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= 0008.0082.p
         (225 letters)

Database: BlastDatabases/689/689 
           4735 sequences; 1,619,870 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300312901|ref|YP_003776993.1| 16S rRNA uridine-516 pseudourid...    87   9e-19

>gi|300312901|ref|YP_003776993.1| 16S rRNA uridine-516
           pseudouridylate synthase [Herbaspirillum seropedicae
           SmR1]
          Length = 560

 Score = 87.4 bits (215), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 49/60 (81%), Positives = 51/60 (85%), Gaps = 3/60 (5%)

Query: 74  AKPKAAAPEAAAPAPAAPELPKVIVTVGEEVVAPPVLLDAPVDPNRAKPARRGVRGPRAL 133
           AKP   A + AAPAPA  ELPKVIVTVG+EVVAPPVLLDAP DPNR KPARRGVRGPRAL
Sbjct: 19  AKP-VEAEQIAAPAPA--ELPKVIVTVGDEVVAPPVLLDAPADPNRNKPARRGVRGPRAL 75


  Database: BlastDatabases/689/689
    Posted date:  Apr 10, 2011 12:15 AM
  Number of letters in database: 1,619,870
  Number of sequences in database:  4735
  
Lambda     K      H
   0.311    0.120    0.341 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 4735
Number of Hits to DB: 196,271
Number of extensions: 2862
Number of successful extensions: 14
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 14
Number of HSP's successfully gapped: 1
Length of query: 225
Length of database: 1,619,870
Length adjustment: 82
Effective length of query: 143
Effective length of database: 1,231,600
Effective search space: 176118800
Effective search space used: 176118800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 129 (54.3 bits)