Protein Info for Shew_1209 in Shewanella loihica PV-4
Annotation: pseudouridylate 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
Best Hits
Swiss-Prot: 66% identical to TRUD_SHEON: tRNA pseudouridine synthase D (truD) from Shewanella oneidensis (strain MR-1)
KEGG orthology group: K06176, tRNA pseudouridine synthase D [EC: 5.4.99.12] (inferred from 100% identity to slo:Shew_1209)Predicted SEED Role
"tRNA pseudouridine 13 synthase (EC 4.2.1.-)" in subsystem tRNA processing (EC 4.2.1.-)
KEGG Metabolic Maps
- 1- and 2-Methylnaphthalene degradation
- Benzoate degradation via CoA ligation
- Benzoate degradation via hydroxylation
- Biosynthesis of type II polyketide backbone
- Biosynthesis of unsaturated fatty acids
- Butanoate metabolism
- Fatty acid biosynthesis
- Limonene and pinene degradation
- Nucleotide sugars metabolism
- Phenylalanine, tyrosine and tryptophan biosynthesis
- Porphyrin and chlorophyll metabolism
- Tyrosine metabolism
Isozymes
Compare fitness of predicted isozymes for: 4.2.1.-, 5.4.99.12
Use Curated BLAST to search for 4.2.1.- 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
See A3QC81 at UniProt or InterPro
Protein Sequence (355 amino acids)
>Shew_1209 pseudouridylate synthase (RefSeq) (Shewanella loihica PV-4) MTPLHYLYGQPEASADLRTYNSDFIVQEILPFLPTGEGEHHMLHIRKEGLNTADVARMLS SFAGVHPKEVTFAGQKDRHAITEQWFGVRIPGKSMPDWQSLNSEQLTVLSSARHGKKLRT GALAGNRFTLTLRAVSDMDALVRRIELIKATGVPNYFGEQRFGHDGKNLIFGRQMLSGKK KVKDRNKRSIYLSAVRSYLFNQVVSERLRLHQLKTLDGDCVMLAGSKSYFVANPWDESLY GRLAENDIQLSAPMWGRGLALSEAEALAFEQGVCGQYPEDLAGLEQAGLNQERRPLLLAP QQLSYEIQEDTLVIKFALPAGSFATSVLRELVNYQDVKEREYQARKAAASEQAHD