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= 018012
         (362 letters)

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

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



>pdb|3VOT|A Chain A, Crystal Structure Of L-Amino Acid Ligase From Bacillus
           Licheniformis
 pdb|3VOT|B Chain B, Crystal Structure Of L-Amino Acid Ligase From Bacillus
           Licheniformis
          Length = 425

 Score = 29.6 bits (65), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 26/108 (24%), Positives = 42/108 (38%), Gaps = 9/108 (8%)

Query: 79  ILATASSPAEGSDSAGEAAPVRFFDRY--PALVTGFFFFMWYFLNVIFNILNKRIYNY-- 134
           +L  A  P E S+  GE  PVR    Y  P   +G F  +     V      KR++ +  
Sbjct: 313 VLQNALKPLESSEFEGEIRPVRTAGNYIIPVQGSGTFEKIDGLEEVKQRQEVKRVFQFMR 372

Query: 135 -----FPYPYNVSFAAVAVSFTHTIKALEPFFNAAASQFILGQQLPLT 177
                 PYP+   +    ++  H+ +  E F+     +  +  Q  LT
Sbjct: 373 RGAKILPYPHFSGYPGFILTSHHSYEECEAFYRELDDELHIIYQNNLT 420


  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
   0.324    0.137    0.404 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,984,173
Number of Sequences: 62578
Number of extensions: 341584
Number of successful extensions: 777
Number of sequences better than 100.0: 1
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 777
Number of HSP's gapped (non-prelim): 1
length of query: 362
length of database: 14,973,337
effective HSP length: 100
effective length of query: 262
effective length of database: 8,715,537
effective search space: 2283470694
effective search space used: 2283470694
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: 52 (24.6 bits)