Protein Info for HER17_RS04110 in Pectobacterium carotovorum WPP14

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 22 to 71 (50 residues), 42.6 bits, 2e-14
• TIGR00479: 23S rRNA (uracil-5-)-methyltransferase RumA
  • amino acids 29 to 435 (407 residues), 475.5 bits, E=7.5e-147
• PF05958: tRNA_U5-meth_tr
  • amino acids 124 to 439 (316 residues), 86.7 bits, E=7.3e-28
• PF00398: RrnaAD
  • amino acids 281 to 353 (73 residues), 28.3 bits, E=4.4e-10
• PF01135: PCMT
  • amino acids 283 to 351 (69 residues), 30.9 bits, E=1e-10
• PF05175: MTS
  • amino acids 292 to 375 (84 residues), 26.1 bits, E=2.8e-09
• PF03602: Cons_hypoth95
  • amino acids 297 to 398 (102 residues), 24.1 bits, E=1.2e-08
• PF13847: Methyltransf_31
  • amino acids 298 to 403 (106 residues), 55.3 bits, E=3.1e-18
• PF13649: Methyltransf_25
  • amino acids 301 to 372 (72 residues), 36.9 bits, E=2.2e-12
• PF08241: Methyltransf_11
  • amino acids 302 to 372 (71 residues), 23 bits, E=4.6e-08

Best Hits

Swiss-Prot: 95% identical to RLMD_PECAS: 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD (rlmD) from Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672)

KEGG orthology group: K03215, RNA methyltransferase, TrmA family [EC: 2.1.1.-] (inferred from 95% identity to pwa:Pecwa_3549)

MetaCyc: 62% identical to 23S rRNA m5U1939 methyltransferase (Escherichia coli K-12 substr. MG1655)
RXN-11601 [EC: 2.1.1.190]

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.- or 2.1.1.190

Protein Sequence (449 amino acids)

>HER17_RS04110 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD (Pectobacterium carotovorum WPP14)
MAQFYSPNRRVTTRKAIPAKNLTVTVTSLDPFGQGVARHEGKTVFVTGVLPGEQAEIQLT
EEKRQFSHAKLKRLLTPSPQRVTPPCPHFTRCGGCQQQHADIALQQSSKTAALMRLMTRE
TGAELPAASLIAGTPYAYRRRARLALYFQAKEQRLLMGYRQSNSHDLVDIKACPVLRPEL
EALLQPLRDCLSRLKAVKRLGHVELVQAENGPLLVLRHLDPLHSSDQQALRDFAQQQGVS
VYLAPDADSLTRLQGEEPVYHVAGLTLAFSPRDFIQVNDAVNQQMVAQALAWLDVQPQDR
ILDLFCGMGNFTLPLAQRAASVVGVEGVTALVEKGRENAQRNGLSNVTFFHQNLEDDVTQ
QPWAAQGFDKILLDPARAGAAGVMEQITRLAPERVVYVSCNATTLARDSKVLLAAGYRLA
NVAMLDMFPHTGHLESMALFLHDTGTRKA