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= psy5478
         (1009 letters)

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

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



>pdb|4EZB|A Chain A, Crystal Structure Of The Conserved Hypothetical Protein
           From Sinorhizobium Meliloti 1021
          Length = 317

 Score = 30.4 bits (67), Expect = 4.7,   Method: Composition-based stats.
 Identities = 21/51 (41%), Positives = 28/51 (54%), Gaps = 4/51 (7%)

Query: 35  HLS--ATFEIFLNSCGMSSSANHAVGGVTTPSGSYVENTIIIQYDPYVQEV 83
           HLS  A F I LNS G  + A  A G + T  GS+VE  +  +  PY ++V
Sbjct: 110 HLSDEAVF-IDLNSVGPDTKA-LAAGAIATGKGSFVEGAVXARVPPYAEKV 158



 Score = 30.4 bits (67), Expect = 4.7,   Method: Composition-based stats.
 Identities = 21/51 (41%), Positives = 28/51 (54%), Gaps = 4/51 (7%)

Query: 530 HLS--ATFEIFLNSCGMSSSANHAVGGVTTPSGSYVENTIIIQYDPYVQEV 578
           HLS  A F I LNS G  + A  A G + T  GS+VE  +  +  PY ++V
Sbjct: 110 HLSDEAVF-IDLNSVGPDTKA-LAAGAIATGKGSFVEGAVXARVPPYAEKV 158


  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    0.136    0.423 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 28,489,077
Number of Sequences: 62578
Number of extensions: 1090375
Number of successful extensions: 2393
Number of sequences better than 100.0: 1
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 2392
Number of HSP's gapped (non-prelim): 2
length of query: 1009
length of database: 14,973,337
effective HSP length: 108
effective length of query: 901
effective length of database: 8,214,913
effective search space: 7401636613
effective search space used: 7401636613
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: 56 (26.2 bits)