Protein Info for Shew_2950 in Shewanella loihica PV-4

Annotation: RluA family pseudouridine synthase (RefSeq)

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 50 100 150 200 250 323 TIGR00005: pseudouridine synthase, RluA family" amino acids 14 to 313 (300 residues), 344 bits, see alignment E=3.6e-107 PF01479: S4" amino acids 18 to 65 (48 residues), 41.7 bits, see alignment 7.5e-15 PF00849: PseudoU_synth_2" amino acids 92 to 242 (151 residues), 109.5 bits, see alignment E=1.9e-35

Best Hits

Swiss-Prot: 66% identical to RLUD_SHIFL: Ribosomal large subunit pseudouridine synthase D (rluD) from Shigella flexneri

KEGG orthology group: K06180, ribosomal large subunit pseudouridine synthase D [EC: 5.4.99.12] (inferred from 100% identity to slo:Shew_2950)

MetaCyc: 66% 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)

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

See A3QH68 at UniProt or InterPro

Protein Sequence (323 amino acids)

>Shew_2950 RluA family pseudouridine synthase (RefSeq) (Shewanella loihica PV-4)
MTQEINLKSEITATQTGQRLDQTLAELFPDYSRTRIKEWIQAGAVYVDGMVQTKPREKVL
EGQEIEIEATLKEEIKAEAQAIDLDIVYEDDHIIVINKQAGLVVHPGAGNSDGTLMNALL
HHCPEIELVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVAALQAREITREYEAIVSGTMT
AGGVVDEPIARHPTKRTHMAVHHSGRPSVTHYRVAEKFRAHTRLRLRLETGRTHQIRVHM
AHIGHILVGDPVYGGRPRPPKKATPELMEALNGFKRQALHAVRLELAHPFTCEIMSWQAP
IPEDMVALTRALRDDTKAHPVEY