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= 040665
         (393 letters)

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

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



>pdb|3NPK|A Chain A, The Crystal Structure Of Geranyltranstransferase From
           Campylobacter Jejuni
 pdb|3NPK|B Chain B, The Crystal Structure Of Geranyltranstransferase From
           Campylobacter Jejuni
          Length = 291

 Score = 29.3 bits (64), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 18/72 (25%), Positives = 34/72 (47%), Gaps = 6/72 (8%)

Query: 98  MCSVISKEEARVLRKEREIAKARKALEKYSSDSSDMKKLNSEDLSQISLAAKCCPSIDSS 157
           + SV+   +  +L +  ++A A + +  YS    D+   ++ D        +  P++  S
Sbjct: 47  LLSVVQSNKPELLNQALDVALALEFIHTYSLIHDDLPAXDNADFR------RGIPTLHKS 100

Query: 158 YDKTTLICEGIA 169
           YD+TT I  G A
Sbjct: 101 YDETTAILVGDA 112


  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
   0.316    0.132    0.373 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,435,262
Number of Sequences: 62578
Number of extensions: 330275
Number of successful extensions: 1010
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1008
Number of HSP's gapped (non-prelim): 7
length of query: 393
length of database: 14,973,337
effective HSP length: 101
effective length of query: 292
effective length of database: 8,652,959
effective search space: 2526664028
effective search space used: 2526664028
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)