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
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)
101	 45.09	-1	109750..111723	-	657	15639096	-	TP0102	-	rep helicase, single-stranded DNA-dependent ATPase (rep)
102	 52.74	0	111788..113611	+	607	15639097	-	TP0103	-	ATP-dependent DNA helicase, putative
103	 48.43	-1	113858..115639	+	593	15639098	-	TP0104	-	5'-nucleotidase (ushA)
104	 44.76	-1	115806..118799	+	997	15639099	-	TP0105	-	DNA polymerase I (polA)
105	 49.18	0	118831..120363	-	510	15639100	-	TP0106	-	carnitine transporter, putative
106	 47.02	-1	120344..121921	-	525	15639101	-	TP0107	-	licC protein (licC)
107	 51.08	0	122275..123660	-	461	15639102	-	TP0108	-	diphosphate--fructose-6-phosphate 1-phosphotransferase
108	 55.29	0	123762..124640	-	292	15639103	-	TP0109	-	rRNA methylase, putative
109	 49.60	0	125181..126914	+	577	15639104	-	TP0110	-	hypothetical protein
110	 47.90	-1	126974..128401	+	475	15639105	-	TP0111	-	RNA polymerase sigma-54 factor (rpoN)
111	 46.86	-1	128398..129750	-	450	15639106	-	TP0112	-	aminopeptidase C (pepC)
112	 46.61	-1	129892..130878	+	328	15639107	-	TP0113	-	lambda CII stability-governing protein (hflK)
113	 49.60	0	130883..131878	+	331	15639108	-	TP0114	-	lambda CII stability-governing protein (hflC)
114	 54.44	0	131903..132712	-	269	15639109	-	TP0115	-	phosphomethypyrimidine kinase (thiD)
115	 45.34	-1	132863..134869	+	668	15639110	-	TP0116	-	excinuclease ABC subunit B
116	 56.26	0	134901..136697	-	598	15639111	-	TP0117	-	TPR protein C (tprC)
117	 55.61	0	136777..138042	-	421	15639112	-	TP0118	-	hypothetical protein
118	 55.15	0	138140..138799	-	219	15639113	-	TP0119	-	amino acid ABC transporter, permease protein (yaeE)
119	 51.98	0	138799..139608	-	269	15639114	-	TP0120	-	amino acid ABC transporter ATP-binding protein
120	 57.21	+1	139738..140805	+	355	15639115	-	TP0121	-	hypothetical protein
121	 53.96	0	141025..142881	-	618	15639116	-	TP0122	-	phosphoenolpyruvate carboxykinase
122	 48.89	0	142987..145557	+	856	15639117	-	TP0123	-	hypothetical protein
123	 52.57	0	145571..146677	+	368	15639118	-	TP0124	-	translation-associated GTPase
124	 56.60	0	146754..147548	+	264	15639119	-	TP0125	-	exodeoxyribonuclease (exoA)
125	 59.02	+1	147612..148487	-	291	15639120	-	TP0126	-	hypothetical protein
126	 55.94	0	148595..149284	+	229	15639121	-	TP0127	-	hypothetical protein
127	 62.64	+2	149473..149820	+	115	15639122	-	TP0128	-	hypothetical protein
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.