RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy1721
         (74 letters)



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

 Score = 49.5 bits (119), Expect = 4e-10
 Identities = 19/41 (46%), Positives = 28/41 (68%)

Query: 1  MRILSKAFFRLKTTLPWVPKDTKLSKLDTLRLATSYILHLK 41
           R +++AF  L++ LP +PK+ KLSK + LRLA  YI  L+
Sbjct: 8  RRKINEAFDELRSLLPTLPKNKKLSKAEILRLAIEYIKSLQ 48


>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 = 46.1 bits (110), Expect = 1e-08
 Identities = 18/45 (40%), Positives = 25/45 (55%)

Query: 1  MRILSKAFFRLKTTLPWVPKDTKLSKLDTLRLATSYILHLKMLLS 45
             ++ AF  L++ LP +P   KLSK + LR A  YI  L+ LL 
Sbjct: 16 RERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELLQ 60


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

 Score = 43.6 bits (104), Expect = 8e-08
 Identities = 18/38 (47%), Positives = 24/38 (63%), Gaps = 1/38 (2%)

Query: 4  LSKAFFRLKTTLPWVPKDTKLSKLDTLRLATSYILHLK 41
          ++ AF  L+  LP  P + KLSK + LRLA  YI HL+
Sbjct: 16 INDAFEELRELLPT-PPNKKLSKAEILRLAIEYIKHLQ 52


>gnl|CDD|165142 PHA02777, PHA02777, major capsid L1 protein; Provisional.
          Length = 555

 Score = 27.7 bits (61), Expect = 0.42
 Identities = 9/30 (30%), Positives = 13/30 (43%)

Query: 14  TLPWVPKDTKLSKLDTLRLATSYILHLKML 43
            LP  P D     LD  + +  Y +H  +L
Sbjct: 516 LLPAQPIDDPYITLDLFQGSMDYDIHPSLL 545


>gnl|CDD|223059 PHA03367, PHA03367, single-stranded DNA binding protein;
           Provisional.
          Length = 1115

 Score = 25.7 bits (57), Expect = 2.6
 Identities = 6/17 (35%), Positives = 9/17 (52%)

Query: 7   AFFRLKTTLPWVPKDTK 23
            F+RL+   P V K  +
Sbjct: 465 LFYRLRDRFPPVLKTQR 481


>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1.  Members
           of this family are necessary for accurate chromosome
           transmission during cell division.
          Length = 804

 Score = 25.5 bits (56), Expect = 3.3
 Identities = 13/49 (26%), Positives = 20/49 (40%), Gaps = 7/49 (14%)

Query: 28  DTLRLATSYIL--HLKMLLSQ-----QQDDPSHTHKEQWTQVLNVRFDR 69
           +   +AT+ I    L  L+S+     Q    S    E W ++ NV F  
Sbjct: 670 NVSFVATTKIGLSLLTTLISRAELIKQDGPVSAEELETWNEIYNVLFTS 718


>gnl|CDD|216094 pfam00747, Viral_DNA_bp, ssDNA binding protein.  This protein is
           found in herpesviruses and is needed for replication.
          Length = 1111

 Score = 25.0 bits (55), Expect = 4.7
 Identities = 9/17 (52%), Positives = 11/17 (64%)

Query: 7   AFFRLKTTLPWVPKDTK 23
            F RL+T LP  PK T+
Sbjct: 487 TFVRLRTRLPPFPKTTR 503


  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
   0.324    0.134    0.420 

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: 3,419,723
Number of extensions: 230992
Number of successful extensions: 193
Number of sequences better than 10.0: 1
Number of HSP's gapped: 193
Number of HSP's successfully gapped: 8
Length of query: 74
Length of database: 10,937,602
Length adjustment: 44
Effective length of query: 30
Effective length of database: 8,986,026
Effective search space: 269580780
Effective search space used: 269580780
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.1 bits)