Protein Info for GFF3074 in Sphingobium sp. HT1-2

Annotation: LSU rRNA pseudouridine(955/2504/2580) synthase (EC 5.4.99.24)

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 50 100 150 200 250 300 350 400 452 TIGR00005: pseudouridine synthase, RluA family" amino acids 103 to 400 (298 residues), 199.5 bits, see alignment E=3.7e-63 PF00849: PseudoU_synth_2" amino acids 194 to 343 (150 residues), 114.1 bits, see alignment E=3.5e-37

Best Hits

KEGG orthology group: K06179, ribosomal large subunit pseudouridine synthase C [EC: 5.4.99.12] (inferred from 78% identity to sjp:SJA_C1-15400)

Predicted SEED Role

"Ribosomal large subunit pseudouridine synthase C (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

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 (452 amino acids)

>GFF3074 LSU rRNA pseudouridine(955/2504/2580) synthase (EC 5.4.99.24) (Sphingobium sp. HT1-2)
MKGRPPGKSGGPARGGKPGGSSAKPGGRSGAPGRARGGAKAASARKQDGDRPFKPGAKSV
GKPRTKAPVAKAAAPAPAVAAKPNPAKGVSLDVRQYRVQADDDGIRLDRWFQRHLPDVGF
NIVSRWSRTGQLRVDGARAAPGDRIAEGQMIRVPPAEPKVAAADKPKRVRVIDLTEDEIA
YVQDMVIHRDKQAIVINKPPGLATQGGTKTDEHVDRLLDGLIFDAESRPKLVHRLDKDTS
GALLLARSSRSAAHFAKAFSSRTARKVYWAIVIGVPSIDDGMIELPITKQPGTGGEKMHV
DEEEGLPARTRYRVIERAGNRAAWVELQPYTGRTHQLRVHMAAIGHPLVGDGKYGGKDSF
LSGSISRKMHLHARRIRVDHPDGGRIDMKAELPEHFLNSLIALGFDLSLGDMPLDDEIDR
TPTREDEKKAARAHAKQIRKGRRGERRGRGEK