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= 020496
         (325 letters)

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

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



>pdb|3Q1Y|A Chain A, Allosteric Regulation By Lysine Residue: A Novel
           Anion-Hole Formation In The Ribokinase Family
          Length = 320

 Score = 28.9 bits (63), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 31/118 (26%), Positives = 59/118 (50%), Gaps = 9/118 (7%)

Query: 12  LRTVTISYSELKDKNAD--LSMKIEQG---FGPNGLGILSVTDVPGFSSLRQNLLHLAPR 66
           LRTV  + + L   N+   L++ +E G     PN   ++++ D    +SL +N+  LA +
Sbjct: 156 LRTVKATGAFLGCDNSGEYLNLAVEMGVDFIKPNEDEVIAILD-EKTNSLEENIRTLAEK 214

Query: 67  LANLPEDV--KKDLEDHHSR-YNFGWSHGKEKLESGNPDMLKGSFYANPLLDVPTTET 121
           +  L   +  K  +  H+ + Y       +E+ ++G  D+  G+F A   +++P TET
Sbjct: 215 IPYLVVSLGAKGSICAHNGKLYQVIPPKVQERNDTGAGDVFVGAFIAGLAMNMPITET 272


  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
   0.320    0.136    0.422 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,170,924
Number of Sequences: 62578
Number of extensions: 437135
Number of successful extensions: 1083
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1082
Number of HSP's gapped (non-prelim): 5
length of query: 325
length of database: 14,973,337
effective HSP length: 99
effective length of query: 226
effective length of database: 8,778,115
effective search space: 1983853990
effective search space used: 1983853990
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: 51 (24.3 bits)