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= psy2824
         (242 letters)

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

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



>pdb|1VZ0|A Chain A, Chromosome Segregation Protein Spo0j From Thermus
           Thermophilus
 pdb|1VZ0|B Chain B, Chromosome Segregation Protein Spo0j From Thermus
           Thermophilus
 pdb|1VZ0|C Chain C, Chromosome Segregation Protein Spo0j From Thermus
           Thermophilus
 pdb|1VZ0|D Chain D, Chromosome Segregation Protein Spo0j From Thermus
           Thermophilus
 pdb|1VZ0|E Chain E, Chromosome Segregation Protein Spo0j From Thermus
           Thermophilus
 pdb|1VZ0|F Chain F, Chromosome Segregation Protein Spo0j From Thermus
           Thermophilus
 pdb|1VZ0|G Chain G, Chromosome Segregation Protein Spo0j From Thermus
           Thermophilus
 pdb|1VZ0|H Chain H, Chromosome Segregation Protein Spo0j From Thermus
           Thermophilus
          Length = 230

 Score = 29.3 bits (64), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 15/42 (35%), Positives = 23/42 (54%)

Query: 11  QEVARRNEQFKPTTVNKLIELEIDPGTLLAFDKNDINLGELR 52
           +EVARR  + + T  N L  L++ P  L A ++ +I  G  R
Sbjct: 138 EEVARRVGKARSTVANALRLLQLPPEALEALERGEITAGHAR 179


>pdb|3PSI|A Chain A, Crystal Structure Of The Spt6 Core Domain From
           Saccharomyces Cerevisiae, Form Spt6(239-1451)
          Length = 1219

 Score = 28.9 bits (63), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 16/51 (31%), Positives = 27/51 (52%)

Query: 180 VARNEYQRLRNIARSNKTKVPSVGVMPHESVLSSRQLREAADVAVVSTASI 230
           +AR  +  L   A     +V S+ + PH+++LSS QL  A + A V   ++
Sbjct: 648 LARYMHSPLLEYANLTSEEVRSLSIHPHQNLLSSEQLSWALETAFVDIVNL 698


>pdb|3PSF|A Chain A, Crystal Structure Of The Spt6 Core Domain From
           Saccharomyces Cerevisiae, Form Spt6(236-1259)
          Length = 1030

 Score = 28.9 bits (63), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 16/51 (31%), Positives = 27/51 (52%)

Query: 180 VARNEYQRLRNIARSNKTKVPSVGVMPHESVLSSRQLREAADVAVVSTASI 230
           +AR  +  L   A     +V S+ + PH+++LSS QL  A + A V   ++
Sbjct: 651 LARYMHSPLLEYANLTSEEVRSLSIHPHQNLLSSEQLSWALETAFVDIVNL 701


  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    0.132    0.382 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,875,557
Number of Sequences: 62578
Number of extensions: 267999
Number of successful extensions: 487
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 484
Number of HSP's gapped (non-prelim): 4
length of query: 242
length of database: 14,973,337
effective HSP length: 96
effective length of query: 146
effective length of database: 8,965,849
effective search space: 1309013954
effective search space used: 1309013954
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: 50 (23.9 bits)