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= psy5086
         (124 letters)

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

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



>pdb|3AGP|A Chain A, Structure Of Viral Polymerase Form I
 pdb|3AGQ|A Chain A, Structure Of Viral Polymerase Form Ii
 pdb|3AVT|A Chain A, Structure Of Viral Rna Polymerase Complex 1
 pdb|3AVU|A Chain A, Structure Of Viral Rna Polymerase Complex 2
 pdb|3AVV|A Chain A, Structure Of Viral Rna Polymerase Complex 3
 pdb|3AVW|A Chain A, Structure Of Viral Rna Polymerase Complex 4
 pdb|3AVX|A Chain A, Structure Of Viral Rna Polymerase Complex 5
 pdb|3AVY|A Chain A, Structure Of Viral Rna Polymerase Complex 6
 pdb|3VNU|A Chain A, Complex Structure Of Viral Rna Polymerase I
 pdb|3VNV|A Chain A, Complex Structure Of Viral Rna Polymerase Ii
 pdb|4FWT|A Chain A, Complex Structure Of Viral Rna Polymerase Form Iii
          Length = 1289

 Score = 30.8 bits (68), Expect = 0.20,   Method: Composition-based stats.
 Identities = 15/27 (55%), Positives = 17/27 (62%)

Query: 84   RSRPRKISSPTGSKDLQMVNISLRVLA 110
            RS P KIS  TG  D+Q +  S RVLA
Sbjct: 1241 RSNPTKISRSTGKFDIQYIACSSRVLA 1267


>pdb|3MMP|G Chain G, Structure Of The Qb Replicase, An Rna-Dependent Rna
           Polymerase Consisting Of Viral And Host Proteins
 pdb|3MMP|F Chain F, Structure Of The Qb Replicase, An Rna-Dependent Rna
           Polymerase Consisting Of Viral And Host Proteins
          Length = 589

 Score = 30.4 bits (67), Expect = 0.26,   Method: Composition-based stats.
 Identities = 15/27 (55%), Positives = 17/27 (62%)

Query: 84  RSRPRKISSPTGSKDLQMVNISLRVLA 110
           RS P KIS  TG  D+Q +  S RVLA
Sbjct: 547 RSNPTKISRSTGKFDIQYIACSSRVLA 573


>pdb|4E8C|A Chain A, Crystal Structure Of Streptococcal Beta-Galactosidase In
           Complex With Galactose
 pdb|4E8C|B Chain B, Crystal Structure Of Streptococcal Beta-Galactosidase In
           Complex With Galactose
 pdb|4E8D|A Chain A, Crystal Structure Of Streptococcal Beta-Galactosidase
 pdb|4E8D|B Chain B, Crystal Structure Of Streptococcal Beta-Galactosidase
          Length = 595

 Score = 29.3 bits (64), Expect = 0.56,   Method: Composition-based stats.
 Identities = 18/57 (31%), Positives = 28/57 (49%), Gaps = 4/57 (7%)

Query: 39  QSMFTVEGGHRAIMFSRIGGVQNNVFAEGLHFRLPWFQYPIIYDIRSRPRKISSPTG 95
           ++M  V  GH+ +  ++  G++  V  + LHF L W  YP+  D    P KI    G
Sbjct: 448 ENMGRVNYGHKFLADTQRKGIRTGV-CKDLHFLLNWKHYPLPLD---NPEKIDFSKG 500


>pdb|2ZT9|B Chain B, Crystal Structure Of The Cytochrome B6f Complex From
          Nostoc Sp. Pcc 7120
 pdb|4H44|B Chain B, 2.70 A Cytochrome B6f Complex Structure From Nostoc Pcc
          7120
          Length = 160

 Score = 28.1 bits (61), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 13/41 (31%), Positives = 20/41 (48%)

Query: 50 AIMFSRIGGVQNNVFAEGLHFRLPWFQYPIIYDIRSRPRKI 90
          A++   + G   N FA  L     W+ YP+   +RS P K+
Sbjct: 55 AVLDPAMTGEPANPFATPLEILPEWYLYPVFQILRSLPNKL 95


>pdb|1VF5|B Chain B, Crystal Structure Of Cytochrome B6f Complex From
          M.Laminosus
 pdb|1VF5|O Chain O, Crystal Structure Of Cytochrome B6f Complex From
          M.Laminosus
 pdb|2D2C|B Chain B, Crystal Structure Of Cytochrome B6f Complex With Dbmib
          From M. Laminosus
 pdb|2D2C|O Chain O, Crystal Structure Of Cytochrome B6f Complex With Dbmib
          From M. Laminosus
          Length = 160

 Score = 26.6 bits (57), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 12/33 (36%), Positives = 16/33 (48%)

Query: 58 GVQNNVFAEGLHFRLPWFQYPIIYDIRSRPRKI 90
          G   N FA  L     W+ YP+   +RS P K+
Sbjct: 63 GEPANPFATPLEILPEWYLYPVFQILRSLPNKL 95


  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    0.139    0.421 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,660,957
Number of Sequences: 62578
Number of extensions: 81221
Number of successful extensions: 138
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 134
Number of HSP's gapped (non-prelim): 5
length of query: 124
length of database: 14,973,337
effective HSP length: 85
effective length of query: 39
effective length of database: 9,654,207
effective search space: 376514073
effective search space used: 376514073
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 45 (21.9 bits)