DISTILLER RESULTS

Modules:

ArcA ArgR CpxR CRP CueR CysB CytR DeoR FadR Fis FlhDC FNR FruR Fur GadE GlpR IHF IscR LexA Lrp MalT MarA MetJ Mlc NagC NarL NarP NsrR NtrC OmpR OxyR PhoB PhoP PurR RcsB SoxS TyrR

ArcA:

Modules	Motifs	No. conditions	No. genes	Functional enrichment
Module 9	ArcA CRP	149	12	Metabolism (-7.8e-13) TCA cycle (6.36e-12) aerobic respiration (1.53e-07) electron donors (0.000187) Central intermediary metabolism (0.00114) fermentation (0.00347) anaerobic respiration (0.00634)
Module 17	ArcA FNR	111	5	Metabolism (-3.25e-12) primary active transporters (5.32e-07) aerobic respiration (1.61e-05) electron acceptors (0.000477) transport (0.0322) fermentation (0.0372) Central intermediary metabolism (0.0476)
Module 18	ArcA CRP	45	4	Carbon compounds (0.0112) Carbon Utilization (0.0247) group translocators (0.0349) Metabolism (0.0472) inner membrane (0.0504) transport (0.0693) membrane (0.0711)
Module 28	ArcA CRP	110	11	Metabolism (-5.78e-12) TCA cycle (1.59e-13) aerobic respiration (8.99e-08) electron donors (0.000141) primary active transporters (0.000814) electron acceptors (0.00256) membrane (0.0223)
Module 90	ArcA	79	14	Metabolism (6.28e-13) Carbon compounds (7.27e-09) Carbon Utilization (1.05e-08) group translocators (0.000405) regulation (0.00166) transport (0.0446) type of regulation (0.0481)
Module 91	ArcA	49	4	Metabolism (-1.64e-12) adaptations (0.00587) TCA cycle (0.0178) amines (0.0363) Cell Processes (0.0455) regulation (0.0646) periplasm (0.114)
Module 92	ArcA	46	4	Metabolism (-8.9e-12) electron donors (0.0294) anaerobic respiration (0.0964) Carbon compounds (0.176) protein related (0.218) Carbon Utilization (0.256) inner membrane (0.355)
Module 93	ArcA	94	4	regulation (0.00515) Metabolism (0.017) electron acceptors (0.028) type of regulation (0.0639) inner membrane (0.0918) anaerobic respiration (0.126) membrane (0.127)
Module 94	ArcA	110	7	Metabolism (-4.69e-12) aerobic respiration (6.31e-07) primary active transporters (1.85e-06) electron acceptors (1.1e-05) electron donors (0.0673) transport (0.0878) membrane (0.0906)
Module 128	ArcA	32	4	primary active transporters (0.0159) electron donors (0.039) Cell Processes (0.0455) aerobic respiration (0.0472) protection (0.121) DNA related (0.121) transport (0.124)
Module 129	ArcA	85	4	Metabolism (-1.64e-12) primary active transporters (0.0159) electron donors (0.039) group translocators (0.0463) aerobic respiration (0.0472) amino acids (0.0608) type of regulation (0.0639)
Module 130	ArcA	54	4	Metabolism (-1.64e-12) amines (0.0363) electron donors (0.039) aerobic respiration (0.0472) unknown (0.0689) periplasm (0.114) transport (0.124)
Module 131	ArcA	44	4	Carbon compounds (0.0112) Carbon Utilization (0.0247) Metabolism (0.298) type of regulation (0.299) regulation (0.3) inner membrane (0.355) transport (0.409)

ArgR:

Modules	Motifs	No. conditions	No. genes	Functional enrichment
Module 10	ArgR	149	11	Metabolism (-5.78e-12) amino acids (-3.04e-12) cytoplasm (0.000543) periplasm (0.283) Extrachromosomal (0.571) transport (0.855)
Module 54	ArgR	52	4	amino acids (3.6e-06) cytoplasm (0.0113) protein related (0.0176) Metabolism (0.0472) unknown (0.0521) Information transfer (0.122) type of regulation (0.299)

CpxR:

Modules	Motifs	No. conditions	No. genes	Functional enrichment
Module 27	CpxR	82	6	Cell Processes (7.33e-05) type of regulation (0.00505) periplasm (0.00505) regulation (0.00515) protection (0.00578) adaptations (0.00587) RNA related (0.402)
Module 52	CpxR	82	4	membrane (0.0152) phospholipid (0.0187) Cell Structure (0.0366) outer membrane (0.0635) inner membrane (0.0918) protection (0.121) protein related (0.28)
Module 101	CpxR	62	4	Cell Processes (7.33e-05) protein related (0.00182) Information transfer (0.0345) Cell division (0.059) type of regulation (0.0639) regulation (0.0646) protection (0.121)

CRP:

Modules	Motifs	No. conditions	No. genes	Functional enrichment
Module 6	DeoR CRP	94	4	Central intermediary metabolism (0.0158) regulation (0.0349) genetic unit regulated (0.114) cytoplasm (0.129) Metabolism (0.298) type of regulation (0.299) RNA related (0.32)
Module 7	GlpR CRP	112	7	Metabolism (-4.69e-12) Central intermediary metabolism (1.19e-08) electron donors (3.07e-05) anaerobic respiration (0.00114) aerobic respiration (0.00286) membrane (0.0906) Cell Structure (0.189)
Module 9	ArcA CRP	149	12	Metabolism (-7.8e-13) TCA cycle (6.36e-12) aerobic respiration (1.53e-07) electron donors (0.000187) Central intermediary metabolism (0.00114) fermentation (0.00347) anaerobic respiration (0.00634)
Module 12	CytR CRP	127	4	Central intermediary metabolism (3.02e-05) Metabolism (0.017) inner membrane (0.443) transport (0.505) membrane (0.51) Cell Structure (0.635) cytoplasm (0.639)
Module 13	Mlc CRP	82	4	Metabolism (-1.64e-12) Carbon compounds (0.000919) Carbon Utilization (0.00305) group translocators (0.0463) Central intermediary metabolism (0.266) transport (0.505) cytoplasm (0.639)
Module 14	Mlc CRP	41	4	regulation (0.000157) genetic unit regulated (0.00887) Metabolism (0.017) Carbon compounds (0.0214) group translocators (0.0463) Carbon Utilization (0.0463) type of regulation (0.0639)
Module 15	Fis CRP	99	5	protein related (0.00429) cytoplasm (0.0104) glycolysis (0.021) fermentation (0.0372) Metabolism (0.0606) Information transfer (0.0724) Cell division (0.0732)
Module 16	IHF CRP	82	4	Metabolism (-1.64e-12) Central intermediary metabolism (0.00155) Carbon Utilization (0.00305) Carbon compounds (0.0214) fatty acids (0.0298) electron donors (0.039) protection (0.121)
Module 18	ArcA CRP	45	4	Carbon compounds (0.0112) Carbon Utilization (0.0247) group translocators (0.0349) Metabolism (0.0472) inner membrane (0.0504) transport (0.0693) membrane (0.0711)
Module 20	FNR CRP	83	4	Metabolism (-1.64e-12) amino acids (1.42e-05) periplasm (0.00505) Central intermediary metabolism (0.03) amines (0.0363) Carbon Utilization (0.0463) regulation (0.0646)
Module 25	IHF FNR CRP	48	4	Metabolism (-1.64e-12) anaerobic respiration (0.0063) aerobic respiration (0.0472) regulation (0.0646) transport (0.124) genetic unit regulated (0.149) cytoplasm (0.22)
Module 26	NagC CRP	114	5	Metabolism (-3.25e-12) group translocators (8.46e-08) Carbon Utilization (0.000353) Carbon compounds (0.00219) transport (0.00291) amines (0.0451) Central intermediary metabolism (0.0476)
Module 28	ArcA CRP	110	11	Metabolism (-5.78e-12) TCA cycle (1.59e-13) aerobic respiration (8.99e-08) electron donors (0.000141) primary active transporters (0.000814) electron acceptors (0.00256) membrane (0.0223)
Module 30	Fis CRP	61	4	Metabolism (-1.64e-12) Carbon Utilization (7.64e-05) fatty acids (0.000328) TCA cycle (0.0178) Carbon compounds (0.0214) Cell Processes (0.0455) aerobic respiration (0.0472)
Module 56	Fis CRP	82	4	Metabolism (-1.64e-12) aerobic respiration (0.000837) anaerobic respiration (0.0063) TCA cycle (0.0178) fatty acids (0.0298) amino acids (0.0608) adaptations (0.122)
Module 71	Fur CRP	82	9	adaptations (0.00235) membrane (0.00807) outer membrane (0.00872) Cell Structure (0.0304) transport (0.0427) Cell Processes (0.0437) Extrachromosomal (0.139)
Module 99	FNR CRP	80	4	Metabolism (-1.64e-12) anaerobic respiration (0.00014) Central intermediary metabolism (0.03) electron donors (0.039) aerobic respiration (0.0472) transport (0.124) membrane (0.127)
Module 100	Mlc CRP	85	4	Metabolism (-1.64e-12) Carbon compounds (1.49e-05) Carbon Utilization (7.64e-05) group translocators (0.0463) regulation (0.0646) genetic unit regulated (0.149) type of regulation (0.377)
Module 114	CRP	42	54	Metabolism (-4.17e-12) Carbon compounds (1.24e-12) Carbon Utilization (2.01e-11) transport (6.86e-07) Central intermediary metabolism (4.34e-06) periplasm (0.000403) amino acids (0.000724)
Module 115	CRP	52	38	Metabolism (-4.81e-12) Carbon Utilization (2.15e-09) Carbon compounds (1.23e-08) transport (2.59e-05) regulation (6.58e-05) fatty acids (0.00152) periplasm (0.00195)
Module 116	CRP	143	11	amino acids (0.000283) Metabolism (0.0135) ribosomes (0.0158) glycolysis (0.0376) Cell Structure (0.118) cytoplasm (0.122) Central intermediary metabolism (0.141)
Module 117	CRP	44	7	transport (1.71e-05) group translocators (0.00198) Metabolism (0.00222) Carbon compounds (0.00418) Carbon Utilization (0.0132) inner membrane (0.0364) membrane (0.0588)
Module 135	CRP	48	14	Metabolism (-8.15e-12) Carbon Utilization (2.24e-11) Carbon compounds (6.13e-10) group translocators (0.000512) fatty acids (0.00474) Central intermediary metabolism (0.0166) transport (0.0605)
Module 136	CRP	54	18	Carbon compounds (0.00011) periplasm (0.000589) Carbon Utilization (0.00102) regulation (0.0147) transport (0.016) Metabolism (0.0301) type of regulation (0.0616)
Module 137	CRP	43	5	regulation (0.000713) type of regulation (0.0116) membrane (0.0334) Carbon compounds (0.0343) fermentation (0.0372) Carbon Utilization (0.0725) Cell Structure (0.0765)
Module 138	CRP	40	10	amino acids (3.57e-06) Metabolism (0.00438) adaptations (0.0252) regulation (0.0511) Carbon compounds (0.0848) Cell Processes (0.166) Carbon Utilization (0.169)
Module 139	CRP	64	4	regulation (0.000157) type of regulation (0.00505) periplasm (0.114) transport (0.124) genetic unit regulated (0.149) Carbon compounds (0.227) Extrachromosomal (0.265)
Module 140	CRP	44	4	Central intermediary metabolism (0.0158) unknown (0.0521) Metabolism (0.298) type of regulation (0.299) regulation (0.3) inner membrane (0.355) transport (0.409)
Module 141	CRP	100	4	amino acids (0.0608) posttranscriptional (0.0866) cytoplasm (0.22) Central intermediary metabolism (0.266) protein related (0.28) type of regulation (0.377) regulation (0.379)
Module 142	CRP	76	4	TCA cycle (0.0178) amino acids (0.0608) adaptations (0.122) Metabolism (0.138) Central intermediary metabolism (0.266) protein related (0.28) Cell Processes (0.323)
Module 143	CRP	67	4	regulation (-3.9e-12) type of regulation (0.00138) genetic unit regulated (0.00455) glycolysis (0.0127) RNA related (0.0401) amino acids (0.046) Information transfer (0.122)
Module 144	CRP	71	4	Carbon compounds (0.000919) Carbon Utilization (0.00305) Metabolism (0.138) type of regulation (0.377) regulation (0.379) RNA related (0.402) inner membrane (0.443)
Module 145	CRP	36	4	Carbon Utilization (0.00082) Carbon compounds (0.0112) fatty acids (0.0225) Metabolism (0.0472) outer membrane (0.048) cytoplasm (0.129) membrane (0.414)
Module 146	CRP	36	4	Metabolism (-8.9e-12) amino acids (0.046) inner membrane (0.0504) transport (0.0693) membrane (0.0711) Cell Structure (0.126) Carbon compounds (0.176)
Module 147	CRP	59	4	extracellular (0.00188) fatty acids (0.0298) Carbon Utilization (0.0463) protection (0.121) transport (0.124) membrane (0.127) Metabolism (0.138)
Module 148	CRP	78	5	Metabolism (-1.64e-12) Central intermediary metabolism (0.03) DNA related (0.121) cytoplasm (0.22) membrane (0.51) Information transfer (0.626) Cell Structure (0.635)
Module 149	CRP	39	4	Carbon compounds (0.0214) Carbon Utilization (0.0463) regulation (0.0646) Metabolism (0.138) genetic unit regulated (0.149) Extrachromosomal (0.265) Central intermediary metabolism (0.266)
Module 150	CRP	87	4	Carbon compounds (0.0214) group translocators (0.0463) Carbon Utilization (0.0463) amino acids (0.0608) Metabolism (0.138) transport (0.505)

CueR:

Modules	Motifs	No. conditions	No. genes	Functional enrichment
Module 31	CueR	79	4	Cell Processes (0.0242) periplasm (0.0865) protection (0.0925) adaptations (0.0931) Metabolism (0.298) inner membrane (0.355) transport (0.409)

CysB:

Modules	Motifs	No. conditions	No. genes	Functional enrichment
Module 23	CysB	124	13	Metabolism (1.35e-05) transport (0.0859) amino acids (0.159) periplasm (0.283) protection (0.3) inner membrane (0.453) membrane (0.557)
Module 38	CysB	52	5	RNA related (0.0739) protection (0.121) membrane (0.127) Information transfer (0.209) Cell Structure (0.216) Cell Processes (0.323) inner membrane (0.443)

CytR:

Modules	Motifs	No. conditions	No. genes	Functional enrichment
Module 12	CytR CRP	127	4	Central intermediary metabolism (3.02e-05) Metabolism (0.017) inner membrane (0.443) transport (0.505) membrane (0.51) Cell Structure (0.635) cytoplasm (0.639)

DeoR:

Modules	Motifs	No. conditions	No. genes	Functional enrichment
Module 6	DeoR CRP	94	4	Central intermediary metabolism (0.0158) regulation (0.0349) genetic unit regulated (0.114) cytoplasm (0.129) Metabolism (0.298) type of regulation (0.299) RNA related (0.32)

FadR:

Modules	Motifs	No. conditions	No. genes	Functional enrichment
Module 34	FadR	91	4	Metabolism (-1.64e-12) fatty acids (1.55e-06) Carbon Utilization (0.00305) phospholipid (0.0187) membrane (0.127) Cell Structure (0.216) Extrachromosomal (0.265)

Fis:

Modules	Motifs	No. conditions	No. genes	Functional enrichment
Module 15	Fis CRP	99	5	protein related (0.00429) cytoplasm (0.0104) glycolysis (0.021) fermentation (0.0372) Metabolism (0.0606) Information transfer (0.0724) Cell division (0.0732)
Module 30	Fis CRP	61	4	Metabolism (-1.64e-12) Carbon Utilization (7.64e-05) fatty acids (0.000328) TCA cycle (0.0178) Carbon compounds (0.0214) Cell Processes (0.0455) aerobic respiration (0.0472)
Module 35	Fis	75	9	Information transfer (-1.26e-12) RNA related (0.000428) cytoplasm (0.000722) DNA related (0.019) protein related (0.0996) unknown (0.117) Central intermediary metabolism (0.419)
Module 56	Fis CRP	82	4	Metabolism (-1.64e-12) aerobic respiration (0.000837) anaerobic respiration (0.0063) TCA cycle (0.0178) fatty acids (0.0298) amino acids (0.0608) adaptations (0.122)
Module 67	Fis	55	4	Carbon compounds (0.121) Metabolism (0.131) Central intermediary metabolism (0.143) Carbon Utilization (0.179) type of regulation (0.211) regulation (0.212)
Module 68	Fis	62	4	Metabolism (-1.64e-12) Central intermediary metabolism (3.02e-05) primary active transporters (0.0159) electron donors (0.039) aerobic respiration (0.0472) anaerobic respiration (0.126) cytoplasm (0.22)
Module 69	Fis	77	4	DNA related (0.000123) Information transfer (0.00224) Cell Structure (0.00244) cytoplasm (0.0377) pilus (0.0399) flagella (0.0409) Cell Processes (0.0455)
Module 111	Fis	101	4	Metabolism (-1.64e-12) primary active transporters (0.0159) electron donors (0.039) group translocators (0.0463) aerobic respiration (0.0472) posttranscriptional (0.0866) DNA related (0.121)
Module 112	Fis	91	4	Information transfer (2.48e-12) DNA related (0.000123) Cell Processes (0.0455) RNA related (0.0739) protection (0.121) cytoplasm (0.22) Metabolism (0.457)
Module 113	Fis	86	5	Metabolism (-3.25e-12) anaerobic respiration (0.000342) Central intermediary metabolism (0.00365) electron acceptors (0.0349) large molecule carriers (0.0485) unknown (0.0853) periplasm (0.14)

FlhDC:

Modules	Motifs	No. conditions	No. genes	Functional enrichment
Module 3	FlhDC	49	32	flagella (-1.04e-11) Cell Processes (-7.66e-12) Cell Structure (-2.46e-12) flagellum (-1.28e-12) Metabolism (4.54e-10) periplasm (0.0125) unknown (0.426)
Module 132	FlhDC	78	4	flagella (0.000313) Cell Structure (0.011) flagellum (0.0252) Extrachromosomal (0.206) Cell Processes (0.254) inner membrane (0.355) membrane (0.414)

FNR:

Modules	Motifs	No. conditions	No. genes	Functional enrichment
Module 1	NarL IHF FNR	81	7	Metabolism (-4.69e-12) anaerobic respiration (7.52e-07) electron acceptors (1.1e-05) inner membrane (0.00843) membrane (0.0162) Cell Structure (0.0478) large molecule carriers (0.0673)
Module 2	NarL NarP FNR	76	5	Metabolism (-3.25e-12) anaerobic respiration (5.7e-06) electron carriers (0.00015) electron acceptors (0.0349) electron donors (0.0485) large molecule carriers (0.0485) periplasm (0.14)
Module 17	ArcA FNR	111	5	Metabolism (-3.25e-12) primary active transporters (5.32e-07) aerobic respiration (1.61e-05) electron acceptors (0.000477) transport (0.0322) fermentation (0.0372) Central intermediary metabolism (0.0476)
Module 20	FNR CRP	83	4	Metabolism (-1.64e-12) amino acids (1.42e-05) periplasm (0.00505) Central intermediary metabolism (0.03) amines (0.0363) Carbon Utilization (0.0463) regulation (0.0646)
Module 25	IHF FNR CRP	48	4	Metabolism (-1.64e-12) anaerobic respiration (0.0063) aerobic respiration (0.0472) regulation (0.0646) transport (0.124) genetic unit regulated (0.149) cytoplasm (0.22)
Module 29	NarL IHF FNR	67	4	Metabolism (-8.9e-12) anaerobic respiration (3.59e-05) electron acceptors (0.000144) primary active transporters (0.012) electron donors (0.0294) large molecule carriers (0.0294) aerobic respiration (0.0356)
Module 45	FNR	98	11	Metabolism (-1.32e-12) anaerobic respiration (4.28e-06) electron acceptors (0.00169) protein related (0.0284) fermentation (0.0659) outer membrane (0.137) membrane (0.17)
Module 49	NarL FNR	71	4	inner membrane (0.009) transport (0.0146) membrane (0.0152) Metabolism (0.017) Carbon compounds (0.0214) Cell Structure (0.0366) electron donors (0.039)
Module 50	NarL FNR	64	4	Metabolism (-1.64e-12) anaerobic respiration (0.00014) electron acceptors (0.028) type of regulation (0.0639) regulation (0.0646) posttranscriptional (0.0866) membrane (0.127)
Module 80	FNR	37	4	Carbon compounds (0.121) Metabolism (0.131) Central intermediary metabolism (0.143) Carbon Utilization (0.179) inner membrane (0.254) transport (0.296) membrane (0.3)
Module 81	FNR	131	4	regulation (2.54e-12) type of regulation (0.000153) fermentation (0.0298) amino acids (0.0608) Metabolism (0.138) genetic unit regulated (0.149) Central intermediary metabolism (0.266)
Module 82	FNR	40	4	Metabolism (0.017) amino acids (0.0608) periplasm (0.114) protection (0.121) anaerobic respiration (0.126) Cell Processes (0.323) transport (0.505)
Module 83	FNR	82	4	Metabolism (0.017) TCA cycle (0.0178) fermentation (0.0298) Cell Processes (0.0455) unknown (0.0689) periplasm (0.114) anaerobic respiration (0.126)
Module 84	FNR	34	6	aerobic respiration (0.0587) transport (0.185) Extrachromosomal (0.319) RNA related (0.474) inner membrane (0.519) membrane (0.59) Metabolism (0.594)
Module 85	FNR	73	4	Central intermediary metabolism (0.03) transposon related (0.0635) DNA related (0.121) adaptations (0.122) cytoplasm (0.22) Extrachromosomal (0.265) Cell Processes (0.323)
Module 86	FNR	70	4	Metabolism (-1.64e-12) anaerobic respiration (0.0063) primary active transporters (0.0159) glycolysis (0.0169) TCA cycle (0.0178) electron donors (0.039) aerobic respiration (0.0472)
Module 87	FNR	68	4	large molecule carriers (0.039) pilus (0.0399) Cell Processes (0.0455) protection (0.121) adaptations (0.122) Cell Structure (0.635) cytoplasm (0.639)
Module 99	FNR CRP	80	4	Metabolism (-1.64e-12) anaerobic respiration (0.00014) Central intermediary metabolism (0.03) electron donors (0.039) aerobic respiration (0.0472) transport (0.124) membrane (0.127)
Module 106	FNR	93	7	Metabolism (0.017) amino acids (0.0608) unknown (0.0689) periplasm (0.114) adaptations (0.122) cytoplasm (0.22) Carbon compounds (0.227)

FruR:

Modules	Motifs	No. conditions	No. genes	Functional enrichment
Module 42	FruR	73	4	regulation (0.00515) Metabolism (0.017) TCA cycle (0.0178) type of regulation (0.0639) anaerobic respiration (0.126) genetic unit regulated (0.149) cytoplasm (0.22)
Module 43	FruR	74	5	Metabolism (-3.25e-12) Carbon compounds (0.00219) Carbon Utilization (0.00709) glycolysis (0.021) group translocators (0.0576) cytoplasm (0.0787) transport (0.185)
Module 88	FruR	92	5	Central intermediary metabolism (0.0476) protein related (0.0527) type of regulation (0.0987) regulation (0.0998) ribosomes (0.106) posttranscriptional (0.107) Metabolism (0.253)
Module 89	FruR	113	4	fermentation (0.000328) regulation (0.00515) TCA cycle (0.0178) protein related (0.0333) Information transfer (0.0345) type of regulation (0.0639) ribosomes (0.0857)

Fur:

Modules	Motifs	No. conditions	No. genes	Functional enrichment
Module 5	Fur	51	33	adaptations (1.72e-11) Cell Processes (4.19e-06) transport (5.01e-05) membrane (0.0041) outer membrane (0.0111) Central intermediary metabolism (0.0179) Cell Structure (0.0405)
Module 21	Fur	77	16	transport (6.43e-05) Extrachromosomal (0.00246) membrane (0.00356) Cell Structure (0.0206) outer membrane (0.0209) adaptations (0.0722) inner membrane (0.111)
Module 70	Fur	60	22	Central intermediary metabolism (3.17e-05) Metabolism (0.00017) adaptations (0.000254) Cell Processes (0.00587) posttranscriptional (0.00812) regulation (0.0146) transport (0.0233)
Module 71	Fur CRP	82	9	adaptations (0.00235) membrane (0.00807) outer membrane (0.00872) Cell Structure (0.0304) transport (0.0427) Cell Processes (0.0437) Extrachromosomal (0.139)
Module 120	Fur	96	10	Metabolism (-7.42e-12) aerobic respiration (4.17e-12) electron acceptors (4.14e-07) primary active transporters (6.3e-06) TCA cycle (8.96e-06) membrane (1.6e-05) electron donors (0.000103)
Module 121	Fur	40	4	amino acids (0.0309) protection (0.0626) Cell Processes (0.177) inner membrane (0.254) transport (0.296) membrane (0.3) Cell Structure (0.396)
Module 122	Fur	46	4	inner membrane (0.009) transport (0.0146) membrane (0.0152) Extrachromosomal (0.0296) Cell Structure (0.0366) transposon related (0.0635) adaptations (0.122)

GadE:

Modules	Motifs	No. conditions	No. genes	Functional enrichment
Module 40	GadE	100	4	amino acids (0.0309) unknown (0.035) Metabolism (0.131) Central intermediary metabolism (0.143) type of regulation (0.211) regulation (0.212) cytoplasm (0.399)

GlpR:

Modules	Motifs	No. conditions	No. genes	Functional enrichment
Module 7	GlpR CRP	112	7	Metabolism (-4.69e-12) Central intermediary metabolism (1.19e-08) electron donors (3.07e-05) anaerobic respiration (0.00114) aerobic respiration (0.00286) membrane (0.0906) Cell Structure (0.189)

IHF:

Modules	Motifs	No. conditions	No. genes	Functional enrichment
Module 1	NarL IHF FNR	81	7	Metabolism (-4.69e-12) anaerobic respiration (7.52e-07) electron acceptors (1.1e-05) inner membrane (0.00843) membrane (0.0162) Cell Structure (0.0478) large molecule carriers (0.0673)
Module 16	IHF CRP	82	4	Metabolism (-1.64e-12) Central intermediary metabolism (0.00155) Carbon Utilization (0.00305) Carbon compounds (0.0214) fatty acids (0.0298) electron donors (0.039) protection (0.121)
Module 25	IHF FNR CRP	48	4	Metabolism (-1.64e-12) anaerobic respiration (0.0063) aerobic respiration (0.0472) regulation (0.0646) transport (0.124) genetic unit regulated (0.149) cytoplasm (0.22)
Module 29	NarL IHF FNR	67	4	Metabolism (-8.9e-12) anaerobic respiration (3.59e-05) electron acceptors (0.000144) primary active transporters (0.012) electron donors (0.0294) large molecule carriers (0.0294) aerobic respiration (0.0356)
Module 74	IHF	59	7	Metabolism (-4.69e-12) amino acids (0.00012) primary active transporters (0.0277) electron acceptors (0.0485) aerobic respiration (0.0812) transport (0.0878) Central intermediary metabolism (0.0905)
Module 75	IHF	91	10	Cell Structure (0.000171) ribosomes (0.00113) protein related (0.00541) outer membrane (0.0108) membrane (0.0649) regulation (0.0925) pilus (0.0969)
Module 76	IHF	66	4	regulation (2.54e-12) type of regulation (0.000153) genetic unit regulated (0.00887) outer membrane (0.0635) adaptations (0.122) Central intermediary metabolism (0.266) Cell Processes (0.323)
Module 77	IHF	86	4	Metabolism (-1.64e-12) amino acids (0.0014) TCA cycle (0.0178) periplasm (0.114) transport (0.124) anaerobic respiration (0.126)
Module 78	IHF	110	4	Information transfer (0.00224) DNA related (0.00578) adaptations (0.00587) protein related (0.0333) cytoplasm (0.0377) Cell Processes (0.0455) periplasm (0.114)
Module 79	IHF	42	4	regulation (0.0014) fermentation (0.0225) type of regulation (0.0345) unknown (0.0521) anaerobic respiration (0.0964) genetic unit regulated (0.114) Metabolism (0.298)
Module 123	IHF	94	4	TCA cycle (0.0178) Extrachromosomal (0.0296) flagella (0.0409) regulation (0.0646) anaerobic respiration (0.126) genetic unit regulated (0.149) Cell Processes (0.323)
Module 124	IHF	71	4	cytoplasm (0.0505) protection (0.0626) Central intermediary metabolism (0.143) Cell Processes (0.177) Metabolism (0.592)
Module 125	IHF	99	4	Metabolism (-1.64e-12) primary active transporters (0.0159) Central intermediary metabolism (0.03) electron donors (0.039) aerobic respiration (0.0472) murein (0.0545) posttranscriptional (0.0866)
Module 126	IHF	70	4	pilus (0.0399) amino acids (0.0608) transport (0.124) Metabolism (0.138) Cell Structure (0.216) cytoplasm (0.22) Carbon compounds (0.227)
Module 127	IHF	41	4	Carbon compounds (0.00389) Carbon Utilization (0.00878) Metabolism (0.131)

IscR:

Modules	Motifs	No. conditions	No. genes	Functional enrichment
Module 48	IscR	95	4	regulation (0.0349) genetic unit regulated (0.114) Central intermediary metabolism (0.207) Metabolism (0.298) type of regulation (0.299) RNA related (0.32) transport (0.409)

LexA:

Modules	Motifs	No. conditions	No. genes	Functional enrichment
Module 33	LexA	55	5	DNA related (-2.06e-12) Cell Processes (-1.49e-12) Information transfer (-2.32e-13) type of regulation (0.000696) regulation (0.000713) posttranscriptional (0.00475) DNA structure level (0.0129)
Module 61	LexA	85	4	Information transfer (2.48e-12) DNA related (9.81e-07) Cell Processes (0.00296) protein related (0.0333) cytoplasm (0.0377) regulation (0.0646) ribosomes (0.0857)
Module 62	LexA	77	4	DNA related (3.15e-05) Cell Processes (0.000795) Information transfer (0.0103) protection (0.0925) cytoplasm (0.129) Metabolism (0.74)
Module 63	LexA	106	4	protection (0.00295) Cell Processes (0.0242) regulation (0.0349) transport (0.0693) genetic unit regulated (0.114) type of regulation (0.299) RNA related (0.32)
Module 102	LexA	75	4	Cell Processes (-2.92e-12) DNA related (9.81e-07) Information transfer (0.00224) protection (0.00578) cytoplasm (0.22) Metabolism (0.834)
Module 103	LexA	101	5	Cell Processes (-1.49e-12) DNA related (3.03e-08) protection (0.000301) Information transfer (0.000486) adaptations (0.15) Extrachromosomal (0.319) inner membrane (0.519)

Lrp:

Modules	Motifs	No. conditions	No. genes	Functional enrichment
Module 64	Lrp	76	4	regulation (0.000157) amino acids (0.0014) type of regulation (0.00505) periplasm (0.00505) protein related (0.0333) Information transfer (0.0345) unknown (0.0689)
Module 65	Lrp	76	4	pilus (0.0399) murein (0.0545) amino acids (0.0608) periplasm (0.114) protection (0.121) Metabolism (0.138) Cell Structure (0.216)
Module 66	Lrp	75	4	amino acids (0.000708) Metabolism (0.0472) Central intermediary metabolism (0.207) inner membrane (0.355) transport (0.409) membrane (0.414) Cell Structure (0.53)
Module 109	Lrp	87	4	Metabolism (-1.64e-12) amino acids (1.42e-05) Central intermediary metabolism (0.00155) protein related (0.28) Information transfer (0.626) cytoplasm (0.639)
Module 110	Lrp	83	4	amino acids (0.0014) outer membrane (0.0635) periplasm (0.114) adaptations (0.122) Cell Processes (0.323) Metabolism (0.457) transport (0.505)

MalT:

Modules	Motifs	No. conditions	No. genes	Functional enrichment
Module 22	MalT	92	6	Metabolism (-9.22e-12) Carbon compounds (5.22e-06) Carbon Utilization (3.93e-05) periplasm (0.0121) transport (0.0568) outer membrane (0.0937) Extrachromosomal (0.37)

MarA:

Modules	Motifs	No. conditions	No. genes	Functional enrichment
Module 4	SoxS MarA	80	4	Cell Processes (0.00296) protection (0.00578) Metabolism (0.017) Central intermediary metabolism (0.03) electron donors (0.039) adaptations (0.122) cytoplasm (0.22)
Module 36	MarA	81	5	Cell Processes (0.000795) adaptations (0.003) outer membrane (0.048) periplasm (0.0865) Central intermediary metabolism (0.207) Metabolism (0.298) membrane (0.414)

MetJ:

Modules	Motifs	No. conditions	No. genes	Functional enrichment
Module 11	MetJ	148	5	Metabolism (-3.25e-12) amino acids (3.52e-05) Central intermediary metabolism (0.00365) cytoplasm (0.0104) unknown (0.0853) type of regulation (0.446) regulation (0.449)
Module 118	MetJ	112	4	regulation (0.000157) Central intermediary metabolism (0.00155) type of regulation (0.00505) Metabolism (0.017) amino acids (0.0608) unknown (0.0689) genetic unit regulated (0.149)

Mlc:

Modules	Motifs	No. conditions	No. genes	Functional enrichment
Module 13	Mlc CRP	82	4	Metabolism (-1.64e-12) Carbon compounds (0.000919) Carbon Utilization (0.00305) group translocators (0.0463) Central intermediary metabolism (0.266) transport (0.505) cytoplasm (0.639)
Module 14	Mlc CRP	41	4	regulation (0.000157) genetic unit regulated (0.00887) Metabolism (0.017) Carbon compounds (0.0214) group translocators (0.0463) Carbon Utilization (0.0463) type of regulation (0.0639)
Module 100	Mlc CRP	85	4	Metabolism (-1.64e-12) Carbon compounds (1.49e-05) Carbon Utilization (7.64e-05) group translocators (0.0463) regulation (0.0646) genetic unit regulated (0.149) type of regulation (0.377)
Module 107	Mlc	41	4	regulation (2.54e-12) genetic unit regulated (0.000237) RNA related (0.00636) Information transfer (0.0345) group translocators (0.0463) type of regulation (0.0639) ribosomes (0.0857)
Module 108	Mlc	48	4	group translocators (0.0234) cytoplasm (0.0505) Carbon compounds (0.121) Carbon Utilization (0.179) type of regulation (0.211) regulation (0.212) RNA related (0.227)

NagC:

Modules	Motifs	No. conditions	No. genes	Functional enrichment
Module 26	NagC CRP	114	5	Metabolism (-3.25e-12) group translocators (8.46e-08) Carbon Utilization (0.000353) Carbon compounds (0.00219) transport (0.00291) amines (0.0451) Central intermediary metabolism (0.0476)
Module 57	NagC	51	4	transposon related (0.0323) outer membrane (0.0323) Extrachromosomal (0.143) membrane (0.3) Cell Structure (0.396)
Module 58	NagC	106	4	unknown (0.035) Carbon compounds (0.121) Carbon Utilization (0.179) type of regulation (0.211) regulation (0.212) Metabolism (0.592)
Module 59	NagC	77	4	Extrachromosomal (0.074)
Module 60	NagC	39	4	inner membrane (0.136) transport (0.161) membrane (0.163) Cell Structure (0.222) Metabolism (0.362)

NarL:

Modules	Motifs	No. conditions	No. genes	Functional enrichment
Module 1	NarL IHF FNR	81	7	Metabolism (-4.69e-12) anaerobic respiration (7.52e-07) electron acceptors (1.1e-05) inner membrane (0.00843) membrane (0.0162) Cell Structure (0.0478) large molecule carriers (0.0673)
Module 2	NarL NarP FNR	76	5	Metabolism (-3.25e-12) anaerobic respiration (5.7e-06) electron carriers (0.00015) electron acceptors (0.0349) electron donors (0.0485) large molecule carriers (0.0485) periplasm (0.14)
Module 29	NarL IHF FNR	67	4	Metabolism (-8.9e-12) anaerobic respiration (3.59e-05) electron acceptors (0.000144) primary active transporters (0.012) electron donors (0.0294) large molecule carriers (0.0294) aerobic respiration (0.0356)
Module 49	NarL FNR	71	4	inner membrane (0.009) transport (0.0146) membrane (0.0152) Metabolism (0.017) Carbon compounds (0.0214) Cell Structure (0.0366) electron donors (0.039)
Module 50	NarL FNR	64	4	Metabolism (-1.64e-12) anaerobic respiration (0.00014) electron acceptors (0.028) type of regulation (0.0639) regulation (0.0646) posttranscriptional (0.0866) membrane (0.127)
Module 55	NarL	114	4	Metabolism (-1.64e-12) electron donors (0.000567) anaerobic respiration (0.0063) fermentation (0.0298) aerobic respiration (0.0472) Carbon compounds (0.227) protein related (0.28)
Module 119	NarL	71	5	Metabolism (-3.25e-12) anaerobic respiration (3.78e-08) electron acceptors (3.16e-06) membrane (0.00306) Cell Structure (0.01) inner membrane (0.0202) electron donors (0.0485)

NarP:

Modules	Motifs	No. conditions	No. genes	Functional enrichment
Module 2	NarL NarP FNR	76	5	Metabolism (-3.25e-12) anaerobic respiration (5.7e-06) electron carriers (0.00015) electron acceptors (0.0349) electron donors (0.0485) large molecule carriers (0.0485) periplasm (0.14)

NsrR:

Modules	Motifs	No. conditions	No. genes	Functional enrichment
Module 51	NsrR	41	4	Central intermediary metabolism (0.0745) Metabolism (0.362)

NtrC:

Modules	Motifs	No. conditions	No. genes	Functional enrichment
Module 19	NtrC	36	7	amino acids (1.6e-08) regulation (0.000302) Metabolism (0.0008) type of regulation (0.00405) posttranscriptional (0.147) periplasm (0.19) genetic unit regulated (0.246)
Module 72	NtrC	95	4	type of regulation (-6.4e-12) regulation (-3.9e-12) unknown (0.0521) adaptations (0.0931) genetic unit regulated (0.114) Cell Processes (0.254) Metabolism (0.298)
Module 73	NtrC	114	4	regulation (0.0349) amino acids (0.046) Metabolism (0.0472) genetic unit regulated (0.114) cytoplasm (0.129) Central intermediary metabolism (0.207) type of regulation (0.299)
Module 133	NtrC	82	4	type of regulation (0.0345) regulation (0.0349) amino acids (0.046) posttranscriptional (0.0657) periplasm (0.0865) DNA related (0.0925) inner membrane (0.355)
Module 134	NtrC	67	5	Metabolism (-1.64e-12) regulation (2.54e-12) type of regulation (0.000153) amino acids (0.0014) posttranscriptional (0.0866) genetic unit regulated (0.149) inner membrane (0.443)

OmpR:

Modules	Motifs	No. conditions	No. genes	Functional enrichment
Module 47	OmpR	89	4	flagella (0.0409) Cell Processes (0.0455) amino acids (0.0608) regulation (0.0646) periplasm (0.114) adaptations (0.122) transport (0.124)

OxyR:

Modules	Motifs	No. conditions	No. genes	Functional enrichment
Module 46	OxyR	37	4	regulation (0.0646) adaptations (0.122) genetic unit regulated (0.149) Information transfer (0.209) cytoplasm (0.22) protein related (0.28) Cell Processes (0.323)

PhoB:

Modules	Motifs	No. conditions	No. genes	Functional enrichment
Module 44	PhoB	40	5	fermentation (0.0225) Metabolism (0.0472) transport (0.0693) periplasm (0.0865) anaerobic respiration (0.0964) inner membrane (0.355) membrane (0.414)

PhoP:

Modules	Motifs	No. conditions	No. genes	Functional enrichment
Module 53	PhoP	76	4	membrane (0.0152) Cell Structure (0.0366) outer membrane (0.0635) type of regulation (0.0639) regulation (0.0646) RNA related (0.402) inner membrane (0.443)
Module 104	PhoP	87	4	type of regulation (0.0639) regulation (0.0646) cytoplasm (0.22) Extrachromosomal (0.265) Central intermediary metabolism (0.266) RNA related (0.402) inner membrane (0.443)
Module 105	PhoP	70	4	type of regulation (0.0124) regulation (0.0126) Central intermediary metabolism (0.143) RNA related (0.227) Information transfer (0.388) cytoplasm (0.399) Metabolism (0.592)

PurR:

Modules	Motifs	No. conditions	No. genes	Functional enrichment
Module 8	PurR	83	9	Metabolism (-1.32e-12) cytoplasm (4.6e-05) amino acids (0.132) Extrachromosomal (0.5) Central intermediary metabolism (0.502) inner membrane (0.732) membrane (0.799)
Module 24	PurR	120	10	Metabolism (-7.42e-12) amino acids (0.0099) Central intermediary metabolism (0.0331) cytoplasm (0.0519) inner membrane (0.403) transport (0.496) membrane (0.503)
Module 39	PurR	75	4	inner membrane (0.009) membrane (0.0152) Central intermediary metabolism (0.03) Cell Structure (0.0366) amino acids (0.0608) transport (0.124) Metabolism (0.138)
Module 95	PurR	118	6	Metabolism (-9.22e-12) Central intermediary metabolism (0.00691) cytoplasm (0.0257) inner membrane (0.584) transport (0.651) membrane (0.657) Cell Structure (0.779)
Module 96	PurR	94	5	Metabolism (-3.25e-12) amino acids (3.52e-05) pilus (0.0497) Central intermediary metabolism (0.321) transport (0.584) Cell Structure (0.716) cytoplasm (0.72)
Module 97	PurR	95	4	Extrachromosomal (0.0296) transport (0.124) Metabolism (0.138) cytoplasm (0.22) Central intermediary metabolism (0.266)

RcsB:

Modules	Motifs	No. conditions	No. genes	Functional enrichment
Module 37	RcsB	74	4	adaptations (0.0631) Cell Processes (0.177) type of regulation (0.211) regulation (0.212)

SoxS:

Modules	Motifs	No. conditions	No. genes	Functional enrichment
Module 4	SoxS MarA	80	4	Cell Processes (0.00296) protection (0.00578) Metabolism (0.017) Central intermediary metabolism (0.03) electron donors (0.039) adaptations (0.122) cytoplasm (0.22)
Module 32	SoxS	113	4	electron donors (0.0294) regulation (0.0349) protection (0.0925) DNA related (0.0925) genetic unit regulated (0.114) Information transfer (0.122) Cell Processes (0.254)

TyrR:

Modules	Motifs	No. conditions	No. genes	Functional enrichment
Module 41	TyrR	107	4	amino acids (1.42e-05) Metabolism (0.138) RNA related (0.402) inner membrane (0.443) transport (0.505) membrane (0.51) Information transfer (0.626)
Module 98	TyrR	80	4	regulation (0.00515) amino acids (0.0608) transposon related (0.0635) type of regulation (0.0639) DNA related (0.121) genetic unit regulated (0.149) Information transfer (0.209)