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= 008317
         (570 letters)

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

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



>pdb|3OCC|A Chain A, Crystal Structure Of Pnp With Dadmeimmh From Yersinia
           Pseudotuberculosis
 pdb|3OCC|B Chain B, Crystal Structure Of Pnp With Dadmeimmh From Yersinia
           Pseudotuberculosis
 pdb|3OCC|C Chain C, Crystal Structure Of Pnp With Dadmeimmh From Yersinia
           Pseudotuberculosis
 pdb|3OCC|D Chain D, Crystal Structure Of Pnp With Dadmeimmh From Yersinia
           Pseudotuberculosis
 pdb|3OCC|E Chain E, Crystal Structure Of Pnp With Dadmeimmh From Yersinia
           Pseudotuberculosis
 pdb|3OCC|F Chain F, Crystal Structure Of Pnp With Dadmeimmh From Yersinia
           Pseudotuberculosis
          Length = 239

 Score = 31.6 bits (70), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 17/59 (28%), Positives = 26/59 (44%)

Query: 410 VYVAAGKIYKAEKYVAPLRQMFPRLETKDTLATPEELAAFKGHSSRLAALDYTVCLHSE 468
           V V  G ++ A+ +  P  QMF  +E    L    E A   G ++   A   T+C  S+
Sbjct: 147 VNVRVGNLFSADLFYTPDPQMFDVMEKYGILGVEMEAAGIYGVAAEFGAKALTICTVSD 205


>pdb|2ZAM|A Chain A, Crystal Structure Of Mouse Skd1VPS4B APO-Form
 pdb|2ZAN|A Chain A, Crystal Structure Of Mouse Skd1VPS4B ATP-Form
 pdb|2ZAO|A Chain A, Crystal Structure Of Mouse Skd1VPS4B ADP-Form
          Length = 444

 Score = 30.4 bits (67), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 12/32 (37%), Positives = 21/32 (65%), Gaps = 6/32 (18%)

Query: 492 GHAKTIKPDKRKL------ALLFDRPNIRWDD 517
           G A++  P+K+KL      A++ +RPN++W D
Sbjct: 104 GEAESDDPEKKKLQNQLQGAIVIERPNVKWSD 135


  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    0.136    0.411 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,357,014
Number of Sequences: 62578
Number of extensions: 665128
Number of successful extensions: 1289
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1288
Number of HSP's gapped (non-prelim): 2
length of query: 570
length of database: 14,973,337
effective HSP length: 104
effective length of query: 466
effective length of database: 8,465,225
effective search space: 3944794850
effective search space used: 3944794850
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: 54 (25.4 bits)