Protein Info for LRK55_RS04745 in Rhodanobacter denitrificans MT42

Annotation: 23S rRNA pseudouridine(1911/1915/1917) synthase RluD

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 50 100 150 200 250 324 TIGR00005: pseudouridine synthase, RluA family" amino acids 15 to 313 (299 residues), 309.7 bits, see alignment E=1.1e-96 PF00849: PseudoU_synth_2" amino acids 90 to 242 (153 residues), 110.4 bits, see alignment E=4.9e-36

Best Hits

Swiss-Prot: 66% identical to RLUD_XANCP: Ribosomal large subunit pseudouridine synthase D (rluD) from Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25)

KEGG orthology group: K06180, ribosomal large subunit pseudouridine synthase D [EC: 5.4.99.12] (inferred from 66% identity to xcb:XC_1070)

MetaCyc: 55% identical to 23S rRNA pseudouridine1911/1915/1917 synthase (Escherichia coli K-12 substr. MG1655)
RXN-11837 [EC: 5.4.99.23]

Predicted SEED Role

"Ribosomal large subunit pseudouridine synthase D (EC 4.2.1.70)" in subsystem Ribosome biogenesis bacterial (EC 4.2.1.70)

MetaCyc Pathways

KEGG Metabolic Maps

Isozymes

Compare fitness of predicted isozymes for: 4.2.1.70, 5.4.99.12

Use Curated BLAST to search for 4.2.1.70 or 5.4.99.12 or 5.4.99.23

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 (324 amino acids)

>LRK55_RS04745 23S rRNA pseudouridine(1911/1915/1917) synthase RluD (Rhodanobacter denitrificans MT42)
MTTIRHEAEVPLGAAGRRFDQALAEMFPDYSRSRLSGWIKSGAVTLDGAQAPPRQLLRGG
ERVCLEVELENEVSSAAEDIALTIVHEDAHLLVLDKPAGLVVHPGAGNPAGTLLNALLHH
DPQLAELPRAGIVHRLDKDTSGLMVVARTLPTYTALVDLLSRHEVERQYEAVVLGTLVAG
GTVDAPIGRSMGDRLRQAVRDEEDGKRAVTHYRLRERFRAHSLLQCQLETGRTHQIRVHL
AHIGHPLIGDPLYGGGLKLPKGASAELAATLRGFRRQALHAEKLSFIHPASGEALSFGAQ
RPADLQALIEALRADLAEHGSDHY