Protein Info for SMa0870 in Sinorhizobium meliloti 1021

Annotation: NodD1 nod-box dependent transcriptional activator

These analyses and tools can help you predict a protein's function, but be skeptical. For enzymes, over 10% of annotations from KEGG or SEED are probably incorrect. For other types of proteins, the error rates may be much higher. MetaCyc and Swiss-Prot have low error rates, but the best hits in these databases are often quite distant, so this protein's function may not be the same. TIGRFam has low error rates. Finally, many experimentally-characterized proteins are not in any of these databases. To find relevant papers, use PaperBLAST.

Protein Families and Features

1 50 100 150 200 250 308 transmembrane" amino acids 99 to 116 (18 residues), see Phobius details PF00126: HTH_1" amino acids 8 to 67 (60 residues), 55.6 bits, see alignment E=4.2e-19 PF03466: LysR_substrate" amino acids 94 to 298 (205 residues), 43.5 bits, see alignment E=2.6e-15

Best Hits

Swiss-Prot: 100% identical to NODD1_RHIME: Nodulation protein D 1 (nodD1) from Rhizobium meliloti (strain 1021)

KEGG orthology group: K14657, LysR family transcriptional regulator, nod-box dependent transcriptional activator (inferred from 100% identity to sme:SMa0870)

Predicted SEED Role

"Nodulation protein D (transcriptional regulator, LysR family)"

Sequence Analysis Tools

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Compare to protein structures

Predict protein localization: PSORTb (Gram-negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the current SEED with FIGfam search

Find homologs in fast.genomics or the ENIGMA genome browser

See P03031 at UniProt or InterPro

Protein Sequence (308 amino acids)

>SMa0870 NodD1 nod-box dependent transcriptional activator (Sinorhizobium meliloti 1021)
MRFRGLDLNLLVALDALMTERKLTAAARRINLSQPAMSAAIARLRTYFGDELFSMQGREL
IPTPRAEALAPAVRDALLHIQLSVIAWDPLNPAQSDRRFRIILSDFMILVFFARIVERVA
REAPGVSFELLPLDDDPHELLRRGDVDFLIFPDVFMSSAHPKAKLFDEALVCVGCPTNKK
LLGNISFETYMSMGHVAAQFGREMKPSVEQWLLLEHGFNRRIELVVPGFTLIPRLLSGTN
RIATLPLRLVKYFEQTIPLRIVTSPLPPLFFTEAIQWPALHNTDPGNIWLREILLQEASR
IDPQSDTC