Protein Info for PP_0478 in Pseudomonas putida KT2440

Annotation: 30S ribosomal 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 50 100 150 206 PF00163: Ribosomal_S4" amino acids 3 to 95 (93 residues), 110.4 bits, see alignment E=5.7e-36 TIGR01017: ribosomal protein uS4" amino acids 3 to 206 (204 residues), 258 bits, see alignment E=2.9e-81 PF01479: S4" amino acids 97 to 143 (47 residues), 74 bits, see alignment 6.2e-25

Best Hits

Swiss-Prot: 100% identical to RS4_PSEPK: 30S ribosomal protein S4 (rpsD) from Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440)

KEGG orthology group: K02986, small subunit ribosomal protein S4 (inferred from 98% identity to ppw:PputW619_4725)

MetaCyc: 73% identical to 30S ribosomal subunit protein S4 (Escherichia coli K-12 substr. MG1655)

Predicted SEED Role

"SSU ribosomal protein S4p (S9e)" in subsystem Ribosome SSU bacterial

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 Q88QL2 at UniProt or InterPro

Protein Sequence (206 amino acids)

>PP_0478 30S ribosomal protein S4 (Pseudomonas putida KT2440)
MARYIGPKCKLSRREGTDLFLKSGVRALESKCNIEAAPGIHGQRRGRQSDYGTQLREKQK
VRRIYGVLERQFRGYYQAAASKKGATGENLLQLLECRLDNVVYRMGFGSTRSESRQLVSH
KAISVNGKTVNIPSYQVRPGDVVAVREKSLGQLRIVQALELCAQRGRVEWVDVDAAKKSG
VFKNVPARSDLSADINENLIVELYSK