Signals, motifs, PWM

Preliminary work

According the task 9 proteins engaged in purine biosynthesis were chosen:
keyword:"Purine biosynthesis [KW-0658]"
organism:"Yersinia pestis"

There are 45 reviewed and there are 5 popular organisms. Among them I chose Yersinia pestis bv. Antiqua (strain Antiqua) which have 9 reviewed proteins. Mnemonic: YERPA. EMBL: CP000308 Genomic DNA.

The list of reviewed proteins of Yersinia pestis bv. Antiqua you can see in the folloing table.

Entry Entry name Protein names Gene names Coordinates + 100 nt upstream

Q1C5E7 PUR4_YERPA Phosphoribosylformylglycinamidine synthase, FGAM synthase, FGAMS, EC 6.3.5.3 purL YPA_2360 complement(2646172..2650035) complement(2650036..2650136)

Q1C8V8 PURT_YERPA Formate-dependent phosphoribosylglycinamide formyltransferase purT YPA_1147 complement(1300219..1301400) complement(1301401..1301501)

Q1C105 PURA_YERPA Formate-dependent phosphoribosylglycinamide formyltransferase purA YPA_3906 complement(4398153..4399451) complement(4399452..4399552)

Q1C4U4 FOLD_YERPA Bifunctional protein FolD folD YPA_2565 2858239..2859105 2858138..2858238

Q1C5J6 GUAA_YERPA GMP synthase [glutamine-hydrolyzing], EC 6.3.5.2 guaA YPA_2311 complement(2587010..2588587) complement(2588588..2588688)

Q1C1V9 PUR9_YERPA GMP synthase [glutamine-hydrolyzing], EC 6.3.5.2 purH YPA_3601 4038210..4039799 4038109..4038209

Q1C1V9 PURR_YERPA HTH-type transcriptional repressor PurR purR YPA_1732 1942437..1943462 1942336..1942436

Q1C5P2 PUR5_YERPA Phosphoribosylformylglycinamidine cyclo-ligase, EC 6.3.3.1 purM YPA_2265 2536453..2537496 2536352..2536452

Q1C5Q7 PUR7_YERPA Phosphoribosylaminoimidazole-succinocarboxamide synthase, EC 6.3.2.6 purC YPA_2250 complement(2523727..2524440) complement(2524441..2524541)

Sequences of upstream regions was cut from FASTA file with genome and saved in 100upstream.fasta. (Syntax: to cut sequenses: 'descseq CP000308.fasta:[xxxx:xxxx:r?] -name **** -description YPA_**** -outseq up*.fasta', to join them: 'seqret up*.fasta 100upstream.fasta)

To find motifs in upstream regions I used 'ememe' installed on kodomo. Syntax: 'ememe -nmotifs 3 -revcomp 100upstream.fasta' (-nmotifs 3 = find 3 motifs, -revcomp = use both forward and reverse sequences). Output files here and the main one - meme.html.

Analysis of motifs

Width - width, sites - number of occurrences in the training set (number of sequences where motif was found), I - information content, llr - log likelihood ratio, E-value - you understand, it is reliability of our findings.

MOTIF 1 width = 10 sites = 9 I = 11.7 bits llr = 76 E-value = 1.7e+002
MOTIF 2 width = 11 sites = 6 I = 15.4 bits llr = 64 E-value = 4.2e+003
MOTIF 3 width = 11 sites = 2 I = 19.0 bits lls = 29 E-value = 1.3e+004

Summary:
Motives 1-3 have E-value > 0.001 and low information content. Motif 1 only was found in all 9 sequenses. I think these motives are not reliable.

Term 4

← Block 1 → Pr 6