IslandPath Analysis: Treponema pallidum subsp. pallidum str. Nichols



Each circle in the graphic corresponds to a predicted protein-coding ORF in the genome.
Circle colours indicate if an ORF has a higher or lower %G+C than cutoffs you set below
--(default is +/- 3.48 of the mean %G+C).
Strike lines across the circles represent regions with dinucleotide bias above a pre-determined cutoff.
Click on a circle to view a different portion of the table presented below the graph (default is the first 100 ORFs).




A yellow circle indicates its %G+C value is bigger than the high value.
A green circle indicates its %G+C value is bigger than the low value and smaller than the high value.
A pink circle indicates its %G+C value is smaller than the low value.

A strike line across the circles indicates the region has dinucleotide bais above 1 STD DEV.
A black verticle bar indicates a transfer RNA gene lies between the two ORFs.
A purple verticle bar indicates a ribosomal RNA gene lies between the two ORFs.
A deep blue verticle bar indicates both a tRNA and rRNA gene lie between the two ORFs.
A black square indicates the dot is annotated as a transposase.
A black triangle indicates the dot is annotated as an integrase.


Low:  High:    Mean: 52.88   STD DEV: 4.31
Treponema pallidum subsp. pallidum str. Nichols, complete genome - 1..1138011
1036 proteins
Pos	%G+C	SD	Location	Strand	Length	PID	Gene	Synonym	Code	Product
1	 40.72	-2	4..1398	+	464	15638996	-	TP0001	-	chromosomal replication initiator protein (dnaA)
2	 41.31	-2	1641..2756	+	371	15638997	-	TP0002	-	DNA polymerase III, subunit beta (dnaN)
3	 43.56	-2	2623..3834	+	403	15638998	-	TP0003	-	recF protein (recF)
4	 47.03	-1	3827..4264	+	145	15638999	-	TP0004	-	hypothetical protein
5	 47.54	-1	4391..6832	+	813	15639000	-	TP0005	-	DNA gyrase, subunit A (gyrA)
6	 45.24	-1	7014..7181	+	55	15639001	-	TP0006	-	Tp75 protein
7	 50.69	0	7317..7967	+	216	15639002	-	TP0007	-	hypothetical protein
8	 48.15	-1	7991..8260	+	89	15639003	-	TP0008	-	hypothetical protein
9	 47.62	-1	10237..10362	+	41	15639004	-	TP0010	-	hypothetical protein
10	 52.55	0	10396..12378	+	660	15639005	-	TP0011	-	TPR protein B (tprB)
11	 48.02	-1	12372..12548	+	58	15639006	-	TP0012	-	hypothetical protein
12	 50.45	0	12545..13210	+	221	15639007	-	TP0013	-	hypothetical protein
13	 48.93	0	13167..13775	+	202	15639008	-	TP0014	-	hypothetical protein
14	 50.08	0	13966..15780	+	604	15639009	pheT	TP0015	-	phenylalanyl-tRNA synthetase subunit beta
15	 50.27	0	15743..18316	+	857	15639010	-	TP0016	-	ATP-dependent protease LA (lon-1)
16	 48.21	-1	18404..19351	+	315	15639011	-	TP0017	-	hypothetical protein
17	 45.14	-1	19418..21391	+	657	15639012	-	TP0018	-	transcription elongation factor
18	 45.40	-1	21558..22046	+	162	15639013	-	TP0019	-	transcription elongation factor (greA)
19	 49.39	0	22046..24169	+	707	15639014	-	TP0020	-	76K protein
20	 42.70	-2	25107..25373	+	88	15639015	-	TP0021	-	hypothetical protein
21	 50.02	0	25328..27496	+	722	15639016	-	TP0022	-	hypothetical protein
22	 47.45	-1	27557..28888	+	443	15639017	-	TP0023	-	sodium- and chloride- dependent transporter
23	 45.15	-1	29068..29778	+	236	15639018	-	TP0024	-	hypothetical protein
24	 50.39	0	29857..32928	-	1023	15639019	-	TP0025	-	hypothetical protein
25	 52.20	0	32957..33979	-	340	15639020	-	TP0026	-	flagellar motor switch protein (fliG-1)
26	 51.39	0	34205..35428	+	407	15639021	-	TP0027	-	hemolysin, putative
27	 49.05	0	35442..36803	+	453	15639022	-	TP0028	-	hemolysin, putative
28	 50.08	0	36911..38188	+	425	15639023	-	TP0029	-	UDP-N-acetylglucosamine 1-carboxyvinyltransferase
29	 50.15	0	38307..39941	+	544	15639024	groEL	TP0030	-	chaperonin GroEL
30	 56.27	0	40005..40283	+	92	15639025	-	TP0031	-	hypothetical protein
31	 51.06	0	40280..41080	-	266	15639026	-	TP0032	-	hypothetical protein
32	 43.63	-2	41077..41688	-	203	15639027	-	TP0033	-	hypothetical protein
33	 48.58	0	41789..42739	-	316	15639028	-	TP0034	-	ABC transporter, periplasmic binding protein
34	 47.84	-1	42937..43653	+	238	15639029	-	TP0035	-	ABC transporter, ATP-binding protein
35	 52.18	0	43653..44453	+	266	15639030	-	TP0036	-	ABC transporter, permease protein
36	 51.51	0	44562..45557	-	331	15639031	-	TP0037	-	D-specific D-2-hydroxyacid dehydrogenase
37	 54.23	0	45654..46706	-	350	15639032	-	TP0038	-	regulatory protein (pfoS/R)
38	 49.06	0	46755..46913	+	52	15639033	-	TP0039	-	hypothetical protein
39	 54.29	0	47591..49384	+	597	15639034	-	TP0040	-	methyl-accepting chemotaxis protein (mcp1)
40	 61.79	+2	49386..49508	+	40	15639035	-	TP0041	-	hypothetical protein
41	 55.41	0	49505..50437	+	310	15639036	-	TP0042	-	hypothetical protein
42	 51.62	0	50418..52550	+	710	15639037	-	TP0043	-	soluble lytic transglycosylase, putative
43	 49.34	0	52590..54482	+	630	15639038	-	TP0044	-	tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA
44	 43.33	-2	54538..55437	-	299	15639039	-	TP0045	-	adenosine deaminase
45	 49.00	0	55799..56500	-	233	15639040	-	TP0046	-	hypothetical protein
46	 46.74	-1	56518..57039	-	173	15639041	-	TP0047	-	hypothetical protein
47	 51.85	0	57045..57476	-	143	15639042	-	TP0048	-	hypothetical protein
48	 53.84	0	57498..58526	-	342	15639043	-	TP0049	-	hypothetical protein
49	 53.37	0	58819..59427	-	202	15639044	-	TP0050	-	hypothetical protein
50	 49.72	0	59578..60633	+	351	15639045	prfA	TP0051	-	peptide chain release factor 1
51	 55.21	0	60603..61649	+	348	15639046	-	TP0052	-	protoporphyrinogen oxidase (hemK)
52	 45.08	-1	61738..62793	-	351	15639047	nrdF	TP0053	-	ribonucleotide-diphosphate reductase subunit beta
53	 53.12	0	62964..63923	+	319	15639048	-	TP0054	-	hypothetical protein
54	 57.81	+1	64130..64366	+	78	15639049	-	TP0055	-	hypothetical protein
55	 54.04	0	64363..66144	+	593	15639050	-	TP0056	-	pyruvate carboxylase subunit B
56	 52.48	0	66156..67565	+	469	15639051	-	TP0057	-	oxaloacetate decarboxylase, subunit beta (oadB)
57	 53.00	0	67640..68956	-	438	15639052	-	TP0058	-	replicative DNA helicase (dnaB)
58	 53.95	0	68940..69167	-	75	15639053	-	TP0059	-	hypothetical protein
59	 47.98	-1	69173..69643	-	156	15639054	rplI	TP0060	-	50S ribosomal protein L9
60	 51.33	0	69749..70048	-	99	15639055	rpsR	TP0061	-	30S ribosomal protein S18
61	 53.86	0	70165..70695	-	176	15639056	-	TP0062	-	single-strand DNA binding protein (ssb)
62	 53.55	0	70704..70985	-	93	15639057	rpsF	TP0063	-	30S ribosomal protein S6
63	 49.65	0	71127..71702	+	191	15639058	-	TP0064	-	hypothetical protein
64	 49.83	0	71776..72363	+	195	15639059	-	TP0065	-	hypothetical protein
65	 52.06	0	72347..72661	+	104	15639060	-	TP0066	-	hypothetical protein
66	 50.34	0	72649..73830	+	393	15639061	-	TP0067	-	hypothetical protein
67	 53.18	0	74011..75033	+	340	15639062	-	TP0068	-	hypothetical protein
68	 52.54	0	75089..75619	-	176	15639063	-	TP0069	-	hypothetical protein
69	 52.97	0	75469..75855	-	128	15639064	-	TP0070	-	hypothetical protein
70	 49.87	0	75906..78542	-	878	15639065	-	TP0071	-	ATP-dependent Clp protease subunit B (clpB)
71	 48.72	0	78746..79018	+	90	15639066	-	TP0072	-	hypothetical protein
72	 52.46	0	79088..80629	-	513	15639067	-	TP0073	-	hypothetical protein
73	 55.11	0	80934..82343	+	469	15639068	-	TP0074	-	sugar ABC transporter, periplasmic binding protein (y4oP)
74	 49.38	0	82462..83352	+	296	15639069	-	TP0075	-	sugar ABC transporter, permease protein (y4oQ)
75	 48.42	-1	83392..84213	+	273	15639070	-	TP0076	-	sugar ABC transporter, permease protein (y4oR)
76	 50.28	0	84254..85870	+	538	15639071	-	TP0077	-	capsular polysaccharide biosynthesis protein (cap5D)
77	 50.04	0	85875..87113	+	412	15639072	-	TP0078	-	spore coat polysaccharide biosynthesis protein (spsC)
78	 50.11	0	87041..89263	+	740	15639073	-	TP0079	-	hypothetical protein
79	 42.95	-2	89260..89727	+	155	15639074	-	TP0080	-	quinoline 2-oxidoreductase
80	 46.64	-1	89734..90582	+	282	15639075	-	TP0081	-	hypothetical protein
81	 52.69	0	90629..92431	-	600	15639076	-	TP0082	-	formate hydrogenlyase transcriptional activator (fhlA)
82	 54.25	0	93177..94457	+	426	15639077	-	TP0083	-	hypothetical protein
83	 53.42	0	94437..94670	-	77	15639078	-	TP0084	-	hypothetical protein
84	 49.89	0	94784..95230	-	148	15639079	-	TP0085	-	PTS system, nitrogen regulatory IIA component (ptsN-1)
85	 53.65	0	95311..96255	+	314	15639080	-	TP0086	-	hypothetical protein
86	 57.41	+1	96258..96797	-	179	15639081	-	TP0087	-	hypothetical protein
87	 48.62	0	96781..97395	-	204	15639082	-	TP0088	-	hypothetical protein
88	 45.39	-1	97425..98660	-	411	15639083	-	TP0089	-	cyclic nucleotide binding protein
89	 57.75	+1	98743..99807	-	354	15639084	-	TP0090	-	UDP-N-acetylmuramate dehydrogenase (murB)
90	 54.51	0	99989..101551	+	520	15639085	-	TP0091	-	cysteinyl-tRNA synthetase (cysS)
91	 54.19	0	101622..102110	+	162	15639086	-	TP0092	-	RNA polymerase sigma-24 factor (rpoE)
92	 55.25	0	102094..102741	+	215	15639087	-	TP0093	-	hypothetical protein
93	 51.43	0	102879..103889	+	336	15639088	-	TP0094	-	phosphate acetyltransferase (pta)
94	 56.65	0	103889..105835	+	648	15639089	-	TP0095	-	hypothetical protein
95	 53.44	0	105909..106271	-	120	15639090	-	TP0096	-	dnaK suppressor, putative
96	 54.79	0	106441..106659	+	72	15639091	-	TP0097	-	translation initiation factor 1 (infA)
97	 60.22	+1	106719..107369	-	216	15639092	-	TP0098	-	heat-shock protein, putative
98	 55.56	0	107373..108128	-	251	15639093	pyrH	TP0099	-	uridylate kinase
99	 54.89	0	108323..108925	+	200	15639094	-	TP0100	-	thioredoxin, putative
100	 55.35	0	108918..109712	+	264	15639095	-	TP0101	-	cytochrome c biogenesis protein (ccdA)
52.88	MEAN

4.31	STD DEV




Last Updated: Dec 04, 2008
      
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.