Protein Info for HMPREF1078_RS01815 in Parabacteroides merdae CL09T00C40

Annotation: 30S ribosomal protein S12 methylthiotransferase RimO

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 50 100 150 200 250 300 350 400 431 TIGR00089: radical SAM methylthiotransferase, MiaB/RimO family" amino acids 5 to 428 (424 residues), 371 bits, see alignment E=7.9e-115 PF00919: UPF0004" amino acids 5 to 106 (102 residues), 73.3 bits, see alignment E=2e-24 TIGR01125: ribosomal protein S12 methylthiotransferase RimO" amino acids 5 to 428 (424 residues), 436.9 bits, see alignment E=9.5e-135 PF04055: Radical_SAM" amino acids 142 to 312 (171 residues), 86.8 bits, see alignment E=2.9e-28 PF18693: TRAM_2" amino acids 369 to 430 (62 residues), 71 bits, see alignment E=1.1e-23

Best Hits

Swiss-Prot: 84% identical to RIMO_PARD8: Ribosomal protein S12 methylthiotransferase RimO (rimO) from Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152)

KEGG orthology group: K14441, ribosomal protein S12 methylthiotransferase [EC: 2.-.-.-] (inferred from 84% identity to pdi:BDI_0942)

Predicted SEED Role

"Ribosomal protein S12p Asp88 (E. coli) methylthiotransferase" in subsystem Ribosomal protein S12p Asp methylthiotransferase

KEGG Metabolic Maps

Isozymes

Compare fitness of predicted isozymes for: 2.-.-.-

Use Curated BLAST to search for 2.-.-.-

Sequence Analysis Tools

PaperBLAST (search for papers about homologs of this protein)

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

Search 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 (431 amino acids)

>HMPREF1078_RS01815 30S ribosomal protein S12 methylthiotransferase RimO (Parabacteroides merdae CL09T00C40)
MRKNKVDIITLGCSKNLVDSEQLMRQFVANGYTVEHDPHKINGEIVVVNTCGFIGDAQEE
SINMILDLGEAKKKGKIGKLFVMGCLSERFLKDLENELPEVDRFYGKFNWKELLNDLGKS
YHRELAADRVLTTPRHYAYLKIAEGCDRTCSYCAIPISTGRYQSIPMEEIEKEVRLLVKQ
GVKEFQVIAQDLTYYGLDLYKRHALPELVERISDIPGVEWIRLHYGYPSHFPYDLLRVMS
ERDNVCKYMDIALQHISDPMLKKMRRNITKEETYALIRRMREEVPGIHLRTTLMVGHPGE
TEQDFEELVEFVKEARFERMGAFAYSHEEGTYSFKHYTDDIDPEVKQDRLDYLMRIQEGI
SAEVNGSKIGKVFKVMIDREEEDFYVGRTEFDSPEVDPEILVSKEKLLIPGMFYNVWIDD
AQAFDLYGSVL