RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254781213|ref|YP_003065626.1| head-to-tail joining protein, putative [Candidatus Liberibacter asiaticus str. psy62] (556 letters) >gnl|CDD|147306 pfam05056, DUF674, Protein of unknown function (DUF674). This family is found in Arabidopsis thaliana and contains several uncharacterized proteins. Length = 462 Score = 30.6 bits (69), Expect = 1.1 Identities = 11/29 (37%), Positives = 16/29 (55%) Query: 113 RSRSGFVGCLQSFYTSVVEFGTGCFYMEA 141 +S+ +GC + Y SVV+ G F EA Sbjct: 56 KSQPVTIGCFNNLYKSVVDMGIDNFETEA 84 >gnl|CDD|99967 cd03793, GT1_Glycogen_synthase_GSY2_like, Glycogen synthase, which is most closely related to the GT1 family of glycosyltransferases, catalyzes the transfer of a glucose molecule from UDP-glucose to a terminal branch of a glycogen molecule, a rate-limit step of glycogen biosynthesis. GSY2, the member of this family in S. cerevisiae, has been shown to possess glycogen synthase activity.. Length = 590 Score = 30.0 bits (68), Expect = 2.0 Identities = 10/30 (33%), Positives = 15/30 (50%) Query: 86 LYKEDARSKKVREWCDQVTDTLFGFRERSR 115 +Y D R K E Q+T ++ F + SR Sbjct: 525 IYIVDRRFKSPDESVQQLTQYMYEFCQLSR 554 >gnl|CDD|33095 COG3285, COG3285, Predicted eukaryotic-type DNA primase [DNA replication, recombination, and repair]. Length = 299 Score = 29.9 bits (67), Expect = 2.1 Identities = 20/84 (23%), Positives = 29/84 (34%), Gaps = 10/84 (11%) Query: 241 VDENRFFEEKQIATFPYIVGRYRVRADEIYGRSPAMEALPTIRRLNETVNELAQFGRLSL 300 + FF++ P V RV S + I + LAQ G L Sbjct: 58 IGGEAFFQKHAPRGAPPWVQTVRV-----TKDSGRTKPYLVIDDA-AGLAWLAQQGALEF 111 Query: 301 HPPTIAVSEAKQRN----FDLKPG 320 HP + + + + FDL PG Sbjct: 112 HPWGATIDDLEHPDERIVFDLDPG 135 >gnl|CDD|173958 cd08199, EEVS, 2-epi-5-epi-valiolone synthase (EEVS). 2-epi-5-epi-valiolone synthases catalyze the cyclization of sedoheptulose 7-phosphate to 2-epi-5-epi-valiolone in the biosynthesis of C(7)N-aminocyclitol-containing products. The cyclization product, 2-epi-5-epi-valiolone ((2S,3S,4S,5R)-5-(hydroxymethyl)cyclohexanon-2,3,4, 5-tetrol), is a precursor of the valienamine moiety. The valienamine unit is responsible for their biological activities as various glycosidic hydrolases inhibitors. Two important microbial secondary metabolites, i.e., validamycin and acarbose, are used in agricultural and biomedical applications. Validamycine A is an antifungal antibiotic which has a strong trehalase inhibitory activity and has been used to control sheath blight disease in rice caused by Rhizoctonia solani. Acarbose is an alpha-glucosidase inhibitor used for the treatment of type II insulin-independent diabetes. Salbostatin produced by Streptomyces albus also belongs to this family. It exhibits strong trehalase inhibitory activity. Length = 354 Score = 28.8 bits (65), Expect = 4.7 Identities = 20/86 (23%), Positives = 31/86 (36%), Gaps = 24/86 (27%) Query: 232 KGFHSKFVSVDEN----------RFFEEKQIATFPYIVGRYRVRADEIYGRSPAMEALPT 281 +G +FV VD+N +F I +V R A EA T Sbjct: 24 EGSGRRFVVVDQNVDKLYGKKLREYFAHHNI-PLTILVLR-------------AGEAAKT 69 Query: 282 IRRLNETVNELAQFGRLSLHPPTIAV 307 + + + V+ L FG P +A+ Sbjct: 70 MDTVLKIVDALDAFGISRRREPVLAI 95 >gnl|CDD|147186 pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle control protein. This family represents Cwf15/Cwc15 (from Schizosaccharomyces pombe and Saccharomyces cerevisiae respectively) and their homologues. The function of these proteins is unknown, but they form part of the spliceosome and are thus thought to be involved in mRNA splicing. Length = 241 Score = 28.5 bits (64), Expect = 5.4 Identities = 7/33 (21%), Positives = 19/33 (57%) Query: 501 AEVEDIRQQREVQRRVMEEQHLQQQLQQTSQDI 533 E+E I+++R ++ EE+ ++ + ++I Sbjct: 149 RELEKIKKERAEEKEREEEEKAAEEEKAREEEI 181 >gnl|CDD|38725 KOG3516, KOG3516, KOG3516, Neurexin IV [Signal transduction mechanisms]. Length = 1306 Score = 28.4 bits (63), Expect = 6.0 Identities = 13/62 (20%), Positives = 25/62 (40%), Gaps = 8/62 (12%) Query: 71 KWHGLAESFSAYQAFLYKEDARSKKVRE-------WCDQVTDTLFGFRERSRSGFVGCLQ 123 +WH + ++ +A L + D K +R + G + GF+GC++ Sbjct: 871 QWHQVRAERNSKEASL-QVDGLPKSIRTSPIPGTRLLQLYSSLFVGGTVSRQRGFLGCIR 929 Query: 124 SF 125 S Sbjct: 930 SL 931 >gnl|CDD|132748 cd06950, NR_LBD_Tlx_PNR_like, The ligand binding domain of Tailless-like proteins, orphan nuclear receptors. The ligand binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like family: This family includes photoreceptor cell-specific nuclear receptor (PNR), Tailless (TLX), and related receptors. TLX is an orphan receptor that is expressed by neural stem/progenitor cells in the adult brain of the subventricular zone (SVZ) and the dentate gyrus (DG). It plays a key role in neural development by promoting cell cycle progression and preventing apoptosis in the developing brain. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TLX and PNR have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 206 Score = 28.4 bits (64), Expect = 6.0 Identities = 11/24 (45%), Positives = 15/24 (62%) Query: 344 LPYHEELNRLKESIRSLFLLDLFQ 367 LP+ ++L L+ES LFLL Q Sbjct: 55 LPFRDQLILLEESWSELFLLGAAQ 78 >gnl|CDD|37150 KOG1939, KOG1939, KOG1939, Oxoprolinase [Amino acid transport and metabolism]. Length = 1247 Score = 28.0 bits (62), Expect = 6.5 Identities = 16/58 (27%), Positives = 29/58 (50%), Gaps = 8/58 (13%) Query: 140 EADVDEKGL--------EEGIRYISVPLSNVYMSVNHQNVVDSVYREFTFTVDQIVSK 189 E VDE+ L ++G++ I+V L + Y +H+ V + +E F+ + SK Sbjct: 162 EKKVDEEALRQDLKELYDKGVKSIAVVLLHSYTYPDHELEVGKIAKEIGFSHVSLSSK 219 >gnl|CDD|80311 cd04861, LigD_Pol_like, LigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. PaeLigD is monomeric, containing an N-terminal phosphoesterase module, a central polymerase (Pol) domain, and a C-terminal ATP-dependent ligase domain. Mycobacterium tuberculosis (Mt)LigD, also found in this group, is monomeric and contains the same modules but these are arranged differently: an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The PaeLigD Pol domain in vitro, in a manganese-dependent fashion, catalyzes templated extensions of 5'-overhang duplex DNA, and nontemplated single-nucleotide additions to blunt-end duplex DNA; it preferentially adds single ribonucleotides at blunt DNA ends. PaeLigD Pol adds a correctly paired rNTP to the DNA primer termini more rapidly than it does a correctly paired dNTP; it has higher infidelity as an RNA polymerase than it does as a DNA polymerase, which is in keeping with the mutagenic property of NHEJ-mediated DNA DSB repair. The MtLigD Pol domain similarly is stimulated by manganese, is error-prone, and prefers adding rNTPs to dNTPs in vitro. The MtLigD Pol domain has been shown to prefer DNA gapped substrates containing a 5'-phosphate group at the gap.. Length = 227 Score = 27.8 bits (62), Expect = 7.2 Identities = 18/83 (21%), Positives = 28/83 (33%), Gaps = 10/83 (12%) Query: 241 VDENRFFEEKQIATFPYIVGRYRVRADEIYGRSPAMEALPTIRRLNETVNELAQFGRLSL 300 +D FF++ A P V V + + LA G + L Sbjct: 33 IDGESFFQKHAPAGAPDWVRTVEVE------SEGGTINYLLVNDA-AGLVWLANLGAIEL 85 Query: 301 HPPTIAVSEAKQRN---FDLKPG 320 HP + ++ + FDL PG Sbjct: 86 HPWLSRADDLERPDRLVFDLDPG 108 >gnl|CDD|114419 pfam05693, Glycogen_syn, Glycogen synthase. This family consists of the eukaryotic glycogen synthase proteins GYS1, GYS2 and GYS3. Glycogen synthase (GS) is the enzyme responsible for the synthesis of -1,4-linked glucose chains in glycogen. It is the rate limiting enzyme in the synthesis of the polysaccharide, and its activity is highly regulated through phosphorylation at multiple sites and also by allosteric effectors, mainly glucose 6-phosphate (G6P). Length = 633 Score = 27.8 bits (62), Expect = 9.3 Identities = 9/30 (30%), Positives = 15/30 (50%) Query: 86 LYKEDARSKKVREWCDQVTDTLFGFRERSR 115 +Y D R K E Q+ ++ F ++SR Sbjct: 520 IYIVDRRFKSPDESVQQLAQFMYEFCQQSR 549 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 0.317 0.133 0.384 Gapped Lambda K H 0.267 0.0670 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 6,514,020 Number of extensions: 339429 Number of successful extensions: 974 Number of sequences better than 10.0: 1 Number of HSP's gapped: 968 Number of HSP's successfully gapped: 23 Length of query: 556 Length of database: 6,263,737 Length adjustment: 99 Effective length of query: 457 Effective length of database: 4,124,446 Effective search space: 1884871822 Effective search space used: 1884871822 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: 60 (27.0 bits)