4. Post-processing for Operon Prediction

Different combinations of genomes produce different clusters. As a result, a gene in a genome can belong to multiple clusters. For example, ureB} gene in urease operon (ureA}, ureB}, ureC}) appear in three different clusters: (ureA ureB ureC}) with T_p=13, T_s=7; (ureB ureC}) with T_p=16, T_s=5; and (ureA ureB}) with T_p=13, T_s=8. Since our goal is to test how gene clusters in B.subtiliss corresponds to known operons in B.subtilis, we need to merge all gene clusters with different dset and set supports with respect to B.subtilis. We performed a simple test for operon prediction using the gene cluster prediction result as follows.

• Gene clusters were predicted with support thresholds T_δ = 200, T_z = 2, T_s = 1, and T_p =$ 2, 3, 4, or 5. The resulting clusters should appear consecutively in 2 or more genomes and smaller clusters are expected with a higher T_p value.
• Another set of gene clusters was predicted with T_δ = 200, T_z = 2, T_p = 1, $T_s = 5, 10 or 15. This set was generated since the T_p = 1 constraint was weak to generate longer family sequences. However, these families were also required to appear in at least 5, 10, or 15 genomes without the proximity constraint.
• Gene clusters that appear in B.subtiliss were collected. Note that gene clusters are supported by different genomes and only portion of the predicted clusters contain genes in B.subtilis.
• Gene clusters were merged together. Gene clusters predicted with strong conditions, higher values of T_p, T_s, tend to be fragmented, so merging clusters is necessary.

Table: Operons detected by gene clusters with (T_p=4,T_s=1) and (T_p=1,T_s=15). Genes in bold font are those in known operons. Among 48 experimentally verified operons with gene clusters, 26 operons are with their excat boundaries. Many extra genes, those outside known operons, in other clusters are indeed functionally related (see the main text).

yjbA appC appB appA appF appD yjaZ fabF fabHA

purD purH purN purM purF purL purQ purS purC purB purK purE yebG yebE yebD yebC

ndk hepT menH hepS mtrB mtrA hbs spoIVA yphF yphE gpsA yphC seaA yphA

pyrR pyrP pyrB pyrC pyrAA pyrAB pyrK pyrD pyrF pyrE

ypkP dfrA thyB ypjQ ypjP

comC folC valS ysxE spoVID hemL hemB hemD hemC hemX hemA

comGA comGB comGC comGD comGE comGF comGG yqzE

pstS pstC pstA pstBA pstBB

acuA acuB acuC

qcrC qcrB qcrA ypiF ypiB ypiA aroE tyrA hisC trpA trpB trpF trpC trpD trpE

spoVAF spoVAE spoVAD spoVAC spoVAB spoVAA sigF spoIIAB spoIIAA dacF

acpS ydcC alr ydcD ydcE rsbR rsbS rsbT rsbU rsbV rsbW sigB rsbX ydcF ydcG

ywtB ywtA ywsC rbsR rbsK rbsD rbsA rbsC rbsB

minD minC mreD mreC mreB radC maf spoIIB

lonA lonB clpX tig ysoA leuD leuC leuB leuA ilvC ilvH ilvB

atpC atpD atpG atpA atpH atpF atpE atpB atpI

argC argJ argB argD carA carB argF yjzC

oppA oppB oppC oppD oppF yjbB yjbC yjbD

gcvT gcvPA gcvPB

gbsA gbsB yuaD

glnA glnR ynbB ynbA

feuA feuB feuC

kapB kinB patB

sdhC sdhA sdhB ysmA gerE

pbpE racX yveF yveG

mutL mutS cotE ymcA ymcB

ureA ureB ureC

cgeC cgeD cgeE

glgP glgA glgD glgC glgB

glpD glpF glpK glpP

yfkQ treP treA treR

opuBA opuBB opuBC opuBD

qoxA qoxB qoxC qoxD

ecsA ecsB ecsC

glnH glnM glnP glnQ

hemE hemH hemY

nrgA nrgB ywoA

dnaG sigA

adaA adaB

spoIVFA spoIVFB

motA motB

glpQ glpT

phoP phoR

sacX sacY

ftsA ftsZ

pbuX xpt

tagG tagH

alsD alsS