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= psy18082
(280 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2IBI|A Chain A, Covalent Ubiquitin-Usp2 Complex
Length = 374
Score = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 22/50 (44%), Positives = 32/50 (64%)
Query: 134 VYELFSIMIHSGSASGGHYYAYIKNFSTDEWYCFNDQSVTRITDEDIHKS 183
VY L+++ HSG+ GGHY AY ++ T EW+ FND SVT ++ + S
Sbjct: 309 VYNLYAVSNHSGTTMGGHYTAYCRSPGTGEWHTFNDSSVTPMSSSQVRTS 358
>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 = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 22/50 (44%), Positives = 32/50 (64%)
Query: 134 VYELFSIMIHSGSASGGHYYAYIKNFSTDEWYCFNDQSVTRITDEDIHKS 183
VY L+++ HSG+ GGHY AY ++ T EW+ FND SVT ++ + S
Sbjct: 302 VYNLYAVSNHSGTTMGGHYTAYCRSPGTGEWHTFNDSSVTPMSSSQVRTS 351
>pdb|2HD5|A Chain A, Usp2 In Complex With Ubiquitin
Length = 359
Score = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 22/50 (44%), Positives = 32/50 (64%)
Query: 134 VYELFSIMIHSGSASGGHYYAYIKNFSTDEWYCFNDQSVTRITDEDIHKS 183
VY L+++ HSG+ GGHY AY ++ T EW+ FND SVT ++ + S
Sbjct: 283 VYNLYAVSNHSGTTMGGHYTAYCRSPGTGEWHTFNDSSVTPMSSSQVRTS 332
>pdb|3NHE|A Chain A, High Resolution Structure (1.26a) Of Usp2a In Complex With
Ubiquitin
Length = 348
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 22/50 (44%), Positives = 32/50 (64%)
Query: 134 VYELFSIMIHSGSASGGHYYAYIKNFSTDEWYCFNDQSVTRITDEDIHKS 183
VY L+++ HSG+ GGHY AY ++ T EW+ FND SVT ++ + S
Sbjct: 283 VYNLYAVSNHSGTTMGGHYTAYCRSPGTGEWHTFNDSSVTPMSSSQVRTS 332
>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 = 48.1 bits (113), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 29/87 (33%), Positives = 43/87 (49%), Gaps = 12/87 (13%)
Query: 116 PPSTSATKDPSMNAKGPYVYELFSIMIHSGSAS-GGHYYAYIKN-FSTDEWYCFNDQSVT 173
PP+ ++PS VY L ++ H G+ S GHY A+I++ ++WY FND V+
Sbjct: 333 PPNLEKGENPSC------VYNLIGVITHQGANSESGHYQAFIRDELDENKWYKFNDDKVS 386
Query: 174 RITDEDIHKSYGGGPARG----YYSGF 196
+ E I GGG + Y GF
Sbjct: 387 VVEKEKIESLAGGGESDSALILXYKGF 413
>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 = 48.1 bits (113), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 23/54 (42%), Positives = 35/54 (64%), Gaps = 2/54 (3%)
Query: 135 YELFSIMIHSG-SASGGHYYAYIKNFSTDEWYCFNDQSVTRITDEDIHKSYGGG 187
Y+L +++ H G S+S GHY +++K DEW F+D V+ +T EDI + GGG
Sbjct: 328 YDLQAVLTHQGRSSSSGHYVSWVKR-KQDEWIKFDDDKVSIVTPEDILRLSGGG 380
>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 = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 130 KGPYVYELFSIMIHSGSASGGHYYAYIKNFSTDEWYCFNDQSVTRITDED-IHKSYGG 186
K P Y L ++++HSG GGHY Y+ +W F+D V+R T E+ I +YGG
Sbjct: 236 KDPANYILHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGG 293
>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 = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 130 KGPYVYELFSIMIHSGSASGGHYYAYIKNFSTDEWYCFNDQSVTRITDED-IHKSYGG 186
K P Y L ++++HSG GGHY Y+ +W F+D V+R T E+ I +YGG
Sbjct: 236 KDPANYILHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGG 293
>pdb|2F1Z|A Chain A, Crystal Structure Of Hausp
pdb|2F1Z|B Chain B, Crystal Structure Of Hausp
Length = 522
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 130 KGPYVYELFSIMIHSGSASGGHYYAYIKNFSTDEWYCFNDQSVTRITDED-IHKSYGG 186
K P Y L ++++HSG GGHY Y+ +W F+D V+R T E+ I +YGG
Sbjct: 405 KDPANYILHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGG 462
>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 = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/66 (39%), Positives = 37/66 (56%), Gaps = 2/66 (3%)
Query: 118 STSATKDPSMNAKGP-YVYELFSIMIHSGSASGGHYYAYIKNFSTDEWYCFNDQSVTRIT 176
ST S N K P +YEL I+ H G+ + GHY A+ K S +W+ FND V+ I+
Sbjct: 398 STKEKDKHSENGKVPDIIYELIGIVSHKGTVNEGHYIAFCK-ISGGQWFKFNDSMVSSIS 456
Query: 177 DEDIHK 182
E++ K
Sbjct: 457 QEEVLK 462
>pdb|3M99|A Chain A, Structure Of The Ubp8-Sgf11-Sgf73-Sus1 Saga Dub Module
Length = 471
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/66 (39%), Positives = 37/66 (56%), Gaps = 2/66 (3%)
Query: 118 STSATKDPSMNAKGP-YVYELFSIMIHSGSASGGHYYAYIKNFSTDEWYCFNDQSVTRIT 176
ST S N K P +YEL I+ H G+ + GHY A+ K S +W+ FND V+ I+
Sbjct: 393 STKEKDKHSENGKVPDIIYELIGIVSHKGTVNEGHYIAFCK-ISGGQWFKFNDSMVSSIS 451
Query: 177 DEDIHK 182
E++ K
Sbjct: 452 QEEVLK 457
>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 = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/66 (39%), Positives = 37/66 (56%), Gaps = 2/66 (3%)
Query: 118 STSATKDPSMNAKGP-YVYELFSIMIHSGSASGGHYYAYIKNFSTDEWYCFNDQSVTRIT 176
ST S N K P +YEL I+ H G+ + GHY A+ K S +W+ FND V+ I+
Sbjct: 398 STKEKDKHSENGKVPDIIYELIGIVSHKGTVNEGHYIAFCK-ISGGQWFKFNDSMVSSIS 456
Query: 177 DEDIHK 182
E++ K
Sbjct: 457 QEEVLK 462
>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 = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 31/49 (63%)
Query: 132 PYVYELFSIMIHSGSASGGHYYAYIKNFSTDEWYCFNDQSVTRITDEDI 180
PYVY+L ++ H G+ GHY AY KN +WY F+D +V+ +++ I
Sbjct: 297 PYVYDLIAVSNHYGAMGVGHYTAYAKNKLNGKWYYFDDSNVSLASEDQI 345
>pdb|2GFO|A Chain A, Structure Of The Catalytic Domain Of Human Ubiquitin
Carboxyl-terminal Hydrolase 8
Length = 396
Score = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 17/36 (47%), Positives = 21/36 (58%)
Query: 135 YELFSIMIHSGSASGGHYYAYIKNFSTDEWYCFNDQ 170
Y LFS+ H G GGHY AY KN + W+ F+D
Sbjct: 337 YNLFSVSNHYGGLDGGHYTAYCKNAARQRWFKFDDH 372
>pdb|3N3K|A Chain A, The Catalytic Domain Of Usp8 In Complex With A Usp8
Specific Inhibitor
Length = 396
Score = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 17/35 (48%), Positives = 21/35 (60%)
Query: 135 YELFSIMIHSGSASGGHYYAYIKNFSTDEWYCFND 169
Y LFS+ H G GGHY AY KN + W+ F+D
Sbjct: 337 YNLFSVSNHYGGLDGGHYTAYCKNAARQRWFKFDD 371
>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 = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 38/78 (48%), Gaps = 6/78 (7%)
Query: 108 GIDISHPEPPSTSATKDPSMNAKGPYVYELFSIMIHSGSASGGHYYAYIKNFSTDEWYCF 167
G+D P + D + + G VY+L+++ HSGS GHY A + W+ +
Sbjct: 290 GVDF----PLQRLSLGDFASDKAGSPVYQLYALCNHSGSVHYGHYTALCR--CQTGWHVY 343
Query: 168 NDQSVTRITDEDIHKSYG 185
ND V+ +++ + S G
Sbjct: 344 NDSRVSPVSENQVASSEG 361
>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 = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 38/78 (48%), Gaps = 6/78 (7%)
Query: 108 GIDISHPEPPSTSATKDPSMNAKGPYVYELFSIMIHSGSASGGHYYAYIKNFSTDEWYCF 167
G+D P + D + + G VY+L+++ HSGS GHY A + W+ +
Sbjct: 284 GVDF----PLQRLSLGDFASDKAGSPVYQLYALCNHSGSVHYGHYTALCR--CQTGWHVY 337
Query: 168 NDQSVTRITDEDIHKSYG 185
ND V+ +++ + S G
Sbjct: 338 NDSRVSPVSENQVASSEG 355
>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 = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 38/78 (48%), Gaps = 6/78 (7%)
Query: 108 GIDISHPEPPSTSATKDPSMNAKGPYVYELFSIMIHSGSASGGHYYAYIKNFSTDEWYCF 167
G+D P + D + + G VY+L+++ HSGS GHY A + W+ +
Sbjct: 271 GVDF----PLQRLSLGDFASDKAGSPVYQLYALCNHSGSVHYGHYTALCR--CQTGWHVY 324
Query: 168 NDQSVTRITDEDIHKSYG 185
ND V+ +++ + S G
Sbjct: 325 NDSRVSPVSENQVASSEG 342
>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
Length = 854
Score = 37.4 bits (85), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 6/74 (8%)
Query: 104 DVDEGIDISHPEPPSTSATKDPSMNAK---GPYVYELFSIMIHSGSAS-GGHYYAYIKNF 159
D + +DIS + S ++ + K GP Y+LF+ + H G+++ GHY +IK
Sbjct: 763 DAEAAMDISEGRSAADSISESVPVGPKVRDGPGKYQLFAFISHMGTSTMCGHYVCHIKK- 821
Query: 160 STDEWYCFNDQSVT 173
W +NDQ V
Sbjct: 822 -EGRWVIYNDQKVC 834
>pdb|1IQ8|A Chain A, Crystal Structure Of Archaeosine Trna-Guanine
Transglycosylase From Pyrococcus Horikoshii
pdb|1IQ8|B Chain B, Crystal Structure Of Archaeosine Trna-Guanine
Transglycosylase From Pyrococcus Horikoshii
pdb|1IT7|A Chain A, Crystal Structure Of Archaeosine Trna-Guanine
Transglycosylase Complexed With Guanine
pdb|1IT7|B Chain B, Crystal Structure Of Archaeosine Trna-Guanine
Transglycosylase Complexed With Guanine
pdb|1IT8|A Chain A, Crystal Structure Of Archaeosine Trna-Guanine
Transglycosylase From Pyrococcus Horikoshii Complexed
With Archaeosine Precursor, Preq0
pdb|1IT8|B Chain B, Crystal Structure Of Archaeosine Trna-Guanine
Transglycosylase From Pyrococcus Horikoshii Complexed
With Archaeosine Precursor, Preq0
pdb|1J2B|A Chain A, Crystal Structure Of Archaeosine Trna-guanine
Transglycosylase Complexed With Lambda-form Trna(val)
pdb|1J2B|B Chain B, Crystal Structure Of Archaeosine Trna-guanine
Transglycosylase Complexed With Lambda-form Trna(val)
Length = 582
Score = 27.3 bits (59), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 3/63 (4%)
Query: 4 IVYKADALSSKHIKLAIHQDKVVDFSGTTSENITIEDLMGVTSVE-TNSPSSEPQYTFRL 62
I+YK + L K ++L IH +++D++G + LM S+E +N E Q+ +
Sbjct: 66 IIYKDEELRRKALELGIH--RMLDYNGIIEVDSGSFQLMKYGSIEVSNREIIEFQHRIGV 123
Query: 63 DYG 65
D G
Sbjct: 124 DIG 126
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
0.308 0.128 0.370
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,105,890
Number of Sequences: 62578
Number of extensions: 397870
Number of successful extensions: 731
Number of sequences better than 100.0: 37
Number of HSP's better than 100.0 without gapping: 18
Number of HSP's successfully gapped in prelim test: 19
Number of HSP's that attempted gapping in prelim test: 702
Number of HSP's gapped (non-prelim): 42
length of query: 280
length of database: 14,973,337
effective HSP length: 98
effective length of query: 182
effective length of database: 8,840,693
effective search space: 1609006126
effective search space used: 1609006126
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 51 (24.3 bits)