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= 0579.0048.p
         (98 letters)

Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF 
           2,715,099 sequences; 757,237,578 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

ref|NP_561434.1| two-component response regulator [Clostridium p...    57   1e-07
ref|ZP_00098048.1| COG3279: Response regulator of the LytR/AlgR ...    56   2e-07
ref|NP_970650.1| DNA-binding response regulator [Treponema denti...    53   2e-06

>ref|NP_561434.1| two-component response regulator [Clostridium perfringens]
 dbj|BAB80224.1| two-component response regulator [Clostridium perfringens str.
          13]
          Length = 238

 Score = 56.6 bits (135), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 33/91 (36%), Positives = 50/91 (54%), Gaps = 1/91 (1%)

Query: 1  VAICDDEDKQRELVKGMLIALSIKANINFEMEEFNSGEQLAAHYEHNEPPFHILILDVEM 60
          +AICDDE  QR ++K ML  +  K N++  ++EF SG  L   Y+ N   + I+  D+ M
Sbjct: 4  IAICDDEKVQRNILKDMLYKICNKNNMDVIIDEFCSGVDLLNVYKRNTKKYSIVFCDILM 63

Query: 61 AGINGIQTAQRIRGLKHLDEQIIFLTNYPEY 91
            +NGI+  ++I  L     Q I +T   EY
Sbjct: 64 DEMNGIELLRKIGELDAF-IQAILITGSEEY 93


>ref|ZP_00098048.1| COG3279: Response regulator of the LytR/AlgR family
          [Desulfitobacterium hafniense]
          Length = 131

 Score = 56.2 bits (134), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 28/86 (32%), Positives = 47/86 (54%), Gaps = 1/86 (1%)

Query: 1  VAICDDEDKQRELVKGMLIALSIKANINFEMEEFNSGEQLAAHYEHNEPPFHILILDVEM 60
          + +CDD   QR  +K ++     ++ + F + EF+SGE L   ++ N   F +  LD  M
Sbjct: 4  ICLCDDGALQRAYLKLIIQEYESRSGVRFNLSEFSSGEDLLEQFQENPTRFDLYFLDQRM 63

Query: 61 AGINGIQTAQRIRGLKHLDEQIIFLT 86
            I G++TA  IR  ++ D  I+F+T
Sbjct: 64 KNITGLETASSIRQ-RNKDCAIVFVT 88


>ref|NP_970650.1| DNA-binding response regulator [Treponema denticola ATCC 35405]
 gb|AAS10531.1| DNA-binding response regulator [Treponema denticola ATCC 35405]
          Length = 239

 Score = 53.1 bits (126), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 32/91 (35%), Positives = 54/91 (59%), Gaps = 2/91 (2%)

Query: 1  VAICDDEDKQRELVKGMLIALSIKANINFEMEEFNSGEQLAAHYEHNEPPFHILILDVEM 60
          +A+ +D + Q  L+K      + K N+  E++ F+SGEQ    +E       I++LD++M
Sbjct: 4  IAVIEDNEVQSRLLKDYANEWANKNNLLPEIKLFSSGEQFWFEFEE-LSDIDIILLDIQM 62

Query: 61 AGINGIQTAQRIRGLKHLDEQIIFLTNYPEY 91
          + I+GI+ A++IR  K  D  IIF+T  P+Y
Sbjct: 63 SRISGIELAKKIRKTKS-DAVIIFITGIPDY 92


  Database: All non-redundant GenBank CDS
  translations+PDB+SwissProt+PIR+PRF
    Posted date:  Mar 24, 2004  1:53 AM
  Number of letters in database: 757,237,578
  Number of sequences in database:  2,715,099
  
Lambda     K      H
   0.320    0.139    0.398 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 2715099
Number of Hits to DB: 134,204,883
Number of extensions: 4386274
Number of successful extensions: 12040
Number of sequences better than 1.0e-05: 5
Number of HSP's gapped: 12060
Number of HSP's successfully gapped: 5
Length of query: 98
Length of database: 757,237,578
Length adjustment: 66
Effective length of query: 32
Effective length of database: 578,041,044
Effective search space: 18497313408
Effective search space used: 18497313408
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: 120 (50.8 bits)