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 ispeg.
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 - Bruce Parrello
NMPDR is 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.