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= 0063.0002.p
         (154 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300312591|ref|YP_003776683.1| tRNA pseudouridine synthase [He...   183   6e-48

>gi|300312591|ref|YP_003776683.1| tRNA pseudouridine synthase
           [Herbaspirillum seropedicae SmR1]
          Length = 300

 Score =  183 bits (464), Expect = 6e-48,   Method: Compositional matrix adjust.
 Identities = 93/150 (62%), Positives = 107/150 (71%), Gaps = 17/150 (11%)

Query: 22  ARARXTLADIGTTCAGRTDSGVHALEQVVHFDTVIARETASWVRGVNAFLPPSIAVRWAC 81
           A  R +   I TTCAGRTDSGVHALEQ+VHFDT IAR++ SWVRG NAFLPP+IAVRWAC
Sbjct: 44  ALQRFSTQPIATTCAGRTDSGVHALEQIVHFDTPIARDSFSWVRGTNAFLPPTIAVRWAC 103

Query: 82  EVPLEEGVG----------INAGER-------EDGFHARFSATARTYHYVLYNHPVRSPL 124
           E+P  +             ++  +R       + GFHARFSA ARTYHYVLYNH VR+PL
Sbjct: 104 ELPYVDDAAIASAASQAAELHGADRAGADSLSQFGFHARFSAIARTYHYVLYNHAVRTPL 163

Query: 125 LAGKAGWTFRPLDAGLMQQGADYLIGMHDF 154
           LAGKAGWTFRPLDA  M + A +LIG HDF
Sbjct: 164 LAGKAGWTFRPLDADRMHRAAQHLIGEHDF 193


  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    0.134    0.421 

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: 468,153
Number of extensions: 18707
Number of successful extensions: 35
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 34
Number of HSP's successfully gapped: 1
Length of query: 154
Length of database: 1,619,870
Length adjustment: 77
Effective length of query: 77
Effective length of database: 1,255,275
Effective search space: 96656175
Effective search space used: 96656175
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 (21.9 bits)
S2: 126 (53.1 bits)