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= 0029.0216.p
         (59 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300311019|ref|YP_003775111.1| GAF domain-containing protein [...   122   4e-30
gi|300311023|ref|YP_003775115.1| GGDEF family protein [Herbaspir...    57   3e-10

>gi|300311019|ref|YP_003775111.1| GAF domain-containing protein
           [Herbaspirillum seropedicae SmR1]
          Length = 144

 Score =  122 bits (307), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 59/59 (100%), Positives = 59/59 (100%)

Query: 1   VRCFAGMRLRLNNGVVFGALCVMDTEPRIFRAREIRTFEGLAQIAEDIYRLFLFERQSH 59
           VRCFAGMRLRLNNGVVFGALCVMDTEPRIFRAREIRTFEGLAQIAEDIYRLFLFERQSH
Sbjct: 86  VRCFAGMRLRLNNGVVFGALCVMDTEPRIFRAREIRTFEGLAQIAEDIYRLFLFERQSH 144


>gi|300311023|ref|YP_003775115.1| GGDEF family protein
           [Herbaspirillum seropedicae SmR1]
          Length = 236

 Score = 57.0 bits (136), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 28/54 (51%), Positives = 37/54 (68%), Gaps = 1/54 (1%)

Query: 2   RCFAGMRLRLNNGVVFGALCVMDTEPRIFRAREIRTFEGLAQIAEDIYRLFLFE 55
           R +AG+RL +  G  FG+LCV+DTEPRI R+ E +  E LA +A DI RL + E
Sbjct: 182 RFYAGVRL-MYEGKAFGSLCVIDTEPRILRSHEQQALEELAMLASDILRLHILE 234


  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
   0.336    0.148    0.449 

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: 159,080
Number of extensions: 4454
Number of successful extensions: 20
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 20
Number of HSP's successfully gapped: 2
Length of query: 59
Length of database: 1,619,870
Length adjustment: 32
Effective length of query: 27
Effective length of database: 1,468,350
Effective search space: 39645450
Effective search space used: 39645450
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 39 (21.7 bits)
S2: 123 (52.0 bits)