B, Cocrystal Structure Of Human Smyd3 With Inhibitor
Sinefungin Bound
Length = 438
Score = 39.3 bits (90), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 22/35 (62%), Gaps = 1/35 (2%)
Query: 77 GNPGSKKCSRCKSVRYCSSKCQTSHWQSGHKRKCK 111
G +CS+C+ +YCS+KCQ W HKR+CK
Sbjct: 57 GKEKLMRCSQCRVAKYCSAKCQKKAW-PDHKRECK 90
>pdb|3PDN|A Chain A, Crystal Structure Of Smyd3 In Complex With
Methyltransferase Inhibitor Sinefungin
pdb|3OXL|A Chain A, Human Lysine Methyltransferase Smyd3 In Complex With
Adohcy (Form Ii)
Length = 428
Score = 39.3 bits (90), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 22/35 (62%), Gaps = 1/35 (2%)
Query: 77 GNPGSKKCSRCKSVRYCSSKCQTSHWQSGHKRKCK 111
G +CS+C+ +YCS+KCQ W HKR+CK
Sbjct: 55 GKEKLMRCSQCRVAKYCSAKCQKKAW-PDHKRECK 88
>pdb|3QWP|A Chain A, Crystal Structure Of Set And Mynd Domain Containing 3;
Zinc Finger Mynd Domain-Containing Protein 1
Length = 429
Score = 39.3 bits (90), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 22/35 (62%), Gaps = 1/35 (2%)
Query: 77 GNPGSKKCSRCKSVRYCSSKCQTSHWQSGHKRKCK 111
G +CS+C+ +YCS+KCQ W HKR+CK
Sbjct: 56 GKEKLMRCSQCRVAKYCSAKCQKKAW-PDHKRECK 89
>pdb|3OXG|A Chain A, Human Lysine Methyltransferase Smyd3 In Complex With
Adohcy (Form Iii)
Length = 464
Score = 39.3 bits (90), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 22/35 (62%), Gaps = 1/35 (2%)
Query: 77 GNPGSKKCSRCKSVRYCSSKCQTSHWQSGHKRKCK 111
G +CS+C+ +YCS+KCQ W HKR+CK
Sbjct: 91 GKEKLMRCSQCRVAKYCSAKCQKKAW-PDHKRECK 124
>pdb|3MEK|A Chain A, Crystal Structure Of Human Histone-Lysine N-
Methyltransferase Smyd3 In Complex With S-Adenosyl-L-
Methionine
Length = 429
Score = 38.9 bits (89), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 22/35 (62%), Gaps = 1/35 (2%)
Query: 77 GNPGSKKCSRCKSVRYCSSKCQTSHWQSGHKRKCK 111
G +CS+C+ +YCS+KCQ W HKR+CK
Sbjct: 56 GKEKLXRCSQCRVAKYCSAKCQKKAW-PDHKRECK 89
>pdb|2D8Q|A Chain A, Solution Structure Of The Mynd Domain Of The Human Zinc
Finger Mynd Domain-Containing Protein 10
Length = 70
Score = 37.7 bits (86), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 29/55 (52%), Gaps = 6/55 (10%)
Query: 73 CIVCGNPGSKKCSRCKSVRYCSSKCQTSHWQSGHKRKCKDIGKINSVQGPRSDFG 127
C C SK+CSRC++ YC +CQ HW+ H + C + + QG R+ G
Sbjct: 18 CAYCSAEASKRCSRCQNEWYCCRECQVKHWEK-HGKTC-----VLAAQGDRAKSG 66
>pdb|2DAN|A Chain A, The Solution Structure Of The Mynd Domain (Leu384-Cys430)
Of Human Zinc Finger Mynd Domain Containing Protein 10
Length = 60
Score = 35.0 bits (79), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 73 CIVCGNPGSKKCSRCKSVRYCSSKCQTSHWQSGHKRKC 110
C C SK+CSRC++ YC +CQ HW+ H + C
Sbjct: 18 CAYCSAEASKRCSRCQNEWYCCRECQVKHWEK-HGKTC 54
>pdb|2ODD|A Chain A, Solution Structure Of The Mynd Domain From Aml1-Eto
Complexed With Smrt, A Corepressor
Length = 64
Score = 34.7 bits (78), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 15/34 (44%), Positives = 18/34 (52%)
Query: 73 CIVCGNPGSKKCSRCKSVRYCSSKCQTSHWQSGH 106
C CG S+ CS C + RYC S CQ W+ H
Sbjct: 20 CWNCGRKASETCSGCNTARYCGSFCQHKDWEKHH 53
>pdb|2OD1|A Chain A, Solution Structure Of The Mynd Domain From Human Aml1-Eto
Length = 60
Score = 33.1 bits (74), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 15/34 (44%), Positives = 18/34 (52%)
Query: 73 CIVCGNPGSKKCSRCKSVRYCSSKCQTSHWQSGH 106
C CG S+ CS C + RYC S CQ W+ H
Sbjct: 16 CWNCGRKASETCSGCNTARYCGSFCQHKDWEKHH 49
>pdb|3N71|A Chain A, Crystal Structure Of Cardiac Specific Histone
Methyltransferase Smyd1
Length = 490
Score = 33.1 bits (74), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 21/48 (43%), Gaps = 1/48 (2%)
Query: 83 KCSRCKSVRYCSSKCQTSHWQSGHKRKCKDIGKINSVQGPRSDFGSKI 130
+C +CK YC CQ W + HK +C I K V ++I
Sbjct: 64 RCGQCKFAHYCDRTCQKDAWLN-HKNECAAIKKYGKVPNENIRLAARI 110
>pdb|2DJ8|A Chain A, Solution Structure Of Zf-Mynd Domain Of Protein Cbfa2ti
(Protein Mtg8)
Length = 60
Score = 32.7 bits (73), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 15/34 (44%), Positives = 18/34 (52%)
Query: 73 CIVCGNPGSKKCSRCKSVRYCSSKCQTSHWQSGH 106
C CG S+ CS C + RYC S CQ W+ H
Sbjct: 18 CWNCGRKASETCSGCNTARYCGSFCQHKDWEKHH 51
>pdb|3RIB|A Chain A, Human Lysine Methyltransferase Smyd2 In Complex With
Adohcy
pdb|3RIB|B Chain B, Human Lysine Methyltransferase Smyd2 In Complex With
Adohcy
Length = 441
Score = 32.7 bits (73), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 80 GSKKCSRCKSVRYCSSKCQTSHWQSGHKRKC 110
G KC RCK YC+ +CQ W HK +C
Sbjct: 61 GLSKCGRCKQAFYCNVECQKEDW-PMHKLEC 90
>pdb|3S7B|A Chain A, Structural Basis Of Substrate Methylation And Inhibition
Of Smyd2
pdb|3S7D|A Chain A, Structural Basis Of Substrate Methylation And Inhibition
Of Smyd2
pdb|3S7F|A Chain A, Structural Basis Of Substrate Methylation And Inhibition
Of Smyd2
pdb|3S7J|A Chain A, Structural Basis Of Substrate Methylation And Inhibition
Of Smyd2
Length = 433
Score = 32.7 bits (73), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 80 GSKKCSRCKSVRYCSSKCQTSHWQSGHKRKC 110
G KC RCK YC+ +CQ W HK +C
Sbjct: 61 GLSKCGRCKQAFYCNVECQKEDW-PMHKLEC 90
>pdb|3TG4|A Chain A, Structure Of Smyd2 In Complex With Sam
pdb|3TG5|A Chain A, Structure Of Smyd2 In Complex With P53 And Sah
Length = 433
Score = 32.3 bits (72), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 80 GSKKCSRCKSVRYCSSKCQTSHWQSGHKRKC 110
G KC RCK YC+ +CQ W HK +C
Sbjct: 61 GLSKCGRCKQAFYCNVECQKEDW-PMHKLEC 90
>pdb|3QWV|A Chain A, Crystal Structure Of Histone Lysine Methyltransferase
Smyd2 In Complex With The Cofactor Product Adohcy
pdb|3QWW|A Chain A, Crystal Structure Of Histone Lysine Methyltransferase
Smyd2 In Complex With The Methyltransferase Inhibitor
Sinefungin
Length = 433
Score = 32.3 bits (72), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 18/41 (43%), Gaps = 1/41 (2%)
Query: 73 CIVCGNPGSKKCSRCKSVRYCSSKCQTSHWQSGHKRKCKDI 113
C G KC RCK YC +CQ W HK +C +
Sbjct: 54 CCFARKEGLSKCGRCKQAFYCDVECQKEDW-PLHKLECSSM 93
>pdb|2JW6|A Chain A, Solution Structure Of The Deaf1 Mynd Domain
Length = 52
Score = 30.0 bits (66), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 73 CIVCGNPGSKKCSRCKSVRYCSSKCQTSHWQ 103
C+ CG +C+ C V YCS+ CQ W+
Sbjct: 12 CVNCGREAMSECTGCHKVNYCSTFCQRKDWK 42
>pdb|4A24|A Chain A, Structural And Functional Analysis Of The Deaf-1 And Bs69
Mynd Domains
Length = 47
Score = 29.6 bits (65), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 73 CIVCGNPGSKKCSRCKSVRYCSSKCQTSHWQ 103
C+ CG +C+ C V YCS+ CQ W+
Sbjct: 7 CVNCGREAMSECTGCHKVNYCSTFCQRKDWK 37
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
0.317 0.133 0.409
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,155,074
Number of Sequences: 62578
Number of extensions: 919880
Number of successful extensions: 1884
Number of sequences better than 100.0: 39
Number of HSP's better than 100.0 without gapping: 31
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 1806
Number of HSP's gapped (non-prelim): 48
length of query: 733
length of database: 14,973,337
effective HSP length: 106
effective length of query: 627
effective length of database: 8,340,069
effective search space: 5229223263
effective search space used: 5229223263
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)