RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy16407
         (59 letters)



>gnl|CDD|173872 cd08507, PBP2_SgrR_like, The C-terminal solute-binding domain of
           DNA-binding transcriptional regulator SgrR is related to
           the ABC-type oligopeptide-binding proteins and contains
           the type 2 periplasmic-binding fold.  A novel family of
           SgrR transcriptional regulator contains a two-domain
           structure with an N terminal DNA-binding domain of the
           winged helix family and a C-terminal solute-binding
           domain. The C-terminal domain shows strong homology with
           the ABC-type oligopeptide-binding protein family, a
           member of the type 2 periplasmic-binding fold protein
           (PBP2) superfamily that also includes the C-terminal
           substrate-binding domain of LysR-type transcriptional
           regulators. SgrR (SugaR transport-related Regulator) is
           negatively autoregulated and activates transcription of
           divergent operon SgrS, which encodes a small RNA
           required for recovery from glucose-phosphate stress.
           Hence, the small RNA SgrS and SgrR, the transcription
           factor that controls sgrS expression, are both required
           for recovery from glucose-phosphate stress. Most of
           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.
          Length = 448

 Score = 25.3 bits (56), Expect = 1.6
 Identities = 7/34 (20%), Positives = 12/34 (35%)

Query: 17  RLFDSHYLVKYSHRRAGATFQGKVYNFLERPSGW 50
           +L D  +L+   H     +F   +        GW
Sbjct: 406 QLVDEAWLLPLFHHWLTLSFHPSLQGVALNSLGW 439


>gnl|CDD|238825 cd01647, RT_LTR, RT_LTR: Reverse transcriptases (RTs) from
           retrotransposons and retroviruses which have long
           terminal repeats (LTRs) in their DNA copies but not in
           their RNA template. RT catalyzes DNA replication from an
           RNA template, and is responsible for the replication of
           retroelements. An RT gene is usually indicative of a
           mobile element such as a retrotransposon or retrovirus.
           RTs are present in a variety of mobile elements,
           including retrotransposons, retroviruses, group II
           introns, bacterial msDNAs, hepadnaviruses, and
           Caulimoviruses.
          Length = 177

 Score = 23.7 bits (52), Expect = 6.5
 Identities = 9/24 (37%), Positives = 10/24 (41%)

Query: 32  AGATFQGKVYNFLERPSGWKCFVY 55
           A ATFQ  +   L    G    VY
Sbjct: 103 APATFQRLMNKILGDLLGDFVEVY 126


>gnl|CDD|182775 PRK10847, PRK10847, hypothetical protein; Provisional.
          Length = 219

 Score = 23.1 bits (50), Expect = 9.3
 Identities = 9/29 (31%), Positives = 15/29 (51%), Gaps = 3/29 (10%)

Query: 10  LLTNPDCRLFDSHYLVK---YSHRRAGAT 35
           L +NP+ ++F   YL K   +  +  G T
Sbjct: 100 LFSNPNSKIFRRSYLDKTHQFYEKHGGKT 128


  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
   0.328    0.140    0.472 

Gapped
Lambda     K      H
   0.267   0.0750    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,014,931
Number of extensions: 198426
Number of successful extensions: 196
Number of sequences better than 10.0: 1
Number of HSP's gapped: 196
Number of HSP's successfully gapped: 3
Length of query: 59
Length of database: 10,937,602
Length adjustment: 31
Effective length of query: 28
Effective length of database: 9,562,628
Effective search space: 267753584
Effective search space used: 267753584
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 (21.7 bits)
S2: 53 (24.2 bits)