Top Geobacteraceae motifs identified by AlignACE most similar to conserved motifs in other bacterial species
op	motif	Similar to conserved bacterial motifsa	CompareACE score	Similar to E.coli motifs	Palindromic	Overlaps with RBS	Overlaps with NNPP prediction
17	7	MP_fusions001_300_m32	0.759631				Yes
264	6	CT_operons003_100_m5	0.73394
264	6	MP_fusions001_100_m17	0.732169
264	6	MP_fusions001_300_m20	0.741118
264	6	MP_sum_all002_100_m28	0.71124
334	4	TM_sum_all096_300_m1	0.712319
334	11	TM_operons004_300_m6	0.802975
334	11	TM_sum_all004_300_m3	0.77026
334	11	TM_sum_all096_300_m1	0.726677
485	4	MP_sum_all002_300_m29	0.730695				Yes
485	4	TH_sum_all009_100_m9	0.799676				Yes
485	6	MP_sum_all002_100_m28	0.714292				Yes
485	9	CY_operons002_300_m1	0.704086
498	9	CY_operons080_100_m1	0.706588
498	9	MP_sum_all002_100_m9	0.709892
502	2	EC_profile007_300_m1	0.73635	malT (0.74)
502	2	EC_sum_all013_300_m1	0.712905	malT (0.74)
502	3	MP_fusions001_100_m23	0.807182
502	6	CT_operons003_100_m5	0.754962
502	10	MP_sum_all002_300_m2	0.720891
674	2	BS_fusions018_300_m4	0.717437		Yes
674	2	BS_operons002_300_m5	0.719031		Yes
674	2	BS_sum_all002_300_m5	0.719031		Yes
674	2	HI_sum_all001_300_m4	0.710481		Yes
674	4	CT_operons029_300_m3	0.715539
674	4	CY_fusions002_300_m14	0.704627
674	4	HI_sum_all029_300_m5	0.705999
674	4	MG_operons010_100_m2	0.783942
674	4	RP_sum_all007_100_m5	0.710057
674	4	TH_operons003_300_m5	0.713737
674	4	TH_sum_all013_300_m1	0.707067
674	4	TM_operons004_100_m8	0.726901
674	4	TM_operons004_100_m8	0.726901
765	2	BS_operons008_300_m8	0.749111			Yes	Yes
765	5	AG_sum_all007_300_m7	0.713655	cynR (0.75)			Yes
765	5	MP_sum_all003_300_m5	0.77668	cynR (0.75)			Yes
765	5	TH_operons014_300_m1	0.703027	cynR (0.75)			Yes
765	8	MP_fusions001_300_m31	0.739203
893	8	MP_fusions001_100_m15	0.864884			Yes
893	8	MP_fusions001_100_m2	0.744639			Yes
893	8	MP_fusions001_100_m9	0.720641			Yes
893	8	MP_fusions001_300_m1	0.773251			Yes
893	8	MP_fusions001_300_m11	0.767133			Yes
893	8	MP_fusions001_300_m32	0.815983			Yes
893	8	MP_fusions001_300_m9	0.713442			Yes
893	8	MP_sum_all002_100_m1	0.725258			Yes
893	8	MP_sum_all002_100_m15	0.834872			Yes
893	8	MP_sum_all002_100_m15	0.834872			Yes
893	8	MP_sum_all002_100_m27	0.70634			Yes
893	8	MP_sum_all002_100_m33	0.865052			Yes
893	8	MP_sum_all002_300_m1	0.752706			Yes
893	8	MP_sum_all002_300_m2	0.703949			Yes
893	10	EC_operons006_100_m1	0.729132
893	10	EC_sum_all005_100_m1	0.74036
893	10	EC_sum_all005_300_m1	0.733328
991	9	TH_operons023_100_m1	0.727243
1294	5	CP_operons036_300_m1	0.71747				Yes
1294	5	MP_sum_all002_100_m23	0.710013				Yes
1294	5	PA_profile026_300_m2	0.711337				Yes
1294	5	PA_sum_all015_300_m3	0.769322				Yes
1294	5	TH_operons003_300_m13	0.77397				Yes
1294	5	TH_sum_all002_300_m13	0.801281				Yes
1294	9	AA_operons042_300_m3	0.771247	iclR (0.72)
1294	9	AA_sum_all047_300_m3	0.771247	iclR (0.72)
1294	9	AG_fusions002_300_m9	0.735575	iclR (0.72)
1294	9	AG_fusions004_300_m4	0.847165	iclR (0.72)
1294	9	AG_fusions013_300_m1	0.788461	iclR (0.72)
1294	9	AG_operons001_300_m1	0.75807	iclR (0.72)
1294	9	AG_operons006_100_m1	0.701548	iclR (0.72)
1294	9	AG_operons006_300_m11	0.728179	iclR (0.72)
1294	9	AG_operons008_300_m2	0.705178	iclR (0.72)
1294	9	AG_operons018_300_m3	0.903484	iclR (0.72)
1294	9	AG_sum_all001_100_m1	0.711858	iclR (0.72)
1294	9	AG_sum_all001_300_m1	0.796655	iclR (0.72)
1294	9	AG_sum_all003_100_m2	0.727772	iclR (0.72)
1294	9	AG_sum_all003_300_m3	0.727936	iclR (0.72)
1294	9	AG_sum_all007_100_m1	0.747738	iclR (0.72)
1294	9	AG_sum_all011_100_m2	0.781599	iclR (0.72)
1294	9	CP_sum_all005_100_m5	0.745307	iclR (0.72)
1294	9	CT_operons021_100_m3	0.777985	iclR (0.72)
1294	9	CY_fusions002_300_m12	0.738091	iclR (0.72)
1294	9	CY_fusions002_300_m14	0.702986	iclR (0.72)
1294	9	HI_profile004_300_m4	0.752981	iclR (0.72)
1294	9	MP_sum_all002_300_m17	0.795835	iclR (0.72)
1294	9	PA_operons013_100_m1	0.810869	iclR (0.72)
1294	9	PA_profile002_100_m1	0.770047	iclR (0.72)
1294	9	PA_profile026_300_m2	0.710293	iclR (0.72)
1294	9	PA_sum_all012_300_m1	0.810869	iclR (0.72)
1294	9	PH_operons005_100_m2	0.705683	iclR (0.72)
1294	9	PH_sum_all001_100_m3	0.757205	iclR (0.72)
1294	9	PH_sum_all005_100_m2	0.705683	iclR (0.72)
1294	9	PH_sum_all020_300_m2	0.711229	iclR (0.72)
1294	9	TH_operons003_300_m13	0.784448	iclR (0.72)
1294	9	TH_operons005_300_m7	0.787668	iclR (0.72)
1294	9	TH_sum_all002_300_m13	0.783062	iclR (0.72)
1294	9	TH_sum_all005_300_m8	0.787668	iclR (0.72)
1294	9	TM_fusions001_300_m6	0.736581	iclR (0.72)
1410	11	PA_operons011_100_m1	0.702476
1410	20	CT_operons003_100_m5	0.712325
1410	23	AG_fusions013_300_m1	0.715511	iclR (0.73)			Yes
1410	23	AG_sum_all003_100_m2	0.731523	iclR (0.73)			Yes
1410	23	AG_sum_all003_300_m3	0.727071	iclR (0.73)			Yes
1410	23	CT_operons004_300_m2	0.777975	iclR (0.73)			Yes
1410	23	CT_operons021_100_m3	0.705805	iclR (0.73)			Yes
1581	1	AA_operons042_300_m3	0.731811		Yes		Yes
1581	1	AA_sum_all047_300_m3	0.731811		Yes		Yes
1581	1	AG_sum_all003_300_m3	0.707247		Yes		Yes
1581	1	PH_operons011_300_m5	0.726892		Yes		Yes
1581	1	PH_sum_all020_300_m1	0.704261		Yes		Yes
1816	4	BS_fusions006_100_m2	0.700256				Yes
1816	4	CP_operons036_300_m1	0.783334				Yes
1816	4	TH_operons003_300_m13	0.752982				Yes
1816	4	TH_sum_all002_300_m13	0.780522				Yes
1816	8	AA_sum_all008_300_m5	0.708206	argR18 (0.73)			Yes
1816	8	AG_fusions004_300_m4	0.703947	argR18 (0.73)			Yes
1816	8	AG_sum_all001_100_m9	0.718658	argR18 (0.73)			Yes
1816	8	AG_sum_all001_100_m9	0.718658	argR18 (0.73)			Yes
1816	8	HI_profile004_300_m4	0.700059	argR18 (0.73)			Yes
1816	8	MP_sum_all002_300_m17	0.820471	argR18 (0.73)			Yes
1816	8	PA_sum_all069_300_m2	0.730739	argR18 (0.73)			Yes
1816	8	TH_operons003_300_m13	0.868	argR18 (0.73)			Yes
1816	8	TH_operons004_300_m1	0.740437	argR18 (0.73)			Yes
1816	8	TH_operons011_300_m1	0.770583	argR18 (0.73)			Yes
1816	8	TH_sum_all002_300_m13	0.902726	argR18 (0.73)			Yes
1816	8	TH_sum_all003_100_m7	0.754946	argR18 (0.73)			Yes
1816	8	TH_sum_all003_300_m1	0.758209	argR18 (0.73)			Yes
1816	8	TH_sum_all005_100_m4	0.744197	argR18 (0.73)			Yes
1816	8	TH_sum_all022_100_m1	0.828351	argR18 (0.73)			Yes
1816	9	EC_sum_all013_100_m1	0.730127
1856	6	CY_sum_all002_300_m1	0.716657		Yes
1856	10	MP_sum_all010_300_m14	0.700584
2029	1	MP_fusions001_100_m23	0.723383			Yes	Yes
2029	7	EC_operons006_100_m1	0.747482
2029	7	EC_sum_all005_100_m1	0.754114
2029	7	EC_sum_all005_300_m1	0.754234
2029	13	CP_sum_all010_300_m4	0.720173				Yes
2029	14	EC_operons006_100_m1	0.75421
2029	14	EC_sum_all005_100_m1	0.768699
2029	14	EC_sum_all005_300_m1	0.76225
2097	2	EC_sum_all013_100_m1	0.721551
2097	2	EC_sum_all013_300_m1	0.727095
2207	1	TM_operons003_100_m6	0.70347
2207	11	AG_fusions002_300_m9	0.783862
2207	11	AG_fusions013_300_m1	0.727197
2207	11	AG_operons006_300_m11	0.752063
2207	11	AG_operons009_300_m1	0.706069
2207	11	AG_operons018_300_m3	0.739765
2207	11	AG_sum_all001_100_m1	0.705267
2207	11	AG_sum_all008_300_m1	0.708915
2207	11	CP_operons006_300_m3	0.701733
2207	11	PA_profile002_100_m1	0.780563
2207	11	PA_profile026_300_m2	0.708746
2207	11	PA_sum_all015_300_m3	0.709345
2207	11	PH_operons005_100_m2	0.840268
2207	11	PH_sum_all001_100_m3	0.790004
2207	11	PH_sum_all005_100_m2	0.840268
2207	11	TH_operons003_100_m7	0.802413
2207	11	TH_operons003_100_m7	0.802413
2207	11	TH_operons003_300_m2	0.745618
2207	11	TH_operons003_300_m3	0.702657
2207	11	TH_operons004_300_m1	0.775666
2207	11	TH_operons005_300_m7	0.762556
2207	11	TH_operons011_300_m1	0.724587
2207	11	TH_profile008_300_m2	0.74726
2207	11	TH_sum_all002_100_m7	0.802413
2207	11	TH_sum_all002_300_m2	0.737727
2207	11	TH_sum_all003_100_m7	0.769951
2207	11	TH_sum_all003_300_m1	0.77757
2207	11	TH_sum_all005_100_m4	0.729554
2207	11	TH_sum_all005_300_m8	0.762556
2207	11	TH_sum_all013_300_m2	0.723071
2207	11	TH_sum_all022_100_m1	0.771291
2207	17	MP_sum_all002_300_m20	0.707715	fur (0.74)
2207	23	AG_fusions004_300_m4	0.71347
2207	23	AG_fusions013_300_m1	0.764051
2207	23	AG_operons006_300_m11	0.758245
2207	23	AG_operons008_300_m2	0.794953
2207	23	AG_operons018_300_m3	0.789225
2207	23	AG_sum_all003_100_m2	0.702359
2207	23	AG_sum_all003_300_m3	0.704383
2207	23	CP_sum_all005_100_m5	0.818142
2207	23	CP_sum_all020_300_m1	0.745386
2207	23	CT_operons004_300_m2	0.754581
2207	23	CT_operons021_100_m3	0.816865
2207	23	CT_sum_all001_300_m7	0.702159
2207	23	CT_sum_all021_100_m1	0.742745
2207	23	PA_profile002_100_m1	0.77599
2207	23	TH_operons013_300_m6	0.751445
2207	23	TH_sum_all009_100_m9	0.811525
2207	23	TH_sum_all014_300_m6	0.732913
Note:
Shown are Geobacteraceae motifs similar to conserved motifs in other prokaryotic species (McGuire, A. M., Church, G. M. 2000. Predicting regulons and their
cis-regulatory motifs by comparative genomics. Nucleic Acids Res. 28, 4523-4530) , with the CompareACE search results ≥ 0.7.  Operon, operon number
assigned by FGENESB; Motif, motif number assigned by AlignACE for a motif in that operon; Similar conserved bacterial motifs, similar motifs identified by
McGuire and Church (2000) in 22 bacterial species (http://arep.med.harvard.edu/regulon_pred/); CompareACE score, provides output score by CompareACE;
Similar to E.coli motifs, similar to known E.coli transcription factor binding sites (Robison et al., 1998) with CompareACE score ≥ 0.7 hit listed in parenthesis.
Palindromic, indicates if a motif was also palindromic with CompareACE score ≥ 0.7 hit listed in parenthesis; Overlaps with RBS, indicates if a motif overlapped
with a predicted ribosomal binding site in G. sulfurreducens; Overlaps with NNPP prediction, indicates if a motif overlapped with a region identified by
the Neural Network Promoter Prediction software.
a  motif name consisting of Organism_group_motif number
For bacterial motifs listed from McGuire and Church (2000), abbreviations for motif names are the same as provided at
http://arep.med.harvard.edu/regulon_pred/ and described by McGuire and Church (2000).  Organism names are abbreviated as follows:
Aquifex aeolicus (AA), Archaeoglobus fulgidus (AG), Aeropyrum pernix (AP), Borrelia burgdorferei (BB), Bacillus subtilis (BS), Chlamydia pneumoniae (CP), Chlamydia trachomatis
(CT), Synechocystis PCC6803 (CY), Escherichia coli K12 (EC), Haemophilus influenzae (HI), Helicobacter pylori (HP), Helicobacter pylori strain J99 (HY), Mycoplasma genitalium
(MG), Methanococcus janaschii (MJ), Mycoplasma pneumoniae (MP), Mycobacterium tuberculosis (MT),  Pyrococcus abysii (PA), Pyrococcus horokoshii (PH), Ricksettia
prowazekii (RP), Methanobacterium thermoautotrophicum (TH), Thermatoga maritima (TM), Trepenoma pallidum (TP)
Group names are assigned as follows:
groups derived from conserved operons: "operons" followed by a 3-digit number (e.g. EC_operons001.ace)
groups derived from protein fusions: "fusions" followed by a 3-digit number (e.g. TM_fusions001.ace)
groups derived from phylogenetic profiles: "profile" followed by a 3-digit number (e.g. AA_profile001.ace)
groups from sum of above three regulon prediction methods: "sum_all" followed by a 3-digit number (e.g. HI_sum_all001.ace)