IslandPath Analysis: Treponema pallidum 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: 52.89   STD DEV: 4.31
Treponema pallidum complete genome - 0..1138011
1036 proteins

Pos	 %G+C  SD      Location		Strand	Length	PID	Gene	Synonym	Code	Product

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

 
 52.89 MEAN 
 
 4.31  STD DEV 




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.