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= 004947
(722 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 = 92.4 bits (228), Expect = 7e-19, Method: Compositional matrix adjust.
Identities = 80/260 (30%), Positives = 111/260 (42%), Gaps = 48/260 (18%)
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-----YGWVESLEDALTQFTSPEDLDGENMYKCARCATYVRARKQ 673
S +E DL+L I G SL D FT E+L+ EN C RC R+ K+
Sbjct: 182 RSTTFEVFCDLSLPIPKKGFAGGKVSLRDCFNLFTKEEELESENAPVCDRCRQKTRSTKK 241
Query: 674 LSIHEAPNILTIVLKRFQVS 693
L++ P IL + L RF S
Sbjct: 242 LTVQRFPRILVLHLNRFSAS 261
>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 = 92.4 bits (228), Expect = 7e-19, Method: Compositional matrix adjust.
Identities = 80/260 (30%), Positives = 111/260 (42%), Gaps = 48/260 (18%)
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-----YGWVESLEDALTQFTSPEDLDGENMYKCARCATYVRARKQ 673
S +E DL+L I G SL D FT E+L+ EN C RC R+ K+
Sbjct: 201 RSTTFEVFCDLSLPIPKKGFAGGKVSLRDCFNLFTKEEELESENAPVCDRCRQKTRSTKK 260
Query: 674 LSIHEAPNILTIVLKRFQVS 693
L++ P IL + L RF S
Sbjct: 261 LTVQRFPRILVLHLNRFSAS 280
>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 = 92.0 bits (227), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 80/260 (30%), Positives = 111/260 (42%), Gaps = 48/260 (18%)
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-----YGWVESLEDALTQFTSPEDLDGENMYKCARCATYVRARKQ 673
S +E DL+L I G SL D FT E+L+ EN C RC R+ K+
Sbjct: 195 RSTTFEVFCDLSLPIPKKGFAGGKVSLRDCFNLFTKEEELESENAPVCDRCRQKTRSTKK 254
Query: 674 LSIHEAPNILTIVLKRFQVS 693
L++ P IL + L RF S
Sbjct: 255 LTVQRFPRILVLHLNRFSAS 274
>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 = 84.0 bits (206), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 68/231 (29%), Positives = 112/231 (48%), Gaps = 20/231 (8%)
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-FGGRLWSKVKCLRCSHESER-YENIMDLTLEIYGWVESL 640
+ ++ I HT F G L S + C C + S+ + +DL+L+I + L
Sbjct: 263 PNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIKD-KKKL 321
Query: 641 EDALTQFTSPEDLDGENMYKCARCATYVRARKQLSIHEAPNILTIVLKRFQ 691
+ L F E L N Y C C + A KQL IH+ P++L + LKRF+
Sbjct: 322 YECLDSFHKKEQLKDFN-YHCGECNSTQDAIKQLGIHKLPSVLVLQLKRFE 371
>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 = 81.6 bits (200), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 67/231 (29%), Positives = 112/231 (48%), Gaps = 20/231 (8%)
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-FGGRLWSKVKCLRCSHESER-YENIMDLTLEIYGWVESL 640
+ ++ I HT F G L S + C C + S+ + +DL+L+I + L
Sbjct: 263 PNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIKD-KKKL 321
Query: 641 EDALTQFTSPEDLDGENMYKCARCATYVRARKQLSIHEAPNILTIVLKRFQ 691
+ L F E L N Y C C + A KQL IH+ P++L + LKRF+
Sbjct: 322 YECLDSFHKKEQLKDFN-YHCGECNSTQDAIKQLGIHKLPSVLVLQLKRFE 371
>pdb|3M99|A Chain A, Structure Of The Ubp8-Sgf11-Sgf73-Sus1 Saga Dub Module
Length = 471
Score = 81.6 bits (200), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 67/231 (29%), Positives = 112/231 (48%), Gaps = 20/231 (8%)
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-FGGRLWSKVKCLRCSHESER-YENIMDLTLEIYGWVESL 640
+ ++ I HT F G L S + C C + S+ + +DL+L+I + L
Sbjct: 258 PNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTIDPFLDLSLDIKD-KKKL 316
Query: 641 EDALTQFTSPEDLDGENMYKCARCATYVRARKQLSIHEAPNILTIVLKRFQ 691
+ L F E L N Y C C + A KQL IH+ P++L + LKRF+
Sbjct: 317 YECLDSFHKKEQLKDFN-YHCGECNSTQDAIKQLGIHKLPSVLVLQLKRFE 366
>pdb|2IBI|A Chain A, Covalent Ubiquitin-Usp2 Complex
Length = 374
Score = 71.2 bits (173), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 67/241 (27%), Positives = 110/241 (45%), Gaps = 26/241 (10%)
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-SLEDALTQFTSPEDLDGENMYKCARCATYVRARKQLSIHEAPNILTIVLKRFQV 692
G+ E +L D + FT + LDG+ C RC R K+ SI P IL + LKRF
Sbjct: 217 RGYPEVTLMDCMRLFTKEDVLDGDAAPTCCRCRGRKRCIKKFSIQRFPKILVLHLKRFSE 276
Query: 693 S 693
S
Sbjct: 277 S 277
>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 = 70.9 bits (172), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 67/241 (27%), Positives = 110/241 (45%), Gaps = 26/241 (10%)
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-SLEDALTQFTSPEDLDGENMYKCARCATYVRARKQLSIHEAPNILTIVLKRFQV 692
G+ E +L D + FT + LDG+ C RC R K+ SI P IL + LKRF
Sbjct: 210 RGYPEVTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKILVLHLKRFSE 269
Query: 693 S 693
S
Sbjct: 270 S 270
>pdb|2HD5|A Chain A, Usp2 In Complex With Ubiquitin
Length = 359
Score = 70.9 bits (172), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 67/241 (27%), Positives = 110/241 (45%), Gaps = 26/241 (10%)
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-SLEDALTQFTSPEDLDGENMYKCARCATYVRARKQLSIHEAPNILTIVLKRFQV 692
G+ E +L D + FT + LDG+ C RC R K+ SI P IL + LKRF
Sbjct: 191 RGYPEVTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKILVLHLKRFSE 250
Query: 693 S 693
S
Sbjct: 251 S 251
>pdb|3N3K|A Chain A, The Catalytic Domain Of Usp8 In Complex With A Usp8
Specific Inhibitor
Length = 396
Score = 69.3 bits (168), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 63/243 (25%), Positives = 100/243 (41%), Gaps = 37/243 (15%)
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-SLEDALTQFTSPEDLDGENMYKCARCATYVRARKQLSIHEAPNILTIVL 687
L+L + + +L+D L F+ E L N + C+ C + K++ I + P +L + L
Sbjct: 238 LSLPLASTSKCTLQDCLRLFSKEEKLTDNNRFYCSHCRARRDSLKKIEIWKLPPVLLVHL 297
Query: 688 KRF 690
KRF
Sbjct: 298 KRF 300
>pdb|3NHE|A Chain A, High Resolution Structure (1.26a) Of Usp2a In Complex With
Ubiquitin
Length = 348
Score = 67.4 bits (163), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 66/241 (27%), Positives = 109/241 (45%), Gaps = 26/241 (10%)
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-SLEDALTQFTSPEDLDGENMYKCARCATYVRARKQLSIHEAPNILTIVLKRFQV 692
G+ E +L D + FT + LDG+ C RC R K+ SI P IL + LKRF
Sbjct: 191 RGYPEVTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKILVLHLKRFSE 250
Query: 693 S 693
S
Sbjct: 251 S 251
>pdb|2GFO|A Chain A, Structure Of The Catalytic Domain Of Human Ubiquitin
Carboxyl-terminal Hydrolase 8
Length = 396
Score = 66.6 bits (161), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 62/243 (25%), Positives = 98/243 (40%), Gaps = 37/243 (15%)
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-SLEDALTQFTSPEDLDGENMYKCARCATYVRARKQLSIHEAPNILTIVL 687
L+L + + +L+D L F+ E L N + C+ C + K++ I + P +L + L
Sbjct: 238 LSLPLASTSKCTLQDCLRLFSKEEKLTDNNRFYCSHCRARRDSLKKIEIWKLPPVLLVHL 297
Query: 688 KRF 690
KRF
Sbjct: 298 KRF 300
>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 = 61.2 bits (147), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 61/261 (23%), Positives = 101/261 (38%), Gaps = 46/261 (17%)
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------------------YGWVESLEDALTQFTSPEDLDGENMYKCARCATYVRARKQL 674
+ +L D + FT+ E L + + C C + +A K+
Sbjct: 188 LPLKKDRVMEGPMLQPQKKKKTTVALRDCIELFTTMETLGEHDPWYCPNCKKHQQATKKF 247
Query: 675 SIHEAPNILTIVLKRFQVSCY 695
+ P IL + LKRF + Y
Sbjct: 248 DLWSLPKILVVHLKRFSYNRY 268
>pdb|2F1Z|A Chain A, Crystal Structure Of Hausp
pdb|2F1Z|B Chain B, Crystal Structure Of Hausp
Length = 522
Score = 55.1 bits (131), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 53/219 (24%), Positives = 94/219 (42%), Gaps = 31/219 (14%)
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 DLDGENMYKCARCATYVRARKQLSIHEAPNILTIVLKRF 690
LDG+N Y A K + P +L + L RF
Sbjct: 334 QLDGDNKYDAGEHGLQ-EAEKGVKFLTLPPVLHLQLMRF 371
>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 = 53.5 bits (127), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 53/219 (24%), Positives = 94/219 (42%), Gaps = 31/219 (14%)
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---------FRGKMVSYIQCKEVDYRSDRREDYYDIQLSIKG-KKNIFESFVDYVAVE 164
Query: 652 DLDGENMYKCARCATYVRARKQLSIHEAPNILTIVLKRF 690
LDG+N Y A K + P +L + L RF
Sbjct: 165 QLDGDNKYDAGEHGLQ-EAEKGVKFLTLPPVLHLQLMRF 202
>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 = 51.6 bits (122), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 55/213 (25%), Positives = 86/213 (40%), Gaps = 19/213 (8%)
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 + + + E LDG+N
Sbjct: 113 -IPKLFRGKXVSYIQCKEVDYRSDRREDYYDIQLSIKGKKNIFE-SFVDYVAVEQLDGDN 170
Query: 658 MYKCARCATYVRARKQLSIHEAPNILTIVLKRF 690
Y A K + P +L + L RF
Sbjct: 171 KYDAGEHGLQ-EAEKGVKFLTLPPVLHLQLXRF 202
>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 = 0.012, 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|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 = 38.5 bits (88), Expect = 0.012, 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|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 = 38.5 bits (88), Expect = 0.012, 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 = 0.012, 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|3OXG|A Chain A, Human Lysine Methyltransferase Smyd3 In Complex With
Adohcy (Form Iii)
Length = 464
Score = 38.5 bits (88), Expect = 0.012, 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|2D8Q|A Chain A, Solution Structure Of The Mynd Domain Of The Human Zinc
Finger Mynd Domain-Containing Protein 10
Length = 70
Score = 38.5 bits (88), Expect = 0.014, 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|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 = 0.016, 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|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 = 37.7 bits (86), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 56/237 (23%), Positives = 96/237 (40%), Gaps = 32/237 (13%)
Query: 477 PRGLLNCGNSCYANAVLQCLTCTKPLVIYLLRRSHSSACCGKDWCLMCELEQHVMMLRE- 535
P GL N GN+CY NA +QC+ L L R + + G+ M + LR+
Sbjct: 14 PCGLTNLGNTCYMNATVQCIRSVPELKDALKRYAGALRASGE----MASAQYITAALRDL 69
Query: 536 ------SAGPLSPGRILSHMRSISCQI------GDGSQEDAHE----FLRLLVASMQSI- 578
++ + P +L + Q G Q+DA+E +R+L +++I
Sbjct: 70 FDSMDKTSSSIPPIILLQFLHMAFPQFAEKGEQGQYLQQDANECWIQMMRVLQQKLEAIE 129
Query: 579 ---CLERHGGESKVDPRLQETTFIQHTFGGRLWSKVKCLRCSHE--SERYENIMDLTLEI 633
E + ++ + I FG + +KC E ++ EN + L+ I
Sbjct: 130 DDSVKETDSSSASAATPSKKKSLIDQFFGVEFETTMKCTESEEEEVTKGKENQLQLSCFI 189
Query: 634 YGWVESLEDALTQFTSPEDLDGENMYKCARCATYVRARKQLSIHEAPNILTIVLKRF 690
V+ L L + E++ ++ R A Y+++ K I P LTI + RF
Sbjct: 190 NQEVKYLFTGL-KLRLQEEITKQSP-TLQRNALYIKSSK---ISRLPAYLTIQMVRF 241
>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 = 33.5 bits (75), Expect = 0.45, 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 = 0.50, 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 = 0.50, 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 = 0.51, 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 = 32.3 bits (72), Expect = 1.0, 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|2EOW|A Chain A, Solution Structure Of The C2h2 Type Zinc Finger (Region
368- 400) Of Human Zinc Finger Protein 347
Length = 46
Score = 29.6 bits (65), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 14/24 (58%)
Query: 656 ENMYKCARCATYVRARKQLSIHEA 679
E YKC C RAR L+IH+A
Sbjct: 10 EKPYKCNECGKAFRARSSLAIHQA 33
>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 = 7.7, 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 = 29.3 bits (64), Expect = 8.8, 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 0.130 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,528,316
Number of Sequences: 62578
Number of extensions: 697550
Number of successful extensions: 1637
Number of sequences better than 100.0: 40
Number of HSP's better than 100.0 without gapping: 30
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 1574
Number of HSP's gapped (non-prelim): 40
length of query: 722
length of database: 14,973,337
effective HSP length: 106
effective length of query: 616
effective length of database: 8,340,069
effective search space: 5137482504
effective search space used: 5137482504
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)