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= psy6250
         (778 letters)

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

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



>pdb|2NVJ|A Chain A, Nmr Structures Of Transmembrane Segment From Subunit A
           From The Yeast Proton V-Atpase
          Length = 25

 Score = 46.2 bits (108), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 20/25 (80%), Positives = 23/25 (92%)

Query: 691 EYVLSTISHTASYLRLWALSLAHAQ 715
           E+ L+ +SHTASYLRLWALSLAHAQ
Sbjct: 1   EFCLNCVSHTASYLRLWALSLAHAQ 25


>pdb|2JTW|A Chain A, Solution Structure Of Tm7 Bound To Dpc Micelles
 pdb|2RPW|X Chain X, Structure Of A Peptide Derived From H+-V-Atpase Subunit A
          Length = 25

 Score = 43.9 bits (102), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 20/20 (100%), Positives = 20/20 (100%)

Query: 698 SHTASYLRLWALSLAHAQLS 717
           SHTASYLRLWALSLAHAQLS
Sbjct: 3   SHTASYLRLWALSLAHAQLS 22


>pdb|3H0G|B Chain B, Rna Polymerase Ii From Schizosaccharomyces Pombe
 pdb|3H0G|N Chain N, Rna Polymerase Ii From Schizosaccharomyces Pombe
          Length = 1210

 Score = 32.0 bits (71), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 20/60 (33%), Positives = 28/60 (46%), Gaps = 1/60 (1%)

Query: 456 MIFGVTLSVIN-HVHFRKPVNILLEFLPQLIFLVLLFGYMVTLMFMKWIMYAPQNPLLTS 514
           MI G+  S+I    H + P N     + +    V L  Y V +  M  I+Y PQ PL T+
Sbjct: 736 MILGILASIIPFPDHNQSPRNTYQSAMGKQAMGVYLTNYQVRMDTMANILYYPQKPLATT 795


  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
   0.326    0.140    0.428 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,094,073
Number of Sequences: 62578
Number of extensions: 896502
Number of successful extensions: 2004
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 2002
Number of HSP's gapped (non-prelim): 3
length of query: 778
length of database: 14,973,337
effective HSP length: 106
effective length of query: 672
effective length of database: 8,340,069
effective search space: 5604526368
effective search space used: 5604526368
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 55 (25.8 bits)