RPSBLAST alignment for GI: 254780282 and conserved domain: cd08480

>gnl|CDD|176169 cd08480, PBP2_CrgA_like_10, 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 10. 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 = 198
 Score = 88.5 bits (220), Expect = 2e-18
 Identities = 51/177 (28%), Positives = 85/177 (48%), Gaps = 17/177 (9%)

Query: 93  GKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRLRKPIQS 152
           G+LR+  ++  G + L   L  FL  YP+I + L L ++ +D+  +  D AIR+  P+  
Sbjct: 1   GRLRVNASVPFGTHFLLPLLPAFLARYPEILVDLSLTDEVVDLLAERTDVAIRV-GPLPD 59

Query: 153 SSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWL---- 208
           SSL+ RKL        A+P YL     PL+ Q+L +HN + F     + + D  W     
Sbjct: 60  SSLVARKLGESRRVIVASPSYLARHGTPLTPQDLARHNCLGFN--FRRALPD--WPFRDG 115

Query: 209 -ATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVKD---NPNLVRIMED 261
              V  P+       + VN   ++ +  + G+G+A L  + V D      LV ++E+
Sbjct: 116 GRIVALPVSGN----ILVNDGEALRRLALAGAGLARLALFHVADDIAAGRLVPVLEE 168