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= 005806
(676 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 70.9 bits (172), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 69/230 (30%), Positives = 95/230 (41%), Gaps = 48/230 (20%)
Query: 479 GLLNCGNSCYANAVLQCLTCTKPLVIYLLRRSHSSACCGKDWCL-MCELEQHV---MMLR 534
GL N GN+C+ NAVLQCL+ T+PL + LRR G + E V +
Sbjct: 5 GLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQELTEAFADVIGALWHP 64
Query: 535 ESAGPLSPGRILSHMRSISCQIGDGSQEDAHEFLRLLVASMQSICLE------------- 581
+S ++P R + + SQ+DA EFL+LL M+ + LE
Sbjct: 65 DSCEAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLL---MERLHLEINRRGRRAPPILA 121
Query: 582 --------RHGGESKVDPRL---------------QETTFIQHTFGGRLWSKVKCLRCSH 618
R GG +P L +E + I F G+L S +KC C +
Sbjct: 122 NGPVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKCQACGY 181
Query: 619 ESERYENIMDLTLEI-----YGWVESLEDALTQFTSPEDLDGENMYKCAR 663
S +E DL+L I G SL D FT E+L+ EN C R
Sbjct: 182 RSTTFEVFCDLSLPIPKKGFAGGKVSLRDCFNLFTKEEELESENAPVCDR 231
>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 = 70.9 bits (172), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 69/230 (30%), Positives = 95/230 (41%), Gaps = 48/230 (20%)
Query: 479 GLLNCGNSCYANAVLQCLTCTKPLVIYLLRRSHSSACCGKDWCL-MCELEQHV---MMLR 534
GL N GN+C+ NAVLQCL+ T+PL + LRR G + E V +
Sbjct: 24 GLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQELTEAFADVIGALWHP 83
Query: 535 ESAGPLSPGRILSHMRSISCQIGDGSQEDAHEFLRLLVASMQSICLE------------- 581
+S ++P R + + SQ+DA EFL+LL M+ + LE
Sbjct: 84 DSCEAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLL---MERLHLEINRRGRRAPPILA 140
Query: 582 --------RHGGESKVDPRL---------------QETTFIQHTFGGRLWSKVKCLRCSH 618
R GG +P L +E + I F G+L S +KC C +
Sbjct: 141 NGPVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKCQACGY 200
Query: 619 ESERYENIMDLTLEI-----YGWVESLEDALTQFTSPEDLDGENMYKCAR 663
S +E DL+L I G SL D FT E+L+ EN C R
Sbjct: 201 RSTTFEVFCDLSLPIPKKGFAGGKVSLRDCFNLFTKEEELESENAPVCDR 250
>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 = 70.5 bits (171), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 69/230 (30%), Positives = 95/230 (41%), Gaps = 48/230 (20%)
Query: 479 GLLNCGNSCYANAVLQCLTCTKPLVIYLLRRSHSSACCGKDWCL-MCELEQHV---MMLR 534
GL N GN+C+ NAVLQCL+ T+PL + LRR G + E V +
Sbjct: 18 GLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQELTEAFADVIGALWHP 77
Query: 535 ESAGPLSPGRILSHMRSISCQIGDGSQEDAHEFLRLLVASMQSICLE------------- 581
+S ++P R + + SQ+DA EFL+LL M+ + LE
Sbjct: 78 DSCEAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLL---MERLHLEINRRGRRAPPILA 134
Query: 582 --------RHGGESKVDPRL---------------QETTFIQHTFGGRLWSKVKCLRCSH 618
R GG +P L +E + I F G+L S +KC C +
Sbjct: 135 NGPVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKCQACGY 194
Query: 619 ESERYENIMDLTLEI-----YGWVESLEDALTQFTSPEDLDGENMYKCAR 663
S +E DL+L I G SL D FT E+L+ EN C R
Sbjct: 195 RSTTFEVFCDLSLPIPKKGFAGGKVSLRDCFNLFTKEEELESENAPVCDR 244
>pdb|2HD5|A Chain A, Usp2 In Complex With Ubiquitin
Length = 359
Score = 58.5 bits (140), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 52/204 (25%), Positives = 93/204 (45%), Gaps = 26/204 (12%)
Query: 479 GLLNCGNSCYANAVLQCLTCTKPLVIYLLRRSHSSACCGKDWCLMCELEQHVMMLRE--S 536
GL N GN+C+ N++LQCL+ T+ L Y L+R + +E+ +++ +
Sbjct: 11 GLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQTIWT 70
Query: 537 AGP---LSPGRILSHMRSISCQIGDGSQEDAHEFLRLLVASMQS----ICLERHGGESKV 589
+ P +SP + ++ + + +Q+DA EFLR L+ + + + L +
Sbjct: 71 SSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPENL 130
Query: 590 DPRL--------------QETTFIQHTFGGRLWSKVKCLRCSHESERYENIMDLTLEIY- 634
D +E + I F G+L S + C C + S ++ DL+L I
Sbjct: 131 DHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPIAK 190
Query: 635 -GWVE-SLEDALTQFTSPEDLDGE 656
G+ E +L D + FT + LDG+
Sbjct: 191 RGYPEVTLMDCMRLFTKEDVLDGD 214
>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 = 58.5 bits (140), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 52/204 (25%), Positives = 93/204 (45%), Gaps = 26/204 (12%)
Query: 479 GLLNCGNSCYANAVLQCLTCTKPLVIYLLRRSHSSACCGKDWCLMCELEQHVMMLRE--S 536
GL N GN+C+ N++LQCL+ T+ L Y L+R + +E+ +++ +
Sbjct: 30 GLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQTIWT 89
Query: 537 AGP---LSPGRILSHMRSISCQIGDGSQEDAHEFLRLLVASMQS----ICLERHGGESKV 589
+ P +SP + ++ + + +Q+DA EFLR L+ + + + L +
Sbjct: 90 SSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPENL 149
Query: 590 DPRL--------------QETTFIQHTFGGRLWSKVKCLRCSHESERYENIMDLTLEIY- 634
D +E + I F G+L S + C C + S ++ DL+L I
Sbjct: 150 DHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPIAK 209
Query: 635 -GWVE-SLEDALTQFTSPEDLDGE 656
G+ E +L D + FT + LDG+
Sbjct: 210 RGYPEVTLMDCMRLFTKEDVLDGD 233
>pdb|2IBI|A Chain A, Covalent Ubiquitin-Usp2 Complex
Length = 374
Score = 58.5 bits (140), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 52/204 (25%), Positives = 93/204 (45%), Gaps = 26/204 (12%)
Query: 479 GLLNCGNSCYANAVLQCLTCTKPLVIYLLRRSHSSACCGKDWCLMCELEQHVMMLRE--S 536
GL N GN+C+ N++LQCL+ T+ L Y L+R + +E+ +++ +
Sbjct: 37 GLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQTIWT 96
Query: 537 AGP---LSPGRILSHMRSISCQIGDGSQEDAHEFLRLLVASMQS----ICLERHGGESKV 589
+ P +SP + ++ + + +Q+DA EFLR L+ + + + L +
Sbjct: 97 SSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPENL 156
Query: 590 DPRL--------------QETTFIQHTFGGRLWSKVKCLRCSHESERYENIMDLTLEIY- 634
D +E + I F G+L S + C C + S ++ DL+L I
Sbjct: 157 DHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPIAK 216
Query: 635 -GWVE-SLEDALTQFTSPEDLDGE 656
G+ E +L D + FT + LDG+
Sbjct: 217 RGYPEVTLMDCMRLFTKEDVLDGD 240
>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 = 57.8 bits (138), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 55/202 (27%), Positives = 93/202 (46%), Gaps = 20/202 (9%)
Query: 479 GLLNCGNSCYANAVLQCLTCTKPLVIYLLRRSHSSACCGK--DWCLMCELEQHVMML--- 533
GL+N GN+C+ +++LQCL + + + + HS+ C + D C C L++ V L
Sbjct: 143 GLINMGNTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHELYGA 202
Query: 534 ----RESAGPLSPGRILSHMRSISC------QIGDGSQEDAHEFLRLLVASM-QSICLER 582
+ S+ S R + ++C + SQ+DAHEF + ++ + QS L+
Sbjct: 203 LNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQSYVLDL 262
Query: 583 HGGESKVDPRLQETTFIQHT-FGGRLWSKVKCLRCSHESE-RYENIMDLTLEIYGWVESL 640
+ ++ I HT F G L S + C C + S+ + +DL+L+I + L
Sbjct: 263 PNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIKD-KKKL 321
Query: 641 EDALTQFTSPEDLDGENMYKCA 662
+ L F E L N Y C
Sbjct: 322 YECLDSFHKKEQLKDFN-YHCG 342
>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 = 55.5 bits (132), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 54/202 (26%), Positives = 93/202 (46%), Gaps = 20/202 (9%)
Query: 479 GLLNCGNSCYANAVLQCLTCTKPLVIYLLRRSHSSACCGK--DWCLMCELEQHVMML--- 533
GL+N G++C+ +++LQCL + + + + HS+ C + D C C L++ V L
Sbjct: 143 GLINMGSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHELYGA 202
Query: 534 ----RESAGPLSPGRILSHMRSISC------QIGDGSQEDAHEFLRLLVASM-QSICLER 582
+ S+ S R + ++C + SQ+DAHEF + ++ + QS L+
Sbjct: 203 LNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQSYVLDL 262
Query: 583 HGGESKVDPRLQETTFIQHT-FGGRLWSKVKCLRCSHESE-RYENIMDLTLEIYGWVESL 640
+ ++ I HT F G L S + C C + S+ + +DL+L+I + L
Sbjct: 263 PNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIKD-KKKL 321
Query: 641 EDALTQFTSPEDLDGENMYKCA 662
+ L F E L N Y C
Sbjct: 322 YECLDSFHKKEQLKDFN-YHCG 342
>pdb|3M99|A Chain A, Structure Of The Ubp8-Sgf11-Sgf73-Sus1 Saga Dub Module
Length = 471
Score = 55.5 bits (132), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 54/202 (26%), Positives = 93/202 (46%), Gaps = 20/202 (9%)
Query: 479 GLLNCGNSCYANAVLQCLTCTKPLVIYLLRRSHSSACCGK--DWCLMCELEQHVMML--- 533
GL+N G++C+ +++LQCL + + + + HS+ C + D C C L++ V L
Sbjct: 138 GLINMGSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHELYGA 197
Query: 534 ----RESAGPLSPGRILSHMRSISC------QIGDGSQEDAHEFLRLLVASM-QSICLER 582
+ S+ S R + ++C + SQ+DAHEF + ++ + QS L+
Sbjct: 198 LNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHEFWQFIINQIHQSYVLDL 257
Query: 583 HGGESKVDPRLQETTFIQHT-FGGRLWSKVKCLRCSHESE-RYENIMDLTLEIYGWVESL 640
+ ++ I HT F G L S + C C + S+ + +DL+L+I + L
Sbjct: 258 PNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIKD-KKKL 316
Query: 641 EDALTQFTSPEDLDGENMYKCA 662
+ L F E L N Y C
Sbjct: 317 YECLDSFHKKEQLKDFN-YHCG 337
>pdb|3NHE|A Chain A, High Resolution Structure (1.26a) Of Usp2a In Complex With
Ubiquitin
Length = 348
Score = 55.1 bits (131), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 51/204 (25%), Positives = 92/204 (45%), Gaps = 26/204 (12%)
Query: 479 GLLNCGNSCYANAVLQCLTCTKPLVIYLLRRSHSSACCGKDWCLMCELEQHVMMLRE--S 536
GL N GN+ + N++LQCL+ T+ L Y L+R + +E+ +++ +
Sbjct: 11 GLRNLGNTXFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQTIWT 70
Query: 537 AGP---LSPGRILSHMRSISCQIGDGSQEDAHEFLRLLVASMQS----ICLERHGGESKV 589
+ P +SP + ++ + + +Q+DA EFLR L+ + + + L +
Sbjct: 71 SSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPENL 130
Query: 590 DPRL--------------QETTFIQHTFGGRLWSKVKCLRCSHESERYENIMDLTLEIY- 634
D +E + I F G+L S + C C + S ++ DL+L I
Sbjct: 131 DHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPIAK 190
Query: 635 -GWVE-SLEDALTQFTSPEDLDGE 656
G+ E +L D + FT + LDG+
Sbjct: 191 RGYPEVTLMDCMRLFTKEDVLDGD 214
>pdb|3N3K|A Chain A, The Catalytic Domain Of Usp8 In Complex With A Usp8
Specific Inhibitor
Length = 396
Score = 52.8 bits (125), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 54/215 (25%), Positives = 85/215 (39%), Gaps = 37/215 (17%)
Query: 479 GLLNCGNSCYANAVLQCLTCTKPLVIYLLRRSHSSACCGKDWCLMCELEQHVMMLRESAG 538
GL N GN+CY N++LQCL C P + R+ C +D L H + E G
Sbjct: 64 GLRNLGNTCYMNSILQCL-CNAPHLADYFNRN-----CYQDDINRSNLLGHKGEVAEEFG 117
Query: 539 P------------LSPGRILSHMRSISCQIGDGSQEDAHEFLRLLVASMQSIC------- 579
+SP + I+ Q SQ+D+ E L L+ +
Sbjct: 118 IIMKALWTGQYRYISPKDFKITIGKINDQFAGYSQQDSQELLLFLMDGLHEDLNKADNRK 177
Query: 580 -LERHGGESKVDPRLQETTFIQH----------TFGGRLWSKVKCLRCSHESERYENIMD 628
+ + D + E + +H F G+ S V+CL C +S +E M
Sbjct: 178 RYKEENNDHLDDFKAAEHAWQKHKQLNESIIVALFQGQFKSTVQCLTCHKKSRTFEAFMY 237
Query: 629 LTLEIYGWVE-SLEDALTQFTSPEDLDGENMYKCA 662
L+L + + +L+D L F+ E L N + C+
Sbjct: 238 LSLPLASTSKCTLQDCLRLFSKEEKLTDNNRFYCS 272
>pdb|2F1Z|A Chain A, Crystal Structure Of Hausp
pdb|2F1Z|B Chain B, Crystal Structure Of Hausp
Length = 522
Score = 50.1 bits (118), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 46/191 (24%), Positives = 84/191 (43%), Gaps = 30/191 (15%)
Query: 479 GLLNCGNSCYANAVLQCLTCTKPL--VIYLLRRSHSSACCGKDWCLMCELEQHVMMLRES 536
GL N G +CY N++LQ L T L +Y++ + + L++ L+ S
Sbjct: 177 GLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPTEGDDSSKS----VPLALQRVFYELQHS 232
Query: 537 AGPLSPGRILSHMRSISCQIGDG-SQEDAHEFLRLLVAS----MQSICLERHGGESKVDP 591
P+ ++ +S + D Q D E R+L+ + M+ C+E P
Sbjct: 233 DKPVGTKKL---TKSFGWETLDSFMQHDVQELCRVLLDNVENKMKGTCVE------GTIP 283
Query: 592 RLQETTFIQHTFGGRLWSKVKCLRCSHESERYENIMDLTLEIYGWVESLEDALTQFTSPE 651
+L F G++ S ++C + S+R E+ D+ L I G +++ ++ + + E
Sbjct: 284 KL---------FRGKMVSYIQCKEVDYRSDRREDYYDIQLSIKG-KKNIFESFVDYVAVE 333
Query: 652 DLDGENMYKCA 662
LDG+N Y
Sbjct: 334 QLDGDNKYDAG 344
>pdb|2GFO|A Chain A, Structure Of The Catalytic Domain Of Human Ubiquitin
Carboxyl-terminal Hydrolase 8
Length = 396
Score = 49.7 bits (117), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 53/215 (24%), Positives = 83/215 (38%), Gaps = 37/215 (17%)
Query: 479 GLLNCGNSCYANAVLQCLTCTKPLVIYLLRRSHSSACCGKDWCLMCELEQHVMMLRESAG 538
GL N GN+CY N++LQCL C P + R+ C +D L H + E G
Sbjct: 64 GLRNLGNTCYXNSILQCL-CNAPHLADYFNRN-----CYQDDINRSNLLGHKGEVAEEFG 117
Query: 539 P------------LSPGRILSHMRSISCQIGDGSQEDAHEFLRLLVASMQSIC------- 579
+SP + I+ Q SQ+D+ E L L +
Sbjct: 118 IIXKALWTGQYRYISPKDFKITIGKINDQFAGYSQQDSQELLLFLXDGLHEDLNKADNRK 177
Query: 580 -LERHGGESKVDPRLQETTFIQHT----------FGGRLWSKVKCLRCSHESERYENIMD 628
+ + D + E + +H F G+ S V+CL C +S +E
Sbjct: 178 RYKEENNDHLDDFKAAEHAWQKHKQLNESIIVALFQGQFKSTVQCLTCHKKSRTFEAFXY 237
Query: 629 LTLEIYGWVE-SLEDALTQFTSPEDLDGENMYKCA 662
L+L + + +L+D L F+ E L N + C+
Sbjct: 238 LSLPLASTSKCTLQDCLRLFSKEEKLTDNNRFYCS 272
>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 = 46/191 (24%), Positives = 84/191 (43%), Gaps = 30/191 (15%)
Query: 479 GLLNCGNSCYANAVLQCLTCTKPL--VIYLLRRSHSSACCGKDWCLMCELEQHVMMLRES 536
GL N G +CY N++LQ L T L +Y++ + + L++ L+ S
Sbjct: 8 GLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPTEGDDSSK----SVPLALQRVFYELQHS 63
Query: 537 AGPLSPGRILSHMRSISCQIGDG-SQEDAHEFLRLLVAS----MQSICLERHGGESKVDP 591
P+ ++ +S + D Q D E R+L+ + M+ C+E P
Sbjct: 64 DKPVGTKKL---TKSFGWETLDSFMQHDVQELCRVLLDNVENKMKGTCVE------GTIP 114
Query: 592 RLQETTFIQHTFGGRLWSKVKCLRCSHESERYENIMDLTLEIYGWVESLEDALTQFTSPE 651
+L F G++ S ++C + S+R E+ D+ L I G +++ ++ + + E
Sbjct: 115 KL---------FRGKMVSYIQCKEVDYRSDRREDYYDIQLSIKGK-KNIFESFVDYVAVE 164
Query: 652 DLDGENMYKCA 662
LDG+N Y
Sbjct: 165 QLDGDNKYDAG 175
>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 = 46.2 bits (108), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 47/185 (25%), Positives = 79/185 (42%), Gaps = 18/185 (9%)
Query: 479 GLLNCGNSCYANAVLQCLTCTKPLVIYLLRRSHSSACCGKDWCLMCELEQHVMMLRESAG 538
GL N G +CY N++LQ L T L + K L L++ L+ S
Sbjct: 8 GLKNQGATCYXNSLLQTLFFTNQLRKAVYXXPTEGDDSSKSVPLA--LQRVFYELQHSDK 65
Query: 539 PLSPGRILSHMRSISCQIGDG-SQEDAHEFLRLLVASMQSICLERHGGESKVDPRLQETT 597
P+ ++ +S + D Q D E R+L+ ++ E+K E T
Sbjct: 66 PVGTKKL---TKSFGWETLDSFXQHDVQELCRVLLDNV----------ENKXKGTCVEGT 112
Query: 598 FIQHTFGGRLWSKVKCLRCSHESERYENIMDLTLEIYGWVESLEDALTQFTSPEDLDGEN 657
I F G+ S ++C + S+R E+ D+ L I G +++ ++ + + E LDG+N
Sbjct: 113 -IPKLFRGKXVSYIQCKEVDYRSDRREDYYDIQLSIKG-KKNIFESFVDYVAVEQLDGDN 170
Query: 658 MYKCA 662
Y
Sbjct: 171 KYDAG 175
>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 = 44.3 bits (103), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 43/181 (23%), Positives = 72/181 (39%), Gaps = 28/181 (15%)
Query: 479 GLLNCGNSCYANAVLQCLTCTKPLVIYLLR--------RSHSSACCGKDWCLMCELEQHV 530
GL N GN+ + N+ LQCL+ T PL Y L+ R + G+ EL + +
Sbjct: 10 GLGNLGNTXFMNSALQCLSNTAPLTDYFLKDEYEAEINRDNPLGMKGEIAEAYAELIKQM 69
Query: 531 MMLRESAGPLSPGRILSHMRSISCQIGDGSQEDAHEFLRLLVASM--------QSICLER 582
R++ ++P + + + Q Q+D+ E L L+ + + LE
Sbjct: 70 WSGRDAH--VAPRMFKTQVGRFAPQFSGYQQQDSQELLAFLLDGLHEDLNRVKKKPYLEL 127
Query: 583 HGGESKVDP----------RLQETTFIQHTFGGRLWSKVKCLRCSHESERYENIMDLTLE 632
+ D RL+ + I TF G S + C C+ S ++ LTL
Sbjct: 128 KDANGRPDAVVAKEAWENHRLRNDSVIVDTFHGLFKSTLVCPECAKVSVTFDPFCYLTLP 187
Query: 633 I 633
+
Sbjct: 188 L 188
>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 = 38.9 bits (89), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 27/52 (51%), Gaps = 3/52 (5%)
Query: 102 LCARCF--APATTRCSRCKSVRYCSGKCQIIHWRQVHKQECQQLEKTSSSSP 151
+C RC RCS+C+ +YCS KCQ W HK+EC+ L+ P
Sbjct: 50 VCDRCLLGKEKLMRCSQCRVAKYCSAKCQKKAWPD-HKRECKCLKSCKPRYP 100
>pdb|3OXG|A Chain A, Human Lysine Methyltransferase Smyd3 In Complex With
Adohcy (Form Iii)
Length = 464
Score = 38.9 bits (89), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 27/52 (51%), Gaps = 3/52 (5%)
Query: 102 LCARCF--APATTRCSRCKSVRYCSGKCQIIHWRQVHKQECQQLEKTSSSSP 151
+C RC RCS+C+ +YCS KCQ W HK+EC+ L+ P
Sbjct: 84 VCDRCLLGKEKLMRCSQCRVAKYCSAKCQKKAWPD-HKRECKCLKSCKPRYP 134
>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 = 38.9 bits (89), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 27/52 (51%), Gaps = 3/52 (5%)
Query: 102 LCARCF--APATTRCSRCKSVRYCSGKCQIIHWRQVHKQECQQLEKTSSSSP 151
+C RC RCS+C+ +YCS KCQ W HK+EC+ L+ P
Sbjct: 48 VCDRCLLGKEKLMRCSQCRVAKYCSAKCQKKAWPD-HKRECKCLKSCKPRYP 98
>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 = 38.5 bits (88), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 27/52 (51%), Gaps = 3/52 (5%)
Query: 102 LCARCF--APATTRCSRCKSVRYCSGKCQIIHWRQVHKQECQQLEKTSSSSP 151
+C RC RCS+C+ +YCS KCQ W HK+EC+ L+ P
Sbjct: 48 VCDRCLLGKEKLMRCSQCRVAKYCSAKCQKKAWPD-HKRECKCLKSCKPRYP 98
>pdb|3QWP|A Chain A, Crystal Structure Of Set And Mynd Domain Containing 3;
Zinc Finger Mynd Domain-Containing Protein 1
Length = 429
Score = 38.5 bits (88), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 27/52 (51%), Gaps = 3/52 (5%)
Query: 102 LCARCF--APATTRCSRCKSVRYCSGKCQIIHWRQVHKQECQQLEKTSSSSP 151
+C RC RCS+C+ +YCS KCQ W HK+EC+ L+ P
Sbjct: 49 VCDRCLLGKEKLMRCSQCRVAKYCSAKCQKKAWPD-HKRECKCLKSCKPRYP 99
>pdb|3MEK|A Chain A, Crystal Structure Of Human Histone-Lysine N-
Methyltransferase Smyd3 In Complex With S-Adenosyl-L-
Methionine
Length = 429
Score = 38.1 bits (87), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 27/52 (51%), Gaps = 3/52 (5%)
Query: 102 LCARCF--APATTRCSRCKSVRYCSGKCQIIHWRQVHKQECQQLEKTSSSSP 151
+C RC RCS+C+ +YCS KCQ W HK+EC+ L+ P
Sbjct: 49 VCDRCLLGKEKLXRCSQCRVAKYCSAKCQKKAWPD-HKRECKCLKSCKPRYP 99
>pdb|2D8Q|A Chain A, Solution Structure Of The Mynd Domain Of The Human Zinc
Finger Mynd Domain-Containing Protein 10
Length = 70
Score = 38.1 bits (87), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 18/38 (47%), Positives = 25/38 (65%), Gaps = 1/38 (2%)
Query: 103 CARCFAPATTRCSRCKSVRYCSGKCQIIHWRQVHKQEC 140
CA C A A+ RCSRC++ YC +CQ+ HW + H + C
Sbjct: 18 CAYCSAEASKRCSRCQNEWYCCRECQVKHWEK-HGKTC 54
>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 = 37.7 bits (86), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 18/38 (47%), Positives = 25/38 (65%), Gaps = 1/38 (2%)
Query: 103 CARCFAPATTRCSRCKSVRYCSGKCQIIHWRQVHKQEC 140
CA C A A+ RCSRC++ YC +CQ+ HW + H + C
Sbjct: 18 CAYCSAEASKRCSRCQNEWYCCRECQVKHWEK-HGKTC 54
>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 = 33.9 bits (76), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 22/42 (52%)
Query: 477 PRGLLNCGNSCYANAVLQCLTCTKPLVIYLLRRSHSSACCGK 518
P GL N GN+CY NA +QC+ L L R + + G+
Sbjct: 14 PCGLTNLGNTCYMNATVQCIRSVPELKDALKRYAGALRASGE 55
>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 = 33.1 bits (74), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 22/43 (51%), Gaps = 3/43 (6%)
Query: 103 CARCFA--PATTRCSRCKSVRYCSGKCQIIHWRQVHKQECQQL 143
C CFA ++C RCK YC +CQ W +HK EC +
Sbjct: 52 CECCFARKEGLSKCGRCKQAFYCDVECQKEDW-PLHKLECSSM 93
>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 = 33.1 bits (74), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 3/43 (6%)
Query: 103 CARCFA--PATTRCSRCKSVRYCSGKCQIIHWRQVHKQECQQL 143
C CF ++C RCK YC+ +CQ W +HK EC +
Sbjct: 52 CEYCFTRKEGLSKCGRCKQAFYCNVECQKEDW-PMHKLECSPM 93
>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 = 33.1 bits (74), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 3/43 (6%)
Query: 103 CARCFA--PATTRCSRCKSVRYCSGKCQIIHWRQVHKQECQQL 143
C CF ++C RCK YC+ +CQ W +HK EC +
Sbjct: 52 CEYCFTRKEGLSKCGRCKQAFYCNVECQKEDW-PMHKLECSPM 93
>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 = 33.1 bits (74), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 3/43 (6%)
Query: 103 CARCFA--PATTRCSRCKSVRYCSGKCQIIHWRQVHKQECQQL 143
C CF ++C RCK YC+ +CQ W +HK EC +
Sbjct: 52 CEYCFTRKEGLSKCGRCKQAFYCNVECQKEDW-PMHKLECSPM 93
>pdb|3N71|A Chain A, Crystal Structure Of Cardiac Specific Histone
Methyltransferase Smyd1
Length = 490
Score = 32.0 bits (71), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 21/46 (45%), Gaps = 3/46 (6%)
Query: 102 LCARCFA--PATTRCSRCKSVRYCSGKCQIIHWRQVHKQECQQLEK 145
+C CF RC +CK YC CQ W HK EC ++K
Sbjct: 51 VCHTCFKRQEKLHRCGQCKFAHYCDRTCQKDAWLN-HKNECAAIKK 95
>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 = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 12/20 (60%), Positives = 13/20 (65%)
Query: 477 PRGLLNCGNSCYANAVLQCL 496
P G N GN+CY NA LQ L
Sbjct: 24 PVGFKNXGNTCYLNATLQAL 43
>pdb|3A3J|A Chain A, Crystal Structures Of Penicillin Binding Protein 5 From
Haemophilus Influenzae
Length = 344
Score = 30.0 bits (66), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 645 TQFTSPEDLDGENMYKCARFVNLVEAHFF 673
T FT+P LD N Y AR + ++ AH
Sbjct: 134 TNFTTPHGLDDPNQYSSARDMAIIGAHII 162
>pdb|2ODD|A Chain A, Solution Structure Of The Mynd Domain From Aml1-Eto
Complexed With Smrt, A Corepressor
Length = 64
Score = 29.3 bits (64), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 16/34 (47%)
Query: 103 CARCFAPATTRCSRCKSVRYCSGKCQIIHWRQVH 136
C C A+ CS C + RYC CQ W + H
Sbjct: 20 CWNCGRKASETCSGCNTARYCGSFCQHKDWEKHH 53
>pdb|2DJ8|A Chain A, Solution Structure Of Zf-Mynd Domain Of Protein Cbfa2ti
(Protein Mtg8)
Length = 60
Score = 28.9 bits (63), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 17/36 (47%)
Query: 101 QLCARCFAPATTRCSRCKSVRYCSGKCQIIHWRQVH 136
+ C C A+ CS C + RYC CQ W + H
Sbjct: 16 ESCWNCGRKASETCSGCNTARYCGSFCQHKDWEKHH 51
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 0.129 0.390
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,819,763
Number of Sequences: 62578
Number of extensions: 670763
Number of successful extensions: 1457
Number of sequences better than 100.0: 44
Number of HSP's better than 100.0 without gapping: 30
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 1398
Number of HSP's gapped (non-prelim): 44
length of query: 676
length of database: 14,973,337
effective HSP length: 105
effective length of query: 571
effective length of database: 8,402,647
effective search space: 4797911437
effective search space used: 4797911437
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)