RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy1838
         (80 letters)



>gnl|CDD|148369 pfam06726, BC10, Bladder cancer-related protein BC10.  This
          family consists of a series of short proteins of around
          90 residues in length. The human protein BC10 has been
          implicated in bladder cancer where the transcription of
          the gene coding for this protein is nearly completely
          abolished in highly invasive transitional cell
          carcinomas (TCCs). The protein is a small globular
          protein containing two transmembrane helices, and it is
          a multiply edited transcript. All the editing sites are
          found in either the 5'-UTR or the N-terminal section of
          the protein, which is predicted to be outside the
          membrane. The three coding edits are all non-synonymous
          and predicted to encode exposed residues. The function
          of this family is unknown.
          Length = 65

 Score = 77.5 bits (191), Expect = 6e-21
 Identities = 31/65 (47%), Positives = 41/65 (63%)

Query: 1  MYCLQWLIPVLLIPKPLNPALLQTHVMFMVLYLTGFFLERKPCTICSLVFIIAVFLICYS 60
          M+CL+W IPVLLIP P N +L+    MF VL+L GF+LE +PC  CS+   I +F IC  
Sbjct: 1  MFCLRWNIPVLLIPVPSNRSLVNASPMFAVLFLIGFYLELRPCVYCSITLGIFIFAICRP 60

Query: 61 GIGNC 65
             + 
Sbjct: 61 NWSDF 65


>gnl|CDD|205779 pfam13601, HTH_34, Winged helix DNA-binding domain. 
          Length = 80

 Score = 24.8 bits (55), Expect = 3.1
 Identities = 5/12 (41%), Positives = 8/12 (66%)

Query: 37 FLERKPCTICSL 48
          F+ +KP TI  +
Sbjct: 50 FVGKKPRTIYRI 61


>gnl|CDD|221252 pfam11833, DUF3353, Protein of unknown function (DUF3353).  This
           family of proteins are functionally uncharacterized.
           This protein is found in bacteria and eukaryotes.
           Proteins in this family are typically between 205 to 258
           amino acids in length.
          Length = 193

 Score = 25.3 bits (56), Expect = 3.8
 Identities = 11/35 (31%), Positives = 21/35 (60%)

Query: 4   LQWLIPVLLIPKPLNPALLQTHVMFMVLYLTGFFL 38
           L  L+P  ++P  L+P  +Q+   +++L+L   FL
Sbjct: 159 LAVLLPPFILPGSLSPEQIQSLPAYLLLWLGSLFL 193


>gnl|CDD|184668 PRK14417, PRK14417, membrane protein; Provisional.
          Length = 232

 Score = 24.4 bits (53), Expect = 8.4
 Identities = 12/30 (40%), Positives = 17/30 (56%), Gaps = 2/30 (6%)

Query: 28  FMVLYLTGFFLERKPCTICSLVFIIAVFLI 57
            M  Y  GFF  ++P T+ +  F I +FLI
Sbjct: 152 VMSGYFHGFFGVQEPQTV-TWGF-IGIFLI 179


  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
   0.335    0.148    0.527 

Gapped
Lambda     K      H
   0.267   0.0612    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,017,084
Number of extensions: 313924
Number of successful extensions: 707
Number of sequences better than 10.0: 1
Number of HSP's gapped: 706
Number of HSP's successfully gapped: 46
Length of query: 80
Length of database: 10,937,602
Length adjustment: 49
Effective length of query: 31
Effective length of database: 8,764,256
Effective search space: 271691936
Effective search space used: 271691936
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 39 (21.6 bits)
S2: 53 (24.4 bits)