RPS-BLAST 2.2.26 [Sep-21-2011]

Database: CDD.v3.10 
           44,354 sequences; 10,937,602 total letters

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

Query= psy11497
         (69 letters)



>gnl|CDD|178500 PLN02912, PLN02912, oxidoreductase, 2OG-Fe(II) oxygenase family
           protein.
          Length = 348

 Score = 28.1 bits (62), Expect = 0.30
 Identities = 16/37 (43%), Positives = 22/37 (59%)

Query: 26  LTALLDQQVCALLVQNLERLDETVKEESDGVHNTLGK 62
           +TA     V AL++  LE + E++  E D V NTLGK
Sbjct: 158 VTAEYATSVRALVLTLLEAISESLGLEKDRVSNTLGK 194


>gnl|CDD|239443 cd03327, MR_like_2, Mandelate racemase (MR)-like subfamily of the
          enolase superfamily, subgroup 2. Enzymes of this
          subgroup share three conserved carboxylate ligands for
          the essential divalent metal ion (usually Mg2+), two
          aspartates and a glutamate, and conserved catalytic
          residues,  a Lys-X-Lys motif and a conserved
          histidine-aspartate dyad. This subgroup's function is
          unknown.
          Length = 341

 Score = 25.8 bits (57), Expect = 1.8
 Identities = 7/29 (24%), Positives = 13/29 (44%)

Query: 17 ESEEGTESLLTALLDQQVCALLVQNLERL 45
          E+++GT            C ++ Q+L R 
Sbjct: 17 ETDDGTVGYANTTGGPVACWIVDQHLARF 45


>gnl|CDD|218602 pfam05478, Prominin, Prominin.  The prominins are an emerging
           family of proteins that among the multispan membrane
           proteins display a novel topology. Mouse prominin and
           human prominin (mouse)-like 1 (PROML1) are predicted to
           contain five membrane spanning domains, with an
           N-terminal domain exposed to the extracellular space
           followed by four, alternating small cytoplasmic and
           large extracellular, loops and a cytoplasmic C-terminal
           domain. The exact function of prominin is unknown
           although in humans defects in PROM1, the gene coding for
           prominin, cause retinal degeneration.
          Length = 807

 Score = 25.0 bits (55), Expect = 3.8
 Identities = 10/34 (29%), Positives = 17/34 (50%)

Query: 31  DQQVCALLVQNLERLDETVKEESDGVHNTLGKLV 64
            QQ+  +L QN +   + V ++ DG    LG  +
Sbjct: 194 PQQIDHVLAQNYQETQDQVSKDLDGAGEHLGGRI 227


>gnl|CDD|107260 cd01575, PBP1_GntR, Ligand-binding domain of DNA transcription
          repressor GntR specific for gluconate, a member of the
          LacI-GalR family of bacterial transcription regulators.
           This group represents the ligand-binding domain of DNA
          transcription repressor GntR specific for gluconate, a
          member of the LacI-GalR family of bacterial
          transcription regulators. The ligand-binding domain of
          GntR is structurally homologous to the periplasmic
          sugar-binding domain of ABC-type transporters and both
          domains contain the type I periplasmic binding
          protein-like fold. The LacI-GalR family repressors are
          composed of two functional domains: an N-terminal HTH
          (helix-turn-helix) domain, which is responsible for the
          DNA-binding specificity, and a C-terminal
          ligand-binding domain, which is homologous to the type
          I periplasmic binding proteins. As also observed in the
          periplasmic binding proteins, the C-terminal domain of
          the bacterial transcription repressor undergoes a
          conformational change upon ligand binding, which in
          turn changes the DNA binding affinity of the repressor.
          Length = 268

 Score = 24.8 bits (55), Expect = 4.0
 Identities = 11/33 (33%), Positives = 17/33 (51%)

Query: 18 SEEGTESLLTALLDQQVCALLVQNLERLDETVK 50
          S E  E LL  LL ++   L++  LE  + T +
Sbjct: 40 SPEREEELLRTLLSRRPAGLILTGLEHTERTRQ 72


>gnl|CDD|233594 TIGR01844, type_I_sec_TolC, type I secretion outer membrane
           protein, TolC family.  Members of This model are outer
           membrane proteins from the TolC subfamily within the RND
           (Resistance-Nodulation-cell Division) efflux systems.
           These proteins, unlike the NodT subfamily, appear not to
           be lipoproteins. All are believed to participate in type
           I protein secretion, an ABC transporter system for
           protein secretion without cleavage of a signal sequence,
           although they may, like TolC, participate also in the
           efflux of smaller molecules as well. This family
           includes the well-documented examples TolC (E. coli),
           PrtF (Erwinia), and AprF (Pseudomonas aeruginosa)
           [Protein fate, Protein and peptide secretion and
           trafficking, Transport and binding proteins, Porins].
          Length = 415

 Score = 24.6 bits (54), Expect = 4.4
 Identities = 9/29 (31%), Positives = 14/29 (48%)

Query: 23  ESLLTALLDQQVCALLVQNLERLDETVKE 51
           E+ +  L  Q++ AL   NL  L E +  
Sbjct: 117 EAYMEVLRAQEILALAEANLAALKEQLDL 145


  Database: CDD.v3.10
    Posted date:  Mar 20, 2013  7:55 AM
  Number of letters in database: 10,937,602
  Number of sequences in database:  44,354
  
Lambda     K      H
   0.312    0.131    0.354 

Gapped
Lambda     K      H
   0.267   0.0722    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,222,414
Number of extensions: 231205
Number of successful extensions: 153
Number of sequences better than 10.0: 1
Number of HSP's gapped: 153
Number of HSP's successfully gapped: 7
Length of query: 69
Length of database: 10,937,602
Length adjustment: 39
Effective length of query: 30
Effective length of database: 9,207,796
Effective search space: 276233880
Effective search space used: 276233880
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 53 (24.2 bits)