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= 0025.0143.p
         (152 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300311237|ref|YP_003775329.1| GGDEF domain-containing protein...    87   6e-19

>gi|300311237|ref|YP_003775329.1| GGDEF domain-containing protein
           [Herbaspirillum seropedicae SmR1]
          Length = 585

 Score = 87.0 bits (214), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 57/129 (44%), Positives = 83/129 (64%)

Query: 1   MSLNRLFWLVSVALMLLFSVLAARIVLIEWEAYRRGARSVDAVRVVQLTMLAMEKVSIER 60
           MSLNRLF L+S+AL+LLF   A  +V  EW +YR GA SV A+R  +L ++A+EK+S ER
Sbjct: 1   MSLNRLFRLISIALLLLFLAFAVSLVWTEWNSYRNGANSVPALRTFRLALVALEKLSAER 60

Query: 61  GPSNALMGGEGDALPALRKRLDEARRNSDEALFRVLDSLRLEADVRYAPAIRKIEAVRQA 120
           GP+NA MG       A+  +L  AR  +D AL  +  +L+    +R + ++ K++ V+QA
Sbjct: 61  GPANAFMGASASQREAVADKLKNARAETDAALAALRQALQSHPRLRQSWSLDKVKTVQQA 120

Query: 121 LGPARDRVD 129
           L PAR  +D
Sbjct: 121 LEPARAAID 129


  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
   0.326    0.137    0.380 

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: 419,611
Number of extensions: 15161
Number of successful extensions: 106
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 106
Number of HSP's successfully gapped: 1
Length of query: 152
Length of database: 1,619,870
Length adjustment: 77
Effective length of query: 75
Effective length of database: 1,255,275
Effective search space: 94145625
Effective search space used: 94145625
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 126 (53.1 bits)