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= 040775
         (183 letters)

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

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



>pdb|2D4G|A Chain A, Structure Of Yjcg Protein, A Putative 2'-5' Rna Ligase
           From Bacillus Subtilis
 pdb|2D4G|B Chain B, Structure Of Yjcg Protein, A Putative 2'-5' Rna Ligase
           From Bacillus Subtilis
          Length = 171

 Score = 33.1 bits (74), Expect = 0.084,   Method: Compositional matrix adjust.
 Identities = 26/110 (23%), Positives = 48/110 (43%), Gaps = 10/110 (9%)

Query: 42  PHITL---FSSPTIEPAKLESIIKIHASKQEPLPLCLSTIGSFCNDNNVLFLAPTPSIPL 98
           PH+TL   F     +  +L S ++  A +  PL L  +   SF   NNV+++   P+  L
Sbjct: 33  PHLTLRASFECAEEKADQLVSHLRNIAKESHPLVLKXTKYSSFAPVNNVIYIKAEPTEEL 92

Query: 99  LQFQSQLCEAFKREGIECGDEFRPENWIPYCPVAQEVPKTRMAEAFCVLR 148
                +L       G+  G++    N++P+  V Q +     ++    L+
Sbjct: 93  KTLNEKLY-----TGVLAGEQ--EYNFVPHVTVGQNLSDDEHSDVLGQLK 135


  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    0.137    0.413 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,297,666
Number of Sequences: 62578
Number of extensions: 197595
Number of successful extensions: 378
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: 378
Number of HSP's gapped (non-prelim): 1
length of query: 183
length of database: 14,973,337
effective HSP length: 93
effective length of query: 90
effective length of database: 9,153,583
effective search space: 823822470
effective search space used: 823822470
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: 48 (23.1 bits)