RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy17810
         (62 letters)



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

 Score = 30.6 bits (70), Expect = 0.006
 Identities = 11/26 (42%), Positives = 15/26 (57%), Gaps = 1/26 (3%)

Query: 1  MLPLPAAITSQLDKASIIRLTISYLK 26
          +LP       +L KA I+RL I Y+K
Sbjct: 21 LLP-TLPKNKKLSKAEILRLAIEYIK 45


>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 = 29.9 bits (68), Expect = 0.014
 Identities = 9/26 (34%), Positives = 14/26 (53%), Gaps = 1/26 (3%)

Query: 1  MLPLPAAITSQLDKASIIRLTISYLK 26
          +LP       +L KA I+R  + Y+K
Sbjct: 29 LLPTLPPSK-KLSKAEILRKAVDYIK 53


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

 Score = 27.8 bits (63), Expect = 0.068
 Identities = 11/23 (47%), Positives = 14/23 (60%)

Query: 4  LPAAITSQLDKASIIRLTISYLK 26
          LP     +L KA I+RL I Y+K
Sbjct: 27 LPTPPNKKLSKAEILRLAIEYIK 49


>gnl|CDD|218123 pfam04516, CP2, CP2 transcription factor.  This family represents a
           conserved region in the CP2 transcription factor family.
          Length = 237

 Score = 26.9 bits (60), Expect = 0.51
 Identities = 9/14 (64%), Positives = 10/14 (71%)

Query: 44  SPSKSVKGIPHNLQ 57
           S SK VKG+P  LQ
Sbjct: 174 SSSKGVKGVPLRLQ 187


  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
   0.313    0.134    0.402 

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: 3,091,263
Number of extensions: 208362
Number of successful extensions: 89
Number of sequences better than 10.0: 1
Number of HSP's gapped: 89
Number of HSP's successfully gapped: 4
Length of query: 62
Length of database: 10,937,602
Length adjustment: 33
Effective length of query: 29
Effective length of database: 9,473,920
Effective search space: 274743680
Effective search space used: 274743680
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 (21.9 bits)
S2: 53 (24.1 bits)