5. Analysis of E. coli virulence plasmid pO157 (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
etpC		GCGTTTTATT	1 (1,0)	-9	2589 3464 876	n/a	tagA etpC etpD	3336999	H-NS & etpC	Type II secretion pathway related protein
etpE		TCGTTTAATC	1 (1,0)	-151	5432 6937 1506	n/a	etpD etpE etpF	3337001	H-NS & etpE	Type II secretion pathway related protein
etpO		GCGATACAAT	1 (0,1)	+29	13803 14204 402	n/a	etpN etpO IS911	3337011	H-NS & etpO	Type II secretion pathway related protein
hlyC		GCGATAATAA TCTTTACATT	2 (2,0)	-172, -62	16119 16610 492	n/a	hlyC hlyA	3337014	H-NS & hlyC	Hemolysin C
hlyA		TAGATAAAAA	1 (1,0)	-107	16612 19608 2997	n/a	hlyC hlyA hlyB	3337015	H-NS & hlyA	Hemolysin A
hlyB		TCTTTATATA TCGTTAAAGT	2 (2,0)	-114, -69	19658 21778 2121	n/a	hlyA hlyB hlyD	3337016	H-NS & hlyB	Hemolysin B
papX		TGGATATAAT	1 (1,0)	-113	23512 23796 285	n/a	hlyD papX	3337018	H-NS & papX	PapX protein
PID 3337019		GCGATTTATT	1 (1,0)	-86	24316 25056 741	n/a	PID 3337019 PID 3337020 repFIB	3337019	H-NS & PID 3337019	recombinase
PID 3337034		TCGTTTAATC	1 (0,1)	+36	38075 38977 903	n/a	PID 3337033 PID 3337034 PID 3337035 PID 3337036	3337034	H-NS & PID 3337034	-
PID 3337036		TGGATAAAAC	1 (0,1)	+8	39363 40046 684	n/a	PID 3337034 PID 3337035 PID 3337036 PID 3337037	3337036	H-NS & PID 3337036	hemagglutinin-associated protein
ssb		CCGTTACATC	1 (0,1)	+63	47130 47582 453	n/a	ssb PID 3337048 PID 3337046	3337047	H-NS & ssb	single-strand binding protein
PID 3337048		TCGATAAAGA	1 (1,0)	-207	47938 49896 1959	n/a	ssb PID 3337048 psiB psiA	3337048	H-NS & PID 3337048	-
toxB		TCTACTAATT	1 (1,0)	-113	55981 65490 9510	n/a	IS21 toxB IS3 IS629	3337056	H-NS & toxB	Toxin B
IS3		TGGATAAAAA	1 (1,0)	-227	65582 65854 273	n/a	toxB IS3 traI IS629	3337057	H-NS & IS3	transposase Tra5
PID 3337064		TCGATAAACT TCATTTAATT	2 (2,0)	-156, -132	71421 71759 339	n/a	PID 3337063 PID 3337064 repA2	3337064	H-NS & PID 3337064	-
PID 3337069		TACATAAATA GAGATAAAAT	2 (2,0)	-136, -7	74979 75185 207	n/a	PID 3337067 PID 3337068 PID 3337069 IS91 IS600	3337069	H-NS & PID 3337069	-
PID 3337074		TGGATAAAAA	1 (0,1)	+89	79190 79531 342	n/a	katP PID 3337074 IS629	3337074	H-NS & PID 3337074	-
PID 3337079		GAGATTAATA	1 (1,0)	-212	87659 88765 1107	n/a	PID 3337078 PID 3337079 PID 3337080	3337079	H-NS & PID 3337079	-
PID 4589745		GCGTTACATC	1 (1,0)	-87	27540 28223 684	n/a	letA PID 4589744 PID 4589745	4589745	H-NS & PID 4589745	KfrAs
tagA		GCGACTTATT	1 (1,0)	-52	92527 2502 -90024	n/a	tagA etpC	4666293	H-NS & tagA	ToxR-regulated lipoprotein

20 of 83 genes (or 24.1%) contained a predicted H-NS binding site. These are:

etpC, etpE, etpO, hlyC, hlyA, hlyB, papX, PID 3337019, PID 3337034, PID 3337036, ssb, PID 3337048, toxB, IS3, PID 3337064, PID 3337069, PID 3337074, PID 3337079, PID 4589745, tagA

No strong binding sites were predicted for the following genes (63 of 83):

etpD, etpF, etpG, etpH, etpI, etpJ, etpK, etpL, etpM, etpN, IS911, hlyD, PID 3337020, PID 3337022, letA, letB, PID 3337027, IS629, IS629, rep, sopB, PID 3337033, PID 3337035, PID 3337037, PID 3337038, klcA, PID 3337041, PID 3337042, PID 3337044, PID 3337045, PID 3337046, psiB, psiA, parB, PID 3337053, IS3, IS21, IS629, traI, traX, PID 3337061, finO, PID 3337063, repA2, repA1, PID 3337067, PID 3337068, IS91, IS600, IS91, katP, IS629, espP, PID 3337078, PID 3337080, PID 3337081, repFIB, PID 4589744, sopA, PID 4589747, PID 4589748, nikB, PID 4666292