RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780715|ref|YP_003065128.1| 50S ribosomal protein L19 [Candidatus Liberibacter asiaticus str. psy62] (141 letters) >gnl|CDD|144730 pfam01245, Ribosomal_L19, Ribosomal protein L19. Length = 113 Score = 168 bits (428), Expect = 6e-43 Identities = 70/116 (60%), Positives = 87/116 (75%), Gaps = 5/116 (4%) Query: 1 MNIIDELDHEEMVRIESKRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGIN 60 MN+I E++ E++ K+ LP+F GDT+ V I EG+K RIQ +EGV IAR GRG+N Sbjct: 1 MNLIKEIEAEQL-----KKDLPEFRVGDTVRVHVKIKEGNKERIQVFEGVVIARRGRGLN 55 Query: 61 KNFTVRKISYGEGMNRLFPLYSPMIQDITVIRRGKVRRSKLYYLQDLRGKAARIKE 116 FTVRKIS G G+ R+FPL+SP I I V+RRGKVRR+KLYYL+DL GKAARIKE Sbjct: 56 STFTVRKISQGVGVERVFPLHSPRIDSIEVVRRGKVRRAKLYYLRDLSGKAARIKE 111 >gnl|CDD|30683 COG0335, RplS, Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]. Length = 115 Score = 141 bits (356), Expect = 9e-35 Identities = 69/117 (58%), Positives = 90/117 (76%), Gaps = 5/117 (4%) Query: 1 MNIIDELDHEEMVRIESKRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGIN 60 + II +L+ E++ K+ +P F PGDT+ V I EG K R+QA+EGV IAR GRGI+ Sbjct: 3 IPIIQQLEQEQI-----KKDIPSFRPGDTVRVHVKIVEGSKERVQAFEGVVIARRGRGIS 57 Query: 61 KNFTVRKISYGEGMNRLFPLYSPMIQDITVIRRGKVRRSKLYYLQDLRGKAARIKEN 117 + FTVRKISYG G+ R+FPL+SP+I+ I V+RRGKVRR+KLYYL++ RGKAARIKE Sbjct: 58 ETFTVRKISYGVGVERVFPLHSPLIESIEVVRRGKVRRAKLYYLRERRGKAARIKEK 114 >gnl|CDD|177023 CHL00084, rpl19, ribosomal protein L19. Length = 117 Score = 126 bits (319), Expect = 2e-30 Identities = 53/115 (46%), Positives = 77/115 (66%), Gaps = 5/115 (4%) Query: 2 NIIDELDHEEMVRIESKRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINK 61 ++ E++ E + K++LPK GDT+ V +I EG+K R+Q YEG IA+ G+N Sbjct: 6 QLVKEIESEFL-----KKNLPKIRVGDTVKVGVLIQEGNKERVQFYEGTVIAKKNSGLNT 60 Query: 62 NFTVRKISYGEGMNRLFPLYSPMIQDITVIRRGKVRRSKLYYLQDLRGKAARIKE 116 TVRK+ G G+ R+F L+SP + I V+RR KVRR+KLYYL++ GKAAR+K+ Sbjct: 61 TITVRKVFQGIGVERVFLLHSPKLASIEVLRRSKVRRAKLYYLRNRVGKAARLKQ 115 >gnl|CDD|36911 KOG1698, KOG1698, KOG1698, Mitochondrial/chloroplast ribosomal protein L19 [Translation, ribosomal structure and biogenesis]. Length = 201 Score = 80.8 bits (199), Expect = 1e-16 Identities = 40/127 (31%), Positives = 71/127 (55%), Gaps = 1/127 (0%) Query: 3 IIDELDHEEMVRIESKRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKN 62 I++ LD + ++ R +P+F G + V + E +K ++ ++G+CI R G+N Sbjct: 76 IMEILDRQAVLERRKVRDIPEFKVGSIVRVTSEDPE-NKRKVSRFKGICIRRRNAGLNAT 134 Query: 63 FTVRKISYGEGMNRLFPLYSPMIQDITVIRRGKVRRSKLYYLQDLRGKAARIKENTGKRA 122 F +R + G G+ +FPLYSP I++I V++ K RR+KLYYL+D + + N + Sbjct: 135 FLLRNVIAGVGVEIVFPLYSPNIKEIKVLKLEKRRRAKLYYLRDALPELSTFDANMRPKK 194 Query: 123 KALNEEV 129 + +V Sbjct: 195 EENGHKV 201 >gnl|CDD|34147 COG4469, CoiA, Competence protein [General function prediction only]. Length = 342 Score = 26.4 bits (58), Expect = 3.1 Identities = 14/47 (29%), Positives = 20/47 (42%) Query: 95 KVRRSKLYYLQDLRGKAARIKENTGKRAKALNEEVRRAALPEKEMSK 141 + R KL +DLRGK + L EE R +K++ K Sbjct: 173 QKTRLKLLIHEDLRGKHKYLASEVSFGIIHLMEEFRLPYHRQKKLHK 219 >gnl|CDD|133066 cd00596, Peptidase_M14_like, The M14 family of metallocarboxypeptidases (MCPs) are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavage. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others. Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism. Length = 196 Score = 25.9 bits (57), Expect = 3.6 Identities = 10/38 (26%), Positives = 14/38 (36%), Gaps = 8/38 (21%) Query: 58 GINKNFTVRKISYGEGMNRLFP-------LYSPMIQDI 88 G RK + G +NR FP L P + + Sbjct: 51 GYEAVNW-RKNANGVDLNRNFPGLWGKGPLSEPETRAL 87 >gnl|CDD|37391 KOG2180, KOG2180, KOG2180, Late Golgi protein sorting complex, subunit Vps53 [Intracellular trafficking, secretion, and vesicular transport]. Length = 793 Score = 25.0 bits (54), Expect = 6.8 Identities = 19/77 (24%), Positives = 34/77 (44%), Gaps = 7/77 (9%) Query: 59 INKNFTVRKISYGEGMNRLFPLYSPM--IQDITVIRRGKVRRSKLYYLQDLRGKAARIKE 116 IN+ + ++ E +N LFP + I + +G++RR L +R +E Sbjct: 10 INQMIPTPEFNFVEYINELFPAEQSLTNIDSLIQKIQGEIRRVDKNLLAVVRT-----QE 64 Query: 117 NTGKRAKALNEEVRRAA 133 N+G R K + + A Sbjct: 65 NSGTRGKENLADAQAAI 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 0.318 0.136 0.377 Gapped Lambda K H 0.267 0.0828 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,647,592 Number of extensions: 79370 Number of successful extensions: 187 Number of sequences better than 10.0: 1 Number of HSP's gapped: 186 Number of HSP's successfully gapped: 20 Length of query: 141 Length of database: 6,263,737 Length adjustment: 84 Effective length of query: 57 Effective length of database: 4,448,581 Effective search space: 253569117 Effective search space used: 253569117 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: 52 (23.6 bits)