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= 0025.0046.p
         (307 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...   419   e-118

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

 Score =  419 bits (1076), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 205/291 (70%), Positives = 233/291 (80%), Gaps = 17/291 (5%)

Query: 34  ALHRVVLGIQYDGNSWQGWQTQPHGLTVQDKLEAALKKFTLTDIDTTCAGRTDSGVHALE 93
            L RVVLG+QYDG SWQGWQTQPH  TVQD+LEAAL++F+   I TTCAGRTDSGVHALE
Sbjct: 10  GLRRVVLGVQYDGASWQGWQTQPHRQTVQDQLEAALQRFSTQPIATTCAGRTDSGVHALE 69

Query: 94  QVVHFDTVIARETASWVRGVNAFLPPSIAVRWACEVALEE----------ASGLNPGER- 142
           Q+VHFDT IAR++ SWVRG NAFLPP+IAVRWACE+   +          A+ L+  +R 
Sbjct: 70  QIVHFDTPIARDSFSWVRGTNAFLPPTIAVRWACELPYVDDAAIASAASQAAELHGADRA 129

Query: 143 ------EDGFHARFSATARTYHYVLYNHPVRSPLLAGKAGWTFRPLDVGLMQQGADHLIG 196
                 + GFHARFSA ARTYHYVLYNH VR+PLLAGKAGWTFRPLD   M + A HLIG
Sbjct: 130 GADSLSQFGFHARFSAIARTYHYVLYNHAVRTPLLAGKAGWTFRPLDADRMHRAAQHLIG 189

Query: 197 MHDFSSFRAVECQARSPVRTMESLQVRRHGDMIVFTLKANAFLHHMVRNIVGSLIYVGNG 256
            HDF+SFRAVECQA+SPVR MES+ VRRHGDMIVFTLKANAFLHHMVRNIVGSL+ VG+G
Sbjct: 190 EHDFTSFRAVECQAKSPVRKMESIAVRRHGDMIVFTLKANAFLHHMVRNIVGSLVVVGSG 249

Query: 257 RQPPQWIAEVLAQKDRGCAAPTFMPDGLYLAKVDYPARWQLPQEAAAWPWL 307
           +Q P W+ +VLA +DR  AAPTFMPDGLYLA+VDYP  W LPQE+ AWPWL
Sbjct: 250 KQEPDWMGQVLALRDRSRAAPTFMPDGLYLARVDYPDAWALPQESRAWPWL 300


  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    0.135    0.432 

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: 1,047,448
Number of extensions: 44689
Number of successful extensions: 125
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 124
Number of HSP's successfully gapped: 1
Length of query: 307
Length of database: 1,619,870
Length adjustment: 85
Effective length of query: 222
Effective length of database: 1,217,395
Effective search space: 270261690
Effective search space used: 270261690
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: 130 (54.7 bits)