RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780790|ref|YP_003065203.1| hypothetical protein
CLIBASIA_03405 [Candidatus Liberibacter asiaticus str. psy62]
         (129 letters)



>gnl|CDD|146661 pfam04138, GtrA, GtrA-like protein.  Members of this family are
           predicted to be integral membrane proteins with three or
           four transmembrane spans. They are involved in the
           synthesis of cell surface polysaccharides. The GtrA
           family are a subset of this family. GtrA is predicted to
           be an integral membrane protein with 4 transmembrane
           spans. It is involved is in O antigen modification by
           Shigella flexneri bacteriophage X (SfX), but does not
           determine the specificity of glucosylation. Its function
           remains unknown, but it may play a role in translocation
           of undecaprenyl phosphate linked glucose (UndP-Glc)
           across the cytoplasmic membrane. Another member of this
           family is a DTDP-glucose-4-keto-6-deoxy-D-glucose
           reductase, which catalyses the conversion of
           dTDP-4-keto-6-deoxy-D-glucose to dTDP-D-fucose, which is
           involved in the biosynthesis of the serotype-specific
           polysaccharide antigen of Actinobacillus
           actinomycetemcomitans Y4 (serotype b). This family also
           includes the teichoic acid glycosylation protein, GtcA,
           which is a serotype-specific protein in some Listeria
           innocua and monocytogenes strains. Its exact function is
           not known, but it is essential for decoration of cell
           wall teichoic acids with glucose and galactose.
          Length = 116

 Score = 35.6 bits (83), Expect = 0.004
 Identities = 27/114 (23%), Positives = 52/114 (45%), Gaps = 2/114 (1%)

Query: 7   FIINIVVVFFIDVMGFFILMK-CGADPFYSRIFSIAVAFLVTWIPSRLFIFLKLRRKSFL 65
           F++  V+   +D+  F +L+   G     +   +  VA L  ++ +R + F    R S  
Sbjct: 2   FLLVGVLGTLVDLGVFLLLLNLLGLSYLLANAIAFLVAILFNYLLNRRWTFRSRGRGSLR 61

Query: 66  ETVRYGVMYFMLSILNYAFYVKLLLTFQGLQPLLATVLSAVSSMLFVFLLYIRF 119
           + +R+ ++  +  +LN      LL+   GL PLLA ++      +  FLL   +
Sbjct: 62  QFLRFFLVSLLGLLLNLLLLY-LLVDLLGLDPLLAKLIGIAVVTVVNFLLSKFW 114


>gnl|CDD|153393 cd07923, Gallate_dioxygenase_C, The C-terminal domain of Gallate
          Dioxygenase, which catalyzes the oxidization and
          subsequent ring-opening of gallate.  Gallate
          Dioxygenase catalyzes the oxidization and subsequent
          ring-opening of gallate, an intermediate in the
          degradation of the aromatic compound, syringate. The
          reaction product of gallate dioxygenase is
          4-oxalomesaconate. The amino acid sequence of the
          N-terminal and C-terminal regions of gallate
          dioxygenase exhibits homology with the sequence of the
          PCA 4,5-dioxygenase B (catalytic) and A subunits,
          respectively. This model represents the C-terminal
          domain, which is similar to the A subunit of PCA
          4,5-dioxygenase (or LigAB). The enzyme is estimated to
          be a homodimer according to the Escherichia coli
          enzyme. Since enzymes in this subfamily have fused A
          and B subunits, the dimer interface may resemble the
          tetramer interface of classical LigAB enzymes. This
          enzyme belongs to the class III extradiol dioxygenase
          family, composed of enzymes which use a non-heme Fe(II)
          to cleave aromatic rings between a hydroxylated carbon
          and an adjacent non-hydroxylated carbon.
          Length = 94

 Score = 25.9 bits (57), Expect = 3.4
 Identities = 7/19 (36%), Positives = 15/19 (78%)

Query: 59 LRRKSFLETVRYGVMYFML 77
          +R + ++  +RYGV++F+L
Sbjct: 45 IRNRDWIGMIRYGVIFFVL 63


>gnl|CDD|37513 KOG2302, KOG2302, KOG2302, T-type voltage-gated Ca2+ channel,
            pore-forming alpha1I subunit [Inorganic ion transport and
            metabolism, Signal transduction mechanisms].
          Length = 1956

 Score = 25.4 bits (55), Expect = 4.4
 Identities = 15/47 (31%), Positives = 26/47 (55%), Gaps = 5/47 (10%)

Query: 76   MLSILNYAFYVKLLLTFQGLQPLLATVLSAVSS-----MLFVFLLYI 117
            ++ +L  A  +KLL    G++ LL TV+ A+       +LF+ L +I
Sbjct: 1540 IMRVLRIARVLKLLKMATGMRALLDTVVQALPQVGNLGLLFMLLFFI 1586


>gnl|CDD|33895 COG4139, BtuC, ABC-type cobalamin transport system, permease
           component [Coenzyme metabolism].
          Length = 326

 Score = 24.9 bits (54), Expect = 6.4
 Identities = 12/38 (31%), Positives = 19/38 (50%)

Query: 86  VKLLLTFQGLQPLLATVLSAVSSMLFVFLLYIRFMTRR 123
           +  +L  QG  P  A  L A++  L + L+ +RF  R 
Sbjct: 102 IAAVLLGQGQLPNWALGLCAIAGALIITLILLRFARRH 139


  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
   0.345    0.153    0.464 

Gapped
Lambda     K      H
   0.267   0.0839    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,672,217
Number of extensions: 90515
Number of successful extensions: 850
Number of sequences better than 10.0: 1
Number of HSP's gapped: 831
Number of HSP's successfully gapped: 135
Length of query: 129
Length of database: 6,263,737
Length adjustment: 83
Effective length of query: 46
Effective length of database: 4,470,190
Effective search space: 205628740
Effective search space used: 205628740
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 38 (21.6 bits)
S2: 52 (23.6 bits)