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= 027999
         (215 letters)

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

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



>pdb|2HCN|A Chain A, Crystal Structure Of Rna Dependent Rna Polymerase Domain
           From West Nile Virus
 pdb|2HCS|A Chain A, Crystal Structure Of Rna Dependant Rna Polymerase Domain
           Of West Nile Virus
          Length = 595

 Score = 30.0 bits (66), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 23/82 (28%), Positives = 36/82 (43%), Gaps = 12/82 (14%)

Query: 109 TEALEFAQTKLTPFGKVQKYVEKLEDFMALLAYEEPEKSPMFHLLSLEYRQHVADNLNRA 168
           T     A T  TPFG+ + + EK++      A E PE         ++Y  +   N   A
Sbjct: 28  TNVTTMAMTDTTPFGQQRVFKEKVD----TKAPEPPE--------GVKYVLNETTNWLWA 75

Query: 169 ILAHAERPRYAAMERLIQQTTA 190
            LA  +RPR  + E  I++  +
Sbjct: 76  FLAREKRPRMCSREEFIRKVNS 97


>pdb|2HFZ|A Chain A, Crystal Structure Of Rna Dependent Rna Polymerase Domain
           From West Nile Virus
          Length = 639

 Score = 29.6 bits (65), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 23/82 (28%), Positives = 36/82 (43%), Gaps = 12/82 (14%)

Query: 109 TEALEFAQTKLTPFGKVQKYVEKLEDFMALLAYEEPEKSPMFHLLSLEYRQHVADNLNRA 168
           T     A T  TPFG+ + + EK++      A E PE         ++Y  +   N   A
Sbjct: 72  TNVTTMAMTDTTPFGQQRVFKEKVD----TKAPEPPE--------GVKYVLNETTNWLWA 119

Query: 169 ILAHAERPRYAAMERLIQQTTA 190
            LA  +RPR  + E  I++  +
Sbjct: 120 FLAREKRPRMCSREEFIRKVNS 141


>pdb|3R23|A Chain A, Crystal Structure Of D-Alanine--D-Alanine Ligase From
          Bacillus Anthracis
 pdb|3R23|B Chain B, Crystal Structure Of D-Alanine--D-Alanine Ligase From
          Bacillus Anthracis
 pdb|3R5X|A Chain A, Crystal Structure Of D-Alanine--D-Alanine Ligase From
          Bacillus Anthracis Complexed With Atp
 pdb|3R5X|B Chain B, Crystal Structure Of D-Alanine--D-Alanine Ligase From
          Bacillus Anthracis Complexed With Atp
 pdb|3R5X|C Chain C, Crystal Structure Of D-Alanine--D-Alanine Ligase From
          Bacillus Anthracis Complexed With Atp
 pdb|3R5X|D Chain D, Crystal Structure Of D-Alanine--D-Alanine Ligase From
          Bacillus Anthracis Complexed With Atp
          Length = 307

 Score = 28.1 bits (61), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 14/34 (41%), Positives = 21/34 (61%)

Query: 65 LEGNALKAIELTEELAQDLLEKNKDLHFDLLSLH 98
          L+ N  + + +T     DL+EK KD+ F LL+LH
Sbjct: 31 LDKNKYEIVPITLNEKXDLIEKAKDIDFALLALH 64


  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    0.135    0.390 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,635,817
Number of Sequences: 62578
Number of extensions: 199887
Number of successful extensions: 588
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 587
Number of HSP's gapped (non-prelim): 8
length of query: 215
length of database: 14,973,337
effective HSP length: 95
effective length of query: 120
effective length of database: 9,028,427
effective search space: 1083411240
effective search space used: 1083411240
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: 49 (23.5 bits)