Protein Info for GFF1912 in Xanthobacter sp. DMC5

Annotation: Ribosome maturation factor RimM

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 50 100 150 184 TIGR02273: 16S rRNA processing protein RimM" amino acids 5 to 166 (162 residues), 133 bits, see alignment E=3.5e-43 PF01782: RimM" amino acids 7 to 85 (79 residues), 74.3 bits, see alignment E=1.1e-24 PF05239: PRC" amino acids 93 to 165 (73 residues), 41.5 bits, see alignment E=1.6e-14 PF24986: PRC_RimM" amino acids 99 to 164 (66 residues), 47.2 bits, see alignment E=2.2e-16

Best Hits

Swiss-Prot: 79% identical to RIMM_XANP2: Ribosome maturation factor RimM (rimM) from Xanthobacter autotrophicus (strain ATCC BAA-1158 / Py2)

KEGG orthology group: K02860, 16S rRNA processing protein RimM (inferred from 79% identity to xau:Xaut_2512)

Predicted SEED Role

"16S rRNA processing protein RimM" in subsystem Ribosome biogenesis bacterial

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

Find the best match in UniProt

Protein Sequence (184 amino acids)

>GFF1912 Ribosome maturation factor RimM (Xanthobacter sp. DMC5)
MTDRVLVARIGAPHGVRGEVRLFVFTEDPAAILDYDPLTDATGRTRYRITALRAAKDHFV
ARLANVADRTAAEALTNVDLYVPREALPAPEDEDTFYHADLIGLAVEDEAGARIGTVTAL
HDFGAGDILEYAPALPGIRAKTLMVPFTRAAVPVVDVKARRLVVAEAFVERRDPEPEAGE
DKEG