RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254781219|ref|YP_003065632.1| hypothetical protein CLIBASIA_05630 [Candidatus Liberibacter asiaticus str. psy62] (200 letters) >gnl|CDD|31918 COG1732, OpuBC, Periplasmic glycine betaine/choline-binding (lipo)protein of an ABC-type transport system (osmoprotectant binding protein) [Cell envelope biogenesis, outer membrane]. Length = 300 Score = 27.9 bits (62), Expect = 2.2 Identities = 8/51 (15%), Positives = 21/51 (41%), Gaps = 8/51 (15%) Query: 29 YSPESYSNTYREQKLRDKIIELRRKFAKENGLKTVTEVCPKPKDITYSLSH 79 P ++NTY + +R+ A++ L+T++++ + Sbjct: 129 LKPAGFNNTY--------ALAVRKDVAEKYNLETISDLAKHSNQLKLGADS 171 >gnl|CDD|145760 pfam02776, TPP_enzyme_N, Thiamine pyrophosphate enzyme, N-terminal TPP binding domain. Length = 172 Score = 27.2 bits (61), Expect = 3.3 Identities = 12/50 (24%), Positives = 21/50 (42%), Gaps = 7/50 (14%) Query: 143 ALIRYLEDFYKEIKHTFGNPADALSPHISELADEIHTTCFTLQFVVNPSE 192 AL L+ + H FG P ++ P + LA +++V+ E Sbjct: 6 ALAEALKAL--GVDHVFGVPGGSILPLLDALAKS-----PGIRYVLVRHE 48 >gnl|CDD|36613 KOG1399, KOG1399, KOG1399, Flavin-containing monooxygenase [Secondary metabolites biosynthesis, transport and catabolism]. Length = 448 Score = 26.9 bits (59), Expect = 4.2 Identities = 11/47 (23%), Positives = 17/47 (36%) Query: 110 LHDKLNKILKKSVRNYSRDSGHLNRDVIFHSRYALIRYLEDFYKEIK 156 ++ L L K + YS F S ++ YL D+ K Sbjct: 58 VYKSLRTNLPKEMMGYSDFPFPERDPRYFPSHREVLEYLRDYAKHFD 104 >gnl|CDD|31075 COG0731, COG0731, Fe-S oxidoreductases [Energy production and conversion]. Length = 296 Score = 26.8 bits (59), Expect = 4.3 Identities = 21/70 (30%), Positives = 30/70 (42%), Gaps = 7/70 (10%) Query: 135 DVIFHSRYALIRYLEDFYKEIKH-TF---GNPADALSPHISELADEIH-TTCFTLQFVVN 189 + I L+ Y D E H T G P L P++ EL +EI T V N Sbjct: 60 ESILEELKLLLGYKGDEATEPDHVTISLSGEPT--LYPNLGELIEEIKKRGKKTTFLVTN 117 Query: 190 PSEAELLEKV 199 S ++LE++ Sbjct: 118 GSLPDVLEEL 127 >gnl|CDD|153437 cd07968, OBF_DNA_ligase_IV, The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase IV is a DNA-binding module that is part of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase IV is required for DNA non-homologous end joining pathways, including recombination of the V(D)J immunoglobulin gene segments in cells of the mammalian immune system. DNA ligase IV is stabilized by forming a complex with XRCC4, a nuclear phosphoprotein, which is phosphorylated by DNA-dependent protein kinase. DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and C-terminal oligouncleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. The OB-fold domain contacts the nicked DNA substrate and is required for the ATP-dependent DNA ligase nucleotidylation step. The RxDK motif (motif VI), which is essential for ATP hydrolysis, is located in the OB-fold domain. Length = 140 Score = 26.4 bits (59), Expect = 5.5 Identities = 12/56 (21%), Positives = 26/56 (46%), Gaps = 6/56 (10%) Query: 77 LSHFIEGLIESERSKITEKFKPLAVAKVVS----DELLHDKLNKILKKSVRNYSRD 128 +S F+ G+ E + + + + KV S +EL D++ + LK + + + Sbjct: 22 VSSFLCGVAEDDDPESDKPSVFYSFCKVGSGFSDEEL--DEIRRKLKPHWKPFDKK 75 >gnl|CDD|163692 cd08061, MPN_NPL4, Mov34/MPN/PAD-1 family: nuclear protein localization-4 (Npl4) domain. Npl4p (nuclear protein localization-4) is identical to Hmg-CoA reductase degradation 4 (HRD4) protein and contains a domain that is part of the pfam clan MPN/Mov34-like. Npl4 plays an intermediate role between endoplasmic reticulum-associated degradation (ERAD) substrate ubiquitylation and proteasomal degradation. Npl4p associates with Cdc48p (Cdc48 in yeast and p97 or valosin-containing protein (VCP) in higher eukaryotes), the highly conserved ATPase of the AAA family, via ubiquitin fusion degradation-1 protein (Ufd1p) to form a Cdc48p-Ufd1p-Npl4p complex which then functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation. This family of eukaryotic MPN-like domains lacks the key residues that coordinate a metal ion and therefore does not show catalytic isopeptidase activity. Length = 274 Score = 26.2 bits (58), Expect = 5.8 Identities = 16/58 (27%), Positives = 23/58 (39%), Gaps = 5/58 (8%) Query: 25 CEALYSPESYSNTYREQKLRDKIIELRRKFAKENGLKTV----TEVCPKPKDITYSLS 78 EA+Y P + L D + A GL+ V T++ + KD Y LS Sbjct: 58 VEAIYEPPQEGTPDGFELLEDPNADTVDAIAAALGLERVGWIFTDLPREDKD-GYFLS 114 >gnl|CDD|63877 cd04408, RhoGAP_GMIP, RhoGAP_GMIP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of GMIP (Gem interacting protein). GMIP plays important roles in neurite growth and axonal guidance, and interacts with Gem, a member of the RGK subfamily of the Ras small GTPase superfamily, through the N-terminal half of the protein. GMIP contains a C-terminal RhoGAP domain. GMIP inhibits RhoA function, but is inactive towards Rac1 and Cdc41. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.. Length = 200 Score = 26.1 bits (57), Expect = 7.6 Identities = 21/81 (25%), Positives = 33/81 (40%), Gaps = 3/81 (3%) Query: 8 QFKNYLHEDVKFYLDKWCEALYSPE-SYSNTYREQKLRDKIIELRRKFAKENGLKTVTEV 66 Q E+V F + + + + YR + ++ +L + F ENG V Sbjct: 7 QLPRDFPEEVPFVVVRCTAEIENRALGVQGIYRISGSKARVEKLCQAF--ENGRDLVDLS 64 Query: 67 CPKPKDITYSLSHFIEGLIES 87 P DIT L HF++ L E Sbjct: 65 GHSPHDITSVLKHFLKELPEP 85 >gnl|CDD|145366 pfam02171, Piwi, Piwi domain. This domain is found in the protein Piwi and its relatives. The function of this domain is the dsRNA guided hydrolysis of ssRNA. Determination of the crystal structure of Argonaute reveals that PIWI is an RNase H domain, and identifies Argonaute as Slicer, the enzyme that cleaves mRNA in the RNAi RISC complex. In addition, Mg+2 dependence and production of 3'-OH and 5' phosphate products are shared characteristics of RNaseH and RISC. The PIWI domain core has a tertiary structure belonging to the RNase H family of enzymes. RNase H fold proteins all have a five-stranded mixed beta-sheet surrounded by helices. By analogy to RNase H enzymes which cleave single-stranded RNA guided by the DNA strand in an RNA/DNA hybrid, the PIWI domain can be inferred to cleave single-stranded RNA, for example mRNA, guided by double stranded siRNA. Length = 296 Score = 25.7 bits (57), Expect = 7.9 Identities = 8/36 (22%), Positives = 18/36 (50%) Query: 104 VVSDELLHDKLNKILKKSVRNYSRDSGHLNRDVIFH 139 S + L + L I+K+S+R++ + +I + Sbjct: 113 QASGQELIESLKDIIKESLRSFYKSRKKKPERIIIY 148 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 0.135 0.387 Gapped Lambda K H 0.267 0.0737 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,453,725 Number of extensions: 127267 Number of successful extensions: 447 Number of sequences better than 10.0: 1 Number of HSP's gapped: 447 Number of HSP's successfully gapped: 30 Length of query: 200 Length of database: 6,263,737 Length adjustment: 89 Effective length of query: 111 Effective length of database: 4,340,536 Effective search space: 481799496 Effective search space used: 481799496 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 (21.7 bits) S2: 55 (24.9 bits)