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)