RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780528|ref|YP_003064941.1| chemotaxis protein [Candidatus Liberibacter asiaticus str. psy62] (396 letters) >gnl|CDD|31660 COG1471, RPS4A, Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]. Length = 241 Score = 31.0 bits (70), Expect = 0.65 Identities = 22/82 (26%), Positives = 35/82 (42%), Gaps = 16/82 (19%) Query: 90 IISQDLSVVDDLIAKDTK---GYFDIA----------IVYALKKYF---SGQLEESSKEL 133 I+S+ +VD + KD K G D+ ++ K EE+S +L Sbjct: 63 ILSEGKVLVDGKVRKDYKFPVGLMDVISIPKTGEHYRVLPDEKGRLVLHPISAEEASYKL 122 Query: 134 SKIKDKDNTRGIVPYLHLLIGR 155 K+K+K +G L+L GR Sbjct: 123 CKVKNKTTVKGGRIQLNLHDGR 144 >gnl|CDD|173732 cd06628, STKc_MAPKKK_Byr2_like, Catalytic domain of fungal Byr2-like MAP Kinase Kinase Kinases. Serine/threonine kinases (STKs), mitogen-activated protein kinase (MAPK) kinase kinase (MAPKKK) subfamily, fungal Byr2-like proteins, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The MAPKKK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. Members of this group include the MAPKKKs Schizosaccharomyces pombe Byr2, Saccharomyces cerevisiae and Cryptococcus neoformans Ste11, and related proteins. They contain an N-terminal SAM (sterile alpha-motif) domain, which mediates protein-protein interaction, and a C-terminal catalytic domain. MAPKKKs phosphorylate and activate MAPK kinases (MAPKKs or MKKs or MAP2Ks), which in turn phosphorylate and activate MAPKs during signaling cascades that are important in mediating cellular responses to extracellular signals. Fission yeast Byr2 is regulated by Ras1. It responds to pheromone signaling and controls mating through the MAPK pathway. Budding yeast Ste11 functions in MAPK cascades that regulate mating, high osmolarity glycerol, and filamentous growth responses. Length = 267 Score = 29.0 bits (65), Expect = 2.5 Identities = 12/41 (29%), Positives = 28/41 (68%), Gaps = 2/41 (4%) Query: 40 QRALDEAMRGDISLQKKI--PDIVKETGVQLRATHMDVFVD 78 +R++ +A+ +I+L K++ +IV+ G L A H+++F++ Sbjct: 46 KRSMLDALAREIALLKELQHENIVQYLGSSLDADHLNIFLE 86 >gnl|CDD|36262 KOG1044, KOG1044, KOG1044, Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms, Cytoskeleton]. Length = 670 Score = 28.5 bits (63), Expect = 3.0 Identities = 13/43 (30%), Positives = 21/43 (48%), Gaps = 6/43 (13%) Query: 287 LDYKDLATIQLYENILNIPFVDIMSLQRSTCNIPYYSLMEQDR 329 LDYKDLA I + I +I D+++ + P+Y+ Sbjct: 291 LDYKDLAAIPKNKAIYDIERPDLITYE------PFYTSGYDGM 327 >gnl|CDD|72880 cd02883, Nudix_Hydrolase, Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of nudix hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase.. Length = 123 Score = 28.3 bits (62), Expect = 4.1 Identities = 20/83 (24%), Positives = 32/83 (38%), Gaps = 5/83 (6%) Query: 177 PGTFLEEIALRNLLEITQNEVGERAFGYIRAYVTQFHHSIYKDHFISVLLRFFLHGQ-LK 235 PG LEE A+R + E E G V + +H + + L G Sbjct: 36 PGETLEEAAIREVRE----ETGLDVDVLRLLGVYEVESPDEGEHAVVFVFLARLVGGEPT 91 Query: 236 LPDEDIVFTISFFSLEEQRAIYL 258 L D + + + +L+E A+ L Sbjct: 92 LLPPDEISEVRWVTLDELPALAL 114 >gnl|CDD|144568 pfam01027, UPF0005, Uncharacterized protein family UPF0005. The Pfam entry finds members not in the Prosite definition. Length = 203 Score = 27.1 bits (61), Expect = 9.3 Identities = 10/33 (30%), Positives = 18/33 (54%), Gaps = 3/33 (9%) Query: 282 RIIDRLDYKD--LATIQLYENILNIPFVDIMSL 312 II R D +A + LY + +N+ FV ++ + Sbjct: 169 NIIKRGGETDYIMAAVSLYLDFINL-FVRLLQI 200 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 0.325 0.140 0.392 Gapped Lambda K H 0.267 0.0647 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 4,784,615 Number of extensions: 264861 Number of successful extensions: 777 Number of sequences better than 10.0: 1 Number of HSP's gapped: 777 Number of HSP's successfully gapped: 16 Length of query: 396 Length of database: 6,263,737 Length adjustment: 96 Effective length of query: 300 Effective length of database: 4,189,273 Effective search space: 1256781900 Effective search space used: 1256781900 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 58 (26.3 bits)