BLASTP 2.2.18 [Mar-02-2008]


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= 0012.0026.p
         (243 letters)

Database: COG 
           115,334 sequences; 38,378,431 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

NMA0908 [J] COG0564 Pseudouridylate synthases, 23S RNA-specific       109   4e-24

>NMA0908 [J] COG0564 Pseudouridylate synthases, 23S RNA-specific
          Length = 120

 Score =  109 bits (272), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 51/96 (53%), Positives = 66/96 (68%)

Query: 23  EAGLLPAVVQDADSLEVLMFAYMNKESLQLSLESGQTWFWSRSRGELWHKGGTSGNTQAI 82
           E GL+ AVVQD  S EVLM AYMN+E+L+ ++++G   FWSRSR +LW KG TSG+ Q +
Sbjct: 10  ENGLILAVVQDQKSREVLMCAYMNREALEKTVKTGIAHFWSRSRKQLWKKGETSGHLQKV 69

Query: 83  TSIHYDCDSDTLLVKVVPEGPACHTGETSCFFRELP 118
             I  DCD D++L+ V   G ACH G  SCF+R L 
Sbjct: 70  KEIRIDCDMDSVLLLVEQVGGACHMGYRSCFYRNLK 105


  Database: COG
    Posted date:  Aug 3, 2010  9:58 AM
  Number of letters in database: 38,378,431
  Number of sequences in database:  115,334
  
Lambda     K      H
   0.314    0.132    0.381 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 115334
Number of Hits to DB: 16,942,512
Number of extensions: 704691
Number of successful extensions: 908
Number of sequences better than 1.0e-05: 1
Number of HSP's gapped: 908
Number of HSP's successfully gapped: 1
Length of query: 243
Length of database: 38,378,431
Length adjustment: 103
Effective length of query: 140
Effective length of database: 26,499,029
Effective search space: 3709864060
Effective search space used: 3709864060
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 114 (48.5 bits)