RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

Searching..................................................done

Query= gi|254780519|ref|YP_003064932.1| flagellar biosynthesis protein
FliQ [Candidatus Liberibacter asiaticus str. psy62]
         (88 letters)



>gnl|CDD|32170 COG1987, FliQ, Flagellar biosynthesis pathway, component FliQ
          [Cell motility and secretion / Intracellular
          trafficking and secretion].
          Length = 89

 Score = 69.8 bits (171), Expect = 1e-13
 Identities = 41/86 (47%), Positives = 58/86 (67%)

Query: 1  MNEADVLEIARAAMWTILSSSAPVLFSAMFLGILIAFLQALTQIQEVTLTFVPKIIAVFI 60
          M E DVL+I + A+W +L  SAPVL  A+ +G++I+  QA TQIQE TL+F+PKIIAVF+
Sbjct: 1  MTEEDVLDIGQEAIWLVLMLSAPVLLVALVVGLVISIFQAATQIQEQTLSFIPKIIAVFL 60

Query: 61 TLIISAPFIGGQISSFVTLVLSRIQS 86
           LI+  P++  Q+  F   + S I  
Sbjct: 61 VLILLGPWMLNQLLDFTVTIFSNIPQ 86


>gnl|CDD|144785 pfam01313, Bac_export_3, Bacterial export proteins, family 3.
          This family includes the following members; FliQ, MopD,
          HrcS, Hrp, YopS and SpaQ All of these members export
          proteins, that do not possess signal peptides, through
          the membrane. Although the proteins that these
          exporters move may be different, the exporters are
          thought to function in similar ways.
          Length = 76

 Score = 68.7 bits (169), Expect = 3e-13
 Identities = 31/73 (42%), Positives = 53/73 (72%)

Query: 4  ADVLEIARAAMWTILSSSAPVLFSAMFLGILIAFLQALTQIQEVTLTFVPKIIAVFITLI 63
           DV+++ R A+W +L  SAP+L  A+ +G++++  QA TQIQE TL+FVPK++AV +TL+
Sbjct: 1  EDVIDLGRQALWLVLLLSAPLLLVALVVGLVVSLFQAATQIQEQTLSFVPKLLAVLLTLL 60

Query: 64 ISAPFIGGQISSF 76
          ++ P++   +  F
Sbjct: 61 LAGPWMLQTLLDF 73


>gnl|CDD|34403 COG4794, EscS, Type III secretory pathway, component EscS
          [Intracellular trafficking and secretion].
          Length = 89

 Score = 50.6 bits (121), Expect = 9e-08
 Identities = 30/86 (34%), Positives = 51/86 (59%)

Query: 1  MNEADVLEIARAAMWTILSSSAPVLFSAMFLGILIAFLQALTQIQEVTLTFVPKIIAVFI 60
          M+  D++ +   A+W IL  S P +  A  +G+L++ +QALTQIQ+ TL F  K++AV  
Sbjct: 1  MDMDDIVFLTSQALWLILILSLPPVIVASVVGLLVSLVQALTQIQDQTLPFGIKLLAVSA 60

Query: 61 TLIISAPFIGGQISSFVTLVLSRIQS 86
          TL ++A ++G  + +F   +   I  
Sbjct: 61 TLFLTAGWLGATLLNFAEQIFLNIPK 86


>gnl|CDD|35488 KOG0267, KOG0267, KOG0267, Microtubule severing protein katanin p80
           subunit B (contains WD40 repeats) [Cell cycle control,
           cell division, chromosome partitioning].
          Length = 825

 Score = 25.9 bits (56), Expect = 2.3
 Identities = 24/76 (31%), Positives = 36/76 (47%), Gaps = 17/76 (22%)

Query: 4   ADVLEIA--RAAMWTI--LSSSAPVLFSAMFLGILIAFLQALT-QIQEVTLTFVPKIIAV 58
           ADVL I   +  + T+   +   PVL          A L + T +   V+L  + K++AV
Sbjct: 694 ADVLNILTEKIEILTLDLCTQLLPVL---------TALLGSKTERPVNVSLDMLLKLVAV 744

Query: 59  FITLI---ISAPFIGG 71
           F T+I   +SAP   G
Sbjct: 745 FGTVIYSTLSAPRSVG 760


>gnl|CDD|176160 cd08471, PBP2_CrgA_like_2, The C-terminal substrate binding
          domain of an uncharacterized LysR-type transcriptional
          regulator CrgA-like, contains the type 2 periplasmic
          binding fold.  This CD represents the substrate binding
          domain of an uncharacterized LysR-type transcriptional
          regulator (LTTR) CrgA-like 2. The LTTRs are acting as
          both auto-repressors and activators of target
          promoters, controlling operons involved in a wide
          variety of cellular processes such as amino acid
          biosynthesis, CO2 fixation, antibiotic resistance,
          degradation of aromatic compounds, nodule formation of
          nitrogen-fixing bacteria, and synthesis of virulence
          factors, to name a few. In contrast to the tetrameric
          form of other LTTRs, CrgA from Neisseria meningitides
          assembles into an octameric ring, which can bind up to
          four 63-bp DNA oligonucleotides. Phylogenetic cluster
          analysis showed that the CrgA-like regulators form a
          subclass of the LTTRs that function as octamers. The
          CrgA is an auto-repressor of its own gene and activates
          the expression of the mdaB gene which coding for an
          NADPH-quinone reductase and that its action is
          increased by MBL (alpha-methylene-gamma-butyrolactone),
          an inducer of NADPH-quinone oxidoreductase.  The
          structural topology of this substrate-binding domain is
          most similar to that of the type 2 periplasmic binding
          proteins (PBP2), which are responsible for the uptake
          of a variety of substrates such as phosphate, sulfate,
          polysaccharides, lysine/arginine/ornithine, and
          histidine. The PBP2 bind their ligand in the cleft
          between these domains in a manner resembling a Venus
          flytrap. After binding their specific ligand with high
          affinity, they can interact with a cognate membrane
          transport complex comprised of two integral membrane
          domains and two cytoplasmically located ATPase domains.
          This interaction triggers the ligand translocation
          across the cytoplasmic membrane energized by ATP
          hydrolysis.
          Length = 201

 Score = 25.6 bits (57), Expect = 3.3
 Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 2/36 (5%)

Query: 18 LSSSAPVLFSAMFLG-ILIAFLQALTQIQEVTLTFV 52
          L+ +APVLF  + +  I+  FL A  ++  V L  +
Sbjct: 3  LTVTAPVLFGRLHVLPIITDFLDAYPEVS-VRLLLL 37


>gnl|CDD|32387 COG2205, KdpD, Osmosensitive K+ channel histidine kinase [Signal
           transduction mechanisms].
          Length = 890

 Score = 25.2 bits (55), Expect = 4.2
 Identities = 11/62 (17%), Positives = 25/62 (40%), Gaps = 3/62 (4%)

Query: 23  PVLFSAMFLGILIAFLQALTQIQEVTLTF--VPKIIAVFITLIISAPFIGGQISSFVTLV 80
              +S  +L + I      T I      F  +  I+ +F+  ++    + G+  + +  +
Sbjct: 392 QGSWSRDYL-VAILICALATAIAIQLDKFFDLANIVMLFLLGVLVVAVLTGRWPAVLAAL 450

Query: 81  LS 82
           LS
Sbjct: 451 LS 452


>gnl|CDD|144482 pfam00901, Orbi_VP5, Orbivirus outer capsid protein VP5.
           cryoelectron microscopy indicates that VP5 is a trimer
           implying that there are 360 copies of VP5 per virion.
          Length = 508

 Score = 24.2 bits (53), Expect = 8.8
 Identities = 19/93 (20%), Positives = 36/93 (38%), Gaps = 20/93 (21%)

Query: 4   ADVLEIARAAMWTILSSSAPVLFSAMFLGI-----------LIAFLQALTQIQEVTLTFV 52
           AD+LE A        +   P + + +  GI           L   + AL+ I +++    
Sbjct: 219 ADILEHA--------AEEVPFVGAGVATGIATARAIEGAYKLKKVINALSGI-DLSHLET 269

Query: 53  PKIIAVFITLIISAPFIGGQISSFVTLVLSRIQ 85
           PKI    +  ++  P      +S    V S+++
Sbjct: 270 PKIQPKTLETLLEKPTDVIPDASLAVAVSSKLR 302


  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
   0.330    0.139    0.373 

Gapped
Lambda     K      H
   0.267   0.0907    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 941,468
Number of extensions: 42812
Number of successful extensions: 367
Number of sequences better than 10.0: 1
Number of HSP's gapped: 362
Number of HSP's successfully gapped: 85
Length of query: 88
Length of database: 6,263,737
Length adjustment: 57
Effective length of query: 31
Effective length of database: 5,032,024
Effective search space: 155992744
Effective search space used: 155992744
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 51 (23.1 bits)