RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780160|ref|YP_003064573.1| hypothetical protein CLIBASIA_00215 [Candidatus Liberibacter asiaticus str. psy62] (298 letters) >gnl|CDD|35683 KOG0462, KOG0462, KOG0462, Elongation factor-type GTP-binding protein [Translation, ribosomal structure and biogenesis]. Length = 650 Score = 29.9 bits (67), Expect = 0.97 Identities = 14/59 (23%), Positives = 26/59 (44%), Gaps = 1/59 (1%) Query: 240 GESANASPSMVLSEGDYTVIARNKERNYSREFSVLTGKSTIVEVLMRQ-KRMDKNGQHN 297 S ++ PS + ++++ RN+S V GKST+ + L+ +D N Sbjct: 36 LFSEDSKPSAAVGLPEFSLDPVENIRNFSIIAHVDHGKSTLADRLLELTGTIDNNIGQE 94 >gnl|CDD|146080 pfam03266, DUF265, Protein of unknown function, DUF265. Length = 168 Score = 28.3 bits (64), Expect = 2.5 Identities = 8/30 (26%), Positives = 13/30 (43%) Query: 178 TSHYGKYNAIVSTVVKVEPGKIIDVTIQNR 207 H + +V + + KI VT +NR Sbjct: 131 VVHRRSDSPLVERIRRRPDVKIFVVTEENR 160 >gnl|CDD|143644 cd07884, RHD-n_Relish, N-terminal sub-domain of the Rel homology domain (RHD) of the arthropod protein Relish. Proteins containing the Rel homology domain (RHD) are metazoan transcription factors. The RHD is composed of two structural sub-domains; this model characterizes the N-terminal RHD sub-domain of the arthropod Relish protein, in which the RHD domain co-occurs with C-terminal ankyrin repeats. Family members are sometimes referred to as p110 or p68 (proteolytically processed form). Relish is an NF-kappa B-like transcription factor, which plays a role in mediating innate immunity in Drosophila. It is activated via the Imd (immune deficiency) pathway, which triggers phosphorylation of Relish. IKK-dependent proteolytic cleavage of Relish (which involves Dredd) results in a smaller active form (without the C-terminal ankyrin repeats), which is transported into the nucleus and functions as a transactivator. Length = 159 Score = 27.8 bits (62), Expect = 3.4 Identities = 13/43 (30%), Positives = 19/43 (44%), Gaps = 4/43 (9%) Query: 255 DYTVIARNKERNYSREFSVL----TGKSTIVEVLMRQKRMDKN 293 D I + E +Y F + T K I E L ++K M+ N Sbjct: 84 DPHDIEVSPEGDYVAMFQNMGIIHTAKKNIPEELYKKKNMNLN 126 >gnl|CDD|133157 cd05490, Cathepsin_D2, Cathepsin_D2, pepsin family of proteinases. Cathepsin D is the major aspartic proteinase of the lysosomal compartment where it functions in protein catabolism. It is a member of the pepsin family of proteinases. This enzyme is distinguished from other members of the pepsin family by two features that are characteristic of lysosomal hydrolases. First, mature Cathepsin D is found predominantly in a two-chain form due to a posttranslational cleavage event. Second, it contains phosphorylated, N-linked oligosaccharides that target the enzyme to lysosomes via mannose-6-phosphate receptors. Cathepsin D preferentially attacks peptide bonds flanked by bulky hydrophobic amino acids and its pH optimum is between pH 2.8 and 4.0. Two active site aspartic acid residues are essential for the catalytic activity of aspartic proteinases. Like other aspartic proteinases, Cathepsin D is a bilobed molecule; the two evolutionary related lobes are mostly made up of beta-sheets and flank a deep active site cleft. Each of the two related lobes contributes one active site aspartic acid residue and contains a single carbohydrate group. Cathepsin D is an essential enzyme. Mice deficient for proteinase cathepsin D, generated by gene targeting, develop normally during the first 2 weeks, stop thriving in the third week and die in a state of anorexia in the fourth week. The mice develop atrophy of ileal mucosa followed by other degradation of intestinal organs. In these knockout mice, lysosomal proteolysis was normal. These results suggest that vital functions of cathepsin D are exerted by limited proteolysis of proteins regulating cell growth and/or tissue homeostasis, while its contribution to bulk proteolysis in lysosomes appears to be non-critical. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A, clan AA). Length = 325 Score = 27.8 bits (62), Expect = 3.5 Identities = 12/39 (30%), Positives = 21/39 (53%) Query: 220 GGEAVADTAWSILTASGDTVGESANASPSMVLSEGDYTV 258 G EA+ DT S++T + V A ++ L +G+Y + Sbjct: 206 GCEAIVDTGTSLITGPVEEVRALQKAIGAVPLIQGEYMI 244 >gnl|CDD|35345 KOG0123, KOG0123, KOG0123, Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification, Translation, ribosomal structure and biogenesis]. Length = 369 Score = 27.6 bits (61), Expect = 3.9 Identities = 24/88 (27%), Positives = 39/88 (44%), Gaps = 11/88 (12%) Query: 3 ISFSSYAKAENMHTTSTLLNNNISKGKGKRVVDAQRITCEARLTENSTSIDSGVSWHIFD 62 ++F A AE T +N ++ KGK R++ +QR + SID+ ++D Sbjct: 42 VNFQQPADAERALDT---MNFDVLKGKPIRIMWSQRDPSLVFIKNLDESIDNK---SLYD 95 Query: 63 SISNKKNTLS----TTKKIIGGK-VSFD 85 + S N LS T + G V F+ Sbjct: 96 TFSEFGNILSCKVATDENGSKGYFVQFE 123 >gnl|CDD|33903 COG4152, COG4152, ABC-type uncharacterized transport system, ATPase component [General function prediction only]. Length = 300 Score = 27.2 bits (60), Expect = 5.5 Identities = 11/36 (30%), Positives = 18/36 (50%) Query: 177 ITSHYGKYNAIVSTVVKVEPGKIIDVTIQNRAAKIT 212 +T +G A+ + +V PG+I + N A K T Sbjct: 8 VTKSFGDKKAVDNISFEVPPGEIFGLLGPNGAGKTT 43 >gnl|CDD|112512 pfam03702, UPF0075, Uncharacterized protein family (UPF0075). The proteins is this family are about 370 amino acids long and have no known function. Length = 363 Score = 27.3 bits (61), Expect = 5.8 Identities = 10/20 (50%), Positives = 15/20 (75%) Query: 120 ILNAGGIRLYSIYKPGSPIV 139 +LN GGI S+ KPG+P++ Sbjct: 162 VLNIGGIANVSVLKPGAPVL 181 >gnl|CDD|176956 CHL00013, rpoA, RNA polymerase alpha subunit. Length = 327 Score = 26.5 bits (59), Expect = 9.6 Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 4/51 (7%) Query: 236 GDTVGESANASPSMVLSEGDYTVIARNKERNYSREFSVLTG-KSTIVEVLM 285 DT+G A +L E + T I R K E+S + G + +++E+L+ Sbjct: 34 ADTIG---IALRRALLGEIEGTCITRAKIEGVPHEYSTIPGIRESVLEILL 81 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 0.313 0.129 0.353 Gapped Lambda K H 0.267 0.0708 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 3,206,058 Number of extensions: 160176 Number of successful extensions: 310 Number of sequences better than 10.0: 1 Number of HSP's gapped: 310 Number of HSP's successfully gapped: 15 Length of query: 298 Length of database: 6,263,737 Length adjustment: 93 Effective length of query: 205 Effective length of database: 4,254,100 Effective search space: 872090500 Effective search space used: 872090500 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 57 (25.8 bits)