Signals, motifs, PWM

Bacterium: Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
Amount of entries: 18
Reviewed: 12
Genome EMBL link: BA000031.2

Chosen proteins:

Entry	Entry name	Protein name	Gene name	Gene coordinates	Upstream region coordinates
Q87Q53	PURT_VIBPA	Formate-dependent phosphoribosylglycinamide formyltransferase	purT	complement(1376818..1377993)	complement(1377994-1378094)
P40607	PURA_VIBPA	Adenylosuccinate synthetase	purA	complement(2975587..2976903)	complement(2976904 - 2977004)
Q87RB8	FOLD_VIBPA	Bifunctional protein FolD	folD	complement(911485..912345)	complement(912346 - 912446)
Q87KE0	PURK_VIBPA	N5-carboxyaminoimidazole ribonucleotide synthase	purK	3244219..3245352	3244118 - 3244218
Q87QW9	PURR_VIBPA	HTH-type transcriptional repressor PurR	purR	complement(1079009..1080013)	complement(1080014 - 1080114)
Q87MH0	PUR5_VIBPA	Phosphoribosylformylglycinamidine cyclo-ligase	purM	2393407..2394447	2393306 - 2393406
Q87KE1	PURE_VIBPA	N5-carboxyaminoimidazole ribonucleotide mutase	purE	3243729..3244214	3243628 - 3243728
Q87Q87	PUR7_VIBPA	Phosphoribosylaminoimidazole-succinocarboxamide synthase	purC	complement(1337584..1338687)	complement(1338688 - 1338788)

Download:

Upstream file: upstream.fasta
MEME result page: meme.html

Results and discussion:

Motif	Amount of sites	Frequency	E-value
1	22	7/8 genes	1.8e-007
2	11	7/8 genes	2.1e+003
3	8	2/8 genes	1.1e+004

There is no motifs with E-value less than 0.001 (the first has the smallest E-value, 1.8e-007). What is more, none of them [motifs] presented in every gene. Despite its short length, the third motif is the less frequent one, and I find that kinda interesting because of my first (wrong) suggestion "if it's shorter then it's more frequent".

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