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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.

From: A DNA element recognised by the molybdenum-responsive transcription factor ModE is conserved in Proteobacteria, green sulphur bacteria and Archaea

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