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= 040695
         (169 letters)

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

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



>pdb|3VQT|A Chain A, Crystal Structure Analysis Of The Translation Factor Rf3
 pdb|3VQT|B Chain B, Crystal Structure Analysis Of The Translation Factor Rf3
 pdb|3VQT|C Chain C, Crystal Structure Analysis Of The Translation Factor Rf3
 pdb|3VQT|D Chain D, Crystal Structure Analysis Of The Translation Factor Rf3
 pdb|3VR1|A Chain A, Crystal Structure Analysis Of The Translation Factor Rf3
 pdb|3VR1|B Chain B, Crystal Structure Analysis Of The Translation Factor Rf3
 pdb|3VR1|C Chain C, Crystal Structure Analysis Of The Translation Factor Rf3
 pdb|3VR1|D Chain D, Crystal Structure Analysis Of The Translation Factor Rf3
          Length = 548

 Score = 28.1 bits (61), Expect = 2.6,   Method: Composition-based stats.
 Identities = 21/61 (34%), Positives = 26/61 (42%), Gaps = 6/61 (9%)

Query: 66  HTAIFPYPYDYRNAEDSSLGHGGNLRVYLEGLADAENVQEYVRQNPFGQEAITERNPSWG 125
           HTA + Y  D +   D    H G L V      DAE    Y+  NP+  E+  ER P   
Sbjct: 487 HTARWVYCEDKKIFADFQDYHRGELAV------DAEGALAYLAPNPWRLESAMERYPKVE 540

Query: 126 F 126
           F
Sbjct: 541 F 541


>pdb|2G5D|A Chain A, Crystal Structure Of Mlta From Neisseria Gonorrhoeae
           Monoclinic Form
          Length = 422

 Score = 26.9 bits (58), Expect = 5.7,   Method: Compositional matrix adjust.
 Identities = 13/47 (27%), Positives = 25/47 (53%), Gaps = 1/47 (2%)

Query: 93  YLE-GLADAENVQEYVRQNPFGQEAITERNPSWGFYSKIFSTKSQPP 138
           YL+ G    + ++ Y+RQNP     +  +NPS+ F+ ++  +    P
Sbjct: 280 YLKLGQTSMQGIKAYMRQNPQRLAEVLGQNPSYIFFRELAGSGGDGP 326


  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    0.129    0.390 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,120,086
Number of Sequences: 62578
Number of extensions: 199289
Number of successful extensions: 205
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: 203
Number of HSP's gapped (non-prelim): 3
length of query: 169
length of database: 14,973,337
effective HSP length: 92
effective length of query: 77
effective length of database: 9,216,161
effective search space: 709644397
effective search space used: 709644397
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: 48 (23.1 bits)