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= 0003.0053.p
         (91 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300313081|ref|YP_003777173.1| transcription regulator protein...   164   1e-42
gi|300313912|ref|YP_003778004.1| AraC family transcription regul...    94   2e-21
gi|300311850|ref|YP_003775942.1| AraC family transcription regul...    66   6e-13

>gi|300313081|ref|YP_003777173.1| transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 330

 Score =  164 bits (415), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 81/91 (89%), Positives = 89/91 (97%)

Query: 1   VTVDTLAEVACLSRRKFDRSFAAETGQTPARAIEQMRAEAARLRIEQSQDSLESIARATG 60
           +TVD LAEVACLSRR+FDR+FAAETGQTPARAIEQMRAEAARLRIEQSQD+LESIARATG
Sbjct: 228 LTVDLLAEVACLSRRQFDRAFAAETGQTPARAIEQMRAEAARLRIEQSQDTLESIARATG 287

Query: 61  FGDAERMRRACLRLFGQPPQAMRRLARLDEE 91
           FGDA+RMRRACLRLFGQPPQAMRRLAR +++
Sbjct: 288 FGDADRMRRACLRLFGQPPQAMRRLARAEDD 318


>gi|300313912|ref|YP_003778004.1| AraC family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 313

 Score = 93.6 bits (231), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 51/87 (58%), Positives = 61/87 (70%)

Query: 1   VTVDTLAEVACLSRRKFDRSFAAETGQTPARAIEQMRAEAARLRIEQSQDSLESIARATG 60
           +TV+ LAE A LS R+F R F +ETGQ+PA+AIE +R EAARL IEQS+  LE +AR TG
Sbjct: 226 LTVEELAEQANLSARQFTRVFTSETGQSPAKAIEGLRLEAARLMIEQSRHPLEVVARETG 285

Query: 61  FGDAERMRRACLRLFGQPPQAMRRLAR 87
           F D   MR   LR FG  PQ+MRR  R
Sbjct: 286 FRDRRHMREVFLRGFGVAPQSMRREGR 312


>gi|300311850|ref|YP_003775942.1| AraC family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 343

 Score = 65.9 bits (159), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 36/83 (43%), Positives = 51/83 (61%)

Query: 1   VTVDTLAEVACLSRRKFDRSFAAETGQTPARAIEQMRAEAARLRIEQSQDSLESIARATG 60
           + V+ LA  A +S R F R + AETG+TPAR +E MR EAAR  +E+++  L+ IA   G
Sbjct: 241 LHVENLAHRAGMSPRTFARLYVAETGRTPARTVELMRLEAARRALEETRLPLKRIASQAG 300

Query: 61  FGDAERMRRACLRLFGQPPQAMR 83
           +G+ + +RR  LR  G  P   R
Sbjct: 301 YGEEQNLRRVFLRQLGVSPGQYR 323


  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
   0.322    0.131    0.359 

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: 261,081
Number of extensions: 8477
Number of successful extensions: 72
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 74
Number of HSP's successfully gapped: 3
Length of query: 91
Length of database: 1,619,870
Length adjustment: 61
Effective length of query: 30
Effective length of database: 1,331,035
Effective search space: 39931050
Effective search space used: 39931050
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 (22.0 bits)
S2: 123 (52.0 bits)