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= 0001.3253.p
         (298 letters)

Database: BlastDatabases/690/690 
           3295 sequences; 1,000,347 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|134094449|ref|YP_001099524.1| tRNA pseudouridine synthase A [...   354   4e-99

>gi|134094449|ref|YP_001099524.1| tRNA pseudouridine synthase A
           [Herminiimonas arsenicoxydans]
          Length = 275

 Score =  354 bits (908), Expect = 4e-99,   Method: Compositional matrix adjust.
 Identities = 172/287 (59%), Positives = 212/287 (73%), Gaps = 25/287 (8%)

Query: 12  RRVVLGVQYDGASWQGWQTQPHRQTVQDQLEAALQRFSTTSIATTCAGRTDSGVHALEQV 71
           RR+VLGVQYDGA WQGWQTQ +  TVQD+LE AL +F+  +I T CAGRTD+GVHALEQV
Sbjct: 12  RRIVLGVQYDGAPWQGWQTQLNGLTVQDKLEFALYKFTQQTITTACAGRTDAGVHALEQV 71

Query: 72  VHFDTAIARDRFSWVRGTNAFLPPTIAVRWACELPWVDDAAIAGAQAAELHGAEREGAES 131
           VHFDT + RD  SWVRG N FLP +IAVRWA E+                     + AE+
Sbjct: 72  VHFDTTLERDMQSWVRGVNTFLPSSIAVRWASEVA-------------------HDPAEN 112

Query: 132 LAQFGFHARFSAIARTYHYVLYNHAVRSPLLAGKAGWTFRPLDADRMHRAAQHLIGEHDF 191
                FHARFSA +RTYHY+LYN+ VRSPLL GKAGW FR LD  +M  AA HL+G+HDF
Sbjct: 113 -----FHARFSARSRTYHYMLYNNPVRSPLLEGKAGWVFRALDIAKMQEAAAHLLGQHDF 167

Query: 192 TSFRAVECQAKSPVRKMESIAVRRHGDMIVFTLKANAFLHHMVRNIVGSLVVVGSGKQGP 251
           ++FR+V+CQAKSPV+ M +I + R GD+I+FT+ ANAFLHHMVRNIVGSL+ VG+G Q P
Sbjct: 168 SAFRSVQCQAKSPVKTMHAIKIERRGDLIMFTVHANAFLHHMVRNIVGSLIYVGNGTQAP 227

Query: 252 EWMGQVLALRDRSRAAPTFMPDGLYLARVDYPDAWALPQ-EMRSWPW 297
            W+ +VLA ++R  AAPTFMPDGLYLA++DY   W LPQ E++++ W
Sbjct: 228 SWLKEVLAGQERKFAAPTFMPDGLYLAKIDYDPKWQLPQTEIQNFLW 274


  Database: BlastDatabases/690/690
    Posted date:  Apr 9, 2011  4:48 AM
  Number of letters in database: 1,000,347
  Number of sequences in database:  3295
  
Lambda     K      H
   0.323    0.134    0.428 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 3295
Number of Hits to DB: 575,459
Number of extensions: 21807
Number of successful extensions: 91
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 90
Number of HSP's successfully gapped: 1
Length of query: 298
Length of database: 1,000,347
Length adjustment: 81
Effective length of query: 217
Effective length of database: 733,452
Effective search space: 159159084
Effective search space used: 159159084
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 128 (53.9 bits)