6. Analysis of Salmonella typhi plasmid R27 (back)

Predicted H-NS binding sites

Input motif
Resulting motif

Average AT content

Genes with a predicted H-NS binding site (back)
Gene	Binding site logo	Motif alignment	bs (u,d)	rel bs pos.	abs gene pos. + len	fold change	Gene locus	PID	Interactions	Annotation
R0001		TAGATAAATT	1 (1,0)	-60	407 784 378	n/a	R0210 R0001 R0002	10957191	H-NS & R0001	hypothetical protein R27_p002
R0009		TCGATTAAAT TCGATAATTA	2 (2,0)	-21, -236	11659 15879 4221	n/a	trhF R0009 htdK	10957199	H-NS & R0009	hypothetical protein R27_p010
htdA		CCTATACATA	1 (1,0)	-239	17061 17513 453	n/a	htdK htdF htdA	10957202	H-NS & htdA	putative transfer repressor
R0019		CCGTTATATT	1 (0,1)	+44	23081 24088 1008	n/a	R0018 R0019 R0020	10957209	H-NS & R0019	putative partition protein
R0020		GCGTTTAATA	1 (1,0)	-85	24085 25338 1254	n/a	R0019 R0020	10957210	H-NS & R0020	putative partition protein
R0021		GGGTTAAATC	1 (1,0)	-122	26188 26595 408	n/a	R0021	10957211	H-NS & R0021	hypothetical protein R27_p022
R0023		TGGTTAAATT ACGATAAATT	2 (2,0)	-41, -286	27477 27797 321	n/a	R0022 R0023	10957213	H-NS & R0023	hypothetical protein R27_p024
trhC		TGGATTTATT	1 (0,1)	+59	28465 31146 2682	n/a	trhC trhV	10957214	H-NS & trhC	putative transfer protein
trhB		CGGATAAATT	1 (1,0)	-231	33494 34852 1359	n/a	R0028 trhB R0030 R0031	10957218	H-NS & trhB	putative transfer protein
R0030		GGGATAAATT TCGATAAAGC	2 (2,0)	-57, -108	34842 35282 441	n/a	trhB R0030 R0031	10957219	H-NS & R0030	hypothetical protein R27_p030
trhE		TCGTTACTTT	1 (1,0)	-45	36519 37304 786	n/a	R0031 trhE trhL trhA	10957221	H-NS & trhE	hypothetical protein R27_p032
trhA		GCGTTTAATT	1 (1,0)	-168	37685 38038 354	n/a	trhE trhL trhA	10957223	H-NS & trhA	hypothetical protein R27_p034
repHIA		TGGATAAATT	1 (1,0)	-264	39480 40355 876	n/a	R0035 repHIA	10957225	H-NS & repHIA	replication initiation protein
R0037		TGGATAAATT TCGATAAAAA	2 (1,1)	-270, +47	40890 41966 1077	n/a	R0037 R0038 R0039	10957226	H-NS & R0037	hypothetical protein R27_p037
R0038		CCGATAAATT	1 (1,0)	-288	41984 42184 201	n/a	R0037 R0038 R0039	10957227	H-NS & R0038	hypothetical protein R27_p038
R0040		CCGATTTATT	1 (1,0)	-137	43171 43992 822	n/a	R0039 R0040 R0041	10957229	H-NS & R0040	hypothetical protein R27_p040
R0041		CCGATAAAGC TCGACACATT	2 (2,0)	-69, -168	44007 44780 774	n/a	R0040 R0042 R0041	10957230	H-NS & R0041	putative DNA adenine methylase (dam)
R0042		TCGACACATT TCGTTAAAAA	2 (2,0)	-242, -86	45191 46348 1158	n/a	R0042 R0043 R0041	10957231	H-NS & R0042	hypothetical protein R27_p042
R0054		CCGATTAAAT	1 (1,0)	-130	56639 57247 609	n/a	R0055 R0052 R0053 R0054	10957243	H-NS & R0054	hypothetical protein R27_p054
R0055		CCGATTAAAT	1 (1,0)	-120	57498 59882 2385	n/a	R0055 R0056 R0054	10957244	H-NS & R0055	hypothetical protein R27_p055
R0059		TCGTTAATTT	1 (1,0)	-87	61718 62059 342	n/a	R0058 R0059 R0060	10957248	H-NS & R0059	hypothetical protein R27_p059
R0062		CGGATAAATA	1 (1,0)	-38	64185 64511 327	n/a	R0063 R0061 R0062	10957251	H-NS & R0062	hypothetical protein R27_p062
R0063		CGGATAAATA TGGATAAATA	2 (1,1)	-260, +2	64810 65277 468	n/a	R0063 R0062 R0064	10957252	H-NS & R0063	hypothetical protein R27_p063
R0064		GCGATTTATA	1 (1,0)	-77	65319 65540 222	n/a	R0063 R0065 R0064	10957253	H-NS & R0064	hypothetical protein R27_p064
R0065		GCGATTTATA	1 (1,0)	-256	65874 66827 954	n/a	R0065 R0066 R0064	10957254	H-NS & R0065	hypothetical protein R27_p065
R0070		GCAATAAATA TAGTTAAATT	2 (2,0)	-156, -97	69684 72059 2376	n/a	R0069 R0070 R0071	10957259	H-NS & R0070	hypothetical protein R27_p070
R0075		TCGATTCAGT	1 (0,1)	+42	73779 73982 204	n/a	R0073 R0074 R0075 R0076	10957264	H-NS & R0075	hypothetical protein R27_p075
R0076		TCGATTCAGT TCGATATTTT	2 (1,1)	-265, +11	74086 75294 1209	n/a	R0074 R0075 R0076 gltS	10957265	H-NS & R0076	putative IS10 transposase
R0078		TCTTTAAATT	1 (1,0)	-121	77309 77629 321	n/a	R0078 R0079 R0080 gltS	10957267	H-NS & R0078	hypothetical protein R27_p078
tetR		GCAATAAATT	1 (1,0)	-173	78680 79306 627	n/a	R0080 tetA tetR	10957270	H-NS & tetR	tetracycline repressor protein
tetD		GCAATTAATT	1 (1,0)	-296	81384 81800 417	n/a	tetD tetC R0085	10957273	H-NS & tetD	hypothetical protein R27_p084
R0085		TCGATATTTT	1 (0,1)	+19	81810 83018 1209	n/a	tetD R0086 tetC R0085	10957274	H-NS & R0085	IS10 transposase
R0086		TCGATATTTT	1 (1,0)	-293	83293 83541 249	n/a	R0086 R0087 R0085	10957275	H-NS & R0086	hypothetical protein R27_p086
R0090		GCGATAAAAT	1 (0,1)	+44	85108 85368 261	n/a	R0089 R0090 R0091	10957279	H-NS & R0090	hypothetical protein R27_p090
R0091		TCGATATTTT	1 (1,0)	-106	85410 85967 558	n/a	R0089 R0090 R0092 R0093 R0091	10957280	H-NS & R0091	hypothetical protein R27_p091
R0092		TCGATATTTT	1 (0,1)	+50	86024 86248 225	n/a	R0092 R0093 R0091	10957281	H-NS & R0092	hypothetical protein R27_p092
R0093		TCGATATTTT	1 (1,0)	-209	86283 86489 207	n/a	R0092 R0093 R0091 insB	10957282	H-NS & R0093	hypothetical protein R27_p093
stm		TCGTTTAAAA	1 (1,0)	-134	91263 91478 216	n/a	R0100 stm R0102 R0103	10957290	H-NS & stm	plasmid maintenance protein
R0102		GCGATTTAAT	1 (1,0)	-74	91540 91731 192	n/a	stm R0102 R0103	10957291	H-NS & R0102	hypothetical protein R27_p102
R0103		TCGACATATT	1 (1,0)	-209	91650 91916 267	n/a	stm R0104 R0102 R0103	10957292	H-NS & R0103	hypothetical protein R27_p103
R0104		TCGACATATT TCGATTCATT	2 (2,0)	-210, -70	92336 93541 1206	n/a	R0104 R0105 R0106 R0103	10957293	H-NS & R0104	hypothetical protein R27_p104
R0107		GCGATTAATC	1 (1,0)	-262	94240 94428 189	n/a	R0105 R0106 R0107 R0108	10957296	H-NS & R0107	hypothetical protein R27_p107
R0110		GCGATAATAT	1 (0,1)	+71	95604 96149 546	n/a	R0109 R0110 R0111	10957299	H-NS & R0110	hypothetical protein R27_p110
R0111		GCGATTTATT TCGATAAAGA	2 (0,2)	+5, +77	96195 96431 237	n/a	R0110 R0111 R0112	10957300	H-NS & R0111	hypothetical protein R27_p111
R0116		TCTATAAAAT	1 (0,1)	+79	98869 100050 1182	n/a	R0115 R0116 R0117	10957305	H-NS & R0116	hypothetical protein R27_p116
R0117		TCGACAAAAT GGGATTAATT	2 (2,0)	-225, -232	100063 100725 663	n/a	R0116 R0117 R0118	10957306	H-NS & R0117	hypothetical protein R27_p117
R0123		TCGATTATTC	1 (0,1)	+61	108907 109707 801	n/a	R0123 R0124	10957312	H-NS & R0123	hypothetical protein R27_p123
R0125		TCGATAAATT	1 (1,0)	-236	110782 110910 129	n/a	R0125 R0126	10957314	H-NS & R0125	hypothetical protein R27_p125
R0126		TCGATAAATT	1 (1,0)	-288	110834 111880 1047	n/a	R0125 R0126 trhH	10957315	H-NS & R0126	putative pilus assembly and synthesis protein
mucA		TGGTTAAATA CCGTTACATA	2 (1,1)	+37, -52	123349 123846 498	n/a	R0138 mucB mucA	10957326	H-NS & mucA	putative UV protection protein
R0138		CCGTTACATA	1 (1,0)	-278	124177 124575 399	n/a	R0138 R0139 mucA	10957327	H-NS & R0138	hypothetical protein R27_p138
R0139		TAGATAAATT	1 (1,0)	-164	124723 125076 354	n/a	R0138 R0139	10957328	H-NS & R0139	hypothetical protein R27_p139
citA		TCGATTTTTT TCTATACATA	2 (1,1)	+85, -29	130558 131853 1296	n/a	R0143 citA citB	10957333	H-NS & citA	Putative citrate-proton symport protein
R0150		TCGATATAAA TCGATTAATT TCGACAAATC	3 (3,0)	-99, -190, -242	138447 138584 138	n/a	R0149 R0150 R0151	10957339	H-NS & R0150	hypothetical protein R27_p150
R0151		CGGATACATT	1 (1,0)	-277	138638 139417 780	n/a	R0149 R0150 R0151 R0152	10957340	H-NS & R0151	hypothetical protein R27_p151
parB		TGGATAAAAA TCCATAAATT	2 (2,0)	-112, -287	140402 140917 516	n/a	R0154 R0152 parB	10957342	H-NS & parB	putative partition protein
R0154		TGGATAAAAA TCCATAAATT	2 (1,1)	-110, +65	141140 142567 1428	n/a	R0154 R0155 R0156 parB	10957343	H-NS & R0154	EcoRII cytosine methylase
tlpA		TCGTTTAAAT	1 (1,0)	-256	144482 145702 1221	n/a	R0156 R0157 tlpA R0159 R0160	10957347	H-NS & tlpA	hypothetical protein R27_p158
R0159		TCGTTTAAAT	1 (0,1)	+94	145705 146052 348	n/a	tlpA R0159 R0160	10957348	H-NS & R0159	hypothetical protein R27_p159
R0162		TCGATATAAA	1 (1,0)	-216	147691 147963 273	n/a	R0161 R0162 R0163 h-ns	10957351	H-NS & R0162	hypothetical protein R27_p162
R0163		TCGTTAATAT GCGATTATTA TAGATAAAAT	3 (2,1)	-88, -9, +16	147997 148116 120	n/a	R0161 R0162 R0163 h-ns	10957352	H-NS & R0163	hypothetical protein R27_p163
h-ns		GCGATTATTA TAGATAAAAT	2 (2,0)	-237, -212	148225 148629 405	n/a	R0162 R0163 h-ns R0165	10957353	H-NS & h-ns	'DNA binding protein, H-NS-like'
R0165		TCGATAAAGA	1 (1,0)	-257	149031 149327 297	n/a	h-ns R0165 R0166	10957354	H-NS & R0165	hypothetical protein R27_p165
R0166		CCGTTAAAAA	1 (1,0)	-110	149397 149846 450	n/a	R0165 R0166 R0167	10957355	H-NS & R0166	hypothetical protein R27_p166
R0169		CGGTTAAATT	1 (1,0)	-223	151891 152220 330	n/a	R0168 R0169 R0171 R0172	10957358	H-NS & R0169	hypothetical protein R27_p169
R0171		CGGTTAAATT CCGTTAAATA	2 (1,1)	+42, -176	152087 152485 399	n/a	R0169 R0171 R0172	10957359	H-NS & R0171	hypothetical protein R27_p170
R0175		CCGATATAGT TCGTTAATTC	2 (2,0)	-30, -206	154290 155363 1074	n/a	R0174 R0175 R0176 insB	10957363	H-NS & R0175	hypothetical protein R27_p174
R0176		TCGTTAATTC	1 (0,1)	+30	155234 155599 366	n/a	R0175 R0176 insB	10957364	H-NS & R0176	hypothetical protein R27_p175
insB		GCGTTTAAAT	1 (1,0)	-269	158185 158688 504	n/a	insB insA	10957368	H-NS & insB	IS1 transposase
insA		GCGTTTAAAT GCGATAAATT	2 (2,0)	-66, -270	158607 158891 285	n/a	insB insA hha	10957369	H-NS & insA	IS1 transposase
R0188		TCCATTAATT	1 (1,0)	-122	163352 163579 228	n/a	R0186 R0187 R0188 R0189 R0190	10957376	H-NS & R0188	hypothetical protein R27_p187
R0194		TCGTTATAAT	1 (1,0)	-75	166237 166686 450	n/a	R0193 R0194 R0195	10957382	H-NS & R0194	hypothetical protein R27_p193
R0197		GCGATTAAAA	1 (1,0)	-207	167524 167889 366	n/a	R0195 R0197 R0198	10957384	H-NS & R0197	IS2 hypothetical orf
R0199		GCTATAAATA TCGATAAAGC	2 (2,0)	-135, -148	168706 169641 936	n/a	R0198 R0199 R0200	10957386	H-NS & R0199	hypothetical protein R27_p197
R0200		GCGATTTATA	1 (0,1)	+15	169714 170634 921	n/a	R0199 R0200 R0201	10957387	H-NS & R0200	hypothetical protein R27_p198
R0202		TCGATATAAC	1 (1,0)	-103	171718 172596 879	n/a	R0201 R0202 R0203	10957389	H-NS & R0202	hypothetical protein R27_p200
R0203		TCGTTAAATA GCGATACATC	2 (2,0)	-16, -108	172674 173198 525	n/a	R0202 R0203 R0204	10957390	H-NS & R0203	hypothetical protein R27_p201
R0204		TGGATAAAAC TAGATACATC	2 (2,0)	-131, -183	173473 174726 1254	n/a	R0203 R0204 R0205 R0206	10957391	H-NS & R0204	hypothetical protein R27_p202
R0208		TGGATACATT	1 (1,0)	-160	178401 178670 270	n/a	R0207 R0208 R0209	10957395	H-NS & R0208	hypothetical protein R27_p206
R0210		TCGATTCAAA	1 (1,0)	-273	179821 346 -179474	n/a	R0209 R0210 R0001 R0002	10957397	H-NS & R0210	hypothetical protein R27_p001

80 of 207 genes (or 38.6%) contained a predicted H-NS binding site. These are:

R0001, R0009, htdA, R0019, R0020, R0021, R0023, trhC, trhB, R0030, trhE, trhA, repHIA, R0037, R0038, R0040, R0041, R0042, R0054, R0055, R0059, R0062, R0063, R0064, R0065, R0070, R0075, R0076, R0078, tetR, tetD, R0085, R0086, R0090, R0091, R0092, R0093, stm, R0102, R0103, R0104, R0107, R0110, R0111, R0116, R0117, R0123, R0125, R0126, mucA, R0138, R0139, citA, R0150, R0151, parB, R0154, tlpA, R0159, R0162, R0163, h-ns, R0165, R0166, R0169, R0171, R0175, R0176, insB, insA, R0188, R0194, R0197, R0199, R0200, R0202, R0203, R0204, R0208, R0210

No strong binding sites were predicted for the following genes (127 of 207):

R0002, trhI, R0004, trhN, trhU, trhW, trhF, htdK, htdF, R0013, stbA, R0015, R0016, R0017, R0018, R0022, trhV, htdT, R0028, R0031, trhL, R0035, R0039, R0043, R0044, R0045, R0046, R0047, R0048, R0049, repHIB, R0051, R0052, R0053, R0056, R0057, R0058, R0060, R0061, R0066, R0067, R0068, R0069, R0071, R0072, R0073, R0074, gltS, R0079, R0080, tetA, tetC, R0087, R0088, R0089, insB, insA, corA, R0097, R0098, R0099, R0100, R0105, R0106, R0108, R0109, R0112, R0113, R0114, R0115, R0118, traG, traI, R0121, R0122, R0124, trhH, R0128, R0129, bfpH, dsbC, R0132, R0133, R0134, R0135, mucB, R0140, R0141, R0142, R0143, citB, R0146, nac, R0148, R0149, R0152, R0155, R0156, R0157, R0160, R0161, R0167, R0168, R0172, R0173, R0174, insB, insA, repFIB, hha, R0183, R0184, R0185, R0186, R0187, R0189, R0190, R0191, R0192, R0193, R0195, R0198, R0201, R0205, R0206, R0207, R0209