RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy2115
         (77 letters)



>gnl|CDD|216316 pfam01130, CD36, CD36 family.  The CD36 family is thought to be a
          novel class of scavenger receptors. There is also
          evidence suggesting a possible role in signal
          transduction. CD36 is involved in cell adhesion.
          Length = 460

 Score = 52.2 bits (126), Expect = 1e-09
 Identities = 13/27 (48%), Positives = 17/27 (62%)

Query: 15 FNWTNPEDIRNNETKPNFVEMGPYRFH 41
          FN TNPE++ N   KP   E+GPY + 
Sbjct: 58 FNVTNPEEVLNGGAKPIVEEVGPYVYR 84


>gnl|CDD|149257 pfam08075, NOPS, NOPS (NUC059) domain.  This domain is found at
          the C-terminus of NONA and PSP1 proteins adjacent to 1
          or 2 pfam00076 domains.
          Length = 52

 Score = 25.4 bits (56), Expect = 1.0
 Identities = 9/34 (26%), Positives = 16/34 (47%)

Query: 14 KFNWTNPEDIRNNETKPNFVEMGPYRFHYGDKYK 47
          K    +P+  +  E  P F + G +   YG ++K
Sbjct: 19 KLVKKSPDYHKEREQGPRFAQPGSFEHEYGSRWK 52


>gnl|CDD|240583 cd12948, NOPS_PSF, NOPS domain, including C-terminal coiled-coil
          region, in polypyrimidine tract-binding protein
          (PTB)-associated-splicing factor (PSF) and similar
          proteins.  This model contains the NOPS (NONA and PSP1)
          domain PSF (also termed proline- and glutamine-rich
          splicing factor, or 100 kDa DNA-pairing protein
          (POMp100), or 100 kDa subunit of DNA-binding p52/p100
          complex), with a long helical C-terminal extension. PSF
          is a multifunctional protein that mediates diverse
          activities in the cell. It is ubiquitously expressed
          and highly conserved in vertebrates. PSF binds not only
          RNA but also single-stranded DNA (ssDNA) as well as
          double-stranded DNA (dsDNA) and facilitates the
          renaturation of complementary ssDNAs. Additionally, it
          promotes the formation of D-loops in superhelical
          duplex DNA, and is involved in cell proliferation. PSF
          can also interact with multiple factors. It is an
          RNA-binding component of spliceosomes and binds to
          insulin-like growth factor response element (IGFRE).
          Moreover, PSF functions as a transcriptional repressor
          interacting with Sin3A and mediating silencing through
          the recruitment of histone deacetylases (HDACs) to the
          DNA binding domain (DBD) of nuclear hormone receptors.
          As an RNA-binding component of spliceosomes, PSF binds
          to the insulin-like growth factor response element
          (IGFRE), and acts as an independent negative regulator
          of the transcriptional activity of the porcine P-450
          cholesterol side-chain cleavage enzyme gene (P450scc)
          IGFRE. PSF is an essential pre-mRNA splicing factor and
          is dissociated from PTB and binds to U1-70K and
          serine-arginine (SR) proteins during apoptosis. In
          addition, PSF forms a heterodimer with the nuclear
          protein p54nrb, also known as non-POU domain-containing
          octamer-binding protein (NONO). The PSF/p54nrb complex
          displays a variety of functions, such as DNA
          recombination and RNA synthesis, processing, and
          transport. PSF contains two conserved RNA recognition
          motifs (RRMs), also termed RBDs (RNA binding domains)
          or RNPs (ribonucleoprotein domains), which are
          responsible for interactions with RNA and for the
          localization of the protein in speckles. It also
          contains an N-terminal region rich in proline, glycine,
          and glutamine residues, which may play a role in
          interactions recruiting other molecules. The NOPS
          domain specifically binds to the second RNA recognition
          motif (RRM2) domain of the partner DBHS protein via a
          substantial interaction surface. Its highly conserved
          C-terminal residues are critical for functional DBHS
          dimerization while the highly conserved C-terminal
          helical extension, forming a right-handed antiparallel
          heterodimeric coiled-coil, is essential for
          localization of these proteins to subnuclear bodies.
          Length = 97

 Score = 24.3 bits (52), Expect = 5.3
 Identities = 11/35 (31%), Positives = 17/35 (48%)

Query: 14 KFNWTNPEDIRNNETKPNFVEMGPYRFHYGDKYKS 48
          K    NP   +  ET P F + G + + Y  ++KS
Sbjct: 21 KLAQKNPMYQKERETPPRFAQPGTFEYEYSQRWKS 55


  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
   0.314    0.135    0.448 

Gapped
Lambda     K      H
   0.267   0.0694    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,987,031
Number of extensions: 283088
Number of successful extensions: 158
Number of sequences better than 10.0: 1
Number of HSP's gapped: 158
Number of HSP's successfully gapped: 5
Length of query: 77
Length of database: 10,937,602
Length adjustment: 46
Effective length of query: 31
Effective length of database: 8,897,318
Effective search space: 275816858
Effective search space used: 275816858
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (24.3 bits)