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= psy3598
         (175 letters)

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

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



>pdb|4IIL|A Chain A, Crystal Structure Of Rfua (tp0298) Of T. Pallidum Bound To
           Riboflavin
          Length = 346

 Score = 28.9 bits (63), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 17/54 (31%), Positives = 29/54 (53%), Gaps = 6/54 (11%)

Query: 36  EKAATQKRDLARALNKFIIKTEPIEHIFDE------ADDRFTLIVPKPEMLPYL 83
           E+A TQ+R   R++   II+  P + ++ E      A+ R+ LIV     LP++
Sbjct: 57  ERAVTQERATGRSIGLDIIEAGPNQALWREKLAHLAAEQRYRLIVSSNPALPHV 110


>pdb|1T9H|A Chain A, The Crystal Structure Of Yloq, A Circularly Permuted
           Gtpase
          Length = 307

 Score = 26.9 bits (58), Expect = 5.7,   Method: Compositional matrix adjust.
 Identities = 13/35 (37%), Positives = 22/35 (62%), Gaps = 1/35 (2%)

Query: 68  DRFTLIVPKPEMLPYLCLIPKDQVFEED-EDNIQA 101
           DRF ++V   ++ P +C+   D + ++D ED IQA
Sbjct: 107 DRFLVLVEANDIQPIICITKMDLIEDQDTEDTIQA 141


  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
   0.314    0.132    0.371 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,477,730
Number of Sequences: 62578
Number of extensions: 100025
Number of successful extensions: 133
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: 133
Number of HSP's gapped (non-prelim): 2
length of query: 175
length of database: 14,973,337
effective HSP length: 92
effective length of query: 83
effective length of database: 9,216,161
effective search space: 764941363
effective search space used: 764941363
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 48 (23.1 bits)