Protein Info for CSW01_12410 in Vibrio cholerae E7946 ATCC 55056

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

1 50 100 150 200 250 300 350 400 440 PF01938: TRAM" amino acids 17 to 68 (52 residues), 40.4 bits, see alignment 1.1e-13 TIGR00479: 23S rRNA (uracil-5-)-methyltransferase RumA" amino acids 25 to 431 (407 residues), 429.9 bits, see alignment E=5.5e-133 PF05958: tRNA_U5-meth_tr" amino acids 100 to 438 (339 residues), 112.9 bits, see alignment E=8.9e-36 PF00398: RrnaAD" amino acids 277 to 355 (79 residues), 28.1 bits, see alignment E=5.5e-10 PF01135: PCMT" amino acids 278 to 348 (71 residues), 29.3 bits, see alignment E=3.6e-10 PF02475: TRM5-TYW2_MTfase" amino acids 291 to 344 (54 residues), 32 bits, see alignment 6.3e-11 PF13847: Methyltransf_31" amino acids 294 to 370 (77 residues), 50.6 bits, see alignment E=8.6e-17 PF09445: Methyltransf_15" amino acids 295 to 375 (81 residues), 23.5 bits, see alignment E=1.9e-08 PF13649: Methyltransf_25" amino acids 297 to 352 (56 residues), 32.4 bits, see alignment 6e-11 PF08241: Methyltransf_11" amino acids 298 to 352 (55 residues), 21.4 bits, see alignment 1.6e-07

Best Hits

Swiss-Prot: 100% identical to RLMD_VIBCM: 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD (rlmD) from Vibrio cholerae serotype O1 (strain M66-2)

KEGG orthology group: K03215, RNA methyltransferase, TrmA family [EC: 2.1.1.-] (inferred from 100% identity to vch:VC2452)

Predicted SEED Role

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

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 (440 amino acids)

>CSW01_12410 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD (Vibrio cholerae E7946 ATCC 55056)
MARFFQPKKHSTLDTKHQPVTIERLDHQGSGLAFLHKKPLFVDGALPGEEVLIQLTENKS
KYARGQLIKVLKPSAERVAPFCAHYAQCGGCDLQHLDRAGQIHHKQQALSQLMVKFAGQS
LALSAPVCSDDQGYRRRARLSLMWDKKTQQLQLGFRRKQSKAIVNVTHCPVLEPSLNALL
PDLNALLSEWSQPERLGHVELVKGDNTRVLVLRHLGALIEQDQQRLTDFASQNQLTLYLM
LEAGELQHVQGEAPYCEETGSRLSFLPSHFIQVNRAVNQHMVVQALNWLEVSPQERVLDL
FCGLGNFTLPLAKQAQAVVGVEGVDEMVQHATHNAKLNQINNVAFYQANLEQDMTSASWA
QQKFAKVLLDPARAGAEGIVDQLSALGAKRVVYVSCNPATLARDSQSLLSQGFRLEKLGM
LDMFPHTSHLESMALFVKKG