RPS-BLAST 2.2.26 [Sep-21-2011]

Database: CDD.v3.10 
           44,354 sequences; 10,937,602 total letters

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

Query= psy8271
         (65 letters)



>gnl|CDD|107275 cd06280, PBP1_LacI_like_4, Ligand-binding domain of
          uncharacterized DNA-binding regulatory proteins that
          are members of the LacI-GalR family of bacterial
          transcription repressors.  This group includes the
          ligand-binding domain of uncharacterized DNA-binding
          regulatory proteins that are members of the LacI-GalR
          family of bacterial transcription repressors. The
          LacI-GalR family repressors are composed of two
          functional domains: an N-terminal HTH
          (helix-turn-helix) domain, which is responsible for the
          DNA-binding specificity, and a C-terminal
          ligand-binding domain, which is homologous to the
          sugar-binding domain of ABC-type transport systems that
          contain the type I periplasmic binding protein-like
          fold.  As also observed in the periplasmic binding
          proteins, the C-terminal domain of the bacterial
          transcription repressor undergoes a conformational
          change upon ligand binding which in turn changes the
          DNA binding affinity of the repressor.
          Length = 263

 Score = 27.7 bits (62), Expect = 0.33
 Identities = 11/25 (44%), Positives = 15/25 (60%)

Query: 24 TRDSLSVKDANKKHVYRVIQCHEDE 48
          T  S +V+DA  +   RVI C+ DE
Sbjct: 15 TAVSRAVEDAAYRAGLRVILCNTDE 39


>gnl|CDD|165411 PHA03139, PHA03139, helicase-primase primase subunit; Provisional.
          Length = 860

 Score = 24.9 bits (54), Expect = 3.5
 Identities = 10/39 (25%), Positives = 20/39 (51%)

Query: 11  IAELVRLIKDRICTRDSLSVKDANKKHVYRVIQCHEDEL 49
           I EL+  I D+ C +++LS  D   + ++  +    + L
Sbjct: 689 IEELIYSITDKGCPKENLSFMDLKSRQLWNKVNIATETL 727


>gnl|CDD|234123 TIGR03153, cytochr_NrfH, cytochrome c nitrate reductase, small
           subunit.  Members of this protein family are NrfH, a
           tetraheme cytochrome c. NrfH is the cytochrome c nitrate
           reductase small subunit, and forms a heterodimer with
           NrfA, the catalytic subunit. While NrfA can act as a
           monomer, NrfH can bind to and anchor NrfA in the
           membrane and enables electron transfer to NrfA from
           quinones [Energy metabolism, Electron transport].
          Length = 135

 Score = 24.6 bits (54), Expect = 4.0
 Identities = 8/35 (22%), Positives = 18/35 (51%), Gaps = 1/35 (2%)

Query: 26  DSLSVKDANKKHVY-RVIQCHEDELTQMVSTMSDG 59
           D + + + ++K V    ++CH   +T++V    D 
Sbjct: 89  DVIRISEHSRKVVQENCVRCHAGLVTELVPNHDDE 123


  Database: CDD.v3.10
    Posted date:  Mar 20, 2013  7:55 AM
  Number of letters in database: 10,937,602
  Number of sequences in database:  44,354
  
Lambda     K      H
   0.321    0.131    0.385 

Gapped
Lambda     K      H
   0.267   0.0598    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,035,720
Number of extensions: 202679
Number of successful extensions: 191
Number of sequences better than 10.0: 1
Number of HSP's gapped: 191
Number of HSP's successfully gapped: 5
Length of query: 65
Length of database: 10,937,602
Length adjustment: 36
Effective length of query: 29
Effective length of database: 9,340,858
Effective search space: 270884882
Effective search space used: 270884882
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 (21.9 bits)
S2: 53 (24.5 bits)