Prokaryote name: Methanobacterium thermoautotrophicum

Data Set 1: COG0013

Protein ID Organism Name PID

MTH1683 Methanobacterium thermoautotrophicum 15679677

MJ0564 Methanococcus jannaschii 15668744

AF2255 Archaeoglobus fulgidus 11499836

VNG2283G Halobacterium sp. NRC-1 15791093

Ta0849 Thermoplasma acidophilum 16081904

Phylogentic Tree from Clustal W results:

(((15679677:0.24348,15668744:0.25026):0.02898,16081904:0.34550):0.00465,

11499836:0.26165,15791093:0.28117)

FootPrinter Parameters
Motif Size: 6
Max Mutations: 4
Max Mutations per branch: 1
Subregion Change Cost: 1
Subregion Size: 50

Allow Regulatory Element Losses: No

Motifs found using FootPrinter

Motif #1
Parsimony score: 4.00
15679677           -50  aaaaat
15668744          -136  aaaaat
15668744           -33  gaaaat
16081904           -84  gaaaat
16081904           -29  agaaat
11499836           -50  cgaaat
15791093           -37  ggaact

Motif #2
Parsimony score: 4.00
15679677           -50  aaaaat
15668744          -136  aaaaat
16081904           -29  agaaat
11499836           -50  cgaaat
15791093           -37  ggaact

Motif #3
Parsimony score: 4.00
15679677           -22  tattta
15668744          -169  tattta
16081904           -88  tattga
11499836           -30  gatata
15791093           -31  gtttta

Motif #4
Parsimony score: 4.00
15679677            -7  ttttca
15668744          -155  ttttca
16081904           -42  ctttca
11499836           -22  catcca

Motif #5
Parsimony score: 4.00
15679677           -20  tttata
15668744          -180  tttata
16081904           -18  tttaaa
11499836           -30  gatata
15791093           -31  gtttta

I was not able to find any motifs with FootPrinter when max mutation parameter is smaller than 4. Even if max mutation is set as high as 4, none of the above 5 found motifs seem to have strong alignments across the five non-coding upstream sequences. Quite possibly this is because two of the five input sequences are short (barely over 50bp). For the same sequences, Clustal W doesn’t find any motifs at all. DiAlign only can find 2 identical motifs, but neither of them appear in all five sequences.

Data Set 2: COG0143

Protein ID Organism Name PID

MTH587_1 Methanobacterium thermoautotrophicum 15678615

PH0993_1 Pyrococcus horikoshii 14590837

MJ1263_1 Methanococcus jannaschii 15669449

Ta1162 Thermoplasma acidophilum 16082174

TVN1220 Thermoplasma volcanium 0013542051

Phylogentic Tree from Clustal W results:

(((16082174:0.13623,13542051:0.14002):0.17937,

14590837:0.24179):0.04867,15678615:0.25362,15669449:0.25665)

FootPrinter Parameters
Motif Size: 6
Max Mutations: 2
Max Mutations per branch: 1
Subregion Change Cost: 1
Subregion Size: 50
Allow Regulatory Element Losses: No

Motifs found using FootPrinter

Motif #1
Parsimony score: 2.00
16082174           -55  aatatt
13542051           -55  aatatt
14590837           -40  aatttt
15678615          -100  aaattt
15669449           -96  aaattt

Motif #2
Parsimony score: 2.00
16082174           -67  taattt
16082174           -56  taatat
16082174           -55  aatatt
16082174           -39  taattt
13542051           -56  taatat
13542051           -55  aatatt
14590837           -41  taattt
14590837           -40  aatttt
15678615          -100  aaattt
15669449           -96  aaattt

With the motif length set to 6 and the max mutation set to 2, FootPrinter successfully finds two motifs, between which the first one looks better. Clustal W was not able to find either of the above motifs. DiAlign found more motifs, among which one closely resembles the motif #2 above.