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= 0204.0008.p
         (320 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300311231|ref|YP_003775323.1| recombination factor RarA prote...   349   2e-97

>gi|300311231|ref|YP_003775323.1| recombination factor RarA protein
           [Herbaspirillum seropedicae SmR1]
          Length = 434

 Score =  349 bits (895), Expect = 2e-97,   Method: Compositional matrix adjust.
 Identities = 173/219 (78%), Positives = 187/219 (85%), Gaps = 5/219 (2%)

Query: 104 SVGTELL-AECLGDAL----RRFDKGGDAFYDQISALHKSVRGSSPDGALYWLTRMLDGG 158
           + GT L+ AE L +AL    RRFDKGGD FYDQISALHKSVRGS PD ALYWLTRMLDGG
Sbjct: 216 TTGTRLVTAEFLQNALTLNSRRFDKGGDNFYDQISALHKSVRGSHPDAALYWLTRMLDGG 275

Query: 159 TDPRYLARRIVRMAWEDIGLADPRAMTIANDAAATYERLGSPEGELALAQAVIYLAIAAK 218
            DPRYL+RRIVRMAWEDIGLADPRAM IANDAA TYERLGSPEGELAL QAVIYLA+AAK
Sbjct: 276 ADPRYLSRRIVRMAWEDIGLADPRAMQIANDAALTYERLGSPEGELALGQAVIYLAVAAK 335

Query: 219 SNAGYMAYNQARAFVAKDKSRGVPEHLRNAPTKLMKQLGYGKLYRYAHDEPEGYAAGETY 278
           SNAGY AYN ARAFV +DKSR VP HLRNAPTKLMK+LGYG  YRYAHDEP  YAAGETY
Sbjct: 336 SNAGYNAYNAARAFVKQDKSREVPVHLRNAPTKLMKELGYGHEYRYAHDEPNAYAAGETY 395

Query: 279 LPEGIPDPHWYQPVPRGLEAKIGDKMAHLRELDREYKKN 317
           LP+GI +P WYQPVPRGLE KIG+K+A LR+ D E +K+
Sbjct: 396 LPDGIEEPGWYQPVPRGLEIKIGEKLATLRQWDEEARKD 434



 Score =  140 bits (353), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 65/87 (74%), Positives = 75/87 (86%)

Query: 3  SAPLAERLRPHSFDDVIGQQHLLGAGKPLRVAFESGEPHSMILWGPPGVGKTTLARIMAD 62
          +APLAE LRP + D+VIGQ HLLG GKPLR+AF+SG+PHSMI WGPPGVGKTTLAR+ A 
Sbjct: 10 AAPLAEALRPKTLDEVIGQSHLLGEGKPLRLAFQSGKPHSMIFWGPPGVGKTTLARLTAT 69

Query: 63 SFNAEFIALSAVLSGVKDIREAVERAE 89
          +F  EFIALSAV SGVKDIR A+E+AE
Sbjct: 70 AFECEFIALSAVFSGVKDIRAAMEQAE 96


  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
   0.317    0.135    0.399 

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: 1,072,889
Number of extensions: 47853
Number of successful extensions: 221
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 223
Number of HSP's successfully gapped: 2
Length of query: 320
Length of database: 1,619,870
Length adjustment: 85
Effective length of query: 235
Effective length of database: 1,217,395
Effective search space: 286087825
Effective search space used: 286087825
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 (21.7 bits)
S2: 130 (54.7 bits)