4. Analysis of the composite set of genes (back)

Predicted H-NS binding sites

Input motif
Resulting motif

Average AT content

More details

GO term overrepresentation
Propensity	Count	Annotation term
3.187	5	motor activity
3.187	5	flagellum (sensu Bacteria)
2.501	3	structural molecule activity
1.806	2	cytolysis
1.806	2	type II protein secretion system
1.806	2	type II protein secretion system complex
1.642	5	ciliary or flagellar motility
1.405	7	flagellum
1.355	2	ATPase activity, coupled to transmembrane movement of substances
1.260	5	cell adhesion
1.204	2	porin activity
1.032	2	transposase activity

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
acrE		TCGTTAAATA	1 (1,0)	-286	3411886 3413043 1158	n/a	acrE acrF envR	1789665	H-NS & acrE	cytoplasmic membrane lipoprotein cell cycle protein transporter activity protein secretion membrane cell division
ade		GCGATTATTT GGGATTAAAT	2 (2,0)	-233, -153	3841987 3843753 1767	n/a	ade yicO uhpT	1790098	H-NS & ade	cryptic adenine deaminase adenine deaminase activity adenine catabolism hydrolase activity manganese ion binding
agaB		GGGATAAATC CCGATTAATA	2 (2,0)	-150, -130	3282192 3282668 477	n/a	kbaY agaB agaC	1789527	H-NS & agaB	N-acetylgalactosamine-specific enzyme IIB component of PTS sugar porter activity cytoplasm transport protein-N(PI)-phosphohistidine-sugar phosphotransferase activity phosphoenolpyruvate-dependent sugar phosphotransferase system transferase activity
allC		CGGATTAATA	1 (1,0)	-262	543281 544516 1236	n/a	ylbA allC allD	1786726	H-NS & allC	allantoate amidohydrolase purine base metabolism proteolysis metabolism metallopeptidase activity hydrolase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines protein dimerization activity
bdm		CCGATTAATA	1 (1,0)	-167	1554089 1554304 216	n/a	osmC sfcA sra bdm	87081920	H-NS & bdm	biofilm-dependent modulation protein
chbR		TCAATTAATT	1 (1,0)	-33	1816629 1817471 843	n/a	chbF chbR chbA chbC	1788030	H-NS & chbR	DNA-binding transcriptional dual regulator DNA binding transcription factor activity intracellular transcription regulation of transcription, DNA-dependent sequence-specific DNA binding regulation of transcription
cpsB		TCGATAAAGA	1 (1,0)	-43	2121108 2122544 1437	n/a	cpsG cpsB wcaI	1788362	H-NS & cpsB	mannose-1-phosphate guanyltransferase
crcA		TCGTTAAAAA	1 (1,0)	-255	655780 656340 561	n/a	crcA cspE crcB	1786840	H-NS & crcA	palmitoyl transferase for Lipid A
csgD		TCGTTATATT	1 (1,0)	-208	1101769 1102419 651	n/a	csgF csgE csgD	1787277	H-NS & csgD	DNA-binding transcriptional activator in two-component regulatory system DNA binding transcription factor activity intracellular transcription regulation of transcription, DNA-dependent sequence-specific DNA binding
csgE		GCGATAAAGC	1 (1,0)	-2	1101375 1101764 390	n/a	csgG csgF csgE csgD	1787276	H-NS & csgE	predicted transport protein
cspA		CCGATTAATC	1 (1,0)	-225	3718072 3718284 213	n/a	yiaG cspA insJ hokA	1789979	H-NS & cspA	major cold shock protein nucleic acid binding DNA binding transcription regulation of transcription, DNA-dependent
cspI		CAGATAAATT	1 (1,0)	-123	1636479 1636691 213	n/a	ynfN cspI ydfP	1787834	H-NS & cspI	Qin prophage; cold shock protein nucleic acid binding DNA binding transcription regulation of transcription, DNA-dependent
degS		TGGATTAATT	1 (0,1)	+33	3380222 3381289 1068	n/a	degQ degS mdh	1789630	H-NS & degS	serine endoprotease, periplasmic serine-type endopeptidase activity protein binding proteolysis peptidase activity hydrolase activity periplasmic space
dnaK		GCGATTCATT	1 (1,0)	-253	12163 14079 1917	n/a	dnaK dnaJ yaaI	1786196	H-NS & dnaK	chaperone Hsp70, co-chaperone with DnaJ nucleotide binding protein binding ATP binding DNA replication protein folding response to unfolded protein unfolded protein binding
ebgC		TCGTTACAGT TCGATATTTT	2 (1,1)	-240, +83	3223744 3224193 450	n/a	ebgA ebgC ygjI	1789458	H-NS & ebgC	cryptic beta-D-galactosidase, beta subunit molecular function unknown
essQ		TCGATAAAGT	1 (0,1)	+91	1638394 1638609 216	n/a	ydfQ ydfR essQ	87081934	H-NS & essQ	Qin prophage; predicted S lysis protein cell wall catabolism cytolysis
fimA		TCTATAAATA	1 (1,0)	-213	4541138 4541686 549	n/a	fimE fimA fimI	1790769	H-NS & fimA	major type 1 subunit fimbrin (pilin) cell adhesion fimbrium
fimD		CGGTTAAATT	1 (1,0)	-163	4543119 4545755 2637	n/a	fimC fimD fimF	1790772	H-NS & fimD	outer membrane usher protein, type 1 fimbrial synthesis transporter activity transport fimbrium membrane integral to membrane outer membrane
fimI		GCGATAAAAA	1 (1,0)	-14	4541751 4542290 540	n/a	fimA fimI fimC	87082421	H-NS & fimI	fimbrial protein involved in type 1 pilus biosynthesis glycine-tRNA ligase activity ATP binding glycyl-tRNA aminoacylation cell adhesion fimbrium
fixA		TCGTTAATTT	1 (1,0)	-284	42403 43173 771	n/a	fixA fixB caiT	87081682	H-NS & fixA	predicted electron transfer flavoprotein subunit, ETFP adenine nucleotide-binding domain electron transport transport electron carrier activity carnitine metabolism
flgC		CCGTTAATTT	1 (1,0)	-9	1130661 1131065 405	n/a	flgB flgC flgD	1787314	H-NS & flgC	flagellar component of cell-proximal portion of basal-body rod ciliary or flagellar motility motor activity structural molecule activity flagellum (sensu Bacteria) flagellum
flgE		GCGTTTAATC	1 (0,1)	+26	1131797 1133005 1209	n/a	flgD flgE flgF	1787316	H-NS & flgE	flagellar hook protein ciliary or flagellar motility motor activity structural molecule activity flagellum (sensu Bacteria) flagellum flagellar basal body, rod (sensu Bacteria)
flgG		TCGATAAATT	1 (1,0)	-102	1133952 1134734 783	n/a	flgF flgG flgH	1787318	H-NS & flgG	flagellar component of cell-distal portion of basal-body rod ciliary or flagellar motility motor activity structural molecule activity cell motility flagellum (sensu Bacteria) flagellar basal body, distal rod (sensu Bacteria) flagellum flagellum organization and biogenesis
flgM		CCGATAAATA	1 (1,0)	-41	1129058 1129351 294	n/a	mviN flgN flgM flgA	1787311	H-NS & flgM	anti-sigma factor for FliA (sigma 28) transcription regulation of transcription, DNA-dependent negative regulation of transcription transcriptional repressor activity flagellum
flgN		GCGTTAAAAC	1 (1,0)	-97	1128637 1129053 417	n/a	mviN flgN flgM flgA	1787310	H-NS & flgN	export chaperone for FlgK and FlgL flagellum biogenesis flagellum
fliA		CCGATTAAAA TCAATAAATT	2 (2,0)	-57, -227	1999094 1999813 720	n/a	fliZ fliA fliC	1788231	H-NS & fliA	RNA polymerase, sigma 28 (sigma F) factor DNA binding transcription factor activity DNA-directed RNA polymerase activity transcription transcription initiation regulation of transcription, DNA-dependent sigma factor activity regulation of transcription
fliG		TGGATAAATA	1 (1,0)	-15	2012904 2013899 996	n/a	fliF fliG fliH	1788249	H-NS & fliG	flagellar motor switching and energizing component ciliary or flagellar motility motor activity chemotaxis flagellum (sensu Bacteria) membrane flagellum
fliJ		TCGATAAAGC	1 (1,0)	-139	2015970 2016413 444	n/a	fliI fliJ fliK	1788252	H-NS & fliJ	flagellar protein ciliary or flagellar motility motor activity chemotaxis flagellum (sensu Bacteria) membrane flagellum flagellar part (sensu Bacteria)
fliZ		CCGTTTAATA	1 (1,0)	-73	1998497 1999048 552	n/a	fliY fliZ fliA	87082001	H-NS & fliZ	predicted regulator of FliA activity DNA integration
gadA		TCCTTAAATT CGGATAAATC	2 (2,0)	-8, -42	3664203 3665603 1401	n/a	gadX gadA yhjA	1789934	H-NS & gadA	glutamate decarboxylase A, PLP-dependent glutamate decarboxylase activity glutamate metabolism lyase activity carboxy-lyase activity carboxylic acid metabolism pyridoxal phosphate binding
gadE		TCCATATATT TGGATAAATC	2 (2,0)	-175, -157	3656389 3656916 528	n/a	gadE mdtE	1789928	H-NS & gadE	DNA-binding transcriptional activator DNA binding transcription factor activity pyruvate kinase activity intracellular glycolysis transcription regulation of transcription, DNA-dependent sequence-specific DNA binding
gatD		CAGATAAATT	1 (1,0)	-120	2169857 2170897 1041	n/a	insF-5 gatR_2 gatD gatC	1788407	H-NS & gatD	galactitol-1-phosphate dehydrogenase, Zn-dependent and NAD(P)-binding zinc ion binding galactitol-1-phosphate 5-dehydrogenase activity oxidoreductase activity galactitol metabolism metal ion binding
glf		GCGATTAAAA GCGATATAAT	2 (2,0)	-156, -250	2105250 2106353 1104	n/a	wbbH glf rfbX	1788348	H-NS & glf	UDP-galactopyranose mutase, FAD/NAD(P)-binding protein binding UDP-galactopyranose mutase activity lipopolysaccharide biosynthesis isomerase activity
gltF		TCTATATATT	1 (1,0)	-237	3359198 3359962 765	n/a	gltF yhcA	1789608	H-NS & gltF	periplasmic protein membrane integral to membrane
gspD		GCGATAATAT TCAATAAAAT	2 (1,1)	-275, +11	3454399 3456351 1953	n/a	gspC gspD gspE	87082242	H-NS & gspD	general secretory pathway component, cryptic transport protein transporter activity protein secretion type II protein secretion system complex type II protein secretion system membrane outer membrane
gspE		CGGATAAATA	1 (1,0)	-202	3456361 3457842 1482	n/a	gspD gspE gspF	1789723	H-NS & gspE	general secretory pathway component, cryptic nucleotide binding ATP binding intracellular transport protein transporter activity type II protein secretion system complex type II protein secretion system nucleoside-triphosphatase activity
hdeA		TCGATTTAAT	1 (1,0)	-172	3654431 3654763 333	n/a	hdeD hdeB hdeA	1789926	H-NS & hdeA	stress response protein acid-resistance protein periplasmic space
hdeB		GCGTTACATC	1 (1,0)	-96	3653989 3654315 327	n/a	yhiD hdeB hdeA	87082279	H-NS & hdeB	acid-resistance protein
hlyE		GCGACAAATA	1 (1,0)	-282	1228706 1229617 912	n/a	ycgN umuD hlyE	87081853	H-NS & hlyE	hemolysin E pathogenesis membrane integral to membrane cytolysis hemolysis of host red blood cells
idnK		TCAATAAATT	1 (0,1)	+89	4492646 4493209 564	n/a	idnK idnD yjgB	1790719	H-NS & idnK	D-gluconate kinase, thermosensitive nucleotide binding shikimate kinase activity ATP binding carbohydrate metabolism amino acid biosynthesis kinase activity transferase activity D-gluconate metabolism gluconokinase activity
maa		GCGATACAAC	1 (0,1)	+44	478591 479142 552	n/a	ylaC maa hha ybaJ	1786664	H-NS & maa	maltose O-acetyltransferase acyltransferase activity maltose O-acetyltransferase activity transferase activity
mdtF		TCAATAAAAT	1 (0,1)	+11	3658437 3661550 3114	n/a	mdtE mdtF gadW	1789930	H-NS & mdtF	multidrug transporter, RpoS-dependent transporter activity transport membrane integral to membrane response to antibiotic
mdtI		CCGTTAAAAA	1 (1,0)	-192	1670844 1671173 330	n/a	ydgD mdtI mdtJ	1787883	H-NS & mdtI	multidrug efflux system transporter transport membrane integral to membrane
msbA		GCCATTAATT	1 (1,0)	-285	965844 967592 1749	n/a	ycaI msbA lpxK	1787143	H-NS & msbA	fused lipid transporter subunits of ABC superfamily: membrane component/ATP-binding component nucleotide binding ATP binding transport lipid transport cell wall (sensu Proteobacteria) membrane integral to membrane ATPase activity nucleoside-triphosphatase activity ATPase activity, coupled to transmembrane movement of substances
nmpC		GCGATAAATA	1 (0,1)	+14	574981 576108 1128	n/a	insH-2 nmpC	1786765	H-NS & nmpC	DLP12 prophage; truncated outer membrane porin (pseudogene) transporter activity transport ion transport porin activity membrane integral to membrane outer membrane
nrdH		CCGATAAAAA	1 (1,0)	-284	2798745 2798990 246	n/a	ygaM nrdH nrdI nrdE	1789028	H-NS & nrdH	glutaredoxin-like protein electron transport transport electron carrier activity protein disulfide oxidoreductase activity cell redox homeostasis
ompF		TCCTTAAATT	1 (1,0)	-210	985117 986205 1089	n/a	aspC ompF	1787160	H-NS & ompF	outer membrane porin 1a (Ia;b;F) transporter activity transport ion transport detection of virus porin activity membrane integral to membrane outer membrane entry of virus into host cell
osmB		GCGATATAAC	1 (1,0)	-137	1341134 1341352 219	n/a	pyrF yciH osmB yciT	1787539	H-NS & osmB	lipoprotein membrane
osmC		CCGATTAATA	1 (1,0)	-177	1554649 1555080 432	n/a	osmC bdm ddpF	1787757	H-NS & osmC	osmotically inducible, stress-inducible membrane protein peroxidase activity response to stress antioxidant activity oxidoreductase activity peroxiredoxin activity
pinR		TCGTTTATTT TGGTTAAAAT	2 (2,0)	-95, -226	1431108 1431698 591	n/a	tfaR pinR ynaE	1787638	H-NS & pinR	Rac prophage; predicted site-specific recombinase recombinase activity DNA binding DNA recombination transposition, DNA-mediated regulation of transcription
pitB		TCGTTAAAAA GGGATTAATC	2 (2,0)	-81, -235	3132894 3134393 1500	n/a	yghT pitB gss	1789360	H-NS & pitB	phosphate transporter inorganic phosphate transporter activity transport phosphate transport membrane integral to membrane
proV		TCGATATATT TCGATATATT	2 (1,1)	-39, +68	2802837 2804039 1203	n/a	nrdF proV proW	1789032	H-NS & proV	glycine betaine transporter subunit nucleotide binding ATP binding transport amino acid transport amino acid transporter activity membrane ATPase activity nucleoside-triphosphatase activity
rhsA		CCGATAAAAC	1 (1,0)	-20	3760206 3764339 4134	n/a	rhsA yibA yibF	1790020	H-NS & rhsA	rhsA element core protein RshA membrane integral to membrane
rhsD		TGGATAATAT	1 (1,0)	-220	522485 526765 4281	n/a	ybbP rhsD ybbC ylbH	1786706	H-NS & rhsD	rhsD element protein membrane integral to membrane
tatD		GCGTTAATTT	1 (0,1)	+14	4021577 4022359 783	n/a	tatC tatD rfaH	48994985	H-NS & tatD	DNase, magnesium-dependent magnesium ion binding nuclease activity hydrolase activity
tdcC		TGGATACAAT TCGACTAATT	2 (1,1)	+27, -245	3261708 3263039 1332	n/a	tdcD tdcC tdcB	1789504	H-NS & tdcC	L-threonine/L-serine transporter transporter activity transport symporter activity membrane integral to membrane
tdcD		TCGATTAAGT	1 (0,1)	+66	3260474 3261694 1221	n/a	tdcE tdcD tdcC	1789503	H-NS & tdcD	propionate kinase/acetate kinase C, anaerobic protein binding intracellular organic acid metabolism metabolism acetate kinase activity kinase activity phosphorylation transferase activity phosphotransferase activity, carboxyl group as acceptor
tnaA		TCGTTTATTT CCGATTAATT	2 (2,0)	-120, -68	3886753 3888168 1416	n/a	tnaC tnaA tnaB	87082323	H-NS & tnaA	tryptophanase/L-cysteine desulfhydrase, PLP-dependent protein binding amino acid metabolism tryptophan metabolism tryptophan catabolism tryptophanase activity aromatic amino acid family metabolism lyase activity carbon-carbon lyase activity
torZ		GCGTTAAAAT	1 (1,0)	-69	1952602 1955031 2430	n/a	yecP torZ torY	87081994	H-NS & torZ	trimethylamine N-oxide reductase system III, catalytic subunit electron transport oxidoreductase activity molybdenum ion binding periplasmic space trimethylamine-N-oxide reductase (cytochrome c) activity
ugd		GCGTTAAAAC TGGTTAAATC TGGATTAATC	3 (3,0)	-67, -236, -247	2096471 2097637 1167	n/a	cld ugd gnd	1788340	H-NS & ugd	UDP-glucose 6-dehydrogenase UDP-glucose 6-dehydrogenase activity electron transport oxidoreductase activity
uvrC		GCGTTACATT	1 (1,0)	-279	1990898 1992730 1833	n/a	pgsA uvrC uvrY	87081999	H-NS & uvrC	excinuclease UvrABC, endonuclease subunit DNA binding nuclease activity intracellular cytoplasm DNA repair base-excision repair nucleotide-excision repair response to DNA damage stimulus excinuclease ABC complex excinuclease ABC activity SOS response sequence-specific DNA binding
wcaE		GCGTTAAATA CCGTTAAATA	2 (2,0)	-22, -279	2126928 2127674 747	n/a	wcaF wcaE wcaD	1788368	H-NS & wcaE	predicted glycosyl transferase lipopolysaccharide biosynthesis transferase activity
wcaM		TGGTTAAAAT	1 (1,0)	-57	2112526 2113920 1395	n/a	galF wcaM wcaL	1788356	H-NS & wcaM	predicted colanic acid biosynthesis protein lipopolysaccharide biosynthesis
xapR		GCGTTTAAAT	1 (0,1)	+95	2519615 2520499 885	n/a	xapR xapB	2367136	H-NS & xapR	DNA-binding transcriptional activator DNA binding transcription factor activity transcription regulation of transcription, DNA-dependent
ybbD		TCGACAAAAT TGGATTAATA	2 (2,0)	-271, -40	527864 528124 261	n/a	ylbH ybbD	1786709	H-NS & ybbD	predicted protein membrane integral to membrane
ybcW		GCGATAAAAA GCGACAAAAT	2 (2,0)	-237, -7	579103 579309 207	n/a	ybcW ybcV	1786772	H-NS & ybcW	DLP12 prophage; predicted protein
ybfD		TCGTTAAAAT CCGATAATTT	2 (1,1)	-240, +73	737315 738076 762	n/a	ybfL ybfD ybgA	1786924	H-NS & ybfD	conserved protein DNA binding transposase activity transposition, DNA-mediated
ybfH		TGGATAAAGT TCCATACATT	2 (2,0)	-98, -104	715611 715820 210	n/a	ybfP ybfG ybfH potE	87081772	H-NS & ybfH	predicted protein
ybhM		TCAATAAATT GCAATAAATT CCGTTTAATA	3 (1,2)	-48, +23, +56	820016 820729 714	n/a	ybhL ybhM ybhN	1787005	H-NS & ybhM	conserved inner membrane protein membrane integral to membrane
ycbQ		TCTATAAATT	1 (1,0)	-131	997091 997630 540	n/a	ycbQ ycbR ssuE	87081804	H-NS & ycbQ	predicted fimbrial-like adhesin protein cell adhesion fimbrium
ycdP		CCGTTAAATA	1 (1,0)	-268	1085329 1085742 414	n/a	phoH ycdP ycdQ	1787258	H-NS & ycdP	predicted inner membrane protein
yceI		TCGATAAAGA GCCATAAATC	2 (2,0)	-56, -83	1117124 1117699 576	n/a	yceA yceI yceJ	1787295	H-NS & yceI	predicted protein molecular function unknown periplasmic space
ycfR		TCTTTAAATT	1 (1,0)	-134	1168296 1168553 258	n/a	ycfR ycfQ ycfS	1787355	H-NS & ycfR	predicted protein
ycgV		TCGATATAAA TCGTTACTTA	2 (2,0)	-200, -226	1252308 1255175 2868	n/a	dhaR ycgV	1787452	H-NS & ycgV	predicted adhesin cell adhesion
ycjO		GGGATAAAAA	1 (1,0)	-168	1371246 1372127 882	n/a	ycjN ycjO ycjP	1787570	H-NS & ycjO	predicted sugar transporter subunit: membrane component of ABC superfamily transporter activity transport membrane integral to membrane
ydcL		TCGATAAAAA	1 (1,0)	-227	1500481 1501149 669	n/a	tehB ydcL yncK_2 yncK_1	1787701	H-NS & ydcL	predicted lipoprotein membrane
ydcR		TGGTTTAATT	1 (1,0)	-85	1508027 1509433 1407	n/a	ydcQ ydcR ydcS	1787710	H-NS & ydcR	fused predicted DNA-binding transcriptional regulator/predicted amino transferase DNA binding transcription factor activity intracellular transcription regulation of transcription, DNA-dependent transaminase activity biosynthesis transferase activity transferase activity, transferring nitrogenous groups
ydeI		GAGATAAAAT	1 (1,0)	-289	1622129 1622521 393	n/a	ydeJ ydeH ydeI	1787817	H-NS & ydeI	conserved protein
ydeP		TGGATATATA	1 (1,0)	-83	1582231 1584510 2280	n/a	ydeP ydeQ	1787778	H-NS & ydeP	predicted oxidoreductase iron ion binding formate dehydrogenase activity oxidoreductase activity molybdenum ion binding metal ion binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding
ydjI		GCGATTAATT	1 (1,0)	-19	1854957 1855793 837	n/a	ydjH ydjI ydjJ	1788072	H-NS & ydjI	predicted aldolase fructose-bisphosphate aldolase activity glycolysis zinc ion binding
yeaJ		GCGATAAAAT	1 (0,1)	+29	1870065 1871555 1491	n/a	yeaI yeaJ yeaK	87081974	H-NS & yeaJ	predicted diguanylate cyclase molecular function unknown membrane integral to membrane
yeaU		GGGATTAATT	1 (1,0)	-72	1879936 1881021 1086	n/a	yeaU yeaV yeaT	1788101	H-NS & yeaU	predicted dehydrogenase protein binding metabolism tartrate dehydrogenase activity oxidoreductase activity oxidoreductase activity, acting on NADH or NADPH, NAD or NADP as acceptor lyase activity D-malate dehydrogenase (decarboxylating) activity tartrate decarboxylase activity NAD binding
yeeE		TCGATACAAA	1 (1,0)	-109	2082491 2083549 1059	n/a	sbcB yeeD yeeE yeeF	1788323	H-NS & yeeE	predicted inner membrane protein membrane integral to membrane
yeiC		TCATTAAATT GCGATTAAAT	2 (1,1)	+78, -177	2256377 2257318 942	n/a	yeiN yeiC fruA	1788491	H-NS & yeiC	predicted kinase kinase activity transferase activity
yfaO		TCGATAAAGT	1 (1,0)	-126	2362576 2363001 426	n/a	yfaO yfaZ ais	1788585	H-NS & yfaO	predicted NUDIX hydrolase hydrolase activity
yfbE		GCGATAATTC	1 (1,0)	-226	2363932 2365089 1158	n/a	yfbE yfbF ais	87082073	H-NS & yfbE	uridine 5'-(beta-1-threo-pentapyranosyl-4-ulose diphosphate) aminotransferase, PLP-dependent
yffB		TGGTTAAAAT TCGATAATGT	2 (2,0)	-185, -93	2589269 2589625 357	n/a	yffB dapE	1788815	H-NS & yffB	conserved protein electron transport oxidoreductase activity
yfiR		TCGATATTTT	1 (1,0)	-42	2739897 2740415 519	n/a	yfiL yfiR yfiN	1788955	H-NS & yfiR	predicted protein
ygbT		GCGTTTAATA	1 (1,0)	-283	2876877 2877794 918	n/a	ygbF ygbT ygcH	1789113	H-NS & ygbT	conserved protein
ygcI		GCGTTTAATC	1 (1,0)	-155	2878396 2879070 675	n/a	ygcH ygcI ygcJ	87082154	H-NS & ygcI	predicted protein
ygcJ		TCAATTAATT TCGTTAATTC	2 (2,0)	-178, -200	2879073 2880164 1092	n/a	ygcI ygcJ ygcK ygcL	1789116	H-NS & ygcJ	predicted protein
ygcK		TCGATATAAA	1 (0,1)	+35	2880177 2880659 483	n/a	ygcJ ygcK ygcL	1789117	H-NS & ygcK	predicted protein
ygcL		TCGTTTTATT	1 (1,0)	-222	2880652 2882160 1509	n/a	ygcJ ygcK ygcL ygcB	1789118	H-NS & ygcL	predicted protein
ygiL		TCGATTAAGT TCCTTAAATA	2 (2,0)	-132, -59	3183436 3183987 552	n/a	yqiC ygiL insC-5	1789422	H-NS & ygiL	predicted fimbrial-like adhesin protein cell adhesion fimbrium
yhfL		GGGTTAAATT	1 (1,0)	-247	3497470 3497637 168	n/a	cysG yhfL frlA	1789770	H-NS & yhfL	conserved secreted peptide membrane integral to membrane
yhhI		CCGATAATTT	1 (0,1)	+73	3622401 3623537 1137	n/a	yrhC yhhI yhhJ	1789896	H-NS & yhhI	predicted transposase DNA binding transposase activity transposition, DNA-mediated
yhhJ		GGGATAAAAA	1 (1,0)	-67	3623702 3624826 1125	n/a	yhhI yhhJ rbbA	87082274	H-NS & yhhJ	predicted transporter subunit: membrane component of ABC superfamily ATP binding transport membrane integral to membrane ATPase activity, coupled to transmembrane movement of substances
yhiM		CCGATATATA GGGATTAATT GCGATACAAA	3 (0,3)	+8, +29, +56	3632864 3633916 1053	n/a	yhiM yhiL yhiN	87082276	H-NS & yhiM	conserved inner membrane protein membrane integral to membrane
yiaN		GCGATTATTC	1 (1,0)	-153	3742827 3744104 1278	n/a	yiaM yiaN yiaO	48994950	H-NS & yiaN	predicted transporter transport membrane integral to membrane
yiaT		GCGATTAATT	1 (0,1)	+14	3749151 3749891 741	n/a	sgbE yiaU yiaT	1790010	H-NS & yiaT	predicted protein membrane outer membrane
yiaU		GCGATTCATT GCGATTAATT	2 (2,0)	-228, -137	3750015 3750989 975	n/a	yiaU yiaT yiaV	1790011	H-NS & yiaU	predicted DNA-binding transcriptional regulator DNA binding transcription factor activity transcription regulation of transcription, DNA-dependent
yiaW		TCGTTATATA	1 (1,0)	-77	3752128 3752451 324	n/a	yiaV yiaW	1790013	H-NS & yiaW	conserved inner membrane protein membrane integral to membrane
yjbE		CCGTTAAATT	1 (1,0)	-284	4233929 4234171 243	n/a	pgi yjbE yjbF	1790458	H-NS & yjbE	predicted protein
yjhE		TAGATACATT	1 (1,0)	-47	4504884 4505132 249	n/a	yjhC yjhE insN-2 yjhD insI-3	87082407	H-NS & yjhE	KpLE2 phage-like element; predicted membrane protein (pseudogene) transporter activity transport membrane integral to membrane
yjhF		TCGTTAATTA	1 (0,1)	+87	4518694 4520043 1350	n/a	yjhU yjhF yjhG	2367370	H-NS & yjhF	KpLE2 phage-like element; predicted transporter transport gluconate transporter activity gluconate transport membrane integral to membrane
yjhH		CCGATAAAAA	1 (1,0)	-273	4522128 4523033 906	n/a	yjhG yjhH yjhI	87082415	H-NS & yjhH	KpLE2 phage-like element; predicted lyase/synthase catalytic activity metabolism dihydrodipicolinate synthase activity lysine biosynthesis lyase activity diaminopimelate biosynthesis
yjhI		TGGATTCATT	1 (1,0)	-121	4523038 4523826 789	n/a	yjhH yjhI sgcR	1790752	H-NS & yjhI	KpLE2 phage-like element; predicted DNA-binding transcriptional regulator DNA binding transcription regulation of transcription, DNA-dependent
yjiP		TCCATAAAAT	1 (0,1)	+77	4567021 4567332 312	n/a	yjiP yjiQ yjiO	1790795	H-NS & yjiP	predicted transposase (pseudogene)
ykiA		CCGATATATT	1 (1,0)	-112	407893 408174 282	n/a	yaiE ykiA rdgC	1786591	H-NS & ykiA	predicted protein
yliF		TGGATTAATT GCGATATTTT	2 (2,0)	-259, -218	874558 875886 1329	n/a	yliE yliF yliG	1787056	H-NS & yliF	predicted diguanylate cyclase molecular function unknown membrane integral to membrane
ynaK		GCGTTTTATT	1 (1,0)	-25	1423401 1423664 264	n/a	trkG ynaK ydaY	1787628	H-NS & ynaK	Rac prophage; conserved protein DNA binding
yncD		TCCATAAATT CCGTTTCATT	2 (2,0)	-53, -64	1518987 1521089 2103	n/a	yncC yncE yncD	1787723	H-NS & yncD	predicted iron outer membrane transporter receptor activity transporter activity transport membrane outer membrane
ynjI		GCGATAATTT TGGATAAAAT	2 (2,0)	-30, -36	1841855 1842895 1041	n/a	gdhA ynjI topB	87081969	H-NS & ynjI	predicted inner membrane protein membrane integral to membrane
yoaC		TAGATAAAAT CCGTTAAATT TCGTTATAAT	3 (3,0)	-230, -111, -23	1892097 1892456 360	n/a	yoaB yoaC pabB yoaH	1788112	H-NS & yoaC	predicted protein
yobF		CCGATATATC	1 (1,0)	-148	1905472 1905615 144	n/a	rrmA cspC yobF	1788127	H-NS & yobF	predicted protein
yrhA		TCGATTAATA	1 (1,0)	-156	3581064 3581477 414	n/a	yhhZ yrhA insA-6 insB-6	87082266	H-NS & yrhA	conserved protein

116 of 248 genes (or 46.8%) contained a predicted H-NS binding site. These are:

acrE, ade, agaB, allC, bdm, chbR, cpsB, crcA, csgD, csgE, cspA, cspI, degS, dnaK, ebgC, essQ, fimA, fimD, fimI, fixA, flgC, flgE, flgG, flgM, flgN, fliA, fliG, fliJ, fliZ, gadA, gadE, gatD, glf, gltF, gspD, gspE, hdeA, hdeB, hlyE, idnK, maa, mdtF, mdtI, msbA, nmpC, nrdH, ompF, osmB, osmC, pinR, pitB, proV, rhsA, rhsD, tatD, tdcC, tdcD, tnaA, torZ, ugd, uvrC, wcaE, wcaM, xapR, ybbD, ybcW, ybfD, ybfH, ybhM, ycbQ, ycdP, yceI, ycfR, ycgV, ycjO, ydcL, ydcR, ydeI, ydeP, ydjI, yeaJ, yeaU, yeeE, yeiC, yfaO, yfbE, yffB, yfiR, ygbT, ygcI, ygcJ, ygcK, ygcL, ygiL, yhfL, yhhI, yhhJ, yhiM, yiaN, yiaT, yiaU, yiaW, yjbE, yjhE, yjhF, yjhH, yjhI, yjiP, ykiA, yliF, ynaK, yncD, ynjI, yoaC, yobF, yrhA

No strong binding sites were predicted for the following genes (132 of 248):

acrA, acrF, artJ, bcsF, borD, cadA, cchB, citA, cspC, cutC, emrE, emrY, entA, fhuB, fhuC, fimB, fimE, flgA, flgB, flgD, flgF, flgH, flgI, flgJ, flhB, fliC, fliD, fliE, fliF, fliH, fliK, fliL, fliM, fliN, fliQ, fliS, folC, frlB, fxsA, gadC, glpG, gltJ, gmd, hdhA, hipA, hns, kbl, kdsB, mdtJ, mntH, motB, nagA, nudD, parE, pflB, puuR, pyrB, rbsD, rcsA, recA, serB, sgbU, slp, stpA, tauA, wcaA, wcaC, wcaD, wcaF, wzc, wzxE, yadL, yagX, yagZ, yahA, ybaJ, ybjL, yccU, yceJ, ycgH_1, ycgX, yciA, yciF, ydcC, ydeK, ydeS, ydfJ, ydfW, ydiA, ydjJ, yebN, yecR, yedS_2, yedS_3, yedV, yeeN, yegJ, yfdP, yfgH, yfjK, ygaX, yhdX, yhjB, yhjD, yhjR, yiaA, yiaV, yibA, yibJ, yiiS, yjeJ, yjfJ, yjgM, yjhA, yjhG, yjiW, ykgA, ykgB, ykgF, ykgI, ymgD, ymgG, ynaE, ynaI, yncI, yneK, ynfN, yodA, yqeA, yqeI, yraH, ytfT