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= 0024.0013.p
         (114 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...   140   3e-35
gi|300311211|ref|YP_003775303.1| ribosomal large subunit pseudou...    67   5e-13

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

 Score =  140 bits (353), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 73/105 (69%), Positives = 84/105 (80%)

Query: 1   MTAKPAVTHYRRAAVGALDGRAVSLMRCQLETGRTHQIRVHMQSLGFALVGDALYGKSHL 60
           M AKPAVTHYRR A G +D + VSL+ C+LETGRTHQIRVH+QSLGF LVGDALYGK HL
Sbjct: 240 MRAKPAVTHYRRLATGEIDRKPVSLIHCRLETGRTHQIRVHLQSLGFPLVGDALYGKHHL 299

Query: 61  MPFFPRQALQAWKLGLIHPATGKQVEWEVGLPEDFTELLERAGID 105
           +  FPRQAL A +LGL+HP+TGK  +W   LPED   LL+RAGID
Sbjct: 300 VSVFPRQALLAGRLGLLHPSTGKFRQWAAPLPEDIVALLQRAGID 344


>gi|300311211|ref|YP_003775303.1| ribosomal large subunit
           pseudouridine synthase C [Herbaspirillum seropedicae
           SmR1]
          Length = 355

 Score = 66.6 bits (161), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 34/86 (39%), Positives = 46/86 (53%), Gaps = 10/86 (11%)

Query: 24  SLMRCQLETGRTHQIRVHMQSLGFALVGDALYGKSHLMP----------FFPRQALQAWK 73
           +L+  +L+TGRTHQIRVH+ S GF +VGD  YG   L             F R  L AW+
Sbjct: 248 ALLEAELKTGRTHQIRVHLSSSGFPIVGDDKYGDFALNKALQKADGRRIAFKRMFLHAWR 307

Query: 74  LGLIHPATGKQVEWEVGLPEDFTELL 99
           +   HP +G  V  + GLP++    L
Sbjct: 308 ISFRHPESGDTVTLKAGLPQECASFL 333


  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
   0.322    0.136    0.412 

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: 400,542
Number of extensions: 16403
Number of successful extensions: 41
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 40
Number of HSP's successfully gapped: 2
Length of query: 114
Length of database: 1,619,870
Length adjustment: 73
Effective length of query: 41
Effective length of database: 1,274,215
Effective search space: 52242815
Effective search space used: 52242815
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 124 (52.4 bits)