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= psy14104
         (319 letters)

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

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



>pdb|4FU0|A Chain A, Crystal Structure Of Vang D-Ala:d-Ser Ligase From
           Enterococcus Faecalis
 pdb|4FU0|B Chain B, Crystal Structure Of Vang D-Ala:d-Ser Ligase From
           Enterococcus Faecalis
          Length = 357

 Score = 31.2 bits (69), Expect = 0.80,   Method: Compositional matrix adjust.
 Identities = 24/82 (29%), Positives = 37/82 (45%), Gaps = 7/82 (8%)

Query: 209 CLFLGISILITGEIFE------FINFVNKYPSIIYQLFLFSVLSALGQFFI-FLTVTEYG 261
           C  LGI  LI G + E      F ++  KY     ++++ + + A  +  I    VT Y 
Sbjct: 229 CAVLGIDELIVGRVDEIELSSGFFDYTEKYTLKSSKIYMPARIDAEAEKRIQEAAVTIYK 288

Query: 262 PLPCSIVTTTRKFFTVLGSIIF 283
            L CS  +    F+T  G I+F
Sbjct: 289 ALGCSGFSRVDMFYTPSGEIVF 310


  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
   0.329    0.142    0.418 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,834,366
Number of Sequences: 62578
Number of extensions: 287968
Number of successful extensions: 706
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 706
Number of HSP's gapped (non-prelim): 3
length of query: 319
length of database: 14,973,337
effective HSP length: 99
effective length of query: 220
effective length of database: 8,778,115
effective search space: 1931185300
effective search space used: 1931185300
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 51 (24.3 bits)