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= 0013.0002.p
         (143 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309897|ref|YP_003773989.1| transcription regulator protein...   177   3e-46

>gi|300309897|ref|YP_003773989.1| transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 148

 Score =  177 bits (449), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 80/137 (58%), Positives = 107/137 (78%)

Query: 3   DPCPVARSIDVVGDRWALLIIRDAFDGMRRFGEFQKSLGVAKNILSARLRDLVDAGILDV 62
           + CPVARS+DVVGDRWALLI+RDAFDG+RRFG+FQ++L V+KNIL+ RLR LVDA IL++
Sbjct: 10  EHCPVARSVDVVGDRWALLIVRDAFDGIRRFGDFQRNLSVSKNILADRLRKLVDANILEM 69

Query: 63  APASDGSAYQEYLLTAKGKGLFTVVLGLRQWGEGHLFKKGESIAPMVDRDSGKPIPKITL 122
             ASDG++YQEY+LT  G GLF +V+ LRQWGE HLFK+GE  + ++D D+GKP+  +  
Sbjct: 70  QAASDGTSYQEYVLTETGLGLFPLVVALRQWGEAHLFKRGEKHSVLIDTDTGKPVAYMAP 129

Query: 123 HTCEGKPLKPENAFVKR 139
            + +G  L P    V++
Sbjct: 130 ISRDGSHLNPARTLVRK 146


  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
   0.321    0.140    0.420 

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: 487,865
Number of extensions: 20960
Number of successful extensions: 53
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 56
Number of HSP's successfully gapped: 1
Length of query: 143
Length of database: 1,619,870
Length adjustment: 77
Effective length of query: 66
Effective length of database: 1,255,275
Effective search space: 82848150
Effective search space used: 82848150
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 (21.8 bits)
S2: 126 (53.1 bits)