Protein Info for PS417_05870 in Pseudomonas simiae WCS417

Annotation: RNA-binding protein S4

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 50 100 150 200 236 PF01479: S4" amino acids 15 to 47 (33 residues), 26.4 bits, see alignment 2.2e-10

Best Hits

KEGG orthology group: K06182, ribosomal large subunit pseudouridine synthase F [EC: 5.4.99.12] (inferred from 98% identity to pfs:PFLU1201)

Predicted SEED Role

"tRNA pseudouridine synthase A (EC 4.2.1.70)" in subsystem tRNA processing (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)

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

See U1UMX1 at UniProt or InterPro

Protein Sequence (236 amino acids)

>PS417_05870 RNA-binding protein S4 (Pseudomonas simiae WCS417)
MTDPIRLSKRLIELVGCSRREAELFIEGGWVSVDGEVIDEPQFKVTTQKVALDPDAKATV
PEPVTILLHAPAGVDAETAMASISAETLSEEHRFGKRPLKGHFLRLTASADLQAKASGLL
VFTQDWKILRKLTADAAKIEQEYVVEVEGDMVAHGLNRLNHGLTYKGKELPAVKASWQNE
NRLRFAMKNPQPGVIALFCEAVGLKVIAIRRIRIGGVSIGKVPVGQWRYLSGKEKF