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= psy7177
(66 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 = 46.6 bits (109), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 20/43 (46%), Positives = 25/43 (58%)
Query: 11 AGHYTAYTLHPNTKEWHYFNDETVLEQRPQDEDFNNAYILFYK 53
GHYTAY P T EWH FND +V ++AY+LFY+
Sbjct: 324 GGHYTAYCRSPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFYE 366
>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 = 4e-06, Method: Compositional matrix adjust.
Identities = 21/48 (43%), Positives = 26/48 (54%)
Query: 6 SKGVSAGHYTAYTLHPNTKEWHYFNDETVLEQRPQDEDFNNAYILFYK 53
S GHYTAY P T EWH FND +V ++AY+LFY+
Sbjct: 312 SGTTMGGHYTAYCRSPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFYE 359
>pdb|2HD5|A Chain A, Usp2 In Complex With Ubiquitin
Length = 359
Score = 46.2 bits (108), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 21/48 (43%), Positives = 26/48 (54%)
Query: 6 SKGVSAGHYTAYTLHPNTKEWHYFNDETVLEQRPQDEDFNNAYILFYK 53
S GHYTAY P T EWH FND +V ++AY+LFY+
Sbjct: 293 SGTTMGGHYTAYCRSPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFYE 340
>pdb|3NHE|A Chain A, High Resolution Structure (1.26a) Of Usp2a In Complex With
Ubiquitin
Length = 348
Score = 46.2 bits (108), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 21/48 (43%), Positives = 26/48 (54%)
Query: 6 SKGVSAGHYTAYTLHPNTKEWHYFNDETVLEQRPQDEDFNNAYILFYK 53
S GHYTAY P T EWH FND +V ++AY+LFY+
Sbjct: 293 SGTTMGGHYTAYCRSPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFYE 340
>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 = 40.4 bits (93), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 28/51 (54%)
Query: 8 GVSAGHYTAYTLHPNTKEWHYFNDETVLEQRPQDEDFNNAYILFYKKRDED 58
+ GHYTAY + +W+YF+D V AY+LFY++RD++
Sbjct: 311 AMGVGHYTAYAKNKLNGKWYYFDDSNVSLASEDQIVTKAAYVLFYQRRDDE 361
>pdb|3N3K|A Chain A, The Catalytic Domain Of Usp8 In Complex With A Usp8
Specific Inhibitor
Length = 396
Score = 33.5 bits (75), Expect = 0.030, Method: Composition-based stats.
Identities = 17/45 (37%), Positives = 23/45 (51%)
Query: 8 GVSAGHYTAYTLHPNTKEWHYFNDETVLEQRPQDEDFNNAYILFY 52
G+ GHYTAY + + W F+D V + + AYILFY
Sbjct: 348 GLDGGHYTAYCKNAARQRWFKFDDHEVSDISVSSVKSSAAYILFY 392
>pdb|2GFO|A Chain A, Structure Of The Catalytic Domain Of Human Ubiquitin
Carboxyl-terminal Hydrolase 8
Length = 396
Score = 33.5 bits (75), Expect = 0.032, Method: Composition-based stats.
Identities = 17/45 (37%), Positives = 23/45 (51%)
Query: 8 GVSAGHYTAYTLHPNTKEWHYFNDETVLEQRPQDEDFNNAYILFY 52
G+ GHYTAY + + W F+D V + + AYILFY
Sbjct: 348 GLDGGHYTAYCKNAARQRWFKFDDHEVSDISVSSVKSSAAYILFY 392
>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 = 28.9 bits (63), Expect = 0.75, Method: Composition-based stats.
Identities = 18/52 (34%), Positives = 22/52 (42%), Gaps = 2/52 (3%)
Query: 6 SKGVSAGHYTAYTLHPNTKEWHYFNDETVLEQRPQDEDFNNAYILFYKKRDE 57
S V GHYTA L WH +ND V + Y+LFY+ E
Sbjct: 322 SGSVHYGHYTA--LCRCQTGWHVYNDSRVSPVSENQVASSEGYVLFYQLMQE 371
>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 = 28.9 bits (63), Expect = 0.80, Method: Composition-based stats.
Identities = 18/52 (34%), Positives = 22/52 (42%), Gaps = 2/52 (3%)
Query: 6 SKGVSAGHYTAYTLHPNTKEWHYFNDETVLEQRPQDEDFNNAYILFYKKRDE 57
S V GHYTA L WH +ND V + Y+LFY+ E
Sbjct: 316 SGSVHYGHYTA--LCRCQTGWHVYNDSRVSPVSENQVASSEGYVLFYQLMQE 365
>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 = 28.9 bits (63), Expect = 0.83, Method: Composition-based stats.
Identities = 18/52 (34%), Positives = 22/52 (42%), Gaps = 2/52 (3%)
Query: 6 SKGVSAGHYTAYTLHPNTKEWHYFNDETVLEQRPQDEDFNNAYILFYKKRDE 57
S V GHYTA L WH +ND V + Y+LFY+ E
Sbjct: 303 SGSVHYGHYTA--LCRCQTGWHVYNDSRVSPVSENQVASSEGYVLFYQLMQE 352
>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 = 28.5 bits (62), Expect = 1.0, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 1/47 (2%)
Query: 9 VSAGHYTAYTLHPNTKEWHYFNDETVLEQRPQDEDFNNAYILFYKKR 55
V+ GHY A+ + +W FND V ++ AY+LFY R
Sbjct: 428 VNEGHYIAFC-KISGGQWFKFNDSMVSSISQEEVLKEQAYLLFYTIR 473
>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 = 28.5 bits (62), Expect = 1.1, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 1/47 (2%)
Query: 9 VSAGHYTAYTLHPNTKEWHYFNDETVLEQRPQDEDFNNAYILFYKKR 55
V+ GHY A+ + +W FND V ++ AY+LFY R
Sbjct: 428 VNEGHYIAFC-KISGGQWFKFNDSMVSSISQEEVLKEQAYLLFYTIR 473
>pdb|3M99|A Chain A, Structure Of The Ubp8-Sgf11-Sgf73-Sus1 Saga Dub Module
Length = 471
Score = 28.5 bits (62), Expect = 1.1, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 1/47 (2%)
Query: 9 VSAGHYTAYTLHPNTKEWHYFNDETVLEQRPQDEDFNNAYILFYKKR 55
V+ GHY A+ + +W FND V ++ AY+LFY R
Sbjct: 423 VNEGHYIAFC-KISGGQWFKFNDSMVSSISQEEVLKEQAYLLFYTIR 468
>pdb|2O1W|A Chain A, Structure Of N-Terminal Plus Middle Domains (N+m) Of Grp94
pdb|2O1W|B Chain B, Structure Of N-Terminal Plus Middle Domains (N+m) Of Grp94
pdb|2O1W|C Chain C, Structure Of N-Terminal Plus Middle Domains (N+m) Of Grp94
pdb|2O1W|D Chain D, Structure Of N-Terminal Plus Middle Domains (N+m) Of Grp94
pdb|2O1W|E Chain E, Structure Of N-Terminal Plus Middle Domains (N+m) Of Grp94
Length = 506
Score = 26.2 bits (56), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 19/36 (52%)
Query: 25 EWHYFNDETVLEQRPQDEDFNNAYILFYKKRDEDSD 60
+W ND + QRP E ++ Y FYK ++SD
Sbjct: 244 DWELMNDIKPIWQRPSKEVEDDEYKAFYKSFSKESD 279
>pdb|2O1U|A Chain A, Structure Of Full Length Grp94 With Amp-Pnp Bound
pdb|2O1U|B Chain B, Structure Of Full Length Grp94 With Amp-Pnp Bound
pdb|2O1V|A Chain A, Structure Of Full Length Grp94 With Adp Bound
pdb|2O1V|B Chain B, Structure Of Full Length Grp94 With Adp Bound
Length = 666
Score = 26.2 bits (56), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 19/36 (52%)
Query: 25 EWHYFNDETVLEQRPQDEDFNNAYILFYKKRDEDSD 60
+W ND + QRP E ++ Y FYK ++SD
Sbjct: 244 DWELMNDIKPIWQRPSKEVEDDEYKAFYKSFSKESD 279
>pdb|2JH1|A Chain A, Crystal Structure Of Toxoplasma Gondii Micronemal
Protein 1
Length = 246
Score = 25.8 bits (55), Expect = 7.0, Method: Composition-based stats.
Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 2/45 (4%)
Query: 1 MCVRPSKGVSAGHYTAYTLHPNTKEWHYFNDETVLEQRPQDEDFN 45
MCV PS + A + T H NT +W F+ ++LE ++ N
Sbjct: 44 MCV-PSSRIVARNAVGIT-HQNTLQWRCFDTASLLESNQENNGVN 86
>pdb|2V6U|A Chain A, High Resolution Crystal Structure Of Pterin-4a-
Carbinolamine Dehydratase From Toxoplasma Gondii
pdb|2V6U|B Chain B, High Resolution Crystal Structure Of Pterin-4a-
Carbinolamine Dehydratase From Toxoplasma Gondii
Length = 104
Score = 25.0 bits (53), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 11/46 (23%), Positives = 21/46 (45%)
Query: 3 VRPSKGVSAGHYTAYTLHPNTKEWHYFNDETVLEQRPQDEDFNNAY 48
+ P ++A LH +WH + ++++ Q DFN A+
Sbjct: 1 MAPLARLAANSARLLQLHKTVPQWHLTDGHLSIKRKFQFSDFNEAW 46
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
0.315 0.133 0.415
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,352,870
Number of Sequences: 62578
Number of extensions: 84791
Number of successful extensions: 155
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 139
Number of HSP's gapped (non-prelim): 19
length of query: 66
length of database: 14,973,337
effective HSP length: 37
effective length of query: 29
effective length of database: 12,657,951
effective search space: 367080579
effective search space used: 367080579
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 45 (21.9 bits)