Protein Info for GFF6043 in Variovorax sp. SCN45
Annotation: tRNA/rRNA cytosine-C5-methylase
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
KEGG orthology group: K03500, ribosomal RNA small subunit methyltransferase B [EC: 2.1.1.-] (inferred from 96% identity to vpe:Varpa_1380)Predicted SEED Role
"Fmu (Sun) /eukaryotic nucleolar NOL1/Nop2p; tRNA and rRNA cytosine-C5-methylases"
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 (423 amino acids)
>GFF6043 tRNA/rRNA cytosine-C5-methylase (Variovorax sp. SCN45) MHPKALLEATADLVGLVLKFDHPADQVVSRFFRDHREFGPRERAALAETVYTVLRKKLLF DHLSPSGTGSKERRMAILGFYGPRDFLKSALNDTEKRWLDNCDAVKPDDLLERHRHNLPE WLVAPLKAQLGDGFWPLVESLQQPAPLDLRVNALTDKRADVKVELAKAAIKSEVTPFSPW GLRIEGKPALTKLDAFARGAIEVQDEGSQLLALLLDAKRGEMVVDFCAGAGGKTLAIGAT MRNTGRLYAFDTSAHRLDALKPRLARSKLSNVHPAAIAHERDDRIKRLAGKIDRVLVDAP CSGLGTLRRNPDLKWRQSAKAVEELTVKQTAILQSAARLVKSGGRLVYATCSVLPEENEA IAEAFGAANPDFVPVDAAELLQGLKVEGFEALCAGGEGGRRYLRLWPHRHATDGFFAAVW NRK