Protein Info for LRK54_RS17000 in Rhodanobacter denitrificans FW104-10B01

Annotation: 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD

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

• PF01938: TRAM
  • amino acids 13 to 62 (50 residues), 32.1 bits, 2.1e-11
• TIGR00479: 23S rRNA (uracil-5-)-methyltransferase RumA
  • amino acids 19 to 438 (420 residues), 333.5 bits, E=9.3e-104
• PF05958: tRNA_U5-meth_tr
  • amino acids 275 to 439 (165 residues), 77.4 bits, E=2.8e-25
• PF01135: PCMT
  • amino acids 285 to 354 (70 residues), 27.1 bits, E=8.3e-10
• PF13847: Methyltransf_31
  • amino acids 299 to 376 (78 residues), 38.4 bits, E=2.6e-13
• PF13649: Methyltransf_25
  • amino acids 303 to 357 (55 residues), 31.4 bits, 6.4e-11

Best Hits

Swiss-Prot: 62% identical to RLMD_XANC5: 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD (rlmD) from Xanthomonas campestris pv. vesicatoria (strain 85-10)

KEGG orthology group: K03215, RNA methyltransferase, TrmA family [EC: 2.1.1.-] (inferred from 62% identity to xcv:XCV1381)

Predicted SEED Role

"23S rRNA (Uracil-5-) -methyltransferase RumA (EC 2.1.1.-)" (EC 2.1.1.-)

KEGG Metabolic Maps

• Alkaloid biosynthesis I
• Anthocyanin biosynthesis
• Benzoxazinone biosynthesis
• Biosynthesis of alkaloids derived from shikimate pathway
• Carotenoid biosynthesis - General
• Flavonoid biosynthesis
• Histidine metabolism
• Insect hormone biosynthesis
• Naphthalene and anthracene degradation
• Phenylpropanoid biosynthesis
• Porphyrin and chlorophyll metabolism
• Tryptophan metabolism
• Tyrosine metabolism
• Ubiquinone and menaquinone biosynthesis

Isozymes

Compare fitness of predicted isozymes for: 2.1.1.-

Use Curated BLAST to search for 2.1.1.-

Protein Sequence (445 amino acids)

>LRK54_RS17000 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD (Rhodanobacter denitrificans FW104-10B01)
MSRSNSVPSTLFEAHITDLGHDGRGVARVDGKAVFISGALLGEQVTAKLRKRHRHFDEAD
VVEVIVASPHRVEPRCRHFAECSGCSLQHLDAATQIETKQRVLAENFERIGKVAPQAWLP
PLTAEPWGYRRKGRLSVRHVAKKERVLVGFREEQNPRFVTEIRQCEVMHPALGPKVGLLA
DLLGTMDAVNDIPQIEFAAGDDLMALVFRHMQPLSERDRAALIAFGGQHGFAIYLQPGGT
SSVHPLWPENPRLAFRIASGDARFADVELEFQPLDFVQVNAGMNQLMMARALELLDPQPG
DRVLDLFCGLGNFTLPIARRVAEVVGVEGEHGLVERAAQNAVRNGIGNARFHVANLFEDQ
RAADWAKQPWDKLLLDPPRAGADKVLEYLPHKQTRRIVYVSCHPASLARDAGILVERHGF
RLASAGVMDMFPHTSHVESIAVFVR