RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780254|ref|YP_003064667.1| 50S ribosomal protein L16 [Candidatus Liberibacter asiaticus str. psy62] (138 letters) >gnl|CDD|176985 CHL00044, rpl16, ribosomal protein L16. Length = 135 Score = 178 bits (455), Expect = 3e-46 Identities = 73/135 (54%), Positives = 97/135 (71%), Gaps = 1/135 (0%) Query: 1 MLRQPKNTKYPKQFKGRIKGVAKGGSRICFGNFALKAQEANRIGSSEIEAARRAISRGMK 60 ML PK TK+ KQ +GR+KG++ G+RICFG +AL+A E I S +IEA RRAI+R + Sbjct: 1 ML-SPKRTKFRKQHRGRMKGISYRGNRICFGRYALQALEPAWITSRQIEAGRRAITRYAR 59 Query: 61 RAGRVWICVFPDVPVTAKPTEVRMGKGKGNVEKWVCRVKPGRILFEIDGVSEEVARRAFR 120 R G++WI +FPD PVT +P E RMG GKG+ E WV VKPGRIL+E+ GVSE +AR A + Sbjct: 60 RGGKIWIRIFPDKPVTMRPAETRMGSGKGSPEYWVAVVKPGRILYEMGGVSETIARAAIK 119 Query: 121 LGAAKLSVVTKFIQR 135 + A K+ + T+FI Sbjct: 120 IAAYKMPIKTQFIIS 134 >gnl|CDD|144001 pfam00252, Ribosomal_L16, Ribosomal protein L16p/L10e. Length = 129 Score = 169 bits (431), Expect = 2e-43 Identities = 76/129 (58%), Positives = 92/129 (71%), Gaps = 1/129 (0%) Query: 5 PKNTKYPKQFKGRI-KGVAKGGSRICFGNFALKAQEANRIGSSEIEAARRAISRGMKRAG 63 PK TKY K KGR+ G A G+++ FG++ LKA E RI + +IEAAR AI+R +KR G Sbjct: 1 PKRTKYRKYQKGRLEYGGAVPGNKLAFGDYGLKALEPGRITARQIEAARIAINRYLKRGG 60 Query: 64 RVWICVFPDVPVTAKPTEVRMGKGKGNVEKWVCRVKPGRILFEIDGVSEEVARRAFRLGA 123 ++WI VFPD PVT KP E RMGKGKG E W RVKPG+ILFEI GVSEEVA+ A R A Sbjct: 61 KLWIRVFPDKPVTKKPAETRMGKGKGKPEGWAARVKPGQILFEIGGVSEEVAKEALRRAA 120 Query: 124 AKLSVVTKF 132 +KL + TK Sbjct: 121 SKLPIKTKI 129 >gnl|CDD|30546 COG0197, RplP, Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]. Length = 146 Score = 155 bits (393), Expect = 4e-39 Identities = 79/140 (56%), Positives = 97/140 (69%), Gaps = 2/140 (1%) Query: 1 MLRQPKNTKYPKQFKGRIKGV--AKGGSRICFGNFALKAQEANRIGSSEIEAARRAISRG 58 + QPK TKY KQ KGR G+ AKGG+++ FG + L A E +I + +IEAAR A +R Sbjct: 1 HMLQPKRTKYRKQHKGRGPGITIAKGGNKVFFGEYGLVALEPGQITARQIEAARIAANRY 60 Query: 59 MKRAGRVWICVFPDVPVTAKPTEVRMGKGKGNVEKWVCRVKPGRILFEIDGVSEEVARRA 118 +KR G +WI VFPD P+T KP E RMGKGKG E W RVKPGR+LFEI GV EE+AR A Sbjct: 61 LKRGGGLWIRVFPDKPLTEKPGEDRMGKGKGKPEGWAARVKPGRVLFEIAGVPEELAREA 120 Query: 119 FRLGAAKLSVVTKFIQRVVE 138 R AAKL V TKF+ R+ + Sbjct: 121 LRRAAAKLPVKTKFVIRIEK 140 >gnl|CDD|38632 KOG3422, KOG3422, KOG3422, Mitochondrial ribosomal protein L16 [Translation, ribosomal structure and biogenesis]. Length = 221 Score = 123 bits (309), Expect = 2e-29 Identities = 55/136 (40%), Positives = 80/136 (58%), Gaps = 4/136 (2%) Query: 4 QPKNTKYPKQFKGRI-KGVAKGGSRICFGNFALKAQEANRIGSSEIEAARRAISRGMK-- 60 P+ TKY K +GR+ +G ++ G+ + FG + L+A+ + S++ EA R +R M Sbjct: 41 APERTKYRKIQRGRVPRGGSERGTELIFGRYGLRAKSGGILDSAQFEAMRLTRARKMNPR 100 Query: 61 RAGRVWICVFPDVPVTAKPTEVRMGKGKGNVEKWVCRVKPGRILFEIDG-VSEEVARRAF 119 G++W P++PVT K E RMG GKG ++ WV RVK GRILFE+ G V EE AR+A Sbjct: 101 NNGKIWRRPAPNLPVTVKGNETRMGGGKGAIDHWVARVKAGRILFEMGGDVEEEEARQAL 160 Query: 120 RLGAAKLSVVTKFIQR 135 A KL +F+ Sbjct: 161 LQAAHKLPFKYEFVSE 176 >gnl|CDD|88606 cd01433, Ribosomal_L16_L10e, Ribosomal_L16_L10e: L16 is an essential protein in the large ribosomal subunit of bacteria, mitochondria, and chloroplasts. Large subunits that lack L16 are defective in peptidyl transferase activity, peptidyl-tRNA hydrolysis activity, association with the 30S subunit, binding of aminoacyl-tRNA and interaction with antibiotics. L16 is required for the function of elongation factor P (EF-P), a protein involved in peptide bond synthesis through the stimulation of peptidyl transferase activity by the ribosome. Mutations in L16 and the adjoining bases of 23S rRNA confer antibiotic resistance in bacteria, suggesting a role for L16 in the formation of the antibiotic binding site. The GTPase RbgA (YlqF) is essential for the assembly of the large subunit, and it is believed to regulate the incorporation of L16. L10e is the archaeal and eukaryotic cytosolic homolog of bacterial L16. L16 and L10e exhibit structural differences at the N-terminus.. Length = 112 Score = 120 bits (302), Expect = 1e-28 Identities = 61/112 (54%), Positives = 78/112 (69%), Gaps = 2/112 (1%) Query: 24 GGSRICFGNFALKAQEANRIGSSEIEAARRAISRGMKR-AGRVWICVFPDVPVTAKPTEV 82 G+++ FG + L A E RI + ++EAAR AI+R +K+ G++WI VFPD PVT KP E Sbjct: 1 KGNKLFFGEYGLVALEPGRITAEQLEAARIAINRYLKKKGGKLWIRVFPDHPVTKKPLET 60 Query: 83 RMGKGKGNVEKWVCRVKPGRILFEIDGVS-EEVARRAFRLGAAKLSVVTKFI 133 RMGKGKG E WV RVKPG+ILFE+ GV EEVA+ A R A KL + TK + Sbjct: 61 RMGKGKGKPEGWVARVKPGQILFEVRGVPEEEVAKEALRRAAKKLPIKTKIV 112 >gnl|CDD|144080 pfam00350, Dynamin_N, Dynamin family. Length = 168 Score = 30.3 bits (69), Expect = 0.18 Identities = 13/63 (20%), Positives = 24/63 (38%), Gaps = 2/63 (3%) Query: 73 VPVTAKPTEVRMGKGKG-NVEKWVCRVKPGRILFE-IDGVSEEVARRAFRLGAAKLSVVT 130 P T +P +R+G+ G K G FE + EE+ ++ + + Sbjct: 29 GPTTRRPLVLRLGEEPGAIPGAVKVEYKDGLKKFEDFSELREEIEDETDKISGTGKGISS 88 Query: 131 KFI 133 + I Sbjct: 89 EPI 91 >gnl|CDD|39457 KOG4256, KOG4256, KOG4256, Kinetochore component [Cell cycle control, cell division, chromosome partitioning]. Length = 2209 Score = 27.1 bits (59), Expect = 1.9 Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 1/38 (2%) Query: 91 VEKWVC-RVKPGRILFEIDGVSEEVARRAFRLGAAKLS 127 +EK +C KPG L E + + E+ A + G AK S Sbjct: 1873 LEKGLCISEKPGEDLSEEEELEEDEALARLKDGIAKFS 1910 >gnl|CDD|147618 pfam05536, Neurochondrin, Neurochondrin. This family contains several eukaryotic neurochondrin proteins. Neurochondrin induces hydroxyapatite resorptive activity in bone marrow cells resistant to bafilomycin A1, an inhibitor of macrophage- and osteoclast-mediated resorption. Expression of the gene is localized to chondrocyte, osteoblast, and osteocyte in the bone and to the hippocampus and Purkinje cell layer of cerebellum in the brain. Length = 542 Score = 26.6 bits (59), Expect = 2.1 Identities = 10/54 (18%), Positives = 19/54 (35%), Gaps = 12/54 (22%) Query: 41 NRIGSSEIEAARRAISRGMKRAGRVWICVFPDVPVTAKP----------TEVRM 84 +++ S+ + A + + + G WI F V EVR+ Sbjct: 242 SKLTPSQRDPALKLAANLLSALGPQWI--FAGDKVPNSKFLLLLLNLACVEVRV 293 >gnl|CDD|176195 cd08233, butanediol_DH_like, (2R,3R)-2,3-butanediol dehydrogenase. (2R,3R)-2,3-butanediol dehydrogenase, a zinc-dependent medium chain alcohol dehydrogenase, catalyzes the NAD(+)-dependent oxidation of (2R,3R)-2,3-butanediol and meso-butanediol to acetoin. BDH functions as a homodimer. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. The medium chain alcohol dehydrogenase family (MDR) have a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The N-terminal region typically has an all-beta catalytic domain. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit. Sorbitol and aldose reductase are NAD(+) binding proteins of the polyol pathway, which interconverts glucose and fructose. Sorbitol dehydrogenase is tetrameric and has a single catalytic zinc per subunit. Length = 351 Score = 26.0 bits (58), Expect = 3.4 Identities = 15/49 (30%), Positives = 21/49 (42%), Gaps = 8/49 (16%) Query: 17 RIKGVAKGGSRICFGN--------FALKAQEANRIGSSEIEAARRAISR 57 R G G + + G ALKA A++I SE ARR ++ Sbjct: 166 RRSGFKPGDTALVLGAGPIGLLTILALKAAGASKIIVSEPSEARRELAE 214 >gnl|CDD|88404 cd05007, SIS_Etherase, N-acetylmuramic acid 6-phosphate etherase. Members of this family contain the SIS (Sugar ISomerase) domain. The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. The bacterial cell wall sugar N-acetylmuramic acid carries a unique D-lactyl ether substituent at the C3 position. The etherase catalyzes the cleavage of the lactyl ether bond of N-acetylmuramic acid 6-phosphate.. Length = 257 Score = 25.1 bits (55), Expect = 7.0 Identities = 16/46 (34%), Positives = 21/46 (45%), Gaps = 10/46 (21%) Query: 82 VRMGKGKGNV--------EKWVCRVKPGRILFEIDGVSEEVARRAF 119 +R+GK GN+ EK R RI+ E GVS + A A Sbjct: 201 IRLGKVYGNLMVDVRATNEKLRERAI--RIVMEATGVSRDEAEAAL 244 >gnl|CDD|73393 cd04731, HisF, The cyclase subunit of imidazoleglycerol phosphate synthase (HisF). Imidazole glycerol phosphate synthase (IGPS) catalyzes the fifth step of histidine biosynthesis, the formation of the imidazole ring. IGPS converts N1-(5'-phosphoribulosyl)-formimino-5-aminoimidazole-4- carboxamide ribonucleotide (PRFAR) to imidazole glycerol phosphate (ImGP) and 5'-(5-aminoimidazole-4-carboxamide) ribonucleotide (AICAR). This conversion involves two tightly coupled reactions in distinct active sites of IGPS. The two catalytic domains can be fused, like in fungi and plants, or peformed by a heterodimer (HisH-glutaminase and HisF-cyclase), like in bacteria.. Length = 243 Score = 25.1 bits (55), Expect = 7.3 Identities = 10/25 (40%), Positives = 15/25 (60%) Query: 111 SEEVARRAFRLGAAKLSVVTKFIQR 135 S E ARR R GA K+S+ + ++ Sbjct: 82 SLEDARRLLRAGADKVSINSAAVEN 106 >gnl|CDD|29363 cd01941, YeiC_kinase_like, YeiC-like sugar kinase. Found in eukaryotes and bacteria, YeiC-like kinase is part of the ribokinase/pfkB sugar kinase superfamily. Its oligomerization state is unknown at this time.. Length = 288 Score = 24.9 bits (54), Expect = 7.9 Identities = 8/23 (34%), Positives = 10/23 (43%) Query: 100 PGRILFEIDGVSEEVARRAFRLG 122 PG + GV +A RLG Sbjct: 27 PGHVKQSPGGVGRNIAENLARLG 49 >gnl|CDD|107326 cd06331, PBP1_AmiC_like, Type I periplasmic components of amide-binding protein (AmiC) and the active transport system for short-chain and urea (FmdDEF). This group includes the type I periplasmic components of amide-binding protein (AmiC) and the active transport system for short-chain and urea (FmdDEF), found in bacteria and Archaea. AmiC controls expression of the amidase operon by a ligand-triggered conformational switch. In the absence of ligand or presence of butyramide (repressor), AmiC (the ligand sensor and negative regulator) adopts an open conformation and inhibits the transcription antitermination function of AmiR by direct protein-protein interaction. In the presence of inducing ligands such as acetamide, AmiC adopts a closed conformation which disrupts a silencing AmiC-AmiR complex and the expression of amidase and other genes of the operon is induced. FmdDEF is predicted to be an ATP-dependent transporter and closely resembles the periplasmic binding protein and the two transmembrane proteins present in various hydrophobic amino acid-binding transport systems. Length = 333 Score = 24.4 bits (54), Expect = 9.4 Identities = 11/33 (33%), Positives = 15/33 (45%), Gaps = 2/33 (6%) Query: 37 AQEANRIGSSEIEAARRAISRGMKRA--GRVWI 67 A + GS++ EA R A+ A G V I Sbjct: 287 AAAVEKAGSTDPEAVRAALEGVSFDAPQGPVRI 319 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 0.322 0.137 0.409 Gapped Lambda K H 0.267 0.0724 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,617,352 Number of extensions: 78492 Number of successful extensions: 233 Number of sequences better than 10.0: 1 Number of HSP's gapped: 228 Number of HSP's successfully gapped: 22 Length of query: 138 Length of database: 6,263,737 Length adjustment: 84 Effective length of query: 54 Effective length of database: 4,448,581 Effective search space: 240223374 Effective search space used: 240223374 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 52 (23.8 bits)