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= 039379
         (223 letters)

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

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



>pdb|2VUG|A Chain A, The Structure Of An Archaeal Homodimeric Rna Ligase
 pdb|2VUG|B Chain B, The Structure Of An Archaeal Homodimeric Rna Ligase
          Length = 389

 Score = 30.4 bits (67), Expect = 0.78,   Method: Compositional matrix adjust.
 Identities = 18/84 (21%), Positives = 38/84 (45%), Gaps = 6/84 (7%)

Query: 53  IVHPLPPVFTVNSFTVSNFTLLNSRVKGDY------ELVVSIKNPNKKASLSIDRSDDVC 106
           + + LPP +  +  +   F L   R+KG+       EL  ++  P  ++   +++ +D+ 
Sbjct: 265 VFYELPPGYFTSRISRLAFYLAEKRIKGEEFERVAKELGSALLQPFVESIFDVEQEEDIH 324

Query: 107 LMYDKSAAVIATAWMGPLCLEKMG 130
            ++      I TA+      EK+G
Sbjct: 325 ELFKVRVKRIETAYKMVTHFEKLG 348


  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
   0.321    0.135    0.411 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,405,688
Number of Sequences: 62578
Number of extensions: 174695
Number of successful extensions: 449
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: 449
Number of HSP's gapped (non-prelim): 1
length of query: 223
length of database: 14,973,337
effective HSP length: 95
effective length of query: 128
effective length of database: 9,028,427
effective search space: 1155638656
effective search space used: 1155638656
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 49 (23.5 bits)