Protein Info for b1804 in Escherichia coli BW25113

Name: rnd
Annotation: ribonuclease D (NCBI)

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 50 100 150 200 250 300 350 375 PF01612: DNA_pol_A_exo1" amino acids 3 to 169 (167 residues), 179.9 bits, see alignment E=6e-57 TIGR01388: ribonuclease D" amino acids 5 to 372 (368 residues), 545.5 bits, see alignment E=3.3e-168 PF00570: HRDC" amino acids 213 to 279 (67 residues), 56.8 bits, see alignment E=2.6e-19 PF21293: RNAseD_HRDC_C" amino acids 301 to 366 (66 residues), 111.6 bits, see alignment E=1.9e-36

Best Hits

Swiss-Prot: 100% 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 100% identity to eco:b1804)

MetaCyc: 100% 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)

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 P09155 at UniProt or InterPro

Protein Sequence (375 amino acids)

>b1804 ribonuclease D (NCBI) (Escherichia coli BW25113)
MNYQMITTDDALASLCEAVRAFPAIALDTEFVRTRTYYPQLGLIQLFDGEHLALIDPLGI
TDWSPLKAILRDPSITKFLHAGSEDLEVFLNVFGELPQPLIDTQILAAFCGRPMSWGFAS
MVEEYSGVTLDKSESRTDWLARPLTERQCEYAAADVWYLLPITAKLMVETEASGWLPAAL
DECRLMQMRRQEVVAPEDAWRDITNAWQLRTRQLACLQLLADWRLRKARERDLAVNFVVR
EEHLWSVARYMPGSLGELDSLGLSGSEIRFHGKTLLALVEKAQTLPEDALPQPMLNLMDM
PGYRKAFKAIKSLITDVSETHKISAELLASRRQINQLLNWHWKLKPQNNLPELISGWRGE
LMAEALHNLLQEYPQ