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= psy13202
(242 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 = 67.8 bits (164), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 68/242 (28%), Positives = 96/242 (39%), Gaps = 64/242 (26%)
Query: 28 IAHHFEYYRPEDSHEFLLYLIEGIHRSYL------KVISGSNN----------------- 64
I + Y +D+HEF ++I IH+SY+ K +S +NN
Sbjct: 231 INQNLAGYSQQDAHEFWQFIINQIHQSYVLDLPNAKEVSRANNKQCECIVHTVFEGSLES 290
Query: 65 ------------------LELSLDIYQLSSLDEALGQFFAKEYLVRDNLYQCEKCGYKTE 106
L+LSLDI L E L F KE L +D Y C +C +
Sbjct: 291 SIVCPGCQNNSKTTIDPFLDLSLDIKDKKKLYECLDSFHKKEQL-KDFNYHCGECNSTQD 349
Query: 107 ATKQFSIEKPPIVFILLLKRFNYLC----LKISCAVQVPLYL---------------EFG 147
A KQ I K P V +L LKRF +L K+ ++ P YL E G
Sbjct: 350 AIKQLGIHKLPSVLVLQLKRFEHLLNGSNRKLDDFIEFPTYLNMKNYCSTKEKDKHSENG 409
Query: 148 KFMHCRRNLVSAVIHHGSSSFSGHYNCIGSTSSGSYHYFGDDRVQASNLQQV--TNAYVV 205
K L+ V H G+ + GHY S G + F D V + + ++V AY++
Sbjct: 410 KVPDIIYELIGIVSHKGTVN-EGHYIAFCKISGGQWFKFNDSMVSSISQEEVLKEQAYLL 468
Query: 206 IY 207
Y
Sbjct: 469 FY 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 = 67.8 bits (164), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 68/242 (28%), Positives = 96/242 (39%), Gaps = 64/242 (26%)
Query: 28 IAHHFEYYRPEDSHEFLLYLIEGIHRSYL------KVISGSNN----------------- 64
I + Y +D+HEF ++I IH+SY+ K +S +NN
Sbjct: 231 INQNLAGYSQQDAHEFWQFIINQIHQSYVLDLPNAKEVSRANNKQCECIVHTVFEGSLES 290
Query: 65 ------------------LELSLDIYQLSSLDEALGQFFAKEYLVRDNLYQCEKCGYKTE 106
L+LSLDI L E L F KE L +D Y C +C +
Sbjct: 291 SIVCPGCQNNSKTTIDPFLDLSLDIKDKKKLYECLDSFHKKEQL-KDFNYHCGECNSTQD 349
Query: 107 ATKQFSIEKPPIVFILLLKRFNYLC----LKISCAVQVPLYL---------------EFG 147
A KQ I K P V +L LKRF +L K+ ++ P YL E G
Sbjct: 350 AIKQLGIHKLPSVLVLQLKRFEHLLNGSNRKLDDFIEFPTYLNMKNYCSTKEKDKHSENG 409
Query: 148 KFMHCRRNLVSAVIHHGSSSFSGHYNCIGSTSSGSYHYFGDDRVQASNLQQV--TNAYVV 205
K L+ V H G+ + GHY S G + F D V + + ++V AY++
Sbjct: 410 KVPDIIYELIGIVSHKGTVN-EGHYIAFCKISGGQWFKFNDSMVSSISQEEVLKEQAYLL 468
Query: 206 IY 207
Y
Sbjct: 469 FY 470
>pdb|3M99|A Chain A, Structure Of The Ubp8-Sgf11-Sgf73-Sus1 Saga Dub Module
Length = 471
Score = 67.8 bits (164), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 68/242 (28%), Positives = 96/242 (39%), Gaps = 64/242 (26%)
Query: 28 IAHHFEYYRPEDSHEFLLYLIEGIHRSYL------KVISGSNN----------------- 64
I + Y +D+HEF ++I IH+SY+ K +S +NN
Sbjct: 226 INQNLAGYSQQDAHEFWQFIINQIHQSYVLDLPNAKEVSRANNKQCECIVHTVFEGSLES 285
Query: 65 ------------------LELSLDIYQLSSLDEALGQFFAKEYLVRDNLYQCEKCGYKTE 106
L+LSLDI L E L F KE L +D Y C +C +
Sbjct: 286 SIVCPGCQNNSKTTIDPFLDLSLDIKDKKKLYECLDSFHKKEQL-KDFNYHCGECNSTQD 344
Query: 107 ATKQFSIEKPPIVFILLLKRFNYLC----LKISCAVQVPLYL---------------EFG 147
A KQ I K P V +L LKRF +L K+ ++ P YL E G
Sbjct: 345 AIKQLGIHKLPSVLVLQLKRFEHLLNGSNRKLDDFIEFPTYLNMKNYCSTKEKDKHSENG 404
Query: 148 KFMHCRRNLVSAVIHHGSSSFSGHYNCIGSTSSGSYHYFGDDRVQASNLQQV--TNAYVV 205
K L+ V H G+ + GHY S G + F D V + + ++V AY++
Sbjct: 405 KVPDIIYELIGIVSHKGTVN-EGHYIAFCKISGGQWFKFNDSMVSSISQEEVLKEQAYLL 463
Query: 206 IY 207
Y
Sbjct: 464 FY 465
>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 = 53.1 bits (126), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 41/143 (28%), Positives = 67/143 (46%), Gaps = 11/143 (7%)
Query: 76 SLDEALGQFFAKEYLVRDNLYQCEKCGYKTEATKQFSIEKPPIVFILLLKRFNY---LCL 132
SL + F +E L +N C++C KT +TK+ ++++ P + +L L RF+
Sbjct: 220 SLRDCFNLFTKEEELESENAPVCDRCRQKTRSTKKLTVQRFPRILVLHLNRFSASRGSIK 279
Query: 133 KISCAVQVPL-YLEFGKFMHCRRN----LVSAVIHHGSSSFSGHYNCIGSTSSGSYHYFG 187
K S V PL L G F + + A+ +H S GHY + +G +H +
Sbjct: 280 KSSVGVDFPLQRLSLGDFASDKAGSPVYQLYALCNHSGSVHYGHYTALCRCQTG-WHVYN 338
Query: 188 DDRVQASNLQQV--TNAYVVIYE 208
D RV + QV + YV+ Y+
Sbjct: 339 DSRVSPVSENQVASSEGYVLFYQ 361
>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 = 53.1 bits (126), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 41/143 (28%), Positives = 67/143 (46%), Gaps = 11/143 (7%)
Query: 76 SLDEALGQFFAKEYLVRDNLYQCEKCGYKTEATKQFSIEKPPIVFILLLKRFNY---LCL 132
SL + F +E L +N C++C KT +TK+ ++++ P + +L L RF+
Sbjct: 207 SLRDCFNLFTKEEELESENAPVCDRCRQKTRSTKKLTVQRFPRILVLHLNRFSASRGSIK 266
Query: 133 KISCAVQVPL-YLEFGKFMHCRRN----LVSAVIHHGSSSFSGHYNCIGSTSSGSYHYFG 187
K S V PL L G F + + A+ +H S GHY + +G +H +
Sbjct: 267 KSSVGVDFPLQRLSLGDFASDKAGSPVYQLYALCNHSGSVHYGHYTALCRCQTG-WHVYN 325
Query: 188 DDRVQASNLQQV--TNAYVVIYE 208
D RV + QV + YV+ Y+
Sbjct: 326 DSRVSPVSENQVASSEGYVLFYQ 348
>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 = 52.8 bits (125), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 41/143 (28%), Positives = 67/143 (46%), Gaps = 11/143 (7%)
Query: 76 SLDEALGQFFAKEYLVRDNLYQCEKCGYKTEATKQFSIEKPPIVFILLLKRFNY---LCL 132
SL + F +E L +N C++C KT +TK+ ++++ P + +L L RF+
Sbjct: 226 SLRDCFNLFTKEEELESENAPVCDRCRQKTRSTKKLTVQRFPRILVLHLNRFSASRGSIK 285
Query: 133 KISCAVQVPL-YLEFGKFMHCRRN----LVSAVIHHGSSSFSGHYNCIGSTSSGSYHYFG 187
K S V PL L G F + + A+ +H S GHY + +G +H +
Sbjct: 286 KSSVGVDFPLQRLSLGDFASDKAGSPVYQLYALCNHSGSVHYGHYTALCRCQTG-WHVYN 344
Query: 188 DDRVQASNLQQV--TNAYVVIYE 208
D RV + QV + YV+ Y+
Sbjct: 345 DSRVSPVSENQVASSEGYVLFYQ 367
>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 = 47.0 bits (110), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 38/146 (26%), Positives = 68/146 (46%), Gaps = 14/146 (9%)
Query: 76 SLDEALGQFFAKEYLVRDNLYQCEKCGYKTEATKQFSIEKPPIVFILLLKRFN---YLCL 132
+L + + F E L + + C C +ATK+F + P + ++ LKRF+ Y
Sbjct: 212 ALRDCIELFTTMETLGEHDPWYCPNCKKHQQATKKFDLWSLPKILVVHLKRFSYNRYWRD 271
Query: 133 KISCAVQVPLY-LEFGKF---MHCRR---NLVSAVIHHGSSSFSGHYNCIGSTS-SGSYH 184
K+ V+ P+ L +F + R +L++ H+G+ GHY +G ++
Sbjct: 272 KLDTVVEFPIRGLNMSEFVCNLSARPYVYDLIAVSNHYGAMGV-GHYTAYAKNKLNGKWY 330
Query: 185 YFGDDRVQASNLQQVTN--AYVVIYE 208
YF D V ++ Q+ AYV+ Y+
Sbjct: 331 YFDDSNVSLASEDQIVTKAAYVLFYQ 356
Score = 31.2 bits (69), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 12/43 (27%), Positives = 23/43 (53%)
Query: 16 IIPELIINKLKLIAHHFEYYRPEDSHEFLLYLIEGIHRSYLKV 58
+ P + ++ A F Y+ +DS E L +L++G+H +V
Sbjct: 77 VAPRMFKTQVGRFAPQFSGYQQQDSQELLAFLLDGLHEDLNRV 119
>pdb|3NHE|A Chain A, High Resolution Structure (1.26a) Of Usp2a In Complex With
Ubiquitin
Length = 348
Score = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 37/112 (33%), Positives = 58/112 (51%), Gaps = 13/112 (11%)
Query: 109 KQFSIEKPPIVFILLLKRFNYLCL---KISCAVQVPLY-LEFGKFM-----HCRRNLVSA 159
K+FSI++ P + +L LKRF+ + K++ V PL L+ +F H NL A
Sbjct: 230 KKFSIQRFPKILVLHLKRFSESRIRTSKLTTFVNFPLRDLDLREFASENTNHAVYNLY-A 288
Query: 160 VIHHGSSSFSGHYNC-IGSTSSGSYHYFGDDRVQASNLQQV--TNAYVVIYE 208
V +H ++ GHY S +G +H F D V + QV ++AY++ YE
Sbjct: 289 VSNHSGTTMGGHYTAYCRSPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFYE 340
>pdb|2HD5|A Chain A, Usp2 In Complex With Ubiquitin
Length = 359
Score = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 37/112 (33%), Positives = 58/112 (51%), Gaps = 13/112 (11%)
Query: 109 KQFSIEKPPIVFILLLKRFNYLCL---KISCAVQVPLY-LEFGKFM-----HCRRNLVSA 159
K+FSI++ P + +L LKRF+ + K++ V PL L+ +F H NL A
Sbjct: 230 KKFSIQRFPKILVLHLKRFSESRIRTSKLTTFVNFPLRDLDLREFASENTNHAVYNLY-A 288
Query: 160 VIHHGSSSFSGHYNC-IGSTSSGSYHYFGDDRVQASNLQQV--TNAYVVIYE 208
V +H ++ GHY S +G +H F D V + QV ++AY++ YE
Sbjct: 289 VSNHSGTTMGGHYTAYCRSPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFYE 340
>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 = 46.2 bits (108), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 37/112 (33%), Positives = 58/112 (51%), Gaps = 13/112 (11%)
Query: 109 KQFSIEKPPIVFILLLKRFNYLCL---KISCAVQVPLY-LEFGKFM-----HCRRNLVSA 159
K+FSI++ P + +L LKRF+ + K++ V PL L+ +F H NL A
Sbjct: 249 KKFSIQRFPKILVLHLKRFSESRIRTSKLTTFVNFPLRDLDLREFASENTNHAVYNLY-A 307
Query: 160 VIHHGSSSFSGHYNC-IGSTSSGSYHYFGDDRVQASNLQQV--TNAYVVIYE 208
V +H ++ GHY S +G +H F D V + QV ++AY++ YE
Sbjct: 308 VSNHSGTTMGGHYTAYCRSPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFYE 359
>pdb|2IBI|A Chain A, Covalent Ubiquitin-Usp2 Complex
Length = 374
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 37/112 (33%), Positives = 58/112 (51%), Gaps = 13/112 (11%)
Query: 109 KQFSIEKPPIVFILLLKRFNYLCL---KISCAVQVPLY-LEFGKFM-----HCRRNLVSA 159
K+FSI++ P + +L LKRF+ + K++ V PL L+ +F H NL A
Sbjct: 256 KKFSIQRFPKILVLHLKRFSESRIRTSKLTTFVNFPLRDLDLREFASENTNHAVYNLY-A 314
Query: 160 VIHHGSSSFSGHYNC-IGSTSSGSYHYFGDDRVQASNLQQV--TNAYVVIYE 208
V +H ++ GHY S +G +H F D V + QV ++AY++ YE
Sbjct: 315 VSNHSGTTMGGHYTAYCRSPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFYE 366
>pdb|3N3K|A Chain A, The Catalytic Domain Of Usp8 In Complex With A Usp8
Specific Inhibitor
Length = 396
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 37/135 (27%), Positives = 57/135 (42%), Gaps = 11/135 (8%)
Query: 65 LELSLDIYQLSSLDEALGQFFAKEYLVRDNLYQCEKCGYKTEATKQFSIEKPPIVFILLL 124
L L L +L + L F +E L +N + C C + ++ K+ I K P V ++ L
Sbjct: 238 LSLPLASTSKCTLQDCLRLFSKEEKLTDNNRFYCSHCRARRDSLKKIEIWKLPPVLLVHL 297
Query: 125 KRFNY---LCLKISCAVQVPL-------YLEFGKFMHCRRNLVSAVIHHGSSSFSGHYNC 174
KRF+Y K+ +V PL Y+ K + NL S H+G GHY
Sbjct: 298 KRFSYDGRWKQKLQTSVDFPLENLDLSQYVIGPKNNLKKYNLFSVSNHYGGLD-GGHYTA 356
Query: 175 IGSTSSGSYHYFGDD 189
++ + DD
Sbjct: 357 YCKNAARQRWFKFDD 371
Score = 28.5 bits (62), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 28 IAHHFEYYRPEDSHEFLLYLIEGIHRSYLKV 58
I F Y +DS E LL+L++G+H K
Sbjct: 143 INDQFAGYSQQDSQELLLFLMDGLHEDLNKA 173
>pdb|2GFO|A Chain A, Structure Of The Catalytic Domain Of Human Ubiquitin
Carboxyl-terminal Hydrolase 8
Length = 396
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 37/135 (27%), Positives = 57/135 (42%), Gaps = 11/135 (8%)
Query: 65 LELSLDIYQLSSLDEALGQFFAKEYLVRDNLYQCEKCGYKTEATKQFSIEKPPIVFILLL 124
L L L +L + L F +E L +N + C C + ++ K+ I K P V ++ L
Sbjct: 238 LSLPLASTSKCTLQDCLRLFSKEEKLTDNNRFYCSHCRARRDSLKKIEIWKLPPVLLVHL 297
Query: 125 KRFNY---LCLKISCAVQVPL-------YLEFGKFMHCRRNLVSAVIHHGSSSFSGHYNC 174
KRF+Y K+ +V PL Y+ K + NL S H+G GHY
Sbjct: 298 KRFSYDGRWKQKLQTSVDFPLENLDLSQYVIGPKNNLKKYNLFSVSNHYGGLD-GGHYTA 356
Query: 175 IGSTSSGSYHYFGDD 189
++ + DD
Sbjct: 357 YCKNAARQRWFKFDD 371
>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 = 37.7 bits (86), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 2/53 (3%)
Query: 141 PLYLEFGKFMHCRRNLVSAVIHHGSSSFSGHYNCI--GSTSSGSYHYFGDDRV 191
P LE G+ C NL+ + H G++S SGHY ++ F DD+V
Sbjct: 333 PPNLEKGENPSCVYNLIGVITHQGANSESGHYQAFIRDELDENKWYKFNDDKV 385
>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 = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 41/171 (23%), Positives = 64/171 (37%), Gaps = 30/171 (17%)
Query: 66 ELSLDIYQLSSLDEALGQFFAKEYLVRDNLYQCEKCGYKTEATKQFSIEKPPIVFILLLK 125
++ L I ++ E+ + A E L DN Y + G + EA K P V L L
Sbjct: 142 DIQLSIKGKKNIFESFVDYVAVEQLDGDNKYDAGEHGLQ-EAEKGVKFLTLPPVLHLQLX 200
Query: 126 RFNY-----LCLKISCAVQVPLYLEFGKFMHCRRN------LVSAVIHHGSSSFSGHYNC 174
RF Y +KI+ + P L +F+ ++ AV+ H + GHY
Sbjct: 201 RFXYDPQTDQNIKINDRFEFPEQLPLDEFLQKTDPKDPANYILHAVLVHSGDNHGGHYVV 260
Query: 175 -IGSTSSGSYHYFGDDRVQASNLQQV-----------------TNAYVVIY 207
+ G + F DD V ++ TNAY ++Y
Sbjct: 261 YLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGGHDDDLSVRHCTNAYXLVY 311
>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 = 31.6 bits (70), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 40/172 (23%), Positives = 69/172 (40%), Gaps = 32/172 (18%)
Query: 66 ELSLDIYQLSSLDEALGQFFAKEYLVRDNLYQCEKCGYKTEATKQFS-IEKPPIVFILLL 124
++ L I ++ E+ + A E L DN Y + G + EA K + PP++ + L+
Sbjct: 142 DIQLSIKGKKNIFESFVDYVAVEQLDGDNKYDAGEHGLQ-EAEKGVKFLTLPPVLHLQLM 200
Query: 125 KRFNY-----LCLKISCAVQVPLYLEFGKFMHCRRN------LVSAVIHHGSSSFSGHYN 173
RF Y +KI+ + P L +F+ ++ AV+ H + GHY
Sbjct: 201 -RFMYDPQTDQNIKINDRFEFPEQLPLDEFLQKTDPKDPANYILHAVLVHSGDNHGGHYV 259
Query: 174 C-IGSTSSGSYHYFGDDRVQASNLQQV-----------------TNAYVVIY 207
+ G + F DD V ++ TNAY+++Y
Sbjct: 260 VYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGGHDDDLSVRHCTNAYMLVY 311
>pdb|2F1Z|A Chain A, Crystal Structure Of Hausp
pdb|2F1Z|B Chain B, Crystal Structure Of Hausp
Length = 522
Score = 31.6 bits (70), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 40/172 (23%), Positives = 69/172 (40%), Gaps = 32/172 (18%)
Query: 66 ELSLDIYQLSSLDEALGQFFAKEYLVRDNLYQCEKCGYKTEATKQFS-IEKPPIVFILLL 124
++ L I ++ E+ + A E L DN Y + G + EA K + PP++ + L+
Sbjct: 311 DIQLSIKGKKNIFESFVDYVAVEQLDGDNKYDAGEHGLQ-EAEKGVKFLTLPPVLHLQLM 369
Query: 125 KRFNY-----LCLKISCAVQVPLYLEFGKFMHCRRN------LVSAVIHHGSSSFSGHYN 173
RF Y +KI+ + P L +F+ ++ AV+ H + GHY
Sbjct: 370 -RFMYDPQTDQNIKINDRFEFPEQLPLDEFLQKTDPKDPANYILHAVLVHSGDNHGGHYV 428
Query: 174 C-IGSTSSGSYHYFGDDRVQASNLQQV-----------------TNAYVVIY 207
+ G + F DD V ++ TNAY+++Y
Sbjct: 429 VYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGGHDDDLSVRHCTNAYMLVY 480
>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 = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 18/37 (48%)
Query: 155 NLVSAVIHHGSSSFSGHYNCIGSTSSGSYHYFGDDRV 191
+L + + H G SS SGHY + F DD+V
Sbjct: 329 DLQAVLTHQGRSSSSGHYVSWVKRKQDEWIKFDDDKV 365
>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
Length = 854
Score = 27.3 bits (59), Expect = 6.8, Method: Composition-based stats.
Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 1/56 (1%)
Query: 153 RRNLVSAVIHHGSSSFSGHYNCIGSTSSGSYHYFGDDRVQASNLQQVTNAYVVIYE 208
+ L + + H G+S+ GHY C G + + D +V AS Y+ Y+
Sbjct: 796 KYQLFAFISHMGTSTMCGHYVC-HIKKEGRWVIYNDQKVCASEKPPKDLGYIYFYQ 850
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
0.323 0.137 0.411
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,807,413
Number of Sequences: 62578
Number of extensions: 261637
Number of successful extensions: 433
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 400
Number of HSP's gapped (non-prelim): 36
length of query: 242
length of database: 14,973,337
effective HSP length: 96
effective length of query: 146
effective length of database: 8,965,849
effective search space: 1309013954
effective search space used: 1309013954
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 50 (23.9 bits)