Protein Info for GFF2819 in Salmonella enterica subsp. enterica serovar Typhimurium str. MS1868

Annotation: Ribonuclease D (EC 3.1.26.3)

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 50 100 150 200 250 300 371 TIGR01388: ribonuclease D" amino acids 1 to 367 (367 residues), 515.6 bits, see alignment E=4e-159 PF01612: DNA_pol_A_exo1" amino acids 1 to 164 (164 residues), 170 bits, see alignment E=6.5e-54 PF00570: HRDC" amino acids 209 to 275 (67 residues), 54.9 bits, see alignment E=1e-18 PF21293: RNAseD_HRDC_C" amino acids 297 to 362 (66 residues), 107.2 bits, see alignment E=4.5e-35

Best Hits

Swiss-Prot: 87% identical to RND_ECOLI: Ribonuclease D (rnd) from Escherichia coli (strain K12)

KEGG orthology group: K03684, ribonuclease D [EC: 3.1.13.5] (inferred from 98% identity to ses:SARI_01122)

MetaCyc: 87% identical to RNase D (Escherichia coli K-12 substr. MG1655)
Ribonuclease D. [EC: 3.1.13.5]; 3.1.13.5 [EC: 3.1.13.5]; 3.1.13.5 [EC: 3.1.13.5]

Predicted SEED Role

"Ribonuclease D (EC 3.1.26.3)" in subsystem Experimental tye or tRNA processing (EC 3.1.26.3)

MetaCyc Pathways

Isozymes

Compare fitness of predicted isozymes for: 3.1.26.3

Use Curated BLAST to search for 3.1.13.5 or 3.1.26.3

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

Find the best match in UniProt

Protein Sequence (371 amino acids)

>GFF2819 Ribonuclease D (EC 3.1.26.3) (Salmonella enterica subsp. enterica serovar Typhimurium str. MS1868)
MIETDDALASLCEAVRACPAIALDTEFVRTRTYYPQLGLIQLFDGANVALIDPLGISDWS
PLKAVLRDTGITKFLHAGSEDLEVFLNAFGELPEPLIDTQILAAFCGRPLSWGFASMVEE
YTGVALDKSESRTDWLARPLSERQCEYAAADVWYLLPIAKKLMIETEAAGWLPAALDECR
LMQQRRQEIQAPEEAWRDITNAWQLRTRQLACLQLLADWRLRKARERDMAVNFVVREENL
WAVARYMPGSLGELDSLGLSGSEIRFHGKTLISLVAKAQALPEEALPEPLLNLMDMPGYR
KAFKAIKALVAEVSASHHVSGELLASRRQINQLLNWHWKLKPQNGQPELISGWRAELMEE
KLTLLLQEYPL