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= psy4215
(103 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 38.5 bits (88), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 31/57 (54%), Gaps = 4/57 (7%)
Query: 30 STIGVHSGHYTAYAIHE--AQWWHFDDSTVMPVDIPALKKCKPYILFYVRRVPEVTK 84
+GV GHYTAYA ++ +W++FDDS V + Y+LFY RR E K
Sbjct: 310 GAMGV--GHYTAYAKNKLNGKWYYFDDSNVSLASEDQIVTKAAYVLFYQRRDDEFYK 364
>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 = 37.4 bits (85), Expect = 0.002, Method: Composition-based stats.
Identities = 17/42 (40%), Positives = 23/42 (54%)
Query: 34 VHSGHYTAYAIHEAQWWHFDDSTVMPVDIPALKKCKPYILFY 75
VH GHYTA + W ++DS V PV + + Y+LFY
Sbjct: 325 VHYGHYTALCRCQTGWHVYNDSRVSPVSENQVASSEGYVLFY 366
>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 = 37.4 bits (85), Expect = 0.002, Method: Composition-based stats.
Identities = 17/42 (40%), Positives = 23/42 (54%)
Query: 34 VHSGHYTAYAIHEAQWWHFDDSTVMPVDIPALKKCKPYILFY 75
VH GHYTA + W ++DS V PV + + Y+LFY
Sbjct: 319 VHYGHYTALCRCQTGWHVYNDSRVSPVSENQVASSEGYVLFY 360
>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 = 37.4 bits (85), Expect = 0.002, Method: Composition-based stats.
Identities = 18/46 (39%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 34 VHSGHYTAYA-IHEAQWWHFDDSTVMPVDIPALKKCKPYILFYVRR 78
V+ GHY A+ I QW+ F+DS V + + K + Y+LFY R
Sbjct: 428 VNEGHYIAFCKISGGQWFKFNDSMVSSISQEEVLKEQAYLLFYTIR 473
>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 = 37.4 bits (85), Expect = 0.002, Method: Composition-based stats.
Identities = 18/46 (39%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 34 VHSGHYTAYA-IHEAQWWHFDDSTVMPVDIPALKKCKPYILFYVRR 78
V+ GHY A+ I QW+ F+DS V + + K + Y+LFY R
Sbjct: 428 VNEGHYIAFCKISGGQWFKFNDSMVSSISQEEVLKEQAYLLFYTIR 473
>pdb|3M99|A Chain A, Structure Of The Ubp8-Sgf11-Sgf73-Sus1 Saga Dub Module
Length = 471
Score = 37.4 bits (85), Expect = 0.002, Method: Composition-based stats.
Identities = 18/46 (39%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 34 VHSGHYTAYA-IHEAQWWHFDDSTVMPVDIPALKKCKPYILFYVRR 78
V+ GHY A+ I QW+ F+DS V + + K + Y+LFY R
Sbjct: 423 VNEGHYIAFCKISGGQWFKFNDSMVSSISQEEVLKEQAYLLFYTIR 468
>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 = 37.4 bits (85), Expect = 0.002, Method: Composition-based stats.
Identities = 17/42 (40%), Positives = 23/42 (54%)
Query: 34 VHSGHYTAYAIHEAQWWHFDDSTVMPVDIPALKKCKPYILFY 75
VH GHYTA + W ++DS V PV + + Y+LFY
Sbjct: 306 VHYGHYTALCRCQTGWHVYNDSRVSPVSENQVASSEGYVLFY 347
>pdb|3NHE|A Chain A, High Resolution Structure (1.26a) Of Usp2a In Complex With
Ubiquitin
Length = 348
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 29/54 (53%), Gaps = 5/54 (9%)
Query: 29 ASTIGVHSGHYTAY--AIHEAQWWHFDDSTVMPVDIPALKKCKPYILFYVRRVP 80
+T+G GHYTAY + +W F+DS+V P+ ++ Y+LFY P
Sbjct: 294 GTTMG---GHYTAYCRSPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFYELASP 344
>pdb|2IBI|A Chain A, Covalent Ubiquitin-Usp2 Complex
Length = 374
Score = 35.4 bits (80), Expect = 0.009, Method: Composition-based stats.
Identities = 16/41 (39%), Positives = 24/41 (58%), Gaps = 2/41 (4%)
Query: 37 GHYTAY--AIHEAQWWHFDDSTVMPVDIPALKKCKPYILFY 75
GHYTAY + +W F+DS+V P+ ++ Y+LFY
Sbjct: 325 GHYTAYCRSPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFY 365
>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 = 35.4 bits (80), Expect = 0.009, Method: Composition-based stats.
Identities = 16/41 (39%), Positives = 24/41 (58%), Gaps = 2/41 (4%)
Query: 37 GHYTAY--AIHEAQWWHFDDSTVMPVDIPALKKCKPYILFY 75
GHYTAY + +W F+DS+V P+ ++ Y+LFY
Sbjct: 318 GHYTAYCRSPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFY 358
>pdb|2HD5|A Chain A, Usp2 In Complex With Ubiquitin
Length = 359
Score = 35.0 bits (79), Expect = 0.009, Method: Composition-based stats.
Identities = 16/41 (39%), Positives = 24/41 (58%), Gaps = 2/41 (4%)
Query: 37 GHYTAY--AIHEAQWWHFDDSTVMPVDIPALKKCKPYILFY 75
GHYTAY + +W F+DS+V P+ ++ Y+LFY
Sbjct: 299 GHYTAYCRSPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFY 339
>pdb|3N3K|A Chain A, The Catalytic Domain Of Usp8 In Complex With A Usp8
Specific Inhibitor
Length = 396
Score = 32.3 bits (72), Expect = 0.079, Method: Composition-based stats.
Identities = 19/45 (42%), Positives = 27/45 (60%), Gaps = 2/45 (4%)
Query: 33 GVHSGHYTAYAIHEAQ--WWHFDDSTVMPVDIPALKKCKPYILFY 75
G+ GHYTAY + A+ W+ FDD V + + ++K YILFY
Sbjct: 348 GLDGGHYTAYCKNAARQRWFKFDDHEVSDISVSSVKSSAAYILFY 392
>pdb|2GFO|A Chain A, Structure Of The Catalytic Domain Of Human Ubiquitin
Carboxyl-terminal Hydrolase 8
Length = 396
Score = 32.0 bits (71), Expect = 0.084, Method: Composition-based stats.
Identities = 19/45 (42%), Positives = 27/45 (60%), Gaps = 2/45 (4%)
Query: 33 GVHSGHYTAYAIHEAQ--WWHFDDSTVMPVDIPALKKCKPYILFY 75
G+ GHYTAY + A+ W+ FDD V + + ++K YILFY
Sbjct: 348 GLDGGHYTAYCKNAARQRWFKFDDHEVSDISVSSVKSSAAYILFY 392
>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 = 2.5, Method: Composition-based stats.
Identities = 22/67 (32%), Positives = 30/67 (44%), Gaps = 6/67 (8%)
Query: 12 VNDTKNKRQ-FRFDNLLKASTIGVHSGHYTAYAIHEAQWWHFDDSTVMPVDIPALKKCKP 70
V D K Q F F + + ST+ GHY + E +W ++D V + P K
Sbjct: 790 VRDGPGKYQLFAFISHMGTSTM---CGHYVCHIKKEGRWVIYNDQKVCASEKPP--KDLG 844
Query: 71 YILFYVR 77
YI FY R
Sbjct: 845 YIYFYQR 851
>pdb|1BX4|A Chain A, Structure Of Human Adenosine Kinase At 1.50 Angstroms
pdb|2I6A|A Chain A, Human Adenosine Kinase In Complex With 5'-Deoxy-5-
Iodotubercidin
pdb|2I6A|B Chain B, Human Adenosine Kinase In Complex With 5'-Deoxy-5-
Iodotubercidin
pdb|2I6A|C Chain C, Human Adenosine Kinase In Complex With 5'-Deoxy-5-
Iodotubercidin
pdb|2I6A|D Chain D, Human Adenosine Kinase In Complex With 5'-Deoxy-5-
Iodotubercidin
pdb|2I6B|A Chain A, Human Adenosine Kinase In Complex With An Acetylinic
Inhibitor
pdb|2I6B|B Chain B, Human Adenosine Kinase In Complex With An Acetylinic
Inhibitor
Length = 345
Score = 26.2 bits (56), Expect = 4.9, Method: Composition-based stats.
Identities = 12/34 (35%), Positives = 19/34 (55%)
Query: 16 KNKRQFRFDNLLKASTIGVHSGHYTAYAIHEAQW 49
++K + FD L+K + H+G T +I AQW
Sbjct: 42 EDKHKELFDELVKKFKVEYHAGGSTQNSIKVAQW 75
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
0.321 0.133 0.412
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,078,697
Number of Sequences: 62578
Number of extensions: 115654
Number of successful extensions: 247
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 230
Number of HSP's gapped (non-prelim): 16
length of query: 103
length of database: 14,973,337
effective HSP length: 68
effective length of query: 35
effective length of database: 10,718,033
effective search space: 375131155
effective search space used: 375131155
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)