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= 043286
         (298 letters)

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

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



>pdb|3TRF|A Chain A, Structure Of A Shikimate Kinase (Arok) From Coxiella
           Burnetii
 pdb|3TRF|B Chain B, Structure Of A Shikimate Kinase (Arok) From Coxiella
           Burnetii
          Length = 185

 Score = 27.7 bits (60), Expect = 7.5,   Method: Compositional matrix adjust.
 Identities = 21/90 (23%), Positives = 48/90 (53%), Gaps = 9/90 (10%)

Query: 77  GADLQWNSGLEPKRK-RLKEQDFLENNSQISSVDFLQARPVSTGLGLSLDNTRMASSADS 135
           GAD+ W   +E +   R +E++ +E   ++ ++       ++TG G+ LD       +++
Sbjct: 45  GADIAWIFEMEGEAGFRRREREMIEALCKLDNI------ILATGGGVVLDEKNRQQISET 98

Query: 136 ALLSFIGDDIDSELQR--QDAEIDRFLKVQ 163
            ++ ++   ID++L+R  Q  E+ R L ++
Sbjct: 99  GVVIYLTASIDTQLKRIGQKGEMRRPLFIK 128


  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
   0.314    0.130    0.369 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,936,388
Number of Sequences: 62578
Number of extensions: 317965
Number of successful extensions: 615
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 602
Number of HSP's gapped (non-prelim): 30
length of query: 298
length of database: 14,973,337
effective HSP length: 98
effective length of query: 200
effective length of database: 8,840,693
effective search space: 1768138600
effective search space used: 1768138600
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (24.3 bits)