Table 3. Top Geobacteraceae motifs identified by AlignACE most similar to conserved motifs in other bacterial species
Operon	Motif	Motif sequence	Similar to conserved bacterial motifs a	CompareACE score	Additional criteria
334	11	GGGATGGGAT	TM_operons004_300_m6	0.802975
		GGGGTGGGGC
		GGCGTGGGGC
		GTGGTGGGGT
		GGGATCGGAT
		GTGGTGGGGC
		GGGATGGGGC
		GGGATGGGAT
502	3	GAACGAAAAA	MP_fusions001_100_m23	0.807182
		AAAGGAAAAA
		GACCGAAAAA
		GGGCGAAAAA
		AAACGAAGAG
		GGGGGAAAAG
893	8	TATCGCGGTGG	MP_fusions001_300_m32	0.815983	Overlaps with RBS
		TGGCGCGGGGG	MP_sum_all002_100_m15	0.834872
		TGGCGCGGGGG	MP_fusions001_100_m15	0.864884
		TGGCGCGTGGG	MP_sum_all002_100_m33	0.865052
		ATTCGCGTGGG
1294	5	GGCAAAAAAAT	TH_sum_all002_300_m13	0.801281	Overlaps with NNPP prediction
		AGGATAAAAAT
		ATCAGGAAAAA
		GGCACGACAAT
		AGCAGGAAAAT
		GTCATGAAAAG
		ATCAGAAAATT
		GGCAAAAAAAT
	9	AAAAAAATTT	PA_operons013_100_m1	0.810869	iclR
		AAAAAAATTT	PA_sum_all012_300_m1	0.810869
		AACACAATTT	AG_fusions004_300_m4	0.847165
		GAAACAAATT	AG_operons018_300_m3	0.903484
		GACTAAATTT
1816	8	ATGAAAATTC	MP_sum_all002_300_m17	0.820471	argR18
		ATGAAAATCA	TH_sum_all022_100_m1	0.828351	Overlaps with NNPP prediction
		ATGGAAATTC	TH_operons003_300_m13	0.868
		ATAAAAGTTC	TH_sum_all002_300_m13	0.902726
		TTATAAATTC
		ACAAAAATCC
		ATGAAGACTC
		ATATAATTTC
		ATAAAAACCG
2207	11	GAAAATACTCAT	TH_operons003_100_m7	0.802413
		GTAAAATGTTCT	TH_sum_all002_100_m7	0.802413
		GAAAAAATTTAT	PH_operons005_100_m2	0.840268
		CAAAAAAGTTCT	PH_sum_all005_100_m2	0.840268
		CCAAATGATCAT
		CCAAGTGGTTAT
		GTAAGTCTTTAT
		CAAAGTGTTTAT
	23	AGAAAACGCTT	TH_sum_all009_100_m9	0.811525
		AAAAAATTTAT	CT_operons021_100_m3	0.816865
		AAAAAAGTTCT	CP_sum_all005_100_m5	0.818142
		AAAAAAGGTTG
		AAAAAGGCCCT
		AAAAAGTACAG
		AATAAAGACTT
		AAACAATGTTG
		AAAAAGCCTAT
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 ≥ 0.8.
Operon, operon number assigned by FGENESB;
Motif, motif number assigned by AlignACE for a motif in that operon;
Motif sequence, sequence of a motif provided AlignACE, with active columns marked in red;
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;
Additional criteria, provides information on whether a motif was similar to a known E.coli transcription factor binding site with CompareACE score ≥ 0.7
overlapped with a predicted ribosomal binding site (RBS) in G. sulfurreducens or  with a motif found by Neural Network Promoter Prediction (NNPP) software.
a motif name (Organism_group_motif number)
For bacterial motifs listed from McGuire and Church (2000), abbreviations for motif and group names are the same as provided at:
http://arep.med.harvard.edu/regulon_pred/ as 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)