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= 005238
         (706 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>pdb|1VDY|A Chain A, Nmr Structure Of The Hypothetical Enth-Vhs Domain
           At3g16270 From Arabidopsis Thaliana
 pdb|2DCP|A Chain A, Fully Automated Nmr Structure Determination Of The
           Enth-Vhs Domain At3g16270 From Arabidopsis Thaliana
          Length = 140

 Score =  218 bits (555), Expect = 9e-57,   Method: Compositional matrix adjust.
 Identities = 103/128 (80%), Positives = 113/128 (88%)

Query: 11  YWRSRMIDGATSDEDKVTPVYKLEEICELLRSSHVSIGKEVSDFILKRLEHKSPVVKQKA 70
           YWRSRMID  TSDEDKV PVYKLEEIC+LLRSSHVSI KE S+FILKRL++KSP+VKQKA
Sbjct: 10  YWRSRMIDAVTSDEDKVAPVYKLEEICDLLRSSHVSIVKEFSEFILKRLDNKSPIVKQKA 69

Query: 71  LRLIKYSVGKSGTDFRREMQRHSAVVRQLFHYKGQLDPLKGDALNKAVRDMAHEAISAIF 130
           LRLIKY+VGKSG++FRREMQR+S  VR LFHYKG  DPLKGDALNKAVR+ AHE ISAIF
Sbjct: 70  LRLIKYAVGKSGSEFRREMQRNSVAVRNLFHYKGHPDPLKGDALNKAVRETAHETISAIF 129

Query: 131 SEENKPAP 138
           SEEN   P
Sbjct: 130 SEENGSGP 137


>pdb|1X5B|A Chain A, The Solution Structure Of The Vhs Domain Of Human Signal
          Transducing Adaptor Molecule 2
 pdb|2L0T|B Chain B, Solution Structure Of The Complex Of Ubiquitin And The
          Vhs Domain Of Stam2
          Length = 163

 Score = 30.4 bits (67), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 15/42 (35%), Positives = 21/42 (50%)

Query: 48 GKEVSDFILKRLEHKSPVVKQKALRLIKYSVGKSGTDFRREM 89
           K+    I+KR+ HK P V  +AL L+   V   G  F  E+
Sbjct: 50 AKDCLKAIMKRVNHKVPHVALQALTLLGACVANCGKIFHLEV 91


>pdb|4DS1|A Chain A, The Structure Of A Yeast Dyn2-Nup159 Complex And The
          Molecular Basis For The Dynein Light Chain - Nuclear
          Pore Interaction
 pdb|4DS1|C Chain C, The Structure Of A Yeast Dyn2-Nup159 Complex And The
          Molecular Basis For The Dynein Light Chain - Nuclear
          Pore Interaction
          Length = 97

 Score = 30.0 bits (66), Expect = 4.3,   Method: Composition-based stats.
 Identities = 13/35 (37%), Positives = 22/35 (62%)

Query: 19 GATSDEDKVTPVYKLEEICELLRSSHVSIGKEVSD 53
          G+ SDE+K TP+ K  +I + L+   ++I K+  D
Sbjct: 4  GSMSDENKSTPIVKASDITDKLKEDILTISKDALD 38


>pdb|3EGJ|A Chain A, N-Acetylglucosamine-6-Phosphate Deacetylase From Vibrio
           Cholerae.
 pdb|3EGJ|B Chain B, N-Acetylglucosamine-6-Phosphate Deacetylase From Vibrio
           Cholerae.
 pdb|3IV8|A Chain A, N-Acetylglucosamine-6-Phosphate Deacetylase From Vibrio
           Cholerae Complexed With Fructose 6-Phosphate
 pdb|3IV8|B Chain B, N-Acetylglucosamine-6-Phosphate Deacetylase From Vibrio
           Cholerae Complexed With Fructose 6-Phosphate
 pdb|3IV8|C Chain C, N-Acetylglucosamine-6-Phosphate Deacetylase From Vibrio
           Cholerae Complexed With Fructose 6-Phosphate
 pdb|3IV8|D Chain D, N-Acetylglucosamine-6-Phosphate Deacetylase From Vibrio
           Cholerae Complexed With Fructose 6-Phosphate
          Length = 381

 Score = 29.6 bits (65), Expect = 6.4,   Method: Compositional matrix adjust.
 Identities = 27/94 (28%), Positives = 44/94 (46%), Gaps = 20/94 (21%)

Query: 303 ALAMSRALEAK---------LQSPLWQVRMKAICVLESILRKKDDEKFSIILSYFCENND 353
           A+A +R  +AK         L+ P   V  K I  ++ I R  DD     I    C N+D
Sbjct: 110 AIAAAREYQAKYPNQSLGLHLEGPYLNVMKKGIHSVDFI-RPSDDTMIDTI----CANSD 164

Query: 354 VVVKCSESPQSSLREKANKVLSLLGEEQAGGLVS 387
           V+ K + +P+++  E   K++      +AG +VS
Sbjct: 165 VIAKVTLAPENNKPEHIEKLV------KAGIVVS 192


  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
   0.311    0.128    0.358 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,965,218
Number of Sequences: 62578
Number of extensions: 833438
Number of successful extensions: 1401
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1398
Number of HSP's gapped (non-prelim): 8
length of query: 706
length of database: 14,973,337
effective HSP length: 106
effective length of query: 600
effective length of database: 8,340,069
effective search space: 5004041400
effective search space used: 5004041400
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 55 (25.8 bits)