RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy10561
         (73 letters)



>gnl|CDD|234231 TIGR03492, TIGR03492, conserved hypothetical protein.  This
          protein family is restricted to the Cyanobacteria, in
          one or two copies, save for instances in the genus
          Deinococcus. This protein shows some sequence
          similarity, especially toward the C-terminus, to
          lipid-A-disaccharide synthase (TIGR00215 or pfam02684).
          The function is unknown.
          Length = 396

 Score = 27.6 bits (62), Expect = 0.41
 Identities = 11/31 (35%), Positives = 15/31 (48%)

Query: 43 KGKNYNRSLCSRVGITVGLHSGGLGFDSWRG 73
          +G+ Y       +G T  L SGG  + S RG
Sbjct: 37 EGRAYQNLGIPIIGPTKELPSGGFSYQSLRG 67


>gnl|CDD|237342 PRK13303, PRK13303, L-aspartate dehydrogenase; Provisional.
          Length = 265

 Score = 26.1 bits (58), Expect = 1.6
 Identities = 14/36 (38%), Positives = 16/36 (44%), Gaps = 10/36 (27%)

Query: 34  ARDAKLAYPKGKNYNRSLCSRVGITVGLHSGGLGFD 69
           AR+A   +PK  N        V  TV L   GLG D
Sbjct: 176 AREAARLFPKNAN--------VAATVAL--AGLGLD 201


>gnl|CDD|216263 pfam01044, Vinculin, Vinculin family. 
          Length = 850

 Score = 25.8 bits (57), Expect = 2.3
 Identities = 7/19 (36%), Positives = 9/19 (47%)

Query: 10  VEPAVGSGERCLPGDEAHC 28
           ++PA    ERC P  E   
Sbjct: 271 IDPATYIEERCRPSLEERI 289


>gnl|CDD|182741 PRK10799, PRK10799, metal-binding protein; Provisional.
          Length = 247

 Score = 25.1 bits (55), Expect = 3.4
 Identities = 6/18 (33%), Positives = 9/18 (50%)

Query: 27  HCGDGAPARDAKLAYPKG 44
            CGD  P    ++A+  G
Sbjct: 156 WCGDTGPEVVQRVAWCTG 173


>gnl|CDD|183738 PRK12775, PRK12775, putative trifunctional 2-polyprenylphenol
           hydroxylase/glutamate synthase subunit beta/ferritin
           domain-containing protein; Provisional.
          Length = 1006

 Score = 24.5 bits (53), Expect = 6.8
 Identities = 9/26 (34%), Positives = 14/26 (53%)

Query: 8   YNVEPAVGSGERCLPGDEAHCGDGAP 33
           Y++E A+   ERC+   +  C  G P
Sbjct: 321 YSLEDALQEAERCIQCAKPTCIAGCP 346


>gnl|CDD|173862 cd08497, PBP2_NikA_DppA_OppA_like_14, The substrate-binding
           component of an uncharacterized ABC-type
           nickel/dipeptide/oligopeptide-like import system
           contains the type 2 periplasmic binding fold.  This CD
           represents the substrate-binding domain of an
           uncharacterized ATP-binding cassette (ABC) type
           nickel/dipeptide/oligopeptide-like transporter. The
           oligopeptide-binding protein OppA and the
           dipeptide-binding protein DppA show significant sequence
           similarity to NikA, the initial nickel receptor. The
           DppA binds dipeptides and some tripeptides and is
           involved in chemotaxis toward dipeptides, whereas the
           OppA binds peptides of a wide range of lengths (2-35
           amino acid residues) and plays a role in recycling of
           cell wall peptides, which precludes any involvement in
           chemotaxis. Most of other periplasmic binding proteins
           are comprised of only two globular subdomains
           corresponding to domains I and III of the
           dipeptide/oligopeptide binding proteins. The structural
           topology of these domains 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.  Besides transport
           proteins, the PBP2 superfamily includes the
           ligand-binding domains from ionotropic glutamate
           receptors, LysR-type transcriptional regulators,  and
           unorthodox sensor proteins involved in signal
           transduction.
          Length = 491

 Score = 24.0 bits (53), Expect = 7.7
 Identities = 9/16 (56%), Positives = 10/16 (62%)

Query: 2   DFSAPDYNVEPAVGSG 17
           DF    YN+EP  GSG
Sbjct: 163 DFDKKRYNLEPPPGSG 178


>gnl|CDD|183780 PRK12831, PRK12831, putative oxidoreductase; Provisional.
          Length = 464

 Score = 24.2 bits (53), Expect = 8.1
 Identities = 11/26 (42%), Positives = 12/26 (46%)

Query: 8  YNVEPAVGSGERCLPGDEAHCGDGAP 33
          YN E AV    RCL   +  C  G P
Sbjct: 30 YNEEEAVKEASRCLQCKKPKCVKGCP 55


  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
   0.316    0.139    0.454 

Gapped
Lambda     K      H
   0.267   0.0676    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,721,509
Number of extensions: 266859
Number of successful extensions: 175
Number of sequences better than 10.0: 1
Number of HSP's gapped: 175
Number of HSP's successfully gapped: 8
Length of query: 73
Length of database: 10,937,602
Length adjustment: 43
Effective length of query: 30
Effective length of database: 9,030,380
Effective search space: 270911400
Effective search space used: 270911400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (24.3 bits)