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= 020441
         (326 letters)

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

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



>pdb|3C8T|A Chain A, Crystal Structure Of Fumarate Lyase From Mesorhizobium Sp.
           Bnc1
          Length = 451

 Score = 28.9 bits (63), Expect = 4.2,   Method: Compositional matrix adjust.
 Identities = 38/130 (29%), Positives = 57/130 (43%), Gaps = 30/130 (23%)

Query: 124 SLSKSITTLLADVRMLLIIPLFAYSGLQQAF---------VW-AEFTK-----EIVTPAL 168
           S+ K++  L  + R     P+   + LQ A          VW + F +     E ++P +
Sbjct: 129 SVRKALAALARNHR---DTPMAGRTHLQHALPVTFGYKAAVWLSAFDRHAARLEEISPRV 185

Query: 169 GV---SGVGGAMAVYGA--FDAICSLAAGRLTTGLPSITFIVSGGAIAQVVVFLWILINY 223
            V   SG  G +A  G    D    LA   L  G+PSIT+  +  A+A+ V FL      
Sbjct: 186 LVVEFSGASGTLASLGTRGLDVQRELAR-ELNLGVPSITWHSARDAVAETVQFL------ 238

Query: 224 SVTSGVLGTL 233
           ++ SG LG L
Sbjct: 239 ALVSGSLGKL 248


  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
   0.326    0.140    0.414 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,851,074
Number of Sequences: 62578
Number of extensions: 342913
Number of successful extensions: 949
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 937
Number of HSP's gapped (non-prelim): 28
length of query: 326
length of database: 14,973,337
effective HSP length: 99
effective length of query: 227
effective length of database: 8,778,115
effective search space: 1992632105
effective search space used: 1992632105
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (24.3 bits)