Protein Info for PFR28_03748 in Pseudomonas sp. RS175

Annotation: Ribosomal large subunit pseudouridine synthase D

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 50 100 150 200 250 306 TIGR00005: pseudouridine synthase, RluA family" amino acids 3 to 297 (295 residues), 318.4 bits, see alignment E=2.3e-99 PF01479: S4" amino acids 4 to 49 (46 residues), 30.8 bits, see alignment 1.9e-11 PF00849: PseudoU_synth_2" amino acids 77 to 227 (151 residues), 119.3 bits, see alignment E=1.8e-38

Best Hits

Swiss-Prot: 82% identical to RLUD_PSEAE: Ribosomal large subunit pseudouridine synthase D (rluD) from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)

KEGG orthology group: K06180, ribosomal large subunit pseudouridine synthase D [EC: 5.4.99.12] (inferred from 98% identity to pba:PSEBR_a4841)

MetaCyc: 58% 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 (306 amino acids)

>PFR28_03748 Ribosomal large subunit pseudouridine synthase D (Pseudomonas sp. RS175)
MGGQRLDQVAAQLFAEHSRSRLSAWIKDGRLTVDGAVIRPRDIVHGGAILELTAEQEAQG
EWVAQDIALDIVYEDDDILVINKPAGLVVHPAAGHADGTLLNALLHHVPDIINVPRAGIV
HRLDKDTTGLMVVAKTIQAQTQLVAQLQSRSVSRIYECIVIGVVTAGGKINAPIGRHGQQ
RQRMAVMEGGKPAVSHYRVLERFRSHTHVRVKLETGRTHQIRVHMAHINFPLVGDPAYGG
RFRIPPAASMTMVESLKNFPRQALHARFLELDHPTTGKRMSWESPLPDDFVWLLTLLKQD
REAFVG