Protein Info for GFF4489 in Variovorax sp. SCN45
Annotation: 23S rRNA (cytosine(1962)-C(5))-methyltransferase (EC 2.1.1.191)
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
Best Hits
Swiss-Prot: 46% identical to RLMI_ALTMD: Ribosomal RNA large subunit methyltransferase I (rlmI) from Alteromonas mediterranea (strain DSM 17117 / CIP 110805 / LMG 28347 / Deep ecotype)
KEGG orthology group: K06969, ribosomal RNA large subunit methyltransferase I [EC: 2.1.1.-] (inferred from 92% identity to vap:Vapar_0903)Predicted SEED Role
"LSU m5C1962 methyltransferase RlmI" in subsystem Ribosome biogenesis bacterial
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.-
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 (404 amino acids)
>GFF4489 23S rRNA (cytosine(1962)-C(5))-methyltransferase (EC 2.1.1.191) (Variovorax sp. SCN45) MKTLRLKPGKERSMQRRHPWVFESAIARGGADSGETVRVESHDGAFLAWAAFSPASKIRA RAWSFVETQRIDAAFLASVCARAVAARGLFDLQSDGVRVVHGEADGLPGLIVDRYGDTLV AQFLSAGVERWKDVLADALLKATGLAKLYERSDASGREREGLKPVTGWLRGDGPTEIVIR EHGWKLSLDIATGHKTGFYLDQRDSRQRFAELAQHRRFRRVLNCFCYTGGFTVAALAGLK AANALQGAQLVSVDSSLPALERARGHLALNGFEGQGIEAEFLDANVNTVLREFIDQGRTF DAIVLDPPKFAPTAAHAERAARAYKDINRLALKLLEPGGVLLTFSCSGGISADLFHKIVA SAGIDAGVDGYIAERLGAAPDHPMTIEFPEGEYLKGLVVVRKPA