Protein Info for Sama_2039 in Shewanella amazonensis SB2B

Name: yebU
Annotation: rRNA (cytosine-C(5)-)-methyltransferase RsmF (RefSeq)

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 50 100 150 200 250 300 350 400 467 PF17125: Methyltr_RsmF_N" amino acids 4 to 96 (93 residues), 75 bits, see alignment E=1.3e-24 TIGR00446: NOL1/NOP2/sun family putative RNA methylase" amino acids 37 to 304 (268 residues), 318 bits, see alignment E=2.2e-99 PF01189: Methyltr_RsmB-F" amino acids 106 to 302 (197 residues), 160.1 bits, see alignment E=1.4e-50 PF21150: YebU_pre-PUA_dom" amino acids 323 to 399 (77 residues), 64.5 bits, see alignment E=1.7e-21 PF13636: Methyltranf_PUA" amino acids 412 to 460 (49 residues), 45.9 bits, see alignment 1.2e-15

Best Hits

Swiss-Prot: 100% identical to RSMF_SHEAM: Ribosomal RNA small subunit methyltransferase F (rsmF) from Shewanella amazonensis (strain ATCC BAA-1098 / SB2B)

KEGG orthology group: K11392, ribosomal RNA small subunit methyltransferase F [EC: 2.1.1.-] (inferred from 100% identity to saz:Sama_2039)

MetaCyc: 52% identical to 16S rRNA m5C1407 methyltransferase (Escherichia coli K-12 substr. MG1655)
RXN-11593 [EC: 2.1.1.178]

Predicted SEED Role

"Ribosomal RNA small subunit methyltransferase F (EC 2.1.1.-)" (EC 2.1.1.-)

KEGG Metabolic Maps

Isozymes

Compare fitness of predicted isozymes for: 2.1.1.-

Use Curated BLAST to search for 2.1.1.- or 2.1.1.178

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 A1S788 at UniProt or InterPro

Protein Sequence (467 amino acids)

>Sama_2039 rRNA (cytosine-C(5)-)-methyltransferase RsmF (RefSeq) (Shewanella amazonensis SB2B)
MVQLNQKFINSIAQEMPPHLSMDDFVHYCGLPLRLSIRVNTLKITSDALRAILEPRGWQF
EPVPWCEDGFWVTVPDDCQPGNLTEHYQGLFYIQEASSMMPPCALFMDKEPRQLLLDVAS
APGSKTTQLAALMHNQGLIIANEYSASRTKALHANLQRMGVANVAITQFDGRVFGAHLYE
TLDAIQLDAPCSGEGTVRKDPLSLKNWCPDEIEAIAELQRDLIDSAFQALKPGGVLVYST
CTLNRRENEDVCHFLKERYGDAVVFESLNDLFKGADKALTEEGFLHIWPQIYDSEGFFVA
RIRKTASVARNTDDPRFVSKFPFVAANRKELSALEEAMLALGVSLPEDAVIVTRDGEFWL
MPAPLDGLLTKMRFQRIGIRLAETQKHGIKVRHEAVMALPCNQMLSIEPEAAKQYLMGRD
IALDNAGKAQGEKILSLHGAPLGIAKHLGNKLKNSLPRDLCRDNVQN