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= 013968
(433 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 = 79.7 bits (195), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 46/128 (35%), Positives = 70/128 (54%), Gaps = 12/128 (9%)
Query: 9 CKKLVSARKQMSILQSPNILVIQLKRFEGIFGG---KIDKAIAFEEVLVLSSFMCKASQD 65
C A KQ+ I + P++LV+QLKRFE + G K+D I F L + ++ +D
Sbjct: 344 CNSTQDAIKQLGIHKLPSVLVLQLKRFEHLLNGSNRKLDDFIEFPTYLNMKNYCSTKEKD 403
Query: 66 PQPE--------YKLFGTIVHSGFSPDSGHYYAYIKDAIGRWYCCNDSYVSVSTLQEVLS 117
E Y+L G + H G + + GHY A+ K + G+W+ NDS VS + +EVL
Sbjct: 404 KHSENGKVPDIIYELIGIVSHKG-TVNEGHYIAFCKISGGQWFKFNDSMVSSISQEEVLK 462
Query: 118 EKVYILFF 125
E+ Y+LF+
Sbjct: 463 EQAYLLFY 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 = 79.3 bits (194), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 46/128 (35%), Positives = 70/128 (54%), Gaps = 12/128 (9%)
Query: 9 CKKLVSARKQMSILQSPNILVIQLKRFEGIFGG---KIDKAIAFEEVLVLSSFMCKASQD 65
C A KQ+ I + P++LV+QLKRFE + G K+D I F L + ++ +D
Sbjct: 344 CNSTQDAIKQLGIHKLPSVLVLQLKRFEHLLNGSNRKLDDFIEFPTYLNMKNYCSTKEKD 403
Query: 66 PQPE--------YKLFGTIVHSGFSPDSGHYYAYIKDAIGRWYCCNDSYVSVSTLQEVLS 117
E Y+L G + H G + + GHY A+ K + G+W+ NDS VS + +EVL
Sbjct: 404 KHSENGKVPDIIYELIGIVSHKG-TVNEGHYIAFCKISGGQWFKFNDSMVSSISQEEVLK 462
Query: 118 EKVYILFF 125
E+ Y+LF+
Sbjct: 463 EQAYLLFY 470
>pdb|3M99|A Chain A, Structure Of The Ubp8-Sgf11-Sgf73-Sus1 Saga Dub Module
Length = 471
Score = 79.3 bits (194), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 46/128 (35%), Positives = 70/128 (54%), Gaps = 12/128 (9%)
Query: 9 CKKLVSARKQMSILQSPNILVIQLKRFEGIFGG---KIDKAIAFEEVLVLSSFMCKASQD 65
C A KQ+ I + P++LV+QLKRFE + G K+D I F L + ++ +D
Sbjct: 339 CNSTQDAIKQLGIHKLPSVLVLQLKRFEHLLNGSNRKLDDFIEFPTYLNMKNYCSTKEKD 398
Query: 66 PQPE--------YKLFGTIVHSGFSPDSGHYYAYIKDAIGRWYCCNDSYVSVSTLQEVLS 117
E Y+L G + H G + + GHY A+ K + G+W+ NDS VS + +EVL
Sbjct: 399 KHSENGKVPDIIYELIGIVSHKG-TVNEGHYIAFCKISGGQWFKFNDSMVSSISQEEVLK 457
Query: 118 EKVYILFF 125
E+ Y+LF+
Sbjct: 458 EQAYLLFY 465
>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 = 68.2 bits (165), Expect = 9e-12, Method: Compositional matrix adjust.
Identities = 43/124 (34%), Positives = 67/124 (54%), Gaps = 6/124 (4%)
Query: 8 SCKKLVSARKQMSILQSPNILVIQLKRF--EGIFGGKIDKAIAFE-EVLVLSSFMCKASQ 64
+CKK A K+ + P ILV+ LKRF + K+D + F L +S F+C S
Sbjct: 236 NCKKHQQATKKFDLWSLPKILVVHLKRFSYNRYWRDKLDTVVEFPIRGLNMSEFVCNLSA 295
Query: 65 DPQPEYKLFGTIVHSGFSPDSGHYYAYIKDAI-GRWYCCNDSYVSVSTLQEVLSEKVYIL 123
P Y L H G + GHY AY K+ + G+WY +DS VS+++ +++++ Y+L
Sbjct: 296 RPYV-YDLIAVSNHYG-AMGVGHYTAYAKNKLNGKWYYFDDSNVSLASEDQIVTKAAYVL 353
Query: 124 FFIR 127
F+ R
Sbjct: 354 FYQR 357
>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 = 52.0 bits (123), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 37/127 (29%), Positives = 62/127 (48%), Gaps = 7/127 (5%)
Query: 9 CKKLVSARKQMSILQSPNILVIQLKRFEGIFGGKIDKAIAFE---EVLVLSSFMCKASQD 65
C++ + K++++ + P ILV+ L RF G ++ + + L L F + +
Sbjct: 251 CRQKTRSTKKLTVQRFPRILVLHLNRFSASRGSIKKSSVGVDFPLQRLSLGDF--ASDKA 308
Query: 66 PQPEYKLFGTIVHSGFSPDSGHYYAYIKDAIGRWYCCNDSYVSVSTLQEVLSEKVYILFF 125
P Y+L+ HSG S GHY A + G W+ NDS VS + +V S + Y+LF+
Sbjct: 309 GSPVYQLYALCNHSG-SVHYGHYTALCRCQTG-WHVYNDSRVSPVSENQVASSEGYVLFY 366
Query: 126 IRANQRP 132
+ P
Sbjct: 367 QLMQEPP 373
>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 = 52.0 bits (123), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 37/127 (29%), Positives = 62/127 (48%), Gaps = 7/127 (5%)
Query: 9 CKKLVSARKQMSILQSPNILVIQLKRFEGIFGGKIDKAIAFE---EVLVLSSFMCKASQD 65
C++ + K++++ + P ILV+ L RF G ++ + + L L F + +
Sbjct: 245 CRQKTRSTKKLTVQRFPRILVLHLNRFSASRGSIKKSSVGVDFPLQRLSLGDF--ASDKA 302
Query: 66 PQPEYKLFGTIVHSGFSPDSGHYYAYIKDAIGRWYCCNDSYVSVSTLQEVLSEKVYILFF 125
P Y+L+ HSG S GHY A + G W+ NDS VS + +V S + Y+LF+
Sbjct: 303 GSPVYQLYALCNHSG-SVHYGHYTALCRCQTG-WHVYNDSRVSPVSENQVASSEGYVLFY 360
Query: 126 IRANQRP 132
+ P
Sbjct: 361 QLMQEPP 367
>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 = 51.6 bits (122), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 37/127 (29%), Positives = 62/127 (48%), Gaps = 7/127 (5%)
Query: 9 CKKLVSARKQMSILQSPNILVIQLKRFEGIFGGKIDKAIAFE---EVLVLSSFMCKASQD 65
C++ + K++++ + P ILV+ L RF G ++ + + L L F + +
Sbjct: 232 CRQKTRSTKKLTVQRFPRILVLHLNRFSASRGSIKKSSVGVDFPLQRLSLGDF--ASDKA 289
Query: 66 PQPEYKLFGTIVHSGFSPDSGHYYAYIKDAIGRWYCCNDSYVSVSTLQEVLSEKVYILFF 125
P Y+L+ HSG S GHY A + G W+ NDS VS + +V S + Y+LF+
Sbjct: 290 GSPVYQLYALCNHSG-SVHYGHYTALCRCQTG-WHVYNDSRVSPVSENQVASSEGYVLFY 347
Query: 126 IRANQRP 132
+ P
Sbjct: 348 QLMQEPP 354
>pdb|2GFO|A Chain A, Structure Of The Catalytic Domain Of Human Ubiquitin
Carboxyl-terminal Hydrolase 8
Length = 396
Score = 48.9 bits (115), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 40/121 (33%), Positives = 64/121 (52%), Gaps = 6/121 (4%)
Query: 9 CKKLVSARKQMSILQSPNILVIQLKRF--EGIFGGKIDKAIAFE-EVLVLSSFMCKASQD 65
C+ + K++ I + P +L++ LKRF +G + K+ ++ F E L LS ++ ++
Sbjct: 274 CRARRDSLKKIEIWKLPPVLLVHLKRFSYDGRWKQKLQTSVDFPLENLDLSQYVI-GPKN 332
Query: 66 PQPEYKLFGTIVHSGFSPDSGHYYAYIKDAI-GRWYCCNDSYVSVSTLQEVLSEKVYILF 124
+Y LF H G D GHY AY K+A RW+ +D VS ++ V S YILF
Sbjct: 333 NLKKYNLFSVSNHYG-GLDGGHYTAYCKNAARQRWFKFDDHEVSDISVSSVKSSAAYILF 391
Query: 125 F 125
+
Sbjct: 392 Y 392
>pdb|2IBI|A Chain A, Covalent Ubiquitin-Usp2 Complex
Length = 374
Score = 48.5 bits (114), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 37/113 (32%), Positives = 54/113 (47%), Gaps = 7/113 (6%)
Query: 17 KQMSILQSPNILVIQLKRFEG--IFGGKIDKAIAFE-EVLVLSSFMCKASQDPQPEYKLF 73
K+ SI + P ILV+ LKRF I K+ + F L L F + + Y L+
Sbjct: 256 KKFSIQRFPKILVLHLKRFSESRIRTSKLTTFVNFPLRDLDLREFASENTN--HAVYNLY 313
Query: 74 GTIVHSGFSPDSGHYYAYIKD-AIGRWYCCNDSYVSVSTLQEVLSEKVYILFF 125
HSG + GHY AY + G W+ NDS V+ + +V + Y+LF+
Sbjct: 314 AVSNHSG-TTMGGHYTAYCRSPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFY 365
>pdb|3N3K|A Chain A, The Catalytic Domain Of Usp8 In Complex With A Usp8
Specific Inhibitor
Length = 396
Score = 48.5 bits (114), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 40/121 (33%), Positives = 64/121 (52%), Gaps = 6/121 (4%)
Query: 9 CKKLVSARKQMSILQSPNILVIQLKRF--EGIFGGKIDKAIAFE-EVLVLSSFMCKASQD 65
C+ + K++ I + P +L++ LKRF +G + K+ ++ F E L LS ++ ++
Sbjct: 274 CRARRDSLKKIEIWKLPPVLLVHLKRFSYDGRWKQKLQTSVDFPLENLDLSQYVI-GPKN 332
Query: 66 PQPEYKLFGTIVHSGFSPDSGHYYAYIKDAI-GRWYCCNDSYVSVSTLQEVLSEKVYILF 124
+Y LF H G D GHY AY K+A RW+ +D VS ++ V S YILF
Sbjct: 333 NLKKYNLFSVSNHYG-GLDGGHYTAYCKNAARQRWFKFDDHEVSDISVSSVKSSAAYILF 391
Query: 125 F 125
+
Sbjct: 392 Y 392
>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 = 48.5 bits (114), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 37/113 (32%), Positives = 54/113 (47%), Gaps = 7/113 (6%)
Query: 17 KQMSILQSPNILVIQLKRFEG--IFGGKIDKAIAFE-EVLVLSSFMCKASQDPQPEYKLF 73
K+ SI + P ILV+ LKRF I K+ + F L L F + + Y L+
Sbjct: 249 KKFSIQRFPKILVLHLKRFSESRIRTSKLTTFVNFPLRDLDLREFASENTN--HAVYNLY 306
Query: 74 GTIVHSGFSPDSGHYYAYIKD-AIGRWYCCNDSYVSVSTLQEVLSEKVYILFF 125
HSG + GHY AY + G W+ NDS V+ + +V + Y+LF+
Sbjct: 307 AVSNHSG-TTMGGHYTAYCRSPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFY 358
>pdb|3NHE|A Chain A, High Resolution Structure (1.26a) Of Usp2a In Complex With
Ubiquitin
Length = 348
Score = 48.1 bits (113), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 37/113 (32%), Positives = 54/113 (47%), Gaps = 7/113 (6%)
Query: 17 KQMSILQSPNILVIQLKRFEG--IFGGKIDKAIAFE-EVLVLSSFMCKASQDPQPEYKLF 73
K+ SI + P ILV+ LKRF I K+ + F L L F + + Y L+
Sbjct: 230 KKFSIQRFPKILVLHLKRFSESRIRTSKLTTFVNFPLRDLDLREFASENTN--HAVYNLY 287
Query: 74 GTIVHSGFSPDSGHYYAYIKD-AIGRWYCCNDSYVSVSTLQEVLSEKVYILFF 125
HSG + GHY AY + G W+ NDS V+ + +V + Y+LF+
Sbjct: 288 AVSNHSG-TTMGGHYTAYCRSPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFY 339
>pdb|2HD5|A Chain A, Usp2 In Complex With Ubiquitin
Length = 359
Score = 48.1 bits (113), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 37/113 (32%), Positives = 54/113 (47%), Gaps = 7/113 (6%)
Query: 17 KQMSILQSPNILVIQLKRFEG--IFGGKIDKAIAFE-EVLVLSSFMCKASQDPQPEYKLF 73
K+ SI + P ILV+ LKRF I K+ + F L L F + + Y L+
Sbjct: 230 KKFSIQRFPKILVLHLKRFSESRIRTSKLTTFVNFPLRDLDLREFASENTN--HAVYNLY 287
Query: 74 GTIVHSGFSPDSGHYYAYIKD-AIGRWYCCNDSYVSVSTLQEVLSEKVYILFF 125
HSG + GHY AY + G W+ NDS V+ + +V + Y+LF+
Sbjct: 288 AVSNHSG-TTMGGHYTAYCRSPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFY 339
>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 = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/56 (39%), Positives = 33/56 (58%), Gaps = 2/56 (3%)
Query: 64 QDPQPEYKLFGTIVHSGFSPDSGHYYAYIKDAI--GRWYCCNDSYVSVSTLQEVLS 117
++P Y L G I H G + +SGHY A+I+D + +WY ND VSV +++ S
Sbjct: 340 ENPSCVYNLIGVITHQGANSESGHYQAFIRDELDENKWYKFNDDKVSVVEKEKIES 395
>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
Length = 854
Score = 38.1 bits (87), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 29/58 (50%), Gaps = 3/58 (5%)
Query: 70 YKLFGTIVHSGFSPDSGHYYAYIKDAIGRWYCCNDSYVSVSTLQEVLSEKVYILFFIR 127
Y+LF I H G S GHY +IK GRW ND V S ++ + YI F+ R
Sbjct: 797 YQLFAFISHMGTSTMCGHYVCHIKKE-GRWVIYNDQKVCAS--EKPPKDLGYIYFYQR 851
>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 = 37.0 bits (84), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 25/47 (53%)
Query: 70 YKLFGTIVHSGFSPDSGHYYAYIKDAIGRWYCCNDSYVSVSTLQEVL 116
Y L + H G S SGHY +++K W +D VS+ T +++L
Sbjct: 328 YDLQAVLTHQGRSSSSGHYVSWVKRKQDEWIKFDDDKVSIVTPEDIL 374
>pdb|3IFE|A Chain A, 1.55 Angstrom Resolution Crystal Structure Of Peptidase T
(Pept-1) From Bacillus Anthracis Str. 'ames Ancestor'
Length = 434
Score = 28.9 bits (63), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 13/45 (28%), Positives = 26/45 (57%), Gaps = 2/45 (4%)
Query: 366 EKVLSYMR--SRKRQCAHEVGITPGDIDLKKLLIRDAKSTFLSQI 408
E+ Y++ ++ + +H V TPG I+ KLL+ + K L+++
Sbjct: 31 ERFTRYVKIDTQSNEDSHTVPTTPGQIEFGKLLVEELKEVGLTEV 75
>pdb|2PQY|A Chain A, E. Coli Rnase 1 (in Vitro Refolded With Dsba Only)
pdb|2PQX|A Chain A, E. Coli Rnase 1 (In Vivo Folded)
pdb|2EA1|A Chain A, Crystal Structure Of Ribonuclease I From Escherichia Coli
Complexed With Guanylyl-2(Prime),5(Prime)-Guanosine
pdb|2Z70|A Chain A, E.Coli Rnase 1 In Complex With D(Cgcgatcgcg)
Length = 245
Score = 28.9 bits (63), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 29/108 (26%), Positives = 42/108 (38%), Gaps = 10/108 (9%)
Query: 196 KFSISGSSGCKGVPPTSNGKVNVHKSQSVKMNGVVK---DSVPKEKSGKD---PFINTNG 249
++ + C G P + V +Q +K + K D+ K S +D F + G
Sbjct: 127 RYEYAKHGACFGFDPDAYFGTMVRLNQEIKESEAGKFLADNYGKTVSRRDFDAAFAKSWG 186
Query: 250 SYKSKRVDLVGRGND--LASVSTSENGDTQSVGL--NPVKPDPHEGNC 293
K V L +GN L + S D + L N P PH GNC
Sbjct: 187 KENVKAVKLTCQGNPAYLTEIQISIKADAINAPLSANSFLPQPHPGNC 234
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
0.313 0.130 0.373
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,579,174
Number of Sequences: 62578
Number of extensions: 511788
Number of successful extensions: 874
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 851
Number of HSP's gapped (non-prelim): 26
length of query: 433
length of database: 14,973,337
effective HSP length: 102
effective length of query: 331
effective length of database: 8,590,381
effective search space: 2843416111
effective search space used: 2843416111
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (25.0 bits)