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= 033936
         (108 letters)

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

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



>pdb|1X18|X Chain X, Contact Sites Of Era Gtpase On The Thermus Thermophilus
           30s Subunit
          Length = 292

 Score = 25.8 bits (55), Expect = 6.3,   Method: Compositional matrix adjust.
 Identities = 11/32 (34%), Positives = 19/32 (59%)

Query: 32  HFPSDLISIQDRKDEALQVLRSDLMATLNKEV 63
           HFP D I+ + ++  A +++R  LM  L  E+
Sbjct: 176 HFPEDYITDRSQRFMASEIIREKLMRFLGAEL 207


>pdb|1EGA|A Chain A, Crystal Structure Of A Widely Conserved Gtpase Era
 pdb|1EGA|B Chain B, Crystal Structure Of A Widely Conserved Gtpase Era
 pdb|1X1L|X Chain X, Interaction Of Era,A Gtpase Protein, With The 3'minor
           Domain Of The 16s Rrna Within The Thermus Thermophilus
           30s Subunit.
 pdb|3IEU|A Chain A, Crystal Structure Of Era In Complex With Gdp
 pdb|3IEU|B Chain B, Crystal Structure Of Era In Complex With Gdp
          Length = 301

 Score = 25.8 bits (55), Expect = 6.4,   Method: Compositional matrix adjust.
 Identities = 11/32 (34%), Positives = 19/32 (59%)

Query: 32  HFPSDLISIQDRKDEALQVLRSDLMATLNKEV 63
           HFP D I+ + ++  A +++R  LM  L  E+
Sbjct: 179 HFPEDYITDRSQRFMASEIIREKLMRFLGAEL 210


  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
   0.309    0.125    0.346 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,979,899
Number of Sequences: 62578
Number of extensions: 99799
Number of successful extensions: 191
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 189
Number of HSP's gapped (non-prelim): 3
length of query: 108
length of database: 14,973,337
effective HSP length: 72
effective length of query: 36
effective length of database: 10,467,721
effective search space: 376837956
effective search space used: 376837956
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 45 (21.9 bits)