^{version 1.0}

An aid to the identification of genomics islands, including pathogenicity islands, of potentially horizontally transferred genes

See the help file for more information, plus analyses that illustrate the utility of IslandPath.

Select the button below for a given organism to view a graphical representation of the organism's genome with some features commonly associated with genomic islands marked. These features include abnormal %G+C, dinucleotide bias, proximity to tRNA and other structural RNA and the presence of mobility genes (transposases and integrases). Plain text tables of the ORF %G+C data and ORF-cluster dinucleotide bias data are also available by request. A cautionary note: This analysis does not definitely identify islands of horizontally transferred genes, but rather should be considered a guide for the identification of clusters of genes that are more likely to have horizontal origins. A reminder that such analysis only identifies a subset of potential recent horizontal transfers (i.e. those that involve genetic exchange between organisms of differing DNA signatures). See the publication associated with IslandPath for further information (William Hsiao, Ivan Wan, Steven J. Jones, and Fiona S.L. Brinkman, Bioinformatics, Feb 2003 PMID:12584130). We thank the National Centre for Biotechnology Information (NCBI), particularly Tatiana Tatusov, for providing helpful files for IslandPath and acknowledge the efforts of the many microbial and other genome projects that have made such an analysis possible.

IslandPath is maintained by William Hsiao of the Brinkman Laboratory at Simon Fraser University, BC, Canada. Email islandpath-mail@sfu.ca with any questions/comments. If you wish to be notified of changes to islandpath, you can subscribe to the islandpath-update mailing list by sending an email to maillist@sfu.ca with "subscribe islandpath-update" in the subject or body of the message.

The tables below list organisms according to a measure of %G+C variance in the genome. You may also view this data alphabetically. The gene G+C variance for a bacterial genome appears to reflect the number of incidences of recent horizontal gene exchange with organisms of differing G+C ratios, for extreme cases.

• Pathogenic Bacteria
• Bacteria that are primarily non-pathogenic
• Archaea
  

Pathogenic Bacteria

Organism	Approximate host range	"Primary" Disease	Intracellular?	No. of protein coding ORFs	%G+C Mean (all ORFs)	%G+C S.D. (all ORFs)	%G+C Mean (ORFs >300bp)	%G+C S.D. (ORFs >300bp)	Genome Dinucleotide Bias Mean	Genome Dinucleotide Bias S.D.	Interactive Graphical View of ORFs
Chlamydophila caviae GPIC	guinea pig	guinea pig inclusion conjunctivitis (GPIC)	Intracellular	998	39.40	2.70	39.70	2.20	39.90	14.80
Chlamydia trachomatis D	humans	chlamydia	obligate Intracellular	894	41.50	2.30	41.50	2.30	39.60	14.50
Chlamydophila pneumoniae TW-183	humans	chlamydial pneumonia	obligate Intracellular	1113	40.62	3.18	41.05	2.58	40.39	16.40
Chlamydophila pneumoniae J138	humans	chlamydial pneumonia	obligate Intracellular	1070	40.90	2.80	41.10	2.60	39.90	16.60
Agrobacterium tumefaciens C58 Cereon Circular	plants	crown gall	Extracellular	2721	59.40	3.30	59.80	2.70	38.20	16.20
Agrobacterium tumefaciens C58 Uwash Circular	plant	Crown Gall	Extracellular	2785	59.40	3.40	59.86	2.75	38.60	16.30
Bartonella quintana str. Toulose	humans	trench fever	Facultative Intracellular	1142	40.09	2.95	40.15	2.80	40.18	17.48
Brucella melitensis choromosome II	goats, sheep, and humans	Malta fever in human	Facultative Intracellular	1139	57.71	3.41	58.13	2.81	40.10	15.70
Mycobacterium leprae	humans	Leprosy	obligate intraceullular	2720	59.70	3.20	60.00	2.90	34.20	12.70
Brucella suis 1330 chromosome II	humans and other animals	brucellosis (a zoonotic disease)	Facultative Intracellular	1148	56.92	4.54	58.11	2.95	40.87	17.63
Vibrio parahaemolyticus RIMD 2210633 chromosome I	humans	watery diarrhea	Extracellular(?)	3080	45.40	3.50	45.90	3.00	46.80	21.30
Helicobacter hepaticus	mice and rat	chronic hepatitis and liver cancer	Extracellular	1875	35.80	3.58	36.22	3.03	43.55	20.50
Agrobacterium tumefaciens C58 Uwash Lineaer	Plant	Crown Gall	Extracellular	1876	59.30	3.50	59.73	3.04	38.80	16.30
Staphylococcus aureus subsp. aureus strain MRSA252	humans	methicillin-resistance Staphylococcus aureus;	Extracellular	2656	32.95	3.41	33.19	3.05	51.72	24.46
Staphylococcus aureus subsp. aureus MW2	humans	methicillin-resistance Staphylococcus aureus (MRSA); septicaemia, septic arthritis	Extracellular	3371	32.85	3.41	33.13	3.10	51.62	24.35
Leptospira interrogans chromosome II	humans and other animals	leptospirosis, Fort Bragg fever, Weil's syndrome, aseptic meningitis(a zoonotic disease)	Extracellular	367	35.09	4.66	36.53	3.11	47.88	21.86
Mycoplasma gallisepticum	avians (including chicken)	chronic respiratory disease	Facultative Intracellular	726	31.65	3.21	31.64	3.15	52.68	22.05
Bacillus anthracis A2012	humans, cattle, sheep, goats, horses, pigs	anthrax	Extracellular	5544	35.61	3.48	35.80	3.19	52.54	19.86
Vibrio vulnificus CMCP6 chromosome II	humans, shellfish	vomiting, diarrhea, abdominal pain; septicemia and blistering skin lesions	Extracellular	1565	47.70	3.40	48.00	3.20	42.50	20.50
Leptospira interrogans serovar Copenhageni, chromosome II	rodents, humans	leptospirosis, Fort Bragg fever, Weil's syndrome, aseptic meningitis(a zoonotic disease)	Extracellular	264	36.46	3.21	36.43	3.21	42.63	17.29
Listeria monocytogenes strain EGD-e	Mammals, birds, fish, crustaceans and insects	meningoencephalitis and/or septicemia	Facultative Intracellular	2846	38.00	3.40	38.12	3.23	45.40	20.60
Listeria monocytogenes str. 4b F2365	Mammals, birds, fish, crustaceans and insects	meningoencephalitis and/or septicemia	Facultative Intracellular	2821	37.91	3.60	38.22	3.25	45.56	20.38
Clostridium perfringens	humans	gas gangrene, enterotoxaemia, myonecrotic lesions	Extracellular	2660	29.10	3.50	29.18	3.29	53.40	22.70
Vibrio vulnificus CMCP6 chromosome I	humans, shellfish	vomiting, diarrhea, abdominal pain; septicemia and blistering skin lesions	Extracellular	2972	47.10	3.50	47.20	3.30	47.40	23.80
Streptococcus agalactiae 2603V/R	humans	bacterial sepsis, pneumonia, and meningitis	Extracellular	2124	35.44	3.78	35.81	3.31	47.61	23.16
Mycobacterium bovis subsp. bovis AF2122/97	animals and humans	tuberculosis	Facultative Intracellular	3920	65.47	3.40	65.58	3.33	42.09	20.19
Vibrio vulnificus YJ016 chromosome II	humans, shellfish	vomiting, diarrhea, abdominal pain; septicemia and blistering skin lesions	Extracellular	1696	47.09	4.03	47.73	3.34	41.08	15.90
Bacillus cereus ATCC 10987	humans	endophthalmitis, food poisoning (opportunistic pathogen)	Extracellular	5603	35.34	4.00	35.86	3.36	52.15	21.31
Mycobacterium avium paratuberculosis	animals and human (opportunistic)	Johne disease (in ruminants) and possible cause of Crohn disease (in human)	Obligate Intracellular	4350	69.39	3.47	69.49	3.37	39.84	13.95
Streptococcus agalactiae NEM316	humans	septicaemia, meningitis and pneumonia in neonates	Extracellular	2094	35.70	3.50	35.70	3.40	46.90	22.40
Rickettsia typhi strain wilmington	mammals (including humans) and anthropod vector	murine typhus, meningoencephalitis, interstitial pneumonia, and disseminated vascular lesions	Obligate Intracellular	838	29.88	3.61	30.16	3.42	39.71	16.63
Leptospira interrogans serovar Copenhageni, chromosome I	rodents, humans	leptospirosis, Fort Bragg fever, Weil's syndrome, aseptic meningitis(a zoonotic disease)	Extracellular	3394	36.17	3.74	36.47	3.44	46.38	19.41
Leptospira interrogans chromosome I	humans and other animals	leptospirosis, Fort Bragg fever, Weil's syndrome, aseptic meningitis(a zoonotic disease)	Extracellular	4360	35.02	4.84	36.42	3.47	50.74	21.25
Streptococcus pyogenes SSI-1	humans	scarlet fever, toxic shock like syndrome	Extracellular	1861	38.50	3.80	38.80	3.50	50.20	23.00
Streptococcus pyogenes MGAS10394	humans	macrolide-resistant strain; scarlet fever, toxic shock like syndrome	Extracellular	1886	38.65	3.80	38.99	3.52	49.01	22.31
Haemophilus ducreyi 35000HP	humans	chancroid (genital ulcer disease)	Extracellular	1717	38.08	4.33	38.64	3.54	48.61	24.39
Streptococcus pyogenes strain MGAS8232	humans	scarlet fever, toxic shock like syndrome	Extracellular	1845	38.55	3.80	38.85	3.56	49.40	22.90
Streptococcus pyogenes	humans	scarlet fever, toxic shock like syndrome	Extracellular	1696	38.60	3.70	38.90	3.60	47.40	21.90
Streptococcus mutans UA159	humans	dental caries	Extracellular	1963	37.10	3.90	37.30	3.61	44.01	19.25
Bordetella pertussis	humans	whooping cough	Extracellular	3436	67.71	3.90	67.94	3.67	44.11	17.21
Vibrio cholerae chromosome I	humans, zooplankton, other aquatic life	cholera	Extracellular	2736	47.40	4.30	48.10	3.70	44.80	20.60
Vibrio vulnificus YJ016 chromosome I	humans, shellfish	vomiting, diarrhea, abdominal pain; septicemia and blistering skin lesions	Extracellular	3259	46.27	4.02	46.74	3.71	47.77	22.21
Xanthomonas axonopodis pv. citri str. 306	most citrus cultivars	citrus canker	Extracellular	4312	64.78	3.84	64.91	3.78	49.84	22.40
Ureaplasma urealyticum serovar3	humans	urethritis	Extracellular	613	25.80	3.80	25.80	3.80	50.60	22.10
Pseudomonas syringae pv tomato str DC3000	plants	bacterial speck	Extracellular(?)	5471	58.60	4.10	59.00	3.90	42.30	16.40
Shigella flexneri 2a 2457T	humans	severe gastroenteritis (bacillary dysentery)	Facultative Intracellular	4068	51.57	4.04	51.79	3.91	43.70	18.69
Xanthomonas campestris	plants	black rot	Extracellular	4181	65.30	4.10	65.50	4.00	49.80	21.40
Bordetella bronchiseptica	animals	chronic respiratory infections	Extracellular	4994	68.04	4.24	68.29	4.02	47.62	19.49
Shigella flexneri 2a	humans	severe gastroenteritis (bacillary dysentery)	Facultative Intracellular	4180	51.28	4.24	51.46	4.15	43.29	18.44
Treponema pallidum Nichols	humans	syphillis	Extracellular	1031	52.90	4.30	51.40	4.20	44.10	16.80
Ralstonia solanacearum	plants	wilt disease (Southern wilt, bacterial wilt, and brown rot of potato)	Extracellular(?)	3440	67.00	4.60	67.29	4.23	48.50	19.50
Vibrio cholerae chromosome II	humans, zooplankton, other aquatic life	cholera	Extracellular	1092	46.00	4.80	46.90	4.30	46.10	20.40
Streptococcus pneumoniae TIGR4	humans	bacterial pneumonia, meningitis, sepsis, and otitis media	Extracellular	2094	39.50	5.00	40.30	4.40	49.50	24.30
Onion yellows phytoplasma	plant and insect vector	virescence, yellowing, phyllody, stunting	Obligate Intracellular	754	28.56	4.59	28.58	4.45	76.96	27.61
Corynebacterium diphtheriae	humans	diphtheria (toxin)	Extracellular	2272	53.75	4.65	53.97	4.49	46.76	20.73
Yersinia pestis KIM	hymans, other animals	bubonic plague and Pneumonic plague	Facultative Intracellular	4090	48.00	5.00	48.30	4.60	42.00	18.20
Porphyromonas gingivalis W83	humans	periodontal disease	Extracellular	1909	48.73	4.83	49.22	4.62	41.63	18.98
Yersinia pestis biovar Mediaevails	humans, other animals	bubonic plague and Pneumonic plague	Facultative Intracellular	3895	47.77	5.00	48.29	4.63	41.13	17.96
Yersinia pestis CO92	humans, other animals	bubonic plague and Pneumonic plague	Facultative Intracellular	3885	47.90	4.90	48.30	4.70	41.50	17.90
Escherichia coli CFT073	human	urinary tract infection	Extracellular(?)	5389	50.10	5.60	51.00	4.80	49.50	24.30
Yersinia pseudotuberculosis IP32953 chromosome	animals and humans	yersiniosis	Extracellular(?)	3901	48.01	4.97	48.26	4.82	41.62	19.07
Xylella fastidiosa Temecula1	plants	Pierce's disease	Extracellular	2034	52.20	5.20	52.50	4.90	49.70	22.10
Erwinia carotovora subsp. atroseptica SCRI1043	potato	soft rot and blackleg in potato	Extracellular(?)	4472	51.14	5.41	51.61	5.04	42.47	19.47
Salmonella enterica subsp. enterica serovar Typhi	humans	enteric (typhoid) fever	Facultative Intracellular	4395	52.17	5.59	52.71	5.18	48.20	26.30
Salmonella typhimurium LT2	humans and other animals	Gastroenteritis	Facultative Intracellular	4451	52.39	5.40	52.76	5.19	44.50	21.10
Salmonella enterica subsp. enterica serovar Typhi Ty2	humans	enteric (typhoid) fever	Facultative Intracellular	4323	52.20	5.60	52.80	5.20	47.70	26.10
Escherichia coli O157_EDL933	warm blooded animals, including humans	diarrhea	Facultative Intracellular	5349	50.40	5.90	51.00	5.30	50.90	23.00
Treponema denticola ATCC 35405	humans	periodontal disease	Extracellular	2767	37.25	5.76	37.80	5.31	55.64	26.51
Xylella fastidiosa 9a5c	plants	citrus variegated chlorosis	Extracellular	2766	52.20	6.20	53.40	5.40	54.20	23.90
Photorhabdus luminescens	insects, nematodes vector	toxemia and septicemia in insects	Extracellular(?)	4683	43.10	5.83	43.19	5.78	47.99	19.81
Neisseria meningitidis serogroup A strain Z2491	humans	meningitis	Extracellular	2121	51.70	7.10	52.60	6.50	51.00	28.00
Neisseria meningitidis serogroup B strain MC58	humans	meningitis	Extracellular	2025	51.40	7.60	52.40	6.90	54.10	30.10

Bacteria that are primarily non-pathogenic

Organism	No. of protein coding ORFs	%G+C Mean (all ORFs)	%G+C S.D. (all ORFs)	%G+C Mean (ORFs >300bp)	%G+C S.D. (ORFs >300bp)	Genome Dinucleotide Bias Mean	Genome Dinucleotide Bias S.D.	Graphical analysis
Pirellula sp.	7325	54.91	2.96	55.41	2.32	42.49	18.95
Wolbachia endosymbiont of Drosophila melanogaster	1195	35.43	3.58	35.09	2.71	43.69	17.22
Thermotoga maritima MSB8	1846	46.10	3.40	46.30	3.10	42.20	19.20
Bdellovibrio bacteriovorus	3587	50.40	3.19	50.68	2.75	40.38	16.54
Sinorhizobium meliloti 1021	3341	63.00	3.00	63.30	2.80	39.50	16.40
Parachlamydia sp.UWE25	2031	35.64	3.37	36.08	2.86	42.66	18.06
Rhodopseudomonas palustris CGA009	4813	65.23	3.17	65.44	2.99	40.29	16.07
Lactobacillus johnsonii NCC 533	1821	34.52	3.16	34.59	3.00	48.78	20.50
Propionibacterium acnes KPA171202	2297	60.05	3.20	60.22	3.03	38.19	15.57
Oceanobacillus iheyensis	3496	35.64	3.25	35.79	3.05	43.64	18.81
Clostridium acetobutylicum ATCC824	3672	31.08	3.28	31.20	3.10	46.90	18.40
Thermus thermophilus HB27 chromosome	1982	69.35	3.27	69.57	3.12	53.78	25.13
Thermosynechococcus elongatus BP-1	2475	54.11	3.25	54.34	3.13	35.27	14.59
Listeria innocua Clip11262	2968	37.40	3.30	37.60	3.17	46.10	18.80
Streptomyces avermitilis MA-4680	7575	70.70	3.30	70.90	3.20	46.70	18.40
Mesorhizobium loti	6752	63.00	3.50	63.20	3.30	42.30	16.30
Wolinella succinogenes	2044	48.62	3.50	48.78	3.39	43.12	18.39
Buchnera aphidicola (Baizongia pistaciae)	504	26.90	3.40	26.90	3.40	43.90	16.60
Streptomyces coelicolor A3	7512	72.07	3.62	72.28	3.42	46.56	16.72
Fusobacterium nucleatum subsp. Nucleatum ATCC25586	2067	27.00	3.80	27.13	3.46	47.20	18.20
Mycoplasma mobile 163K	633	25.29	3.59	25.21	3.48	45.08	16.32
Bradyrhizobium japonicum	8317	64.10	3.80	64.40	3.50	46.63	19.70
Shewanella oneidensis MR-1	4630	46.30	3.80	46.57	3.59	42.30	18.10
Buchnera sp. APS	564	27.30	3.70	27.20	3.60	44.60	18.70
Corynebacterium glutamicum	3040	54.30	3.80	54.56	3.66	46.60	21.30
Prochlorococcus marinus CCMP1375	1882	37.01	4.00	37.02	3.70	46.86	18.30
Thermoanaerobacter tengcongensis strain MB4T	2588	37.40	4.04	37.64	3.78	46.26	19.64
Pseudomonas putida KT2440	5350	61.80	4.00	62.10	3.80	47.20	20.00
Acinetobacter sp. ADP1	3325	40.81	4.14	41.15	3.82	44.46	22.97
Mesoplasma florum L1	683	26.85	3.89	26.77	3.85	44.42	18.30
Buchnera aphidicola str Sg (Schizaphis graminum)	545	26.30	4.00	26.20	3.90	44.92	17.04
Nostoc sp. PCC 7120	5366	42.00	4.11	42.18	3.96	40.80	16.00
Symbiobacterium thermophilum IAM 14863	3337	68.88	4.16	69.17	4.01	44.58	16.71
Prochlorococcus marinus CCMP1378	1712	31.44	4.23	31.42	4.02	45.57	17.77
Wigglesworthia brevipalpis	654	23.41	4.55	23.43	4.06	47.92	20.00
Nitrosomonas europaea	2461	50.82	4.40	51.08	4.16	43.78	19.03
Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough	3379	62.04	5.68	63.22	4.18	45.51	19.92
Deinococcus radiodurans chrom 1	2579	67.20	4.30	67.40	4.20	41.80	17.00
Bifidobacterium longum	1729	60.23	4.40	60.38	4.30	44.33	18.22
Bacillus subtilis 168	4100	43.30	4.60	43.80	4.40	47.90	25.50
Desulfotalea psychrophila LSv54	3118	46.83	4.73	47.16	4.52	44.03	18.34
Gloeobacter violaceus	4430	62.08	4.75	62.48	4.53	38.91	13.62
Chlorobium tepidum TLS	2252	55.49	6.35	57.36	4.62	42.64	18.59
Escherichia coli K12	4289	51.00	4.90	51.30	4.70	42.20	18.20
Prochlorococcus marinus MIT9313	2265	51.74	4.82	52.00	4.79	42.93	15.70
Synechocystis sp PCC6803	3169	48.20	5.00	48.30	4.90	39.50	19.50
Geobacter sulfurreducens	3446	60.71	5.38	61.23	4.94	45.07	17.84
Bacteroides thetaiotaomicron VPI-5482	4778	43.30	5.10	43.60	5.00	44.90	19.60
Deinococcus radiodurans chrom 2	357	67.00	5.10	67.00	5.10	44.60	24.10
Chromobacterium violaceum ATCC 12472	4407	64.93	6.18	65.52	5.47	51.63	20.02
Synechococcus sp. WH8102	2517	60.02	6.10	60.30	6.23	51.98	19.08

Archaea

Organism	No. of protein coding ORFs	%G+C Mean (all ORFs)	%G+C S.D. (all ORFs)	%G+C Mean  (ORFs >300bp)	%G+C S.D. (ORFs >300bp)	Genome Dinucleotide Bias Mean	Genome Dinucleotide Bias S.D.	Graphical analysis
Nanoarchaeum equitans	536	31.09	2.98	31.00	2.81	43.98	16.93
Thermoplasma volcanium	1499	40.90	3.40	41.00	3.30	41.80	19.40
Pyrococcus abyssi GE5	1765	45.00	3.50	44.90	3.40	40.00	16.10
Pyrococcus furiosus DSM 3638	2065	40.87	3.62	40.86	3.42	44.10	17.70
Methanococcus maripaludis	1722	33.73	3.61	33.79	3.57	51.65	22.14
Methanococcus jannaschii DSM2661	1715	31.70	3.80	31.70	3.70	49.10	22.20
Methanobacterium thermoautotrophicum deltaH	1869	49.90	4.40	50.40	3.90	45.80	21.30
sulfolobus tokodaii	2826	33.40	4.40	33.30	4.00	53.60	22.90
Picrophilus torridus DSM 9790	1535	36.84	4.42	36.82	4.24	43.51	19.28
Sulfolobus solfataricus	2977	36.40	4.50	36.30	4.40	49.60	20.30
Methanopyrus kandleri AV19	1687	60.82	4.58	60.94	4.55	46.85	20.00
Pyrobaculum aerophilum	2605	51.51	5.02	51.72	4.71	45.20	17.90
Methanosarcina mazei strain Goe1	3371	43.57	4.98	43.91	4.73	45.63	19.90
Halobacterium sp. NRC1	2058	67.90	5.20	68.40	4.90	50.30	22.00
Aeropyrum pernix K1	2694	57.60	5.60	57.70	5.40	48.70	20.20
Methanosarcina acetivorans str. C2A	4540	44.25	5.60	44.61	5.49	51.24	21.80

Last Updated: SEPT-17-2004 (Note: update adds new organisms but does not affect the existing records)

Funding for this work was provided by the Peter Wall Institute for Advanced Studies. This service is hosted by the Brinkman Laboratory of the Department of Molecular Biology and Biochemistry at Simon Fraser University.