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= 005559
         (691 letters)

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

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



>pdb|2XZM|R Chain R, Crystal Structure Of The Eukaryotic 40s Ribosomal Subunit
           In Complex With Initiation Factor 1. This File Contains
           The 40s Subunit And Initiation Factor For Molecule 1
 pdb|2XZN|R Chain R, Crystal Structure Of The Eukaryotic 40s Ribosomal Subunit
           In Complex With Initiation Factor 1. This File Contains
           The 40s Subunit And Initiation Factor For Molecule 2
          Length = 343

 Score = 33.1 bits (74), Expect = 0.47,   Method: Compositional matrix adjust.
 Identities = 27/73 (36%), Positives = 35/73 (47%), Gaps = 8/73 (10%)

Query: 224 VSPNGNFVACFTHDGRLVVNNTNFSSPVIDESCES-----ALPP--EQIAWCGMDSVLLY 276
           V P   + A    DGRL V NTNF      ++ ES     ++ P  + IA  G D  LL 
Sbjct: 180 VQPFAPYFASVGWDGRLKVWNTNFQIRYTFKAHESNVNHLSISPNGKYIATGGKDKKLLI 239

Query: 277 WNDMLVMVAPQAE 289
           W D+L +  PQ E
Sbjct: 240 W-DILNLTYPQRE 251


>pdb|4F3Y|A Chain A, X-Ray Crystal Structure Of Dihydrodipicolinate Reductase
           From Burkholderia Thailandensis
 pdb|4F3Y|B Chain B, X-Ray Crystal Structure Of Dihydrodipicolinate Reductase
           From Burkholderia Thailandensis
          Length = 272

 Score = 30.8 bits (68), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 23/82 (28%), Positives = 35/82 (42%), Gaps = 18/82 (21%)

Query: 185 PKYTMTGSVEVL----IGTDAGILMLDEDGVQKVDDTLSQKMAVS---------PNGNFV 231
           P  T+ G+++      +G DAG  +  + GV   DD   +++            P G  V
Sbjct: 31  PDATLVGALDRTGSPQLGQDAGAFLGKQTGVALTDDI--ERVCAEADYLIDFTLPEGTLV 88

Query: 232 ---ACFTHDGRLVVNNTNFSSP 250
              A   HD +LV+  T FS P
Sbjct: 89  HLDAALRHDVKLVIGTTGFSEP 110


  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    0.407 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,212,934
Number of Sequences: 62578
Number of extensions: 749426
Number of successful extensions: 1594
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1593
Number of HSP's gapped (non-prelim): 3
length of query: 691
length of database: 14,973,337
effective HSP length: 106
effective length of query: 585
effective length of database: 8,340,069
effective search space: 4878940365
effective search space used: 4878940365
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: 55 (25.8 bits)