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= 0024.0012.p
         (178 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300312307|ref|YP_003776399.1| ribosomal large subunit pseudou...   204   3e-54

>gi|300312307|ref|YP_003776399.1| ribosomal large subunit
           pseudouridine synthase D [Herbaspirillum seropedicae
           SmR1]
          Length = 370

 Score =  204 bits (519), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 103/167 (61%), Positives = 125/167 (74%), Gaps = 1/167 (0%)

Query: 1   MSRTTPPKVVKAFATEPVEIPEGDDSLDEVVE-EFTDGAEPITLKLTDDACGVRLDKVLS 59
           MSR  P ++         ++P+ DD  D     E   G EP+TL+L D+  G RLDKVLS
Sbjct: 1   MSRKKPLQITNGDTPVHTDLPQADDFDDAHDGDEIGPGLEPLTLRLDDEVIGQRLDKVLS 60

Query: 60  GLVPQYSRSRIQQWIEGGYVTVDGNPARTKMTVLGDELVIITPQAAPEDNAFQPEPMDLS 119
           GL+P++SRSRIQQWIE G+VTV+G PA+ KMT+LGDELV + PQ+ P D  + PEPM L 
Sbjct: 61  GLLPEFSRSRIQQWIEDGHVTVNGAPAKAKMTMLGDELVEVAPQSVPSDQPYGPEPMALD 120

Query: 120 ILHEDKAIMVIDKPAGLVVHPAAGNWSGTLLNGLLHHCPALAGVPRG 166
           ILHEDKA++V++KPAGLVVHPAAGNWSGTLLNGLLHHCPALA VPR 
Sbjct: 121 ILHEDKALIVLNKPAGLVVHPAAGNWSGTLLNGLLHHCPALAKVPRA 167


  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
   0.316    0.135    0.411 

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: 647,603
Number of extensions: 28849
Number of successful extensions: 73
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 73
Number of HSP's successfully gapped: 1
Length of query: 178
Length of database: 1,619,870
Length adjustment: 79
Effective length of query: 99
Effective length of database: 1,245,805
Effective search space: 123334695
Effective search space used: 123334695
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: 41 (21.6 bits)
S2: 127 (53.5 bits)