Protein Encoding Gene

Protein encoding gene (PEG), protein coding sequence (CDS), and open reading frame (ORF) are nearly synonymous terms. In the FIG ID, the feature type for a protein encoding gene is peg.

Protein encoding genes are commmonly described as structural or regulatory. Structural genes encode enzymes and structural proteins. Regulatory genes encode proteins that function to regulate the expression of other genes, often by binding specifically to short sequences of the DNA.

PEGs may be labeled as hypothetical when there is an open reading frame (see codon), but no experimental evidence that the encoded protein is expressed, or no suggestion by similarity of the function of the encoded protein.

The table below shows the PEG counts for the NMPDR core organisms along with an indication of how many are hypothetical and how many are known.

Group name Genomes Protein Encoding Genes (PEGs) Named genes in subsystems Named genes not in subsystems Hypothetical genes in subsystems Hypothetical genes not in subsystems RNAs
Campylobacter 15 27,372 12,905 8,942 358 5,691 1,043
Chlamydiaceae 10 10,112 4,439 2,627 58 3,235 419
Haemophilus 9 16,660 8,742 5,826 197 2,336 780
Listeria 16 51,610 22,933 17,040 992 11,658 1,685
Mycoplasma 12 8,900 4,027 2,948 40 2,343 508
Neisseria 5 11,319 4,809 3,462 134 1,679 372
Staphylococcus 17 44,572 20,304 13,096 1,456 11,524 1,995
Streptococcus 46 94,883 39,521 37,732 1,055 20,083 3,890
Treponema 2 3,826 1,171 1,547 10 1,197 134
Ureaplasma 13 8,522 3,654 2,482 47 2,425 583
Vibrio 20 79,814 35,035 27,596 1,152 17,951 3,925
Topic revision: r6 - 16 Jan 2009 - 15:13:15 - TWiki Guest
 
Notice to NMPDR Users - The NMPDR BRC contract has ended and bacterial data from NMPDR has been transferred to PATRIC (http://www.patricbrc.org), a new consolidated BRC for all NIAID category A-C priority pathogenic bacteria. NMPDR was a collaboration among researchers from the Computation Institute of the University of Chicago, the Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the National Center for Supercomputing Applications (NCSA) at the University of Illinois. NMPDR is funded by the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract HHSN266200400042C. Banner images are copyright © Dennis Kunkel.