Table 2

Potential ModE-binding sites identified by scanning archaeal genome sequences against the weight matrix derived from alignment in Figure 3. Sites that fall immediately upstream of genes implicated in molybdenum metabolism are indicated in bold. Scores are Kullback-Leibler distances that have been normalised such that the maximum possible score is 100. Essentially, the higher the score is, the greater the magnitude of the theoretical binding energy [26]. All sites scoring more than 75 are listed. Distances are given (number of bases) between the downstream end of the putative ModE-binding site and the predicted translational start codon.
Organism	Sequence	Score	Distance	Annotation of potential target gene

*Methanosarcina mazei*	TGGCGTTATGTTTATTTAAACATAACGAT	80	-5	MM1564 molybdenum containing formylmethanofuran dehydrogenase isoenzyme I subunit E
Methanosarcina mazei	TAATGTTATATATCTTAATAAATAACTTT	78	524	MM1328 Two component response regulator
Methanosarcina mazei	TAACGATATATTAATAATTAGATTTAGAT	78	299	MM1783 hypothetical protein
Methanosarcina mazei	TATCCATATACTAATGATTATATATCCAT	78	69	MM1790 conserved protein
Methanosarcina mazei	AATATTTATATAGTACACAATATATCAAT	78	39	MM2248 conserved protein
Methanosarcina mazei	CACCCATATATTAGTTTATAAATAACGCT	78	948	MM2931 hydrolase
Methanosarcina mazei	GAAGCGTATATATAAGAGTATATAAAGAG	78	53	MM3131 Fructokinase
Methanosarcina mazei	TTTCTCTCTATACTAGTCTACAGATAGAG	78	191	MM3331 conserved protein
Methanosarcina mazei	GAACAATATATCGTTAACAATATATCCAT	77	48	MM0378 sugar phosphate nucleotydyl transferase
Methanosarcina mazei	AATCTTTATATCATGGAATTTATCGTGAA	77	290	MM0957 Ammonium transporter
Methanosarcina mazei	CATCTTTTTATACTTCCCTATATACTTAA	77	31	tlpC MM1658 methyl accepting chemotaxis protein
Methanosarcina mazei	AAAACATATATAGAAACATACATATCGCA	77	153	MM2159 hypothetical protein
Methanosarcina mazei	TCTCGTTATATTTCTATTTATATATATTT	77	344	MM2777 Acylphosphatase
Methanosarcina mazei	TTTCGCTGTATATCTTATTTCATAAATAG	76	1436	MM0016 translation initiation factor 1A
Methanosarcina mazei	TGACAGTATATAAATTAATAGTTAGAGAT	76	76	MM0211 Cysteine proteinase
Methanosarcina mazei	AGTCATTATCTATATCAATATAAATAGTT	76	527	MM0338 putative phosphomethylpyrimidine kinase
Methanosarcina mazei	AAACATTAAATATTTTAATACATAGTTAT	76	39	MM0659 GDP mannose 4,6 dehydratase
*Methanosarcina mazei*	ATTAGGTTTATAAGTCAATAAATAATGAA	76	43	MM0996 cobalamin biosynthesis protein G
Methanosarcina mazei	TTTAGATTTATATAAGAATTTAAAACTAT	76	276	MM1157 conserved protein
Methanosarcina mazei	TATCGGGATATTCTATGGATTATATCGAA	76	13	MM1281 conserved protein
Methanosarcina mazei	AAACGTTATATACAAGCGAATATGAGTAT	76	156	MM1355 conserved protein
Methanosarcina mazei	CATCAATAAATTAATTTCTATATAAGGTA	76	30	MM1847 hypothetical protein
Methanosarcina mazei	GATTGATATATAATTATTTTCAAACTGAT	76	25	iorA MM2093 Indolepyruvate oxidoreductase, subunit
Methanosarcina mazei	AATTAATATATGATGGATTTTATATAGAT	76	290	MM2747 hypothetical protein
Methanosarcina mazei	TAAATATATATAAATAGAAATATAACGAG	76	101	MM2776 hypothetical protein
Methanosarcina mazei	AAGCGTTATTTATAAACTAATATATGGGT	76	35	MM2932 conserved protein
Methanosarcina mazei	AATCGCTCTATAGAAGTAAACTGAGCGGA	76	377	MM2945 Mannosyltransferase
Methanosarcina mazei	AAACTTTATATATTAAAATATAAATAAAA	76	499	MM3203 hypothetical protein
*Methanosarcina acetivorans*	TATGGTTATGTAATTCTAAACATAACGAA	81	1504	vnfH MA1213 nitrogenase (iron protein)
*Methanosarcina acetivorans*	AATCGTTATGTTTAGGTATACATAACTAC	81	164	modA MA2280 molybdenum ABC transporter, solute binding protein
Methanosarcina acetivorans	TAAAGTTATTTATTAGTATACATAACTAT	80	764	cheY2 MA0016 chemotaxis response regulator
Methanosarcina acetivorans	AAATGAAATATATATATATAGATAACGAT	80	185	MA0724 predicted protein
Methanosarcina acetivorans	TTTCAATATATATTTCAATATATAAAATA	80	378	vhtG MA1146 F420 nonreducing hydrogenase
*Methanosarcina acetivorans*	ATTCGTTATGTTTAGAATTACATAACCAT	80	339	nifI1 MA1212 P II family nitrogen regulatory protein
Methanosarcina acetivorans	AATCTGTATATAATTAACCAGATAGAGTT	80	9	MA2899 conserved hypothetical protein
*Methanosarcina acetivorans*	TGTCGTTATGTTTATTTAAACATAACGGT	79	-6	fmdE MA0304 formylmethanofuran dehydrogenase, subunit E
Methanosarcina acetivorans	CACCGTTATGTTTAAATAAACATAACGAC	79	1483	MA0303 conserved hypothetical protein
Methanosarcina acetivorans	ATTAATTATATAAATGTGTATATAAATAT	79	1375	hypC MA1140 hydrogenase expression/formation protein
Methanosarcina acetivorans	GAACCTTATATATTTTTCTACAGAGAGCT	79	114	MA3892 hypothetical protein (multi domain)
Methanosarcina acetivorans	AGTGGCTATATTTAGCTATATATAACAAA	79	710	MA3957 ABC transporter, ATP binding protein
Methanosarcina acetivorans	ACTCGATATATTATTCAACGAATAGTGAT	78	118	MA1301 predicted protein
Methanosarcina acetivorans	ATCCGTTATGTATGAATGAACATAACGTT	78	27	MA1663 predicted protein
Methanosarcina acetivorans	TATCTTTATGTTTATCCGAACATATCGAT	78	6	MA4536 ABC transporter, solute binding protein
Methanosarcina acetivorans	ATTTACTTTATATCTGTATATATATTGAA	77	529	MA0519 conserved hypothetical protein
Methanosarcina acetivorans	TATCGTTATCTATATATATATATTTCATT	77	114	MA0725 conserved hypothetical protein
Methanosarcina acetivorans	CTATTTTATATATTGAAATATATATTGAA	77	122	MA1145 hypothetical protein (multi domain)
Methanosarcina acetivorans	GTTCCTTTTATATTGCAAATCATAACGTT	77	43	MA2861 response regulator receiver
Methanosarcina acetivorans	AAACGTTATATACAAGCGGATATGAGTAT	76	147	MA0056 conserved hypothetical protein
Methanosarcina acetivorans	AATTCTTTTATATAAATCCATATAACGGT	76	130	MA0459 conserved hypothetical protein
Methanosarcina acetivorans	TACCGTTATATGGATTTATATAAAAGAAT	76	229	MA0458 predicted protein
Methanosarcina acetivorans	CTAGGTTATATAACAGAAATCATAAAGAG	76	17	MA1630 sensory transduction histidine kinase
Methanosarcina acetivorans	TTACGATATATATAAATTTATCTAAAAAA	76	87	MA1757 conserved hypothetical protein
Methanosarcina acetivorans	ATTTTTTAGATAAATTTATATATATCGTA	76	441	MA1756 cell surface protein
Methanosarcina acetivorans	ATCCATTAGATACAAATATTTATATAGAA	76	1467	MA3192 conserved hypothetical protein
Methanosarcina acetivorans	TATATTTATATAAAAATCAACATATCTAT	76	555	cpa MA3604 carboxypeptidase A
Methanosarcina acetivorans	GTACAGTATATATTTTAAAATATAGTTAT	76	507	atpH MA4152 H(+) transporting ATP synthase, subunit H

Studholme and Pau BMC Microbiology 2003 3:24 doi:10.1186/1471-2180-3-24