Predicting Transcription Units
These are predictions of operons based on intergentic distance. This comes from the work:
- Gabriel Moreno-Hagelsieb and Julio Collado-Vides (2002) A powerful non-homology method for the prediction of operons in prokaryotes. Bioinformatics 18 Suppl. 1 (ISMB02 Special Issue) S329-S336.
Prediction of Transcription Units by Intergenic Distances
These files are distance-based predictions. Be aware that for most cases we do expect to have a high confidence on them, but exceptions are possible. The predictions will be put in a better, more informative, format in a future multigenomic version of RegulonDB.
The format:
- 1st column: Replicon
- 2nd column: Strand (forward or reverse)
- 3rd column: The transcription unit genes identified by their protein ID, as of the RefSeq genome database.
Distance Graphs
These files are graphs of the inter-genic distances of all adjacent genes in the same strand in all prokaryotic genomes available. These might indicate the abundance or proportions of genes in operons within each genome. The genomes were downloaded from the RefSeq genome database.
Table of Genome Redundancy
This table corresponds to the published work. Currently, a table can be built at different similarity thresholds here.
Redundant organisms are indicated by an asterisk (*).
Organism | Abbreviation | GenBank Accessions |
---|---|---|
Crenarchaeota | ||
Aeropyrum pernix | A. pernix | NC_000854 |
Pyrobaculum aerophilum | P. aerophilum | NC_003364 |
Sulfolobus solfataricus | S. solfataricus | NC_002754 |
Sulfolobus tokodaii | S. tokodaii | NC_003106 |
Euryarchaeota | ||
Archaeoglobus fulgidus | A. fulgidus | NC_000917 |
Halobacterium sp. NRC-1 | Halobacterium sp | NC_002607, NC_001869, NC_002608 |
Methanococcus jannaschii | M. jannaschii | NC_000909, NC_001732, NC_001733 |
Methanothermobacter thermautotrophicus | M. thermoautotrophicum | NC_000916 |
Pyrococcus abyssi | P. abyssi | NC_000868 |
Pyrococcus furiosus DSM 3638* | P. furiosus | NC_003413 |
Pyrococcus horikoshii* | P. horikoshii | NC_000961 |
Thermoplasma acidophilum | T. acidophilum | NC_002578 |
Thermoplasma volcanium | T. volcanium | NC_002689 |
Aquificae | ||
Aquifex aeolicus | A. aeolicus | NC_000918, NC_001880 |
Chlamydiales | ||
Chlamydia muridarum | C. muridarum | NC_002620, NC_002182 |
Chlamydophila pneumoniae AR39 | C. pneumoniae AR39 | NC_002179 |
Chlamydophila pneumoniae CWL029* | C. pneumoniae CWL029 | NC_000922 |
Chlamydophila pneumoniae J138* | C. pneumoniae J138 | NC_002491 |
Chlamydia trachomatis* | C. trachomatis | NC_000117 |
Cyanobacteria | ||
Nostoc sp. PCC 7120 | Nostoc sp | NC_003272, NC_003276, NC_003240, NC_003273, NC_003270, NC_003267, NC_003241 |
Synechocystis sp. PCC 6803 | Synechocystis PCC6803 | NC_000911 |
Firmicutes | ||
Bacillus halodurans | B. halodurans | NC_002570 |
Bacillus subtilis | B. subtilis | NC_000964 |
Clostridium acetobutylicum | C. acetobutylicum | NC_003030, NC_001988 |
Clostridium perfringens | C. perfringens | NC_003366, NC_003042 |
Listeria innocua | L. innocua | NC_003212, NC_003383 |
Lactococcus lactis subsp. lactis | L. lactis | NC_002662 |
Listeria monocytogenes EGD-e* | L. monocytogenes | NC_003210 |
Mycoplasma genitalium | M. genitalium | NC_000908 |
Mycobacterium leprae | M. leprae | NC_002677 |
Mycoplasma pneumoniae | M. pneumoniae | NC_000912 |
Mycoplasma pulmonis | M. pulmonis | NC_002771 |
Mycobacterium tuberculosis CDC1551* | M. tuberculosis CDC1551 | NC_002755 |
Mycobacterium tuberculosis H37Rv* | M. tuberculosis H37Rv | NC_000962 |
Staphylococcus aureus subsp. aureus Mu50 | S. aureus Mu50 | NC_002758, NC_002774 |
Staphylococcus aureus subsp. aureus N315* | S. aureus N315 | NC_002745, NC_003140 |
Streptococcus pneumoniae R6 | S. pneumoniae R6 | NC_003098 |
Streptococcus pneumoniae TIGR4* | S. pneumoniae TIGR4 | NC_003028 |
Streptococcus pyogenes M1 GAS | S. pyogenes | NC_002737 |
Ureaplasma urealyticum | U. urealyticum | NC_002162 |
Proteobacteria | ||
Agrobacterium tumefaciens str. C58 (Cereon) | A. tumefaciens C58 | NC_003062, NC_003063, NC_003064, NC_003065 |
Agrobacterium tumefaciens str. C58 (U. Washington)* | A. tumefaciens C58 UWash | NC_003304, NC_003305, NC_003306, NC_003308 |
Brucella melitensis | B. melitensis | NC_003317, NC_003318 |
Buchnera sp. APS | Buchnera sp | NC_002528, NC_002253, NC_002252 |
Caulobacter vibrioides | C. crescentus | NC_002696 |
Campylobacter jejuni | C. jejuni | NC_002163 |
Escherichia coli K12 | E. coli K12 | NC_000913 |
Escherichia coli O157:H7* | E. coli O157H7 | NC_002695 |
Escherichia coli O157:H7 EDL933* | E. coli O157H7 EDL933 | NC_002655 |
Haemophilus influenzae Rd | H. influenzae | NC_000907 |
Helicobacter pylori 26695 | H. pylori 26695 | NC_000915 |
Helicobacter pylori J99* | H. pylori J99 | NC_000921 |
Mesorhizobium loti | M. loti | NC_002678, NC_002679, NC_002682 |
Neisseria meningitidis MC58 | N. meningitidis MC58 | NC_003112 |
Neisseria meningitidis Z2491* | N. meningitidis Z2491 | NC_003116 |
Pseudomonas aeruginosa | P. aeruginosa | NC_002516 |
Pasteurella multocida* | P. multocida | NC_002663 |
Rickettsia conorii | R. conorii | NC_003103 |
Rickettsia prowazekii* | R. prowazekii | NC_000963 |
Ralstonia solanacearum | R. solanacearum | NC_003295, NC_003296 |
Sinorhizobium meliloti | S. meliloti | NC_003047, NC_003037, NC_003078 |
Salmonella enterica subsp. enterica serovar Typhi* | S. typhi | NC_003198, NC_003384, NC_003385 |
Salmonella typhimurium LT2* | S. typhimurium LT2 | NC_003197, NC_003277 |
Vibrio cholerae | V. cholerae | NC_002505, NC_002506 |
Xylella fastidiosa 9a5c | X. fastidiosa | NC_002488, NC_002489, NC_002490 |
Yersinia pestis* | Y. pestis | NC_003143, NC_003131, NC_003134, NC_003132 |
Spirochaetales | ||
Borrelia burgdorferi | B. burgdorferi | NC_001318, NC_001903, NC_000948, NC_000949, NC_000950, NC_000951, NC_000952, NC_000953, NC_000954, NC_001904, NC_001849, NC_000955, NC_001850, NC_001851, NC_001852, NC_001853, NC_001854, NC_001855, NC_001856, NC_000957, NC_001857, NC_000956 |
Treponema pallidum | T. pallidum | NC_000919 |
Thermotogales | ||
Thermotoga maritima | T. maritima | NC_000853 |
Thermus/Deinococcus | ||
Deinococcus radiodurans | D. radiodurans | NC_001263, NC_001264, NC_000959, NC_000958 |
(*) Redundant organisms that should be left out to get the non-redundant prokaryotic genomes data set
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