RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

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

Query= gi|254780304|ref|YP_003064717.1| DNA protecting protein DprA
[Candidatus Liberibacter asiaticus str. psy62]
         (34 letters)



>gnl|CDD|145559 pfam02481, DNA_processg_A, DNA recombination-mediator protein A.
           The SMF family, of DNA processing chain A, dprA, are a
           group of bacterial proteins. In H. pylori, dprA is
           required for natural chromosomal and plasmid
           transformation. It has now been shown that DprA is found
           to bind cooperatively to single-stranded DNA (ssDNA) and
           to interact with RecA. In the process, DprA-RecA-ssDNA
           filaments are produced and these filaments catalyse the
           homology-dependent formation of joint molecules. While
           the E.coli SSB protein limits access of RecA to ssDNA,
           DprA alleviates this barrier. It is proposed that DprA
           is a new member of the recombination-mediator protein
           family, dedicated to natural bacterial transformation.
          Length = 210

 Score = 49.4 bits (119), Expect = 2e-07
 Identities = 18/34 (52%), Positives = 23/34 (67%)

Query: 1   MAGGLDCLYPPENRNLLEEIWDNGGIAISEIPFG 34
           +  GLD +YP ENR L EEI + GG+ +SE P G
Sbjct: 102 LGTGLDRIYPKENRKLAEEIAEQGGLLLSEYPPG 135


>gnl|CDD|31101 COG0758, Smf, Predicted Rossmann fold nucleotide-binding protein
           involved in DNA uptake [DNA replication, recombination,
           and repair / Intracellular trafficking and secretion].
          Length = 350

 Score = 38.0 bits (88), Expect = 5e-04
 Identities = 17/33 (51%), Positives = 21/33 (63%), Gaps = 1/33 (3%)

Query: 2   AGGLDCLYPPENRNLLEEIWDNGGIAISEIPFG 34
           A GLD +YP EN  L E+I +NG + ISE P  
Sbjct: 172 ATGLDKIYPRENIKLAEKIAENGLL-ISEYPPD 203


>gnl|CDD|88554 cd05175, PI3Kc_IA_alpha, Phosphoinositide 3-kinase (PI3K), class
           IA, alpha isoform, catalytic domain; The PI3K catalytic
           domain family is part of a larger superfamily that
           includes the catalytic domains of other kinases such as
           the typical serine/threonine/tyrosine protein kinases
           (PKs), aminoglycoside phosphotransferase, choline
           kinase, and RIO kinases. PI3Ks catalyze the transfer of
           the gamma-phosphoryl group from ATP to the 3-hydroxyl of
           the inositol ring of D-myo-phosphatidylinositol (PtdIns)
           or its derivatives. PI3Ks can be divided into three main
           classes (I, II, and III), defined by their substrate
           specificity, regulation, and domain structure. Class I
           PI3Ks are the only enzymes capable of converting
           PtdIns(4,5)P2 to the critical second messenger
           PtdIns(3,4,5)P3. Class I enzymes are heterodimers and
           exist in multiple isoforms consisting of one catalytic
           subunit (out of four isoforms) and one of several
           regulatory subunits. They are further classified into
           class IA (alpha, beta and delta) and IB (gamma). Class
           IA enzymes contain an N-terminal p85 binding domain, a
           Ras binding domain, a lipid binding C2 domain, a PI3K
           homology domain of unknown function, and a C-terminal
           ATP-binding cataytic domain. They associate with a
           regulatory subunit of the p85 family and are activated
           by tyrosine kinase receptors. PI3Kalpha plays an
           important role in insulin signaling. It also mediates
           physiologic heart growth and provides protection from
           stress. Activating mutations of PI3Kalpha is associated
           with diverse forms of cancer at high frequency..
          Length = 366

 Score = 24.6 bits (53), Expect = 5.8
 Identities = 7/19 (36%), Positives = 13/19 (68%)

Query: 16  LLEEIWDNGGIAISEIPFG 34
           ++E IW N G+ +  +P+G
Sbjct: 121 IMENIWQNQGLDLRMLPYG 139


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.318    0.147    0.481 

Gapped
Lambda     K      H
   0.267   0.0832    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 482,954
Number of extensions: 11543
Number of successful extensions: 40
Number of sequences better than 10.0: 1
Number of HSP's gapped: 40
Number of HSP's successfully gapped: 3
Length of query: 34
Length of database: 6,263,737
Length adjustment: 8
Effective length of query: 26
Effective length of database: 6,090,865
Effective search space: 158362490
Effective search space used: 158362490
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: 41 (21.6 bits)
S2: 51 (23.2 bits)