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= 0143.0005.p
         (118 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310430|ref|YP_003774522.1| transcription regulator protein...   177   2e-46

>gi|300310430|ref|YP_003774522.1| transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 286

 Score =  177 bits (449), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 93/124 (75%), Positives = 95/124 (76%), Gaps = 20/124 (16%)

Query: 1   MLLDSIRTHINSLSKSEXSIRTHI--------------------NSLSTVIRFCRAIGYE 40
           MLLDSIRTHINSLSKSE  +   I                     S  TVIRFCRAIGYE
Sbjct: 3   MLLDSIRTHINSLSKSEKKVAATILANPQLALAENLTALAKNAEVSEPTVIRFCRAIGYE 62

Query: 41  GWHDFKLKLAQSLALALPGADESLAQDDLAVDLVNKICSRSINTLLDLRNHLNPDAIQLA 100
           GWHDFKLKLAQSLALALPGADE+LAQDDLA DLVNKICSRSINTLLDLRNHLNPDAIQLA
Sbjct: 63  GWHDFKLKLAQSLALALPGADETLAQDDLAADLVNKICSRSINTLLDLRNHLNPDAIQLA 122

Query: 101 LDVL 104
           LDVL
Sbjct: 123 LDVL 126


  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
   0.324    0.136    0.389 

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: 258,816
Number of extensions: 7125
Number of successful extensions: 44
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 42
Number of HSP's successfully gapped: 1
Length of query: 118
Length of database: 1,619,870
Length adjustment: 74
Effective length of query: 44
Effective length of database: 1,269,480
Effective search space: 55857120
Effective search space used: 55857120
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 124 (52.4 bits)