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= 006399
(647 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2AGA|A Chain A, De-Ubiquitinating Function Of Ataxin-3: Insights From The
Solution Structure Of The Josephin Domain
Length = 190
Score = 32.3 bits (72), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 559 PVIISDNYVPPFFEVLNWEAFSVFVQEKDIPN 590
P +ISD Y+ F L E +S+FV + D+P+
Sbjct: 145 PELISDTYLALFLAQLQQEGYSIFVVKGDLPD 176
>pdb|2JRI|A Chain A, Solution Structure Of The Josephin Domain Of Ataxin-3 In
Complex With Ubiquitin Molecule.
pdb|1YZB|A Chain A, Solution Structure Of The Josephin Domain Of Ataxin-3
Length = 182
Score = 32.3 bits (72), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 559 PVIISDNYVPPFFEVLNWEAFSVFVQEKDIPN 590
P +ISD Y+ F L E +S+FV + D+P+
Sbjct: 140 PELISDTYLALFLAQLQQEGYSIFVVKGDLPD 171
>pdb|2DOS|A Chain A, Structural Basis For The Recognition Of Lys48-Linked
Polyubiquitin Chain By The Josephin Domain Of Ataxin-3,
A Putative Deubiquitinating Enzyme
Length = 176
Score = 32.3 bits (72), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 559 PVIISDNYVPPFFEVLNWEAFSVFVQEKDIPN 590
P +ISD Y+ F L E +S+FV + D+P+
Sbjct: 145 PELISDTYLALFLAQLQQEGYSIFVVKGDLPD 176
>pdb|3RYS|A Chain A, The Crystal Structure Of Adenine Deaminase (Aaur1117) From
Arthrobacter Aurescens
pdb|3RYS|B Chain B, The Crystal Structure Of Adenine Deaminase (Aaur1117) From
Arthrobacter Aurescens
Length = 343
Score = 31.6 bits (70), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 26/117 (22%), Positives = 41/117 (35%), Gaps = 29/117 (24%)
Query: 385 LQNHQDLQNYLKTYVKTISRKYRFWNRTGGTDHFVVACHDWAPKFTGQHLRNCIKALCNA 444
LQ QD + + Y++ + GG H + A G L C+ + NA
Sbjct: 73 LQTEQDFTDMTRAYLERAA--------AGGVRHAEIMMDPQAHTSRGVALETCVNGVANA 124
Query: 445 DVSKGFKIGMDTSLPVTYIR---------------SAEAPLDNLG------GNPPLK 480
+ G+ T L ++R + AP+ +G GNPP K
Sbjct: 125 LATSEEDFGVSTLLIAAFLRDMSEDSALEVLDQLLAMHAPIAGIGLDSAEVGNPPSK 181
>pdb|3LKE|A Chain A, Crystal Structure Of Enoyl-Coa Hydratase From Bacillus
Halodurans
pdb|3LKE|B Chain B, Crystal Structure Of Enoyl-Coa Hydratase From Bacillus
Halodurans
pdb|3LKE|C Chain C, Crystal Structure Of Enoyl-Coa Hydratase From Bacillus
Halodurans
Length = 263
Score = 31.2 bits (69), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 22/35 (62%)
Query: 372 SSQMLRIALSEQKLQNHQDLQNYLKTYVKTISRKY 406
S + LR+ L ++ +N Q+LQ +K Y+K +S Y
Sbjct: 174 SEEALRLGLIQEICENKQELQERVKNYLKAVSEGY 208
>pdb|3NBU|A Chain A, Crystal Structure Of Pgi Glucosephosphate Isomerase
pdb|3NBU|B Chain B, Crystal Structure Of Pgi Glucosephosphate Isomerase
pdb|3NBU|C Chain C, Crystal Structure Of Pgi Glucosephosphate Isomerase
pdb|3NBU|D Chain D, Crystal Structure Of Pgi Glucosephosphate Isomerase
pdb|3NBU|E Chain E, Crystal Structure Of Pgi Glucosephosphate Isomerase
pdb|3NBU|F Chain F, Crystal Structure Of Pgi Glucosephosphate Isomerase
Length = 549
Score = 29.3 bits (64), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 1/55 (1%)
Query: 593 NILLSIPEERYLAMQSRVKMVQKHFLWHKKPKKYDIFHMVLHSIWYNRLFNTRTK 647
+I+LSI + ++ + S + KHF K + + L IWYN F T+
Sbjct: 280 SIVLSIGFDNFVELLSGAHAMDKHFSTTPAEKNLPVL-LALIGIWYNNFFGAETE 333
>pdb|3FHL|A Chain A, Crystal Structure Of A Putative Oxidoreductase From
Bacteroides Fragilis Nctc 9343
pdb|3FHL|B Chain B, Crystal Structure Of A Putative Oxidoreductase From
Bacteroides Fragilis Nctc 9343
pdb|3FHL|C Chain C, Crystal Structure Of A Putative Oxidoreductase From
Bacteroides Fragilis Nctc 9343
pdb|3FHL|D Chain D, Crystal Structure Of A Putative Oxidoreductase From
Bacteroides Fragilis Nctc 9343
Length = 362
Score = 29.3 bits (64), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 32/101 (31%), Positives = 46/101 (45%), Gaps = 10/101 (9%)
Query: 80 MDRGLMVGVENYPNHSFYKLKGENSFNKGVTDDKSLNMGYATSLDNSSTETEAMEIEHGK 139
++R + E YP S + SF K +T+D +++ + DN+ E M +E GK
Sbjct: 37 VERSKELSKERYPQASIVR-----SF-KELTEDPEIDLIVVNTPDNTHYEYAGMALEAGK 90
Query: 140 LEKVEK-VGSTYNFDDDPKATA---GLELGGVQNRASPGDF 176
VEK ST ++ A A GL L QNR DF
Sbjct: 91 NVVVEKPFTSTTKQGEELIALAKKKGLMLSVYQNRRWDADF 131
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
0.319 0.134 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,738,910
Number of Sequences: 62578
Number of extensions: 700171
Number of successful extensions: 1716
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1710
Number of HSP's gapped (non-prelim): 9
length of query: 647
length of database: 14,973,337
effective HSP length: 105
effective length of query: 542
effective length of database: 8,402,647
effective search space: 4554234674
effective search space used: 4554234674
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)