RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy2848
         (86 letters)



>gnl|CDD|215654 pfam00010, HLH, Helix-loop-helix DNA-binding domain. 
          Length = 52

 Score = 42.1 bits (100), Expect = 5e-07
 Identities = 15/29 (51%), Positives = 20/29 (68%)

Query: 9  RRNTANKKERRRTQSINNAFSDLRECIPN 37
          RR   N++ERRR   IN+AF +LRE +P 
Sbjct: 1  RRKAHNERERRRRDRINDAFEELRELLPT 29


>gnl|CDD|238036 cd00083, HLH, Helix-loop-helix domain, found in specific DNA-
          binding proteins that act as transcription factors;
          60-100 amino acids long. A DNA-binding basic region is
          followed by two alpha-helices separated by a variable
          loop region; HLH forms homo- and heterodimers,
          dimerization creates a parallel, left-handed, four
          helix bundle; the basic region N-terminal to the first
          amphipathic helix mediates high-affinity DNA-binding;
          there are several groups of HLH proteins: those
          (E12/E47) which bind specific hexanucleotide sequences
          such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3),
          those lacking the basic domain (Emc, Id) function as
          negative regulators since they fail to bind DNA, those
          (hairy, E(spl), deadpan) which repress transcription
          although they can bind specific hexanucleotide
          sequences such as N-box (5-CACGc/aG-3), those which
          have a COE domain (Collier/Olf-1/EBF) which is involved
          in both in dimerization and in DNA binding, and those
          which bind pentanucleotides ACGTG or GCGTG and have a
          PAS domain which allows the dimerization between PAS
          proteins, the binding of small molecules (e.g.,
          dioxin), and interactions with non-PAS proteins.
          Length = 60

 Score = 37.2 bits (87), Expect = 5e-05
 Identities = 14/31 (45%), Positives = 19/31 (61%)

Query: 7  VKRRNTANKKERRRTQSINNAFSDLRECIPN 37
            RR   N +ERRR + IN+AF +LR  +P 
Sbjct: 2  KSRREAHNLRERRRRERINDAFDELRSLLPT 32


>gnl|CDD|197674 smart00353, HLH, helix loop helix domain. 
          Length = 53

 Score = 31.8 bits (73), Expect = 0.005
 Identities = 12/24 (50%), Positives = 16/24 (66%)

Query: 14 NKKERRRTQSINNAFSDLRECIPN 37
          N +ERRR + IN AF +LR  +P 
Sbjct: 1  NARERRRRRKINEAFDELRSLLPT 24


>gnl|CDD|205352 pfam13171, DUF4004, Protein of unknown function (DUF4004).  This
           family of proteins is functionally uncharacterized. This
           family of proteins is found in bacteria. Proteins in
           this family are approximately 210 amino acids in length.
          Length = 199

 Score = 26.1 bits (58), Expect = 2.1
 Identities = 8/50 (16%), Positives = 18/50 (36%)

Query: 35  IPNILETDDIISIDDFKADLSNHSSHRKNKSQYDSPSEISSNQSSQYVMD 84
           I  I +  D +S+D+     S +    +   +      I S  + +   +
Sbjct: 56  INKIQKMKDDLSLDELAKMFSPNMEEVELTEEELLRKGIVSETALEVFEE 105


  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
   0.311    0.126    0.341 

Gapped
Lambda     K      H
   0.267   0.0777    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,076,550
Number of extensions: 310232
Number of successful extensions: 239
Number of sequences better than 10.0: 1
Number of HSP's gapped: 239
Number of HSP's successfully gapped: 16
Length of query: 86
Length of database: 10,937,602
Length adjustment: 54
Effective length of query: 32
Effective length of database: 8,542,486
Effective search space: 273359552
Effective search space used: 273359552
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 53 (24.1 bits)