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)