Spreadsheet: 24d4eb35-d174-4190-9742-3b2c0240efb7
Sheet: Sheet1

POSSIBLE OPERON ORGANIZATION | GENE | PROMOTER PREDICTION | Unnamed: 3 | Unnamed: 4 | Unnamed: 5 | Unnamed: 6 | GENE.1 | TRANSCRIPTIONAL PROFILING EXPERIMENTS | Unnamed: 9 | Unnamed: 10 | Unnamed: 11 | Unnamed: 12 | Unnamed: 13 | Unnamed: 14 | Unnamed: 15 | Unnamed: 16 | Unnamed: 17 | Unnamed: 18 | Unnamed: 19 | GENE.2 | PRESUMED FUNCTION (SubtiList and Swiss-Prot) | Functional category (SubtiList) | GENE.3 | [NAME] | SEARCH FOR PARALOGS | Unnamed: 26 | GENE.4 | SEARCH FOR ORTHOLOGUES | Unnamed: 29 | Unnamed: 30 | Unnamed: 31 | Unnamed: 32 | Unnamed: 33 | Unnamed: 34 | Unnamed: 35 | GENE.5 | [NAME] SEGMENTS
 |  | -35 | Spacing | -10 | Transcription start site | distance to AUG |  | SigK DATA: |  |  | SigK DATA: |  |  | GerE DATA: |  |  | GerE DATA: |  |  |  |  |  |  |  | high similarity | low similarity |  | B. anthracis | B. cereus | B. halodurans | O. iheyensis | C. acetobutylicum | C. perfringens | L. monocytogenes | L. innocua |  | From TM pred server (http://www.ch.embnet.org/software/TMPRED_form.html)
 |  | GCACAATT | 13-11 | gCATANNNT | (bold and underlined) | (from last bp of -10) |  | INDUCTION |  |  | Hour 4.5 |  |  | Hour 5.5 |  |  | Hour 6.5 |  |  |  |  |  |  |  | BLAST in SUBTILIST | BLAST in SUBTILIST |  | Ames | ATCC 14579 |  | HTE 831 | ATCC 824 | str. 13 | LISTILIST | LISTILIST
 |  |  |  |  |  |  |  | sK |  |  | sK |  |  | GerE |  |  | GerE |  |  |  |  |  |  |  | E value> 1e-20 | 1e-20> E value> 1e-4
GENES IDENTIFIED BY TRANSCRIPTIONAL PROFILING EXPERIMENTS COMPARING sigK+ to sigK- STRAINS: |  |  |  |  |  |  |  | Ratio | Score |  | Ratio | Score |  | Ratio | Score |  | Ratio | Score |  |  |  |  |  |  | genes indicated in bold characters are mother cell-specific genes
1. sK-CONTROLLED GENES REPRESSED BY GerE:
1.1. Previously identified sK-controlled genes (with transcription start site mapped by primer extension):
1.1. A. Also identified by overexpression of sK
1.1. A. 1. repression observed at both time points
cotF | cotF | GAACAACA | 11 | GCATATGCT | [NAME] (mapped sigK promoter) | 35 | cotF | 7.312639493627842 | 0.999858395641782 |  | 8.090958991783824 | 0.997 |  | 0.3466779416066029 | 0.001 |  | 0.1973764413158938 | 0 |  | cotF | spore coat protein, proteolytic cleavage, isolated from yabGD spores | 1.8 (Sporulation) | cotF | no | no | yraD, yraF, yraG, yhcQ | cotF | cotF (BA3121)/BA5241 | no [BC4997 (yusN/cotF)] | BH0743 (yraD/cotF) | OB0829 | CAC0613(yraD/yraF/cotF) | no | no | no | cotF | 0 TM
 |  | GAACA | 14 | GCATATGCTGA | BioOptimizer prediction-correct | 33
yybR (not included in final total) | yybR | downstream of cotF (convergent), antisense? |  |  |  |  | yybR | 0.6595477408939932 | 0.0563173687004376 |  | 5.223961889991199 | 0.998 |  | 0.447244630581293 | 0.015 |  | 0.2484940391987056 | 0.000499999999999945 |  | yybR |  |  | yybR |  |  |  | yybR |  |  |  |  |  |  |  |  | yybR
sigK (spoIVCB-spoIIIC) | spoIVCB | ACACAGAC | 12 | ACATACATT | TACATATAG (mapped sigK promoter) | 41 | spoIVCB | 8.325651787526285 | 0.999901174652454 |  | 2.10862814993329 | 0.975 |  | 0.2596772004272965 | 0 |  | 0.1392909292805548 | 0 |  | spoIVCB | RNA polymerase sporulation mother cell-specific (late) sigma factor (sK N-terminal half) | 3.5.1 (Initiation) | spoIVCB | sigK | sigE, sigF, sigG |  | spoIVCB | sigK (BA4566) | BC4336 | sigK (BH1285) | sigK (OB1999) | CAC1770 | sigK (CPE1768) | no [rpoD (sigA)] | no [rpoD (sigA)] | spoIVCB | 1 TM (prosequence of pro-sigK)
 |  | ACACA | 15 | ACATACATTTA | BioOptimizer prediction-correct | 39
 | spoIIIC |  |  |  |  |  | spoIIIC | 13.32428268072805 | 0.999912411636097 |  | 8.31763771102671 | 1 |  | 0.2937976341247219 | 0.000499999999999945 |  | 0.161147943605784 | 0 |  | spoIIIC | RNA polymerase sporulation mother cell-specific (late) sigma factor (sK C-terminal half) | 3.5.1 (Initiation) | spoIIIC | sigK | sigE, sigF, sigG |  | spoIIIC | sigK (BA4566) | BC4336 | sigK (BH1285) | sigK (OB1999) | CAC1770 | sigK (CPE1768) | no [rpoD (sigA)] | no [rpoD (sigA)] | spoIIIC
spoVK | spoVK | TCACAATC | 11 | GAATATCAT | ATAGAGAGA (mapped sigK promoter) | 23 | spoVK | 5.455325291511844 | 0.999767406939578 |  | 3.311311214825912 | 0.995 |  | 0.306256586965793 | 0.002 |  | 0.1234686035759448 | 0 |  | spoVK | disruption leads to the production of immature spores  (AAA family of ATPases) | 1.8 (Sporulation) | spoVK | spoVJ | no | ftsH | spoVK | spoVK (BA3839) | no [ftsH]/BCE3737 | BH2363 | spoVK (OB1647) | no [CAC0955 (ftsH)] | spoVK (CPE1547) | no [ftsH] | no [ftsH] | spoVK | 0 TM
 |  | TCACA | 14 | GAATATCATAT | BioOptimizer prediction-correct | 21
1.1. A. 2. repression observed at second time point only
cotH | cotH | AATCCTCC | 12 | GTTAAGGAT | GAAGATCCTT (mapped sigK promoter) | 106 | cotH | 4.721295772575592 | 0.999620149200842 |  | 11.48153621496883 | 0.999 |  | 0.5543241306640281 | 0.0395 |  | 0.3637652486876488 | 0.000499999999999945 |  | cotH | spore coat protein (inner) | 1.8 (Sporulation) | cotH | ywrH | yisJ | no | cotH | cotH (BA2046) | BC2031 | no | OB2511 | no | no | no | no | cotH | 0 TM
 |  |  |  |  | BioOptimizer-no prediction | no
cotT-ctaO | cotT | ACACCCAA | 12 | GAATATGGT | AAAAGGAT (mapped sigK promoter) | "+33" | cotT | 1.964587594706079 | 0.962130749597732 |  | 10.86425623617066 | 1 |  | 0.6399438229810559 | 0.053 |  | 0.3696667768565147 | 0.002 |  | cotT | spore coat protein (inner), isolated from yabGD spores | 1.8 (Sporulation) | cotT | no | no | no | cotT | no | no | no | no | no | no | no | no | cotT | 0-1 TM
 |  | ACACC | 15 | GAATATGGTAA | BioOptimizer prediction-correct | "+35"
 |  | TAACA | 15 | TAATACTATGA | BioOptimizer-inaccurate | no
 | ctaO (yjdK) | predicted terminator between cotT and ctaO |  |  |  |  | ctaO (yjdK) | 5.626322378099572 | 0.986989907998706 |  | 2.060629913270001 | 0.981 |  | 0.9185893709186763 | 0.36 |  | 0.7317034621066114 | 0.101 |  | ctaO (yjdK) | heme O synthase activity (similar to cytochrome c oxidase assembly factor) | 1.4 (Membrane bioenergetics (electron transport chain and ATP synthase)) | ctaO (yjdK) | yjdK | ctaB | no | ctaO (yjdK) | no | no | no [ctaB (BH2616)] | no [ctaB (OB1436)] | no | no | no [ctaB] | no [ctaB] | ctaO (yjdK) | 8 TMs
spoVFAB-asd-dapG | spoVFA | TCACCGGT | 12 | TCATAAGAT | GAAGGGGA (mapped sigK promoter) | 56 | spoVFA | 8.782946829383105 | 0.99989100507428 |  | 27.60577856220347 | 1 |  | 0.5851678214748586 | 0.0425 |  | 0.3495734837117816 | 0.002 |  | spoVFA | dipicolinate synthase subunit A | 1.8 (Sporulation) | spoVFA | dpaA | no | no | spoVFA | spoVFA (BA3939) | BC3801 | spoVFA (BH2403) | dpaA (OB1608) | no | no | no [lmo1579 (ald)] | no | spoVFA | 0 TM
 |  | TCACC | 15 | TCATAAGATGA | BioOptimizer prediction-correct | 54
 | spoVFB |  |  |  |  |  | spoVFB | 11.00657538566166 | 0.999950228905448 |  | 41.97589839910077 | 1 |  | 0.5845511003175341 | 0.036 |  | 0.3764375789684021 | 0.00349999999999995 |  | spoVFB | dipicolinate synthase subunit B | 1.8 (Sporulation) | spoVFB | dpaB | no | no | spoVFB | spoVFA (BA3937) | BC3800 | spoVFB (BH2402) | dpaB (OB1609) | no | no | no | no | spoVFB | 0 TM
 | asd |  |  |  |  |  | asd | 1.888583850428808 | 0.985075451804439 |  | 6.823386941416698 | 0.998 |  | 0.5933730169769819 | 0.0375 |  | 0.3447145665343144 | 0.000499999999999945 |  | asd | aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) | 2.2 (Metabolism of amino acids and related molecules) | asd | no | no | argC | asd | asd-2 (BA3937) | BC3799/BC2363 | asd (BH2401) | OB1610 | CAC0568 | asd (CPE1904) | lmo1437 | lin1476 | asd | 0-1 TM
 | dapG |  |  |  |  |  | dapG | 1.831982842363843 | 0.983169789959874 |  | 3.404081897010009 | 0.996 |  | 0.7593255932452794 | 0.1475 |  | 0.5076049584415397 | 0.00549999999999995 |  | dapG | aspartokinase I (alpha and beta subunits) (EC 2.7.2.4) | 2.2 (Metabolism of amino acids and related molecules) | dapG | lssD | lysC, yclM | proJ, argB | dapG | [NAME] (BA1811)/dapG-2 (BA3936) | [NAME]/BC1748 | dapG (BH2400) | dapG (OB1611) | CAC1810 | dapG (CPE1678) | lmo1436 | lin1475 | dapG | 1 TM (Cter)
dapA (not included in final total) | dapA | downstream of dapG (read-through) |  |  |  |  | dapA | 1.535050318928707 | 0.951003979089292 |  | 1.931968317016924 | 0.971 |  | 0.8417298609242647 | 0.247 |  | 0.5970710525824832 | 0.0445 |  | dapA |  |  | dapA |  |  |  | dapA |  |  |  |  |  |  |  |  | dapA
yabG | yabG | GCACCACA | 11 | ACATAGGCT | AGAGAAGGA (mapped sigK promoter) | 114 | yabG | 5.519381530214951 | 0.99960995535469 |  | 16.33051947894335 | 0.998 |  | 0.643116230749252 | 0.065 |  | 0.4303280052107685 | 0.00449999999999995 |  | yabG | sporulation-specific protease involved in the proteolysis and maturation of spore coat proteins | 1.8 (Sporulation) | yabG | no | no | no | yabG | BA0040 | BC0047 (yabG) | BH0058 | OB0051 | CAC2905 | CPE2217 | no | no | yabG | 0 TM
 |  | GCACC | 15 | ACATAGGCTAG | BioOptimizer prediction-correct | 112
1.1. B. below cut-off in sigK+ vs. sigK- experiments but identified by overexpression of sK
1.1. B. 1. repression observed at both time points
none
1.1. B. 2. repression observed at second time point only
cotM | cotM | TCACCCAT | 12 | GCATATGAT | GTAAAGCAA (mapped sigK promoter) | 16 | cotM | 8.764839279724367 | 0.999905883529132 |  | 1.83 | 0.918 |  | 0.5515152412721972 | 0.0275 |  | 0.3199866635331556 | 0.00549999999999995 |  | cotM | spore coat protein (outer) | 1.8 (Sporulation) | cotM | yneL | no | no | cotM | cotM  (BA3681) | BC3621 | no | no | no | no | no | no | cotM | 0 TM
 |  |  |  |  | BioOptimizer-no prediction | no
yneK not included in final total | yneK | downstream of cotM (read-through) |  |  |  |  | yneK | 1.631508391308942 | 0.96220759291427 |  | 1.162422264252223 | 0.714 |  | 0.8872021836206423 | 0.32 |  | 0.5863527359513004 | 0.02 |  | yneK |  |  | yneK |  |  |  | yneK |  |  |  |  |  |  |  |  | yneK
1.1. C. not identified by overexpression of sK
1.1. C. 1. repression observed at both time points
cotE | cotE | GCACACTA | 12 | GCATAAGAT | AACACGAAG (P2-promoter) | 31 | cotE | not on array |  |  | 2.500345361696432 | 0.974 |  | 0.2888417031539744 | 0.003 |  | 0.1261263880871775 | 0 |  | cotE | spore coat protein (outer), morphogenetic protein | 1.8 (Sporulation) | cotE | no | no | no | cotE | cotE (BA3906) | BC3770 | cotE | cotE (OB1630) | no | no | no | no | cotE | 0 TM
 |  | GCACA | 15 | GCATAAGATAA | BioOptimizer prediction-correct | 29
 |  | GCACC | 15 | ACAGAAACTTT | BioOptimizer prediction-inaccurate | no
1.1. C. 2. repression observed at second time point only
cotA | cotA | TAACCATC | 12 | TCATTAACT | ATAGTACC (mapped sigK promoter) | 40 | cotA | 1.576040795916145 | 0.961049287627007 |  | 97.72372209558112 | 1 |  | 0.5360075429725195 | 0.0185 |  | 0.2973916935832524 | 0.001 |  | cotA | spore coat protein (outer), brown pigmentation during sporogenesis | 1.8 (Sporulation) | cotA | pig | no | no | cotA | BA1902 | BC1830 | BH2082 | cotA (OB1346) | no | no | no | no | cotA | 0 TM
 |  |  |  |  | BioOptimizer-no prediction | no
1.2. Previously reported sK-controlled genes (but transcription start site had not been mapped):
1.2. A. also identified by overexpression of sK
1.2. A. 1. repression observed at both time points
1.2. A. 1. a) promoter confirmed by 5'RACE-PCR
none
1.2. A. 1. b) not tested by 5'RACE-PCR
gerPABCDEF | gerPA (yisH) | TCACGCAT | 11 | TCATAAGCT | predicted sigK promoter | 83 | gerPA (yisH) | not on array |  |  | 23.76840286624877 | 1 |  | 0.2848798914062555 | 0.00149999999999995 |  | 0.1399057121224359 | 0 |  | gerPA (yisH) | spore germination protein, involved in the access of germinants to their receptor | 1.9 (Germination) | gerPA (yisH) | yisH | no | [NAME], yueG | gerPA (yisH) | gerPA (BA1149) | gerPA | no | no | no | no | no | no | gerPA (yisH) | 0-1 TM (Nter)
 |  | TCACG | 14 | TCATAAGCTAT | BioOptimizer-prediction | 81
 | gerPB (yisG) |  |  |  |  |  | gerPB (yisG) | 10.5218320964206 | 0.999939464898193 |  | 14.28893958511104 | 1 |  | 0.3607176180863353 | 0.00149999999999995 |  | 0.2205024205849757 | 0.0145 |  | gerPB (yisG) | spore germination protein, involved in the access of germinants to their receptor | 1.9 (Germination) | gerPB (yisG) | yisG | no | no | gerPB (yisG) | gerPB (BA1148) | gerPB | no | no | no | no | no | no | gerPB (yisG) | 0 TM
 | gerPC (yisF) |  |  |  |  |  | gerPC (yisF) | 47.30366835401711 | 0.999976419469445 |  | 42.75628861515863 | 1 |  | 0.2873762850092215 | 0.000499999999999945 |  | 0.1083832705173342 | 0 |  | gerPC (yisF) | spore germination protein, involved in the access of germinants to their receptor | 1.9 (Germination) | gerPC (yisF) | yisF | no | no | gerPC (yisF) | gerPC (BA1147) | gerPC | no | no | no | no | no | no | gerPC (yisF) | 0 TM
 | gerPD (yisE) |  |  |  |  |  | gerPD (yisE) | 12.39445663869671 | 0.999967828410044 |  | 31.04559588128357 | 1 |  | 0.3786037697869826 | 0.00749999999999995 |  | 0.1735770143280821 | 0 |  | gerPD (yisE) | spore germination protein, involved in the access of germinants to their receptor | 1.9 (Germination) | gerPD (yisE) | yisE | no | no | gerPD (yisE) | gerPD (BA1146) | gerPD | no | no | no | no | no | no | gerPD (yisE) | 0 TM
 | gerPE (yisD) |  |  |  |  |  | gerPE (yisD) | 12.1158274405515 | 0.999964115408845 |  | 22.23309890651403 | 1 |  | 0.1984894420629523 | 0.00649999999999995 |  | 0.1289300892773792 | 0 |  | gerPE (yisD) | spore germination protein, involved in the access of germinants to their receptor | 1.9 (Germination) | gerPE (yisD) | yisD | no | no | gerPE (yisD) | gerPE (BA1145) | gerPE | no | no | no | no | no | no | gerPE (yisD) | 0 TM
 | [NAME] (yisC) |  |  |  |  |  | [NAME] (yisC) | 13.29045988971838 | 0.999970937707704 |  | 8.260379495771788 | 1 |  | 0.4911485970909518 | 0.00649999999999995 |  | 0.2051069278048646 | 0.000499999999999945 |  | [NAME] (yisC) | spore germination protein, involved in the access of germinants to their receptor | 1.9 (Germination) | [NAME] (yisC) | yisC | no | gerPA, yueG | [NAME] (yisC) | [NAME] (BA1144)/gerPF-2 (BA2341) | [NAME] | no | no | no | no | no | no | [NAME] (yisC) | 1 TM (Nter)
1.2. A. 2. repression observed at second time point only
1.2. A. 2. a) promoter confirmed by 5'RACE-PCR
tgl | tgl | TTTCATTG | 12 | GCATATCTT | [NAME] (5'RACE) | 23 | tgl | 2.906222876717413 | 0.984456593644286 |  | 12.30268770812382 | 1 |  | 0.5396659559521868 | 0.02 |  | 0.3368051690398098 | 0.002 |  | tgl | transglutaminase (introduces cross-links in spore coat) | 1.8 (Sporulation) | tgl | yuxF, yugV | no | no | tgl | BA4173 | BC3963 | tgl (BH3970) | no | no | no | no | no | tgl | 1 TM (mid)
 |  |  |  |  | BioOptimizer-no prediction | no
yugU (not included in final total) | yugU | downstream of tgl (convergent), antisense? |  |  |  |  | yugU | 0.7438093763071096 | 0.111584274600638 |  | 2.735268726306713 | 0.994 |  | 0.5355925017672154 | 0.0245 |  | 0.3733348750886759 | 0.002 |  | yugU |  |  | yugU |  |  |  | yugU |  |  |  |  |  |  |  |  | yugU
ydgBA-cotP | ydgB | GAACAATT | 12 | GCATAATGT | predicted sigK promoter | 31 | ydgB | 6.750660436421319 | 0.999881482869672 |  | 10.61695557198725 | 0.999 |  | 0.6396184924375227 | 0.0705 |  | 0.3782559806663454 | 0.005 |  | ydgB | unknown | 5.1 (From B. subtilis) | ydgB | no | no | ydgA, ydzH | ydgB | no | no | no | no | no | no | no | no | ydgB | 0 TM
 |  | GAACA | 15 | GCATAATGTAC | BioOptimizer-prediction | 31
 | ydgA |  |  |  |  |  | ydgA | 8.999213601058056 | 0.999923721249115 |  | 13.00169578033291 | 0.996 |  | 0.8606684579036386 | 0.3735 |  | 0.3985480191784691 | 0.014 |  | ydgA | unknown | 5.1 (From B. subtilis) | ydgA | no | ydzH | ydgB | ydgA | no | no | no | no | no | no | no | no | ydgA | 0 TM
 | [NAME] (ydfT) | CTTCACTT | 11 | AAATATTGA | possible promoter-but probably operon with ydgBA | 76 | [NAME] (ydfT) | 8.206509272156207 | 0.999781736307793 |  | 5.584701947368308 | 0.999 |  | 0.4802467796824163 | 0.0395 |  | 0.3592496306398918 | 0.00149999999999995 |  | [NAME] (ydfT) | spore coat protein (probable) | 1.8 (Sporulation) | [NAME] (ydfT) | ydfT | no | yocM | [NAME] (ydfT) | no | no | no | no | no | no | no | no | [NAME] (ydfT) | 0 TM
 |  |  |  |  | BioOptimizer-no prediction | no
1.2. A. 2. b) not tested by 5'RACE-PCR
none
1.2. B. below cut-off in sigK+ vs. sigK- experiments but identified by overexpression of sK
none
1.2. C. not identified by overexpression of sK
1.2. C. 1. repression observed at both time points
none
1.2. C. 2. repression observed at second time point only
1.2. C. 2. a) promoter confirmed by 5'RACE-PCR
ykuD | ykuD | TAGCAGGA | 12 | CAATACTTA | TAAGTAAAAAAGGAGG (5'RACE) | 25 | ykuD | 1.327609851329581 | 0.882363443871344 |  | 3.250872973854344 | 0.998 |  | 0.5796725344006866 | 0.031 |  | 0.3569342570274833 | 0.005 |  | ykuD | probable spore protein, cell wall binding motif (LysM domain),  ErfK domain | 1.8 (Sporulation) | ykuD | no | no | yqjB, lytF | ykuD | no [BA4372 (yqjB)] | no [BC4146 (yqjB)] | BH0811 | no | CAC2416 | no | no | no | ykuD | 0 TM
 |  |  |  |  | BioOptimizer-no prediction | no
1.2. C. 2. b) not tested by 5'RACE-PCR
yfhP | yfhP-P1 | GTACACTA | 11 | CGATAATAT | proposed sigK promoter | 133 | yfhP-P1 | 1.076588372790791 | 0.594474153131186 |  | 1.892343618644976 | 0.951 |  | 0.8473815880220745 | 0.2605 |  | 0.3427694537119391 | 0.000499999999999945 |  | yfhP-P1 | unknown, may act as a negative regulator for the transcription of yfhQ, fabL, [NAME] and yfhP | 5.1 (From B. subtilis) | yfhP-P1 | no | no | no | yfhP-P1 | BA0521 | [NAME] | BH0929 | OB0895 | no | no | lmo1690 | lin1798 | yfhP-P1 | 4 TMs
 | yfhP-P2 | GCACAGTA | 12 | ACATTAAAT | proposed sigK promoter | 121 | yfhP-P2 |  |  |  |  |  |  |  |  |  |  |  |  | yfhP-P2 |  |  | yfhP-P2 |  |  |  | yfhP-P2 |  |  |  |  |  |  |  |  | yfhP-P2
 |  |  |  |  | BioOptimizer-no prediction | no
1.3. Newly identified sK-controlled genes with predicted sK promoter:
1.3. A. also identified by overexpression of sK
1.3. A. 1. repressed at both time points
1.3. A. 1. a) promoter confirmed by 5'RACE-PCR
yhjR | yhjR | GCACATCT | 11 | ACATATACT | TTTACAGAAGCCCAA (5'RACE) | 40 | yhjR | 2.64012170279358 | 0.996769169932089 |  | 19.76969640111862 | 1 |  | 0.3162468089674562 | 0.002 |  | 0.1562947192337386 | 0 |  | yhjR | unknown | 5.1 (From B. subtilis) | yhjR | no | no | no | yhjR | BA3113 | BC3081 | BH1034 | no | CAC3002 | no | no | no | yhjR | 0 TM
 |  | GCACA | 14 | ACATATACTTT | BioOptimizer-confirmed by 5'RACE | 38
yhjQ (not included in final total) | yhjQ | downstream of yhjR (read-through) |  |  |  |  | yhjQ | 5.289629614623924 | 0.999719782292888 |  | 1.2 | 0.69 |  | 0.7234568564995315 | 0.113 |  | 0.6484280237607758 | 0.0415 |  | yhjQ |  |  | yhjQ |  |  |  | yhjQ |  |  |  |  |  |  |  |  | yhjQ
yhjP (not included in final total) | yhjP | downstream of yhjQ (convergent), antisense? |  |  |  |  | yhjP | 1.449695123829893 | 0.925835971431137 |  | 1 | 0.49 |  | 0.8582088201202215 | 0.295 |  | 0.4051199768483305 | 0.001 |  | yhjP |  |  | yhjP |  |  |  | yhjP |  |  |  |  |  |  |  |  | yhjP
yitBA-yisZ | yitB | GAACCTTT | 11 | GAATAGTCT | GCCTATAACTCG (5'RACE) | 53 | yitB | 9.880811094092019 | 0.999942997907172 |  | 40.83193863326923 | 1 |  | 0.2671424378168308 | 0.002 |  | 0.1117043761472921 | 0 |  | yitB | similar to phosphoadenosine phosphosulfate reductase | 2.7 (Metabolism of sulfur) | yitB | no | cysH | no | yitB | [NAME] | BC1421 (cysH/yitB) | cysH (BH1486) | cysH (OB1652) | CAC1200 | no | no | no | yitB | 0-1 (mid) TM
 |  | GAACC | 14 | GAATAGTCTGC | BioOptimizer-confirmed by 5'RACE | 51
 | yitA |  |  |  |  |  | yitA | 17.57364420856431 | 0.999982315452861 |  | 12.05035940371798 | 1 |  | 0.3000824572193529 | 0.000499999999999945 |  | 0.1335387226867053 | 0 |  | yitA | similar to sulfate adenylyltransferase | 2.7 (Metabolism of sulfur) | yitA | no | sat | no | yitA | BA1441 | BC1422 | BH1487 | OB1659 | no | no | no | no | yitA | 0 TM
 | yisZ |  |  |  |  |  | yisZ | 6.076009489049119 | 0.999256893261486 |  | 30.4088502567628 | 0.997 |  | 0.180067515747505 | 0.007 |  | 0.1660970281066435 | 0 |  | yisZ | similar to adenylylsulfate kinase | 2.7 (Metabolism of sulfur) | yisZ | no | cysC | no | yisZ | BA1442 | BC1423 | BH1489 | OB1661 | no [[NAME] (cysC)] | no | no | no | yisZ | 0-1 (mid) TM
yitCD | yitC | GAACCATT | 12 | GAATATGCT | TTTTAGCAAAATGGTTTT (5'RACE) | 37 | yitC | 7.049047275864941 | 0.999837798998336 |  | 27.79713267759289 | 0.998 |  | 0.2777599161179429 | 0.00149999999999995 |  | 0.1283114704501933 | 0 |  | yitC | unknown (putative 2-phosphosulfolactate phosphatase) | 5.2 (From other organisms) | yitC | no | no | no | yitC | no | no | no | no | CAC3233 | CPE2556 | no | no | yitC | 0-1 (mid) TM
 |  | GAACC | 15 | GAATATGCTTT | BioOptimizer-confirmed by 5'RACE | 37
 | yitD |  |  |  |  |  | yitD | 3.112096560704641 | 0.998045846100078 |  | 11.93988104464273 | 1 |  | 0.3023685531742096 | 0.00149999999999995 |  | 0.1165969347941382 | 0 |  | yitD | unknown [putative (2R)-phospho-3-sulfolactate synthase (PSL synthase)] | 5.2 (From other organisms) | yitD | no | no | no | yitD | no | no | no | no | no | no | no | no | yitD | 0 TM
yitE (not included in final total) | yitE | downstream of yitCD (convergent), antisense? |  |  |  |  | yitE | 1.489612457951112 | 0.867261525121438 |  | 2.167704104819695 | 0.98 |  | 0.6943668441274372 | 0.079 |  | 0.4988290946123782 | 0.007 |  | yitE |  |  | yitE |  |  |  | yitE |  |  |  |  |  |  |  |  | yitE
yndL | yndL | GAACAGCG | 12 | GTATATAAT | ATTGTGAAT(primer extension-[NAME]) | 101 | yndL | 4.890005192160674 | 0.999549320377255 |  | 23.38837238659356 | 0.989 |  | 0.4149254792638741 | 0.00749999999999995 |  | 0.1308987214718338 | 0 |  | yndL | unknown, similar to phage-related replication protein | 4.4 (Phage-related functions) | yndL | no | yoqZ, ymaC, yjqB | no | yndL | no | no | no | OB3345 | no | no | no | no | yndL | 1 TM (Nter)
 |  | GAACA | 15 | GTATATAATAT | BioOptimizer-confirmed by primer extension | 99
yndM (not included in final total) | yndM | downstream of yndL (convergent), antisense? |  |  |  |  | yndM | 2.184944808439031 | 0.97126619423268 |  | 1.5 | 0.9 |  | 0.676854457383201 | 0.0775 |  | 0.3912973841563155 | 0.002 |  | yndM |  |  | yndM |  |  |  | yndM |  |  |  |  |  |  |  |  | yndM
yngK | yngK | TCACCCTT | 11 | GAATACCGT | AATAGCGAATAG (5'RACE) | 44 | yngK | 12.72746964555602 | 0.999476347836603 |  | 9.727472237769653 | 1 |  | 0.3576334951868701 | 0.00249999999999995 |  | 0.1862503172454641 | 0 |  | yngK | unknown, similar to fenI (fengycin synthesis, chloramphenicol resistance) | 5.2 (From other organisms) | yngK | yotA | no | no | yngK | BA2460 | fenI (BC2392) | no | OB2153 | no | no | no | no | yngK | 1 TM (Nter)
 |  | TCACC | 14 | GAATACCGTAA | BioOptimizer-confirmed by 5'RACE | 42
ynzE (not included in final total) | ynzE | terminator between yngK and ynzE (read-through?) |  |  |  |  | ynzE | 3.138289952773935 | 0.956331897968555 |  | 1.45 | 0.87 |  | 0.6149553167811279 | 0.043 |  | 0.3017658160951987 | 0.000499999999999945 |  | ynzE |  |  | ynzE |  |  |  | ynzE |  |  |  |  |  |  |  |  | ynzE
[NAME] | [NAME] (oxdD) | [NAME] | 12 | GCATAGGCT | GAAATAAAATCTTG | 35 | [NAME] (oxdD) | 8.866463833005625 | 0.998112739696327 |  | 22.59435770220979 | 0.999 |  | 0.2662616698534965 | 0.00249999999999995 |  | 0.07987794635473543 | 0 |  | [NAME] (oxdD) | oxalate decarboxylase | 5.2 (From other organisms) | [NAME] (oxdD) | oxdD | oxdC (yvrK) | no | [NAME] (oxdD) | BA1742 (oxdC/yoaN) | no | no | no | no | no | no | no | [NAME] (oxdD) | 1 TM (mid)
 |  | GCACA | 15 | GCATAGGCTGA | BioOptimizer-confirmed by 5'RACE | 33
ytlABCD | ytlA | TCACACAT | 11 | TCATACGAT | ATGTAAAGCAAAAAAGG (5'RACE) | 52 | ytlA | 14.50336816526569 | 0.999972735086532 |  | 17.13957307508426 | 1 |  | 0.2753570874300663 | 0.001 |  | 0.1219888521657916 | 0 |  | ytlA | unknown, similar to ABC transporter (substrate binding?) | 6 (No similarity) | ytlA | no | no | no | ytlA | BA5036 | BC4778 | no | OB2316 | CAC0620 | CPE1487 | no | no | ytlA | 1 TM (Nter)
 |  | TCACA | 14 | TCATACGATAT | BioOptimizer-confirmed by 5'RACE | 50
 |  | AAACA | 15 | CTATATGCTTT | BioOptimizer-prediction (inaccurate)
 | ytlB |  |  |  |  |  | ytlB | 13.5096818114068 | 0.999930988166234 |  | 14.55459080581966 | 0.999 |  | 0.2913729049280219 | 0.001 |  | 0.1506239274490601 | 0.000499999999999945 |  | ytlB | unknown, similar to ABC transporter (substrate binding?) | 6 (No similarity) | ytlB | no | no | no | ytlB | BA5036 | BC4778 | no | OB2316 | CAC0620 | no | no | no | ytlB | 0 TM
 | ytlC |  |  |  |  |  | ytlC | 11.89746602351173 | 0.999098825819269 |  | 14.82518085145954 | 0.999 |  | 0.2538220774423586 | 0.002 |  | 0.1187384913686672 | 0 |  | ytlC | similar to anion transport ABC transporter (ATP-binding protein) | 1.2 (Transport/binding proteins and lipoproteins) | ytlC | no | ssuB, opuCA, opuBA, msmX, yurJ, opuAA, ytrE, glnQ |  | ytlC | BA5037 | BC4779 | no [BH1211 (ssuB)] | OB2317 | CAC0619 | no [CPE1270 (yurJ)] | no [opuCA] | no [opuCA] | ytlC | 0-1 TM
 | ytlD |  |  |  |  |  | ytlD | 15.68856111289119 | 0.999979858341506 |  | 22.13094709605638 | 1 |  | 0.2419054421204171 | 0.001 |  | 0.1150237006579943 | 0 |  | ytlD | similar to ABC transporter (permease) | 1.2 (Transport/binding proteins and lipoproteins) | ytlD | no | ssuC | yusB, opuBD,dppC | ytlD | BA5038 | BC4779 | no [BH2681 (ssuC)] | OB2318 | CAC0618 | no | no | no | ytlD | 4 TM
1.3. A. 1. b) not tested by 5'RACE-PCR
ydfR | ydfR | TTGCTAT | 12 | TAATATATC | possible promoter (by visual inspection) | 36 | ydfR | 4.618925032281546 | 0.998903339993282 |  | 2.404362800006933 | 0.981 |  | 0.5039553784165526 | 0.033 |  | 0.2423289869203854 | 0.00449999999999995 |  | ydfR | unknown | 5.2 (From other organisms) | ydfR | no | no | ykjA, ydfS, yetF, yrbG | ydfR | no [BA5379 (ydfS)] | BC2531 | BH1290/BH2720 | no | CAC3372 | no [CPE1348 (yrbG)] | no | no | ydfR | 2 TMs
 |  |  |  |  | BioOptimizer-no prediction | no
 |  | downstream of cotP (same orientation)
ydfS | ydfS | GAACC | 14 | GTATAGATGGA | BioOptimizer-prediction | 74 | ydfS | 5.028892563953583 | 0.999735067827263 |  | 7.095777679633889 | 1 |  | 0.4396754675351368 | 0.013 |  | 0.266149041782178 | 0.001 |  | ydfS | unknown | 5.2 (From other organisms) | ydfS | no | yetF, yrbG, ykjA | ydfR | ydfS | BA5379 | BC5151 | BH1970 | OB1377 | [NAME] | no | no | no | ydfS | 2-3 TMs
 |  | downstream of cotP (convergent), antisense?
yvdH | yvdH | CAGCAATG | 12 | TCATAAAGG | possible promoter (by visual inspection) | 68 | yvdH | 1.95081207113816 | 0.979747323638085 |  | 2.25423921215243 | 0.98 |  | 0.502519120008583 | 0.045 |  | 0.4903671375242341 | 0.036 |  | yvdH | similar to maltodextrin transport system permease | 1.2 (Transport/binding proteins and lipoproteins) | yvdH | no | yvfL, yurN | araP, yesP, amyD, lplB, amyC, yteQ, yurM, lplC | yvdH | malC (BA4228yvfL/yvdH) | BC4012 | BH2020 (yvfL/yvdH)/BH2925 (yvfL/yvdH) | OB2559 (yvfL/yvdH) | no | no | lmo2124 | lin2229 | yvdH | 8-9 TMs
 |  |  |  |  | not included in BioOptimizer list of sequences
1.3. A. 2. repression observed at only one of the two time points
1.3. A. 2. a) promoter confirmed by 5'RACE-PCR
yjcA | yjcA | TCATGAAG | 13 | GCATATATG | TGAAGGGATCAT (5' RACE)-looks more like a sigE promoter | 33 | yjcA | 1.889732802673902 | 0.955639961158137 |  | 5.116818355403078 | 0.993 |  | 0.6598450720906949 | 0.0865 |  | 0.4214001198767204 | 0.007 |  | yjcA | unknown | 5.1 (From B. subtilis) | yjcA | no | no | yngL | yjcA | BA1235 | BC1219 | BH2840 | no | no | no | no | no | yjcA | 3 TMs
 |  | TCATGAAG | 13 | GCATATATG | TGAAGGGATCAT (mapped as a sigE promoter) | 33
 |  | TAACC | 16 | CCATACTCTAT | BioOptimizer-prediction (inaccurate) | no
 |  | GGACA | 16 | GAATAGGGTTT | BioOptimizer-prediction (inaccurate) | no
yrkCD | yrkC | GCACACTC | 11 | GCATAGGAT | ACTATCACAAAAA (5'RACE) | 36 | yrkC | 2.064403671224003 | 0.991198369688533 |  | 6.576578373554206 | 1 |  | 0.5922916428230679 | 0.0545 |  | 0.3037317403751453 | 0.00149999999999995 |  | yrkC | unknown | 5.1 (From B. subtilis) | yrkC | no | no | no | yrkC | no | no | BH2720 | OB0373 | no | no | no | no | yrkC | 0 TM
 |  | GCACA | 14 | GCATAGGATAC | BioOptimizer-confirmed by 5'RACE | 34
 |  | GAACA | 14 | TAATATGAGTT | 2nd BioOptimizer-prediction (inaccurate) | 77
 | yrkD |  |  |  |  |  | yrkD | 2.030472911690248 | 0.973663131870024 |  | 3.491403154785862 | 1 |  | 0.6990862927584431 | 0.1215 |  | 0.4946904153694509 | 0.0165 |  | yrkD | unknown | 5.1 (From B. subtilis) | yrkD | no | no | no | yrkD | BA0775 | no | no | OB2653 | no | no | no | no | yrkD | 0 TM
ysnD | ysnD | GCACTTCT | 12 | GCATACATT | AATGATATCTTG (5'-RACE) | 30 | ysnD | 3.74272965518079 | 0.995512020149494 |  | 5.296634438916579 | 1 |  | 0.6356880058092362 | 0.066 |  | 0.5284955302699159 | 0.0215 |  | ysnD | unknown | 6 (No similarity) | ysnD | no | no | no | ysnD | no | no | no | no | no | no | no | no | ysnD | 0-1 (mid) TM
 |  | GCACT | 15 | GCATACATTAA | BioOptimizer-confirmed by 5'RACE | 28
1.3. A. 2. b) not tested by 5'RACE-PCR
asnO | asnO (yisO) | TCAACTAT | 12 | GCATAAACT | predicted sigK promoter | 130 | asnO (yisO) | 7.569586558164521 | 0.999902932700242 |  | 2.322736796357107 | 0.985 |  | 0.6189892213741867 | 0.0555 |  | 0.4274546669226363 | 0.005 |  | asnO (yisO) | asparagine synthetase (EC 6.3.5.4) | 2.2 (Metabolism of amino acids and related molecules) | asnO (yisO) | yisO, yucB | asnB, asnH | purF | asnO (yisO) | [NAME] (BA1157)/asnO-2 (BA1751)/asnO-3 (BA2251) | BC1152/BC1697/BC2204 | BH1508 | OB2608 | CAC2243-CAC2249 | no | no [asnB] | no [asnB] | asnO (yisO) | 1 TM (mid)
 |  | TCAAC | 15 | GCATAAACTTA | BioOptimizer-prediction | 128
ycgG | ycgG | [NAME] | 12 | TAATATAGT | predicted sigK promoter | 26 | ycgG | 3.801896960093609 | 0.997631388550004 |  | 2.409905428686595 | 0.985 |  | 0.7521462874338642 | 0.1345 |  | 0.4961843470782044 | 0.0185 |  | ycgG | unknown, sigE-controlled operon with ycgF | 5.1 (From B. subtilis) | ycgG | no | yqcI | no | ycgG | no [BA3123 (yqcI)] | no [BC1604 (yqcI)] | no | no [OB3195 (yqcI)] | no | no | no | no | ycgG | 1 TM (mid)
 |  | TCACC | 15 | [NAME] | BioOptimizer-prediction | 24
yjiA | yjiA | TAACTCCA | 12 | CCATTATGT | possible promoter (by visual inspection) | 55 | yjiA | 2.205582034416306 | 0.986659318286272 |  | 2.137962089502232 | 0.973 |  | 0.719190625236885 | 0.1305 |  | 0.4985318689569367 | 0.00549999999999995 |  | yjiA | unknown | 6 (No similarity) | yjiA | no | no | no | yjiA | no | no | no | no | no | no | no | no | yjiA | 1 TM (Nter)
 |  |  |  |  | BioOptimizer-no prediction | no
ykoK | ykoK | AGTCAATC | 11 | CCATATACT | possible promoter (by visual inspection) | 94 | ykoK | 2.012678589759382 | 0.98695771219163 |  | 2.494594726942955 | 0.972 |  | 0.5956477577618047 | 0.044 |  | 0.4699041639085378 | 0.009 |  | ykoK | similar to Mg2+ transporter | 1.2 (Transport/binding proteins and lipoproteins) | ykoK | no | no | no | ykoK | no | no [impdh (guaC)] | ykoK | OB1224 | CAC0684 | CPE1240 | no | no | ykoK | 5 TMs
 |  |  |  |  | BioOptimizer-no prediction | no
yqaN | yqaN | AATCCGTT | 12 | AAATAAAGC | possible promoter (by visual inspection) | 121 | yqaN | 4.482503037668612 | 0.99817240665572 |  | 3.104559588128356 | 0.993 |  | 0.6330752072965661 | 0.077 |  | 0.4527962356817938 | 0.00849999999999995 |  | yqaN | similar to phage-related protein  (within skin element) | 6 (No similarity) | yqaN | no | no | no | yqaN | no | no | no | no | no | no | no | lin1248 | yqaN | 0 TM
[NAME] (not included in final total) | yqaO | inside skin element |  |  | not included in BioOptimizer list of sequences |  | yqaO | 0.945356656083619 | 0.414956430610691 |  | 2.228435149270304 | 0.965 |  | 0.832285983496282 | 0.2385 |  | 0.572162285751139 | 0.0455 |  | yqaO |  |  | yqaO |  |  |  | yqaO |  |  |  |  |  |  |  |  | yqaO
yqfQP | yqfQ | AAGCAAAT | 12 | GCATATTCT | possible promoter (by visual inspection) | 32 | yqfQ | 2.011479396959479 | 0.988920584055307 |  | bad spot on the array |  |  |  |  |  | bad spot on the array |  |  | yqfQ | unknown | 6 (No similarity) | yqfQ | no | no | no | yqfQ | no | no | BH1384 | OB1735 | no | no | no | no | yqfQ | 1 TM (mid)
 |  | AAAGC | 16 | GCATATTCTAA | BioOptimizer-prediction | 30
 |  | GCACA | 14 | TCACATTATAC | BioOptimizer-prediction (unlikely) | 119
 | yqfP |  |  |  |  |  | yqfP | 0.8233222185178841 | 0.196787936988479 |  | 29.78516429429191 | 0.989 |  | 0.6615317441736374 | 0.082 |  | 0.3823355724363187 | 0.001 |  | yqfP | similar to penicillin tolerance (E. coli LytB) | 4.2 (Detoxification) | yqfP | no | no | no | yqfP | lytB (BA4511) | no | BH1382 | no | no [CAC1847 (ypfD)] | lytB (CPE1085) | lmo1451 | no | yqfP | 0 TM
yueE | yueE | GCGCATTT | 12 | GCATATACT | predicted sigK promoter | 123 | yueE | 3.344367412460443 | 0.997626877129705 |  | 2.187761623949553 | 0.97 |  | 0.6439926892900671 | 0.058 |  | 0.4404873186246215 | 0.00349999999999995 |  | yueE | unknown | 5.1 (From B. subtilis) | yueE | no | no | no | yueE | BA4807 | BC4564 | BH2866 | OB0529 | no | no | no | no | yueE | 0 TM
 |  | [NAME] | 15 | GCATATACTGA | BioOptimizer-prediction | 123
yusM | yusM | GATCCTC | 13 | TCATTTTAT | possible promoter (by visual inspection) | 62 | yusM | 2.56548384719482 | 0.982872850159405 |  | 2.009092812608728 | 0.952 |  | 0.7688584743075791 | 0.15 |  | 0.437109165054747 | 0.008 |  | yusM | similar to proline dehydrogenase | 2.2 (Metabolism of amino acids and related molecules) | yusM | no | ycgM | no | yusM | BA5253 | BC5006 (yusM/ycgM) | BH1939 (ycgM/yusM) | OB1350 (ycgM/yusM) | no | no | no | no | yusM | 0 TM
 |  |  |  |  | BioOptimizer-no prediction | no
GENES IN SECTIONS 1.3.B) and 1.3.C)  ARE NOT INCLUDED IN THE FINAL TOTAL OF SIGK-CONTROLLED GENES
1.3. B. below cut-off in sigK+ vs. sigK- experiments but identified by overexpression of sK
1.3. B. 1. repressed at both time points
ybfAB | ybfA | TATCGTTG | 11 | ATATGTGAT | possible promoter (by visual inspection) | 42 | ybfA | 2.784176648689816 | 0.99780681878933 |  | 1.75 | 0.92 |  | 0.5921980409372029 | 0.043 |  | 0.2771982809320935 | 0.004 |  | ybfA |  |  | ybfA |  |  |  | ybfA |  |  |  |  |  |  |  |  | ybfA
 |  |  |  |  | BioOptimizer-no prediction | no
 | ybfB |  |  |  |  |  | ybfB | 3.215628518339988 | 0.998468243362693 |  | 0.9210750328289229 | 0.383 |  | 0.9565751118001907 | 0.431 |  | 0.6209614706073312 | 0.0275 |  | ybfB |  |  | ybfB |  |  |  | ybfB |  |  |  |  |  |  |  |  | ybfB
1.3. B. 2. repressed at only one of the two time points
none
1.3. C. not identified by overexpression of sK , but down-regulated in the presence of GerE
1.3. C. 1. repressed at both time points
1.3.C.1. a) ratio in sigK+ vs. sigK- experiment is high (>3)
mntABCD | mntA (ytgA) | CACATGT | 14 | CATAAGAT | possible promoter (by visual inspection) | 38 | mntA (ytgA) | 0.2042079341568166 | 0.000517922343234556 |  | 3.435579478998747 | 0.99 |  | 0.5350403943012859 | 0.0315 |  | 0.5393440577513986 | 0.031 |  | mntA (ytgA) |  |  | mntA (ytgA) |  |  |  | mntA (ytgA) |  |  |  |  |  |  |  |  | mntA (ytgA)
 | mntB (ytgB) |  |  |  |  |  | mntB (ytgB) | 0.171200740218261 | 0.000175920470494417 |  | 3.793149849736819 | 0.995 |  | 0.5655535444121472 | 0.027 |  | 0.4469498879737244 | 0.00249999999999995 |  | mntB (ytgB) |  |  | mntB (ytgB) |  |  |  | mntB (ytgB) |  |  |  |  |  |  |  |  | mntB (ytgB)
 | mntC (ytgC) |  |  |  |  |  | mntC (ytgC) | 0.3502392063404055 | 0.00211678270224314 |  | 3.147748314101316 | 0.994 |  | 0.5758653154496888 | 0.032 |  | 0.4638592416313982 | 0.0135 |  | mntC (ytgC) |  |  | mntC (ytgC) |  |  |  | mntC (ytgC) |  |  |  |  |  |  |  |  | mntC (ytgC)
 | mntD (ytgD) |  |  |  |  |  | mntD (ytgD) | 0.5830219172735488 | 0.0419740562197393 |  | 1.857804455091699 | 0.969 |  | 0.5715426338347218 | 0.0355 |  | 0.4462899320918267 | 0.00249999999999995 |  | mntD (ytgD) |  |  | mntD (ytgD) |  |  |  | mntD (ytgD) |  |  |  |  |  |  |  |  | mntD (ytgD)
murC | murC | GTCGCAA | 14 | CATATACT | possible promoter (by visual inspection) | 34 | murC | 1.006525997827188 | 0.512061063932376 |  | 3.288516308759831 | 0.995 |  | 0.5356471466442527 | 0.019 |  | 0.3566540308677446 | 0.002 |  | murC |  |  | murC |  |  |  | murC |  |  |  |  |  |  |  |  | murC
pbpA | pbpA | GACCCTT | 13 | GATAATTT | possible promoter (by visual inspection) | 110 | pbpA | 1.559107291650409 | 0.95583415588633 |  | 3.16227766016838 | 0.983 |  | 0.3886901238811535 | 0.005 |  | 0.2591613351552564 | 0.000499999999999945 |  | pbpA |  |  | pbpA |  |  |  | pbpA |  |  |  |  |  |  |  |  | pbpA
yhfA-yhaA | yhfA | GCACCTTC | 11 | GAATAATCT | possible promoter (by visual inspection) | 20 | yhfA | 1.611931131911796 | 0.962704115667368 |  | 10.16248692870695 | 1 |  | 0.2454203310481097 | 0 |  | 0.1370541639779742 | 0.000499999999999945 |  | yhfA |  |  | yhfA |  |  |  | yhfA |  |  |  |  |  |  |  |  | yhfA
 | yhaA |  |  |  |  |  | yhaA | 0.4166732153497304 | 0.0533300093899837 |  | 2.280342072000418 | 0.971 |  | 0.4045674075839039 | 0.009 |  | 0.2776312642852118 | 0 |  | yhaA |  |  | yhaA |  |  |  | yhaA |  |  |  |  |  |  |  |  | yhaA
yisJI | yisJ | [NAME] | 12 | ACATATCAT | possible promoter (by visual inspection) | 31 | yisJ | 0.9573031482966182 | 0.422445722854318 |  | 14.65547840955912 | 1 |  | 0.4814443892154257 | 0.01 |  | 0.3306232285003102 | 0.0165 |  | yisJ |  |  | yisJ |  |  |  | yisJ |  |  |  |  |  |  |  |  | yisJ
 | yisI |  |  |  |  |  | yisI | 0.5015792737195272 | 0.0773233622945384 |  | 2.66072505979881 | 0.97 |  | 0.5855763283470318 | 0.0375 |  | 0.3239482593723854 | 0.0125 |  | yisI |  |  | yisI |  |  |  | yisI |  |  |  |  |  |  |  |  | yisI
yjqC | yjqC | GCACGGTT | 11 | TCATACGCT | possible promoter (by visual inspection) | 33 | yjqC | 1.578024148497242 | 0.957788828531812 |  | 6.902398038402421 | 0.997 |  | 0.5273157428334078 | 0.0145 |  | 0.3760069942189994 | 0.000499999999999945 |  | yjqC |  |  | yjqC |  |  |  | yjqC |  |  |  |  |  |  |  |  | yjqC
ypbGH | ypbG | GCACAAAT | 11 | CTATATTTT | preferred predicted promoter | 97 | ypbG | 1.275066154958108 | 0.829165195396378 |  | 2.540972705549305 | 0.98 |  | 0.5779147998404772 | 0.028 |  | 0.3444104341777378 | 0.00349999999999995 |  | ypbG |  |  | ypbG |  |  |  | ypbG |  |  |  |  |  |  |  |  | ypbG
 |  | GCACA | 14 | CTATATTTTGA | BioOptimizer-prediction | 95
 |  | GAAGG | 16 | TCATATGATGA | BioOptimizer-prediction | 128
 | ypbH |  |  |  |  |  | ypbH | 1.716105073850495 | 0.975306312425828 |  | 5.445026528424212 | 0.995 |  | 0.719270482896732 | 0.1205 |  | 0.4613421138507494 | 0.00449999999999995 |  | ypbH |  |  | ypbH |  |  |  | ypbH |  |  |  |  |  |  |  |  | ypbH
yrzA | yrzA | AACAGTT | 12 | CATATTCT | possible promoter (by visual inspection) | 109 | yrzA | 0.6349509003024153 | 0.0703671900129023 |  | 2.999162518987651 | 0.994 |  | 0.3075966832690371 | 0.0175 |  | 0.4392086381421736 | 0.00949999999999995 |  | yrzA |  |  | yrzA |  |  |  | yrzA |  |  |  |  |  |  |  |  | yrzA
ytaFG | ytaF | AAACACGG | 13 | CCATATATA | possible promoter (by visual inspection) | 73 | ytaF | 1.063222451111664 | 0.608449656165878 |  | 7.925013304804718 | 0.993 |  | 0.5256167325829657 | 0.0225 |  | 0.3223280625049327 | 0.001 |  | ytaF |  |  | ytaF |  |  |  | ytaF |  |  |  |  |  |  |  |  | ytaF
 | ytaG |  |  |  |  |  | ytaG | 1.601695507833738 | 0.961321566870317 |  | 4.623810213992605 | 0.995 |  | 0.4526691614617729 | 0.00649999999999995 |  | 0.2851782314739001 | 0.000499999999999945 |  | ytaG |  |  | ytaG |  |  |  | ytaG |  |  |  |  |  |  |  |  | ytaG
ytwI-citZ | ytwI | CACGCTG | 12 | AATACATT | possible promoter (by visual inspection) | 22 | ytwI | 1.43322868414717 | 0.926128037528369 |  | 4.073802778041128 | 0.996 |  | 0.4992237336841124 | 0.0235 |  | 0.311809837467396 | 0.001 |  | ytwI |  |  | ytwI |  |  |  | ytwI |  |  |  |  |  |  |  |  | ytwI
1.3.C.1. b) ratio in sigK+ vs. sigK- experiment is low (<3)
gcvT (yqhI)-gcvPAB (yqhJK) | gcvT (yqhI) | GACAGAG | 13 | CATGAGGT | possible promoter (by visual inspection) | 60 | gcvT (yqhI) | 0.7047259505402115 | 0.0761028407578044 |  | 1.6 | 0.94 |  | 0.4016626847311606 | 0.00649999999999995 |  | 0.2520369888043806 | 0.00349999999999995 |  | gcvT (yqhI) |  |  | gcvT (yqhI) |  |  |  | gcvT (yqhI) |  |  |  |  |  |  |  |  | gcvT (yqhI)
 | [NAME] (yqhJ) |  |  |  |  |  | [NAME] (yqhJ) | 1.12748812553831 | 0.704395739971811 |  | 1.770108958317421 | 0.961 |  | 0.4058557006414021 | 0.00749999999999995 |  | 0.2623204337793396 | 0 |  | [NAME] (yqhJ) |  |  | [NAME] (yqhJ) |  |  |  | [NAME] (yqhJ) |  |  |  |  |  |  |  |  | [NAME] (yqhJ)
 | gcvPB (yqhK) |  |  |  |  |  | gcvPB (yqhK) | 1.218245573469996 | 0.753753538024156 |  | 1.7 | 0.94 |  | 0.4512897997040985 | 0.014 |  | 0.2938283167237982 | 0.001 |  | gcvPB (yqhK) |  |  | gcvPB (yqhK) |  |  |  | gcvPB (yqhK) |  |  |  |  |  |  |  |  | gcvPB (yqhK)
yhgD | yhgD | AGCAGGT | 13 | CATATGTA | possible promoter (by visual inspection) | 45 | yhgD | 0.7641260724409493 | 0.125650678006041 |  | 2.055890595984142 | 0.966 |  | 0.5852431224311845 | 0.0275 |  | 0.4372430445361696 | 0.004 |  | yhgD |  |  | yhgD |  |  |  | yhgD |  |  |  |  |  |  |  |  | yhgD
yjaZ | yjaZ | AATCTTTA | 11 | TCATAATCA | predicted promoter (overlap with predicted [NAME] promoter) | 72 | yjaZ | 1.675421933664105 | 0.972826649536268 |  | 2.094112455850893 | 0.971 |  | 0.5733799831367705 | 0.0215 |  | 0.3794862873517596 | 0.00249999999999995 |  | yjaZ |  |  | yjaZ |  |  |  | yjaZ |  |  |  |  |  |  |  |  | yjaZ
 |  | TAGCC | 14 | GCATAGGATTA | BioOptimizer-prediction | 17
ykoY | ykoY | TGACAAAT | 11 | GCATATTAT | predicted promoter | 51 | ykoY | 0.521148114534442 | 0.192253171801064 |  | 2.249054605835781 | 0.972 |  | 0.493987243633116 | 0.0185 |  | 0.2879948790598499 | 0.001 |  | ykoY |  |  | ykoY |  |  |  | ykoY |  |  |  |  |  |  |  |  | ykoY
 |  | TGACA | 14 | GCATATTATTG | BioOptimizer-prediction | 49
ypbB | ypbB | ATCACAT | 13 | [NAME] | possible promoter (by visual inspection) | 101 | ypbB | 0.6775705744215943 | 0.0636762711388076 |  | 2.387811282913178 | 0.99 |  | 0.5217376047518979 | 0.023 |  | 0.2859544055188596 | 0.000499999999999945 |  | ypbB |  |  | ypbB |  |  |  | ypbB |  |  |  |  |  |  |  |  | ypbB
ysmA | ysmA | upstream of [NAME], no promoter found |  |  |  |  | ysmA | 1.132879320093236 | 0.704999016289314 |  | 2.238721138568339 | 0.977 |  | 0.2024665289921986 | 0.000499999999999945 |  | 0.1843693917389074 | 0 |  | ysmA |  |  | ysmA |  |  |  | ysmA |  |  |  |  |  |  |  |  | ysmA
ytvB | ytvB | AGCTTAC | 14 | CATATAAT | possible promoter (by visual inspection) | 120 | ytvB | 1.066107442560381 | 0.613480415329876 |  | 1.887991349096294 | 0.958 |  | 0.593399581885315 | 0.033 |  | 0.3593074404984857 | 0.00249999999999995 |  | ytvB |  |  | ytvB |  |  |  | ytvB |  |  |  |  |  |  |  |  | ytvB
yxzF | yxzF | AACAGGT | 14 | [NAME] | possible promoter (by visual inspection) | 20 | yxzF | 1.150941220594085 | 0.7312898178593 |  | 1.9 | 0.898 |  | 0.4621782195850788 | 0.0495 |  | 0.06827676635206525 | 0.001 |  | yxzF |  |  | yxzF |  |  |  | yxzF |  |  |  |  |  |  |  |  | yxzF
yyaK | yyaK | TTCATAG | 13 | AATATATA | possible promoter (by visual inspection) | 36 | yyaK | 1.263896163863543 | 0.78113351657836 |  | 2.558585886905646 | 0.982 |  | 0.5836900303193446 | 0.0535 |  | 0.3663186989297675 | 0.00349999999999995 |  | yyaK |  |  | yyaK |  |  |  | yyaK |  |  |  |  |  |  |  |  | yyaK
1.3. C. 2. repressed at only one of the two time points
1.3.C. 2. a) ratio in sigK+ vs. sigK- experiment is high (>3)
fer | fer | no promoter found, divergent from ypbB |  |  |  |  | fer | 0.5967988665177191 | 0.119260644999924 |  | 3.758374042884442 | 0.973 |  | 0.8009941238645848 | 0.231 |  | 0.3595269841588498 | 0.000499999999999945 |  | fer |  |  | fer |  |  |  | fer |  |  |  |  |  |  |  |  | fer
ycdH | ycdH | no promoter found |  |  |  |  | ycdH | 1.027520807946291 | 0.545099121720426 |  | 3.8 | 0.94 |  | 0.6452778193602507 | 0.05 |  | 0.4275225514351469 | 0.00349999999999995 |  | ycdH |  |  | ycdH |  |  |  | ycdH |  |  |  |  |  |  |  |  | ycdH
ydcI | ydcI | no promoter found |  |  |  |  | ydcI | 0.975420929014981 | 0.457737399622694 |  | 2.128139045982712 | 0.981 |  | 0.6896415232719163 | 0.0915 |  | 0.5402303299913706 | 0.0115 |  | ydcI |  |  | ydcI |  |  |  | ydcI |  |  |  |  |  |  |  |  | ydcI
yjnA | yjnA | ACACTCAT | 12 | GAATAGAGA | possible promoter (by visual inspection) | 121 | yjnA | 1.033995852117984 | 0.553007925753968 |  | 6.397348354826484 | 0.999 |  | 0.6523634685049914 | 0.0715 |  | 0.4977566270830797 | 0.037 |  | yjnA |  |  | yjnA |  |  |  | yjnA |  |  |  |  |  |  |  |  | yjnA
ytlR | ytlR | AACGATT | 13 | [NAME] | possible promoter (by visual inspection) | 15 | ytlR | 1.434666177450663 | 0.912461574126312 |  | 3.33426412763235 | 0.99 |  | 0.6731300887159116 | 0.0995 |  | 0.4757295654035384 | 0.022 |  | ytlR |  |  | ytlR |  |  |  | ytlR |  |  |  |  |  |  |  |  | ytlR
yraK | yraK | TATCACCT | 11 | CAATAAAAA | possible promoter (by visual inspection) | 156 | yraK | 1.070357132034774 | 0.617472998815444 |  | 14.75706533275895 | 0.962 |  | 0.7743875813836276 | 0.1695 |  | 0.5027850950203511 | 0.025 |  | yraK |  |  | yraK |  |  |  | yraK |  |  |  |  |  |  |  |  | yraK
ywkF | ywkF | no promoter found |  |  |  |  | ywkF | 0.9486379621867167 | 0.403996527670489 |  | 3.013006024186121 | 0.99 |  | 0.605776914757813 | 0.0515 |  | 0.3466807549364213 | 0.00149999999999995 |  | ywkF |  |  | ywkF |  |  |  | ywkF |  |  |  |  |  |  |  |  | ywkF
1.3.C.2. b) ratio in sigK+ vs. sigK- experiment is low (<3)
lytD | lytD | no promoter found |  |  |  |  | lytD | 1.135867234918529 | 0.692619434521976 |  | 2.818382931264454 | 0.987 |  | 0.6791207700196703 | 0.077 |  | 0.4663869520341771 | 0.00649999999999995 |  | lytD |  |  | lytD |  |  |  | lytD |  |  |  |  |  |  |  |  | lytD
prs | prs | GACGATT | 14 | CATAAAAA | possible promoter (by visual inspection) | 26 | prs | 0.6752792342257969 | 0.0659427288541177 |  | 1.849268618978078 | 0.963 |  | 0.654368355285136 | 0.063 |  | 0.2977947902458409 | 0 |  | prs |  |  | prs |  |  |  | prs |  |  |  |  |  |  |  |  | prs
tagO | tagO | CTCTATA | 13 | CATTTAAT | possible promoter (by visual inspection) | 18 | tagO | 0.5700366998143305 | 0.0881825855439621 |  | 2.798981319634362 | 0.987 |  | 0.7441881103664286 | 0.1325 |  | 0.5729895356611602 | 0.0155 |  | tagO |  |  | tagO |  |  |  | tagO |  |  |  |  |  |  |  |  | tagO
uvrC | uvrC | no promoter found |  |  |  |  | uvrC | 1.585835961135615 | 0.959862975040709 |  | 2.477422057633285 | 0.974 |  | 1.125818658502235 | 0.606 |  | 0.4651924392540023 | 0.00949999999999995 |  | uvrC |  |  | uvrC |  |  |  | uvrC |  |  |  |  |  |  |  |  | uvrC
yddN | yddN | no promoter found |  |  |  |  | yddN | 1.113803844564787 | 0.689677086111338 |  | 2.004472027365162 | 0.962 |  | 0.7313828785704712 | 0.117 |  | 0.4887119224281459 | 0.0215 |  | yddN |  |  | yddN |  |  |  | yddN |  |  |  |  |  |  |  |  | yddN
yhaL | yhaL | CACATAA | 15 | CATATGGT | possible promoter (by visual inspection) | 36 | yhaL | 0.4713899180301805 | 0.0136491052438805 |  | 1.849268618978078 | 0.965 |  | 0.8057505707217283 | 0.215 |  | 0.4664762990480638 | 0.0125 |  | yhaL |  |  | yhaL |  |  |  | yhaL |  |  |  |  |  |  |  |  | yhaL
ykoN | ykoN | CTCCTCA | 12 | CATATTTT | possible promoter (by visual inspection) | 15 | ykoN | 1.385874250772695 | 0.657399361237922 |  | 2.63633138582538 | 0.989 |  | 2.543824915259081 | 0.804 |  | 0.4634584272035353 | 0.004 |  | ykoN |  |  | ykoN |  |  |  | ykoN |  |  |  |  |  |  |  |  | ykoN
ykoP | ykoP | CTCCTAA | 14 | TATATTTT | possible promoter (by visual inspection) | 55 | ykoP | 1.374657134450212 | 0.780356103895818 |  | 2.488857318282391 | 0.983 |  | 0.7377910693492984 | 0.1225 |  | 0.5364795969376991 | 0.015 |  | ykoP |  |  | ykoP |  |  |  | ykoP |  |  |  |  |  |  |  |  | ykoP
yprB | yprB | no promoter found, upstream of cotD |  |  |  |  | yprB | 0.6951405435741624 | 0.0826435699386108 |  | 1.883649089489801 | 0.965 |  | 0.6259548714683503 | 0.049 |  | 0.3499075502328496 | 0.007 |  | yprB |  |  | yprB |  |  |  | yprB |  |  |  |  |  |  |  |  | yprB
yrkRS | yrkR | CACCAAG | 12 | AATAAAAA | downstream of spoIIIC | 28 | yrkR | 1.206962681093756 | 0.734147278796323 |  | 2.404362800006933 | 0.988 |  | 0.8455722218816695 | 0.308 |  | 0.4549794520901208 | 0.018 |  | yrkR |  |  | yrkR |  |  |  | yrkR |  |  |  |  |  |  |  |  | yrkR
 | yrkS |  |  |  | downstream of spoIIIC |  | yrkS | 0.8201146940317409 | 0.221705551578725 |  | 1.635045839319392 | 0.9255 |  | 0.8052220259737839 | 0.19 |  | 0.6011846436857214 | 0.0635 |  | yrkS |  |  | yrkS |  |  |  | yrkS |  |  |  |  |  |  |  |  | yrkS
yugK | yugK | no promoter found |  |  |  |  | yugK | 0.7372184801978288 | 0.18122015431602 |  | 2.07491351745491 | 0.969 |  | 0.7188137754616303 | 0.106 |  | 0.458051235129582 | 0.01 |  | yugK |  |  | yugK |  |  |  | yugK |  |  |  |  |  |  |  |  | yugK
yuiBC | [NAME] | no promoter found |  |  |  |  | [NAME] | 1.237879986440388 | 0.745981530955285 |  | 2.249054605835781 | 0.959 |  | 0.7603118377061954 | 0.17 |  | 0.4915884082025461 | 0.0225 |  | [NAME] |  |  | [NAME] |  |  |  | [NAME] |  |  |  |  |  |  |  |  | [NAME]
 | yuiC |  |  |  |  |  | yuiC | 0.8626911352797677 | 0.255112455852853 |  | 1.734197705580141 | 0.9415 |  | 0.5771032349578878 | 0.0505 |  | 0.4274753118045468 | 0.017 |  | yuiC |  |  | yuiC |  |  |  | yuiC |  |  |  |  |  |  |  |  | yuiC
ywnC | ywnC | CACTTGT | 14 | [NAME] | possible promoter (by visual inspection) | 139 | ywnC | 0.4309668674476025 | 0.00636709400383728 |  | 2.471724145016131 | 0.987 |  |  |  |  | 0.3572131016189015 | 0.006 |  | ywnC |  |  | ywnC |  |  |  | ywnC |  |  |  |  |  |  |  |  | ywnC
yyaJ | yyaJ | no promoter found, divergent from yyaK |  |  |  |  | yyaJ | 0.8790267434658076 | 0.307801001579949 |  | 2.703958364108844 | 0.986 |  | 0.6713013828045845 | 0.082 |  | 0.4083294643073552 | 0.008 |  | yyaJ |  |  | yyaJ |  |  |  | yyaJ |  |  |  |  |  |  |  |  | yyaJ
 |  |  |  |  | BioOptimizer-no prediction | no
yyaTS | yyaT | no promoter found |  |  |  |  | yyaT |  |  |  |  |  |  | 0.9657890193602461 | 0.4715 |  | 0.4342757819088509 | 0.0235 |  | yyaT |  |  | yyaT |  |  |  | yyaT |  |  |  |  |  |  |  |  | yyaT
yyaS | yyaS | GTACGGAT | 14 | TCGTAAGCG | possible promoter (by visual inspection) | 169 | yyaS | 1.950158680405563 | 0.926542846086747 |  | 2.837919028441556 | 0.983 |  | 0.7958966514757803 | 0.2475 |  | 0.5016262540290861 | 0.054 |  | yyaS |  |  | yyaS |  |  |  | yyaS |  |  |  |  |  |  |  |  | yyaS
 |  |  |  |  | BioOptimizer-no prediction | no
2. sK-CONTROLLED GENES ACTIVATED BY GerE:
2.1. Previously identified sK-controlled genes (with mapped transcription start site):
2.1. A. Also identified by overexpression of sK
cgeAB | cgeA | ATACCAAA | 12 | GAATATGAA | TAACGTGAGT (mapped sigK promoter) | 36 | cgeA | 1.836393475891149 | 0.981164298653702 |  | 2.328091257665008 | 0.98 |  | 7.289363306884502 | 1 |  | 17.76153269008994 | 1 |  | cgeA | maturation of the outermost layer of the spore | 1.8 (Sporulation) | cgeA | cgeAA | no | no | cgeA | no | no | no | no | no | no | no | no | cgeA | 0-1 TM (mid)
 |  |  |  |  | BioOptimizer-no prediction | no
 | cgeB |  |  |  |  |  | cgeB | 12.4710838094021 | 0.999857151023492 |  | 1.674942876026438 | 0.937 |  | 27.01194959537318 | 1 |  | 31.76632346911946 | 1 |  | cgeB | maturation of the outermost layer of the spore | 1.8 (Sporulation) | cgeB | cgeAB | no | ykvP | cgeB | no | no | cgeB (BH2839) | no | CAC2177 | no | no | no | cgeB | 0 TM
cotB-ywrJ | cotB | CAACAAAT | 11 | GTATATATG | CAGTATGT (mapped sigK promoter) | 44 | cotB | 1.909879520035382 | 0.976741468785408 |  | 11.06623783977667 | 0.999 |  | 3.286578622526561 | 1 |  | 3.364214417052687 | 0.999 |  | cotB | spore coat protein (outer) | 1.8 (Sporulation) | cotB | no | no | ywrJ | cotB | BA0357 | BC0389/BC0390 | no | no | no | no [CPE0112 (ypuA)] | no | no | cotB | 0 TM
 |  |  |  |  | BioOptimizer-no prediction | no
 | ywrJ |  |  |  |  |  | ywrJ | 4.392591932660268 | 0.998587596125018 |  | 5.081594425605605 | 0.997 |  | 3.246164045786431 | 0.996 |  | 2.730020117677965 | 0.997 |  | ywrJ | unknown | 6 (No similarity) | ywrJ | no | no | cotB | ywrJ | BA0357 | BC0391 | no | no | no | no | no | no | ywrJ | 1-2 TMs
[NAME] (not included in final total) | [NAME] | downstream of ywrJ (convergent),  antisense? |  |  |  |  | [NAME] | 1.026979477821395 | 0.538143712550859 |  | 2.393315756405388 | 0.992 |  | 11.4456735694357 | 0.9995 |  | 15.81994143803255 | 1 |  | [NAME] |  |  | [NAME] |  |  |  | [NAME] |  |  |  |  |  |  |  |  | [NAME]
[NAME] | [NAME] | ATACACTT | 11 | GCGTACTAT | GAGGGTAG (mapped sigK promoter) | 53 | [NAME] | 2.286925653525554 | 0.995037766473735 |  | 5.508076964054035 | 0.998 |  | 8.748543342434985 | 1 |  | 12.12297892902276 | 1 |  | [NAME] | spore coat protein (required for the incorporation of CotB into the coat) | 1.8 (Sporulation) | [NAME] | no | no | no | [NAME] | no | no [BC4731(gerAA)] | no | no | no | no | no | no | [NAME] | 0 TM
 |  |  |  |  | BioOptimizer-no prediction | no
cotSA-cotS-ytxO | cotSA (ytxN) | GCACAAGT | 12 | CCGTATCAT | GATTCTAACT (mapped sigK promoter) | 42 | cotSA (ytxN) | 0.9341489263988959 | 0.382031590590842 |  | 1.522033327611256 | 0.9 |  | 7.851528028116871 | 1 |  | 7.091332857181619 | 0.9995 |  | cotSA (ytxN) | spore coat protein (similarity to glycosyl transferase), assembly into the coat dependent on CotS | 1.8 (Sporulation) | cotSA (ytxN) | ytxN, ytbA | ytcC | yveN, yqgM, ypjH, tuaC | cotSA (ytxN) | BA5012 | BC4756 | BH2305 | OB2890 | no [CAC1053 (yqgM/ypjH)] | CPE0498 | no | no [lin2700 (ypjH)] | cotSA (ytxN) | 0 TM
 |  | GCACA | 14 | CCGTATCATGA | BioOptimizer prediction-correct | 40
 | cotS |  |  |  |  |  | cotS | 1.438750605080461 | 0.92817997236611 |  | 4.688133821452654 | 0.994 |  | 9.459127889253077 | 1 |  | 7.298468899233058 | 1 |  | cotS | spore coat protein (inner), located in the inner coat layer; CotE required for the assembly of CotS in the coat | 1.8 (Sporulation) | cotS | no | cotI (ytaA) | yutH | cotS | cotS (BA 5188) | no [BC4954 (yutH)] | no [BH2306 (cotI)] | no | CAC2906 (cotI/cotS) | CPE2218 (cotS/cotI) | no | no | cotS | 1-2 TMs
 | ytxO |  |  |  |  |  | ytxO | 2.383241391115728 | 0.989291779686719 |  | 12.97179270983956 | 0.996 |  | 5.643466401556307 | 1 |  | 5.059441342318793 | 1 |  | ytxO | unknown | 6 (No similarity) | ytxO | ytbB | no | no | ytxO | no | no | no | no | no | no | no | no | ytxO | 0 TM
cotX | cotX | AGTCAAAA | 12 | TCATTTAAT | AACAGTAA (mapped sigK promoter) | 27 | cotX | 6.462414245922576 | 0.99983596237892 |  | 6.223002851691597 | 0.998 |  | 2.037294845373482 | 0.9895 |  | 2.197645271517719 | 0.9955 |  | cotX | spore coat protein (insoluble fraction) | 1.8 (Sporulation) | cotX | no | no | no | cotX | no | BC2874/BC2872 | cotX | OB0575/OB0574 | no | no | no | no | cotX | 1-2 TMs
 |  | TAACA | 16 | AAATAGGGTTC | BioOptimizer-inaccurate | no
cotYZ | cotY | ACACCAAG | 12 | ACATATGTT | GTTAAGGAC (mapped sigK promoter) | 46 | cotY | 8.951817242026168 | 0.999935342691795 |  | 5.861381645140288 | 0.998 |  | 2.362150665842228 | 0.9925 |  | 1.779470465508628 | 0.981 |  | cotY | spore coat protein (insoluble fraction) | 1.8 (Sporulation) | cotY | no | [NAME] | no | cotY | cotZ-1 (BA1234)/cotZ-2 (BA1238) | BC1218/BC1222 | no | no [OB1226 (cotZ)] | no | no | no | no | cotY | 0 TM
 |  | ACACC | 15 | ACATATGTTGT | BioOptimizer prediction-correct | 44
 | [NAME] |  |  |  |  |  | [NAME] | 8.77693139266097 | 0.999922598781037 |  | 17.13957307508426 | 0.99 |  | 2.830891705089396 | 0.993 |  | 1.80851571544139 | 0.9795 |  | [NAME] | spore coat protein (insoluble fraction) | 1.8 (Sporulation) | [NAME] | no | cotY | no | [NAME] | cotZ-1 (BA1234)/cotZ-2 (BA1238) | BC1218/BC1222 | no | OB1226 | no | no | no | no | [NAME] | 0 TM
2.1. B. below cut-off in sigK+ vs. sigK- experiments but identified by overexpression of sK
cwlC | cwlC | CAAGCAGA | 12 | TCATATCCT | GTAATGAGG (mapped sigK promoter) | 18 | cwlC | 6.871587714979146 | 0.999824418267011 |  | 0.9769918291465723 | 0.46 |  | 2.240526456092728 | 0.9775 |  | 21.95745765974713 | 1 |  | cwlC | N-acetylmuramoyl-L-alanine amidase (sporulation-specific mother cell wall), (EC 3.5.1.28) | 1.1 (Cell wall) | cwlC | no | yqiI, lytC, yrvJ | [NAME] | cwlC | no | BC2207 | cwlC (BH1294) | OB0220 | no [CAC3092 (cwlD)] | no [CPE2367 (cwlD)] | [NAME] | lin0176 | cwlC | 0-1 TM (mid)
 |  | GCACA | 16 | GTATCTGTTGT | BioOptimizer-inaccurate | no
cwlH (yqeE) | cwlH (yqeE) | TGTCCATC | 12 | GCATTCTTA | [NAME] (mapped sigK promoter) | 19 | cwlH (yqeE) | 2.516351314838484 | 0.984888423583009 |  | 0.7999414833737571 | 0.25 |  | 1.321131439952049 | 0.8375 |  | 3.07044812937335 | 0.9995 |  | cwlH (yqeE) | N-acetylmuramoyl-L-alanine amidase (sporulation-specific mother cell wall), (EC 3.5.1.28) | 1.1 (Cell wall) | cwlH (yqeE) | yqeE | xlyA, cwlA, xlyB | blyA | cwlH (yqeE) | BA0870 | BC0888 | no [BH3671 (lytE)] | no | no [CAC0686 (sleB)] | no [CPE0606 (yrvJ)] | no | no [lin1700 (cwlA)] | cwlH (yqeE) | 0 TM
 |  |  |  |  | BioOptimizer-no prediction | no
sspG-yurS | sspG | AATCTCTT | 12 | GAATATCCT | GTCACTATC (mapped sigK promoter) | 29 | sspG | not on the array |  |  | not on the array |  |  | not on the array |  |  | not on the array |  |  | sspG | small acid-soluble spore protein (minor) | 1.8 (Sporulation) | sspG | no | no | no | sspG | no | no | no | no | no | no | no | no | sspG | 0 TM
 |  |  |  |  | BioOptimizer-no prediction | no
 | yurS |  |  |  |  |  | yurS | 3.11780309796024 | 0.992994997780824 |  | 0.8783589964474621 | 0.34 |  | 2.614975084698136 | 0.999 |  | 2.491445030107337 | 0.998 |  | yurS | unknown | 6 (No similarity) | yurS | no | no | no | yurS | no | no | no | no | no | no | no | no | yurS | 1 TM (mid)
2.1. C. not identified by overexpression of sK
cotD | cotD | GAACATGT | 12 | TCATAACTT | AGTATTGTAA (mapped sigK promoter) | 38 | cotD | 1.361106402139658 | 0.894792140083935 |  | 3.475361614432059 | 0.994 |  | 6.109533451184798 | 0.9995 |  | 4.414805662557354 | 1 |  | cotD | spore coat protein (inner) | 1.8 (Sporulation) | cotD | no | no | no | cotD | BA1581 | BC1560 | cotD (BH1767) | OB1024 | no | no | no | no | cotD | 0 TM
 |  |  |  |  | not included in BioOptimizer list of sequences | no
ypsA (not included in final total) | ypsA | terminator between cotD and ypsA |  |  |  |  | ypsA | 0.6321605580775214 | 0.0430473800245346 |  | 1.1 | 0.61 |  | 1.848015725764558 | 0.9715 |  | 2.416446605751659 | 0.995 |  | ypsA |  |  | ypsA |  |  |  | ypsA |  |  |  |  |  |  |  |  | ypsA
2.1. D. identified neither by overexpression of sK nor in sigK+ vs. sigK- experiment
cgeCDE | cgeC | ATACCATA | 12 | ACATATTGT | GAACAGAGA (mapped sigK promoter) | 33 | cgeC | 0.9481214789271848 | 0.459043070068094 |  | 1.21495037339868 | 0.751 |  | 10.48045731846431 | 1 |  | 12.71546988345502 | 0.9995 |  | cgeC | maturation of the outermost layer of the spore | 1.8 (Sporulation) | cgeC | cgeBA | no | no | cgeC | no | no | no | no | no | no | no | no | cgeC | 0 TM
 |  |  |  |  | not included in BioOptimizer list of sequences | no
 | cgeD |  |  |  |  |  | cgeD | 0.977079040127353 | 0.459409756819791 |  | 0.9568138790365877 | 0.44 |  | 5.439418668115384 | 0.999 |  | 9.044611073040459 | 0.9995 |  | cgeD | maturation of the outermost layer of the spore (glycosyl transferase), similar to spsA and glycosyl transferases | 1.8 (Sporulation) | cgeD | cgeBB | spsA | tuaG, [NAME], ggaB, ywdF, yveT | cgeD | no | no [BC1943 (tuaG)] | cgeD (BH3373) | no [OB2925 (tuaG)] | CAC2346 | no | no | no | cgeD | 0 TM
 | cgeE |  |  |  |  |  | cgeE | 0.9787348298052742 | 0.464441285230154 |  | 0.7837396267353417 | 0.2 |  | 6.064266114677564 | 0.999 |  | 7.402663104718043 | 1 |  | cgeE | maturation of the outermost layer of the spore (acetyl transferase) | 1.8 (Sporulation) | cgeE | cgeBC | no | yybD, yyaT | cgeE | no | no | no | no | no | no | no | no | cgeE | 0 TM
cotC | cotC | CAAGCCGC | 12 | [NAME] | AAGCGTA (mapped sigK promoter) | "+126" | cotC | 1.141082801889966 | 0.625441069152691 |  |  |  |  |  |  |  |  |  |  | cotC | spore coat protein (outer), not expressed in resuspension medium | 1.8 (Sporulation) | cotC | no | no | no | cotC | no | no | no | no | no | no | no | no | cotC | 1 TM (Nter)
 |  |  |  |  | not included in BioOptimizer list of sequences | no
yobW | yobW | CTACTATT | 13 | GCATACACT | TCTCAACGGA (mapped sigK promoter) | 24 | yobW | 0.3739157206470199 | 0.0349784456259044 |  | 0.9385496600493631 | 0.42 |  | 2.991788367798409 | 0.9975 |  | 5.923977974072547 | 1 |  | yobW | unknown; sporulation membrane protein | 1.8 (Sporulation) | yobW | csk22 | no | no | yobW | no | no | no | no | no | no | no | no | yobW | 4-5 TMs
 |  |  |  |  | not included in BioOptimizer list of sequences | no
2.2. Previously reported sK-controlled genes (but transcription start site has not been mapped):
2.2. A. also identified by overexpression of sK
2.2. A. 1. promoter confirmed by 5'RACE-PCR
spsABCDEFGIJKL | spsA | GCGCAACT | 12 | ACATAAGAT | AACGATAGTTT (5'RACE) | 44 | spsA | 5.705007627140462 | 0.999726793481435 |  | 10.99005839432521 | 1 |  | 1.517698864163382 | 0.936 |  | 1.634788418877348 | 0.9715 |  | spsA | spore coat polysaccharide synthesis | 1.8 (Sporulation) | spsA | ipa-63d | cgeD | yveO, tuaG, yveR, yveT, ywdF, yfnE | spsA | no | no [BC1941 (tuaG)] | spsA (BH3367) | no [OB2925 (tuaG)] | no [CAC2174 (yveO)] | no [CPE0484 (yveT)] | no [lmo1090 (yveT)] | no | spsA | 0 TM
 |  | [NAME] | 15 | ACATAAGATAA | BioOptimizer-confirmed by 5'RACE | 42
 |  | AAACA | 14 | GCATATTGGTT | 2nd BioOptimizer-prediction (inaccurate) | 83
 | spsB |  |  |  |  |  | spsB | 6.078225300993968 | 0.999798021188025 |  | 11.56112242192099 | 1 |  | 1.631625481077516 | 0.963 |  | 1.981205735255622 | 0.9865 |  | spsB | spore coat polysaccharide synthesis | 1.8 (Sporulation) | spsB | ipa-64d | no | no | spsB | no | no | no | no | no | no | no | no | spsB | 0-1 TM (mid)
 | spsC |  |  |  |  |  | spsC | 8.229155544631272 | 0.99987772359905 |  | 12.07813835106781 | 1 |  | 1.781191181192641 | 0.9645 |  | 2.20558260736416 | 0.9955 |  | spsC | spore coat polysaccharide synthesis | 1.8 (Sporulation) | spsC | ipa-65d | yhjL, yvfE | speA, patA | spsC | no | BC5273 | no | no | CAC2260 | no | no | no | spsC | 1 TM (mid)
 | spsD |  |  |  |  |  | spsD | 6.750660436421319 | 0.999881482869672 |  | 9.74989637717387 | 0.999 |  | 1.724089734475165 | 0.9755 |  | 2.036834756511516 | 0.9855 |  | spsD | spore coat polysaccharide synthesis | 1.8 (Sporulation) | spsD | ipa-66d | no | yhfO | spsD | no | no | no | no | no | no | no | no | spsD | 0 TM
 | spsE |  |  |  |  |  | spsE | 10.67858962891282 | 0.999904556077703 |  | 11.22018454301964 | 1 |  | 1.803655568750732 | 0.97 |  | 2.216438891473849 | 0.994 |  | spsE | spore coat polysaccharide synthesis | 1.8 (Sporulation) | spsE | ipa-67d | no | no | spsE | no | no | no | no | CAC2187 | no | no | no | spsE | 1 TM (mid)
 | [NAME] |  |  |  |  |  | [NAME] | 9.116467260983926 | 0.999928069210026 |  | 11.66809617060963 | 1 |  | 1.892102226599724 | 0.988 |  | 2.033964765824857 | 0.9945 |  | [NAME] | spore coat polysaccharide synthesis | 1.8 (Sporulation) | [NAME] | ipa-68d | no | no | [NAME] | no | no | no | no | CAC2190 | no | no | no | [NAME] | 0-1 TM (mid)
 | spsG |  |  |  |  |  | spsG | 10.21550535979663 | 0.99994578097903 |  | 11.83041555725165 | 1 |  | 1.841221505020744 | 0.9845 |  | 2.318313449585994 | 0.997 |  | spsG | spore coat polysaccharide synthesis | 1.8 (Sporulation) | spsG | ipa-69d, spsH | no | no | spsG | no | no | no | no | CAC2186 | no | no | no | spsG | 1 TM (mid)
 | spsI |  |  |  |  |  | spsI | 7.471371475577616 | 0.999902740858094 |  | 9.931160484209341 | 0.996 |  | 1.962767805502933 | 0.99 |  | 2.290837338449257 | 0.9965 |  | spsI | spore coat polysaccharide synthesis | 1.8 (Sporulation) | spsI | ipa-71d | ytdA, gtaB | yngB, glgC, yfnH | spsI | BA1228 | BC1212 | spsI (BH3363) | OB1129 | CAC2333 | rfbA (CPE0616) | lmo1081 | no | spsI | 0 TM
 | spsJ |  |  |  |  |  | spsJ | 6.806543014996241 | 0.99983366718247 |  | 3.296097121774578 | 0.992 |  | 1.69838422567082 | 0.9625 |  | 2.002220646281898 | 0.9865 |  | spsJ | spore coat polysaccharide synthesis | 1.8 (Sporulation) | spsJ | [NAME] | yfnG, ytcB, galE | yodU, yveM, pksJ | spsJ | rfbB(BA1230) | BC1214 | spsJ (BH3364) | OB2420 | CAC2332 | rfbB (CPE0619) | lmo1083 | no | spsJ | 1 TM (Nter)
 | spsK |  |  |  |  |  | spsK | 6.557295571818407 | 0.999858363448495 |  | 2.716439268839083 | 0.984 |  | 1.600540193563269 | 0.9535 |  | 1.604582518716285 | 0.965 |  | spsK | spore coat polysaccharide synthesis | 1.8 (Sporulation) | spsK | ipa-73d | no | [NAME], yveM | spsK | rfbD(BA1231) | BC1215 | [NAME] (BH3365)/rbfC (BH3366) | OB1127 | CAC2315 | [NAME] (CPE0618) | lmo1084 | no | spsK | 0 TM
 | spsL (spsK) |  |  |  |  |  | spsL (spsK) | 6.557295571818407 | 0.999858363448495 |  | 2.716439268839083 | 0.984 |  | 1.600540193563269 | 0.9535 |  | 1.604582518716285 | 0.965 |  | spsL (spsK) | spore coat polysaccharide synthesis | 1.8 (Sporulation) | spsL (spsK) | ipa-73d | no | [NAME], yveM | spsL (spsK) | rfbD(BA1231) | BA1215 | [NAME] (BH3365)/rbfC (BH3366) | OB1127 | CAC2315 | [NAME] (CPE0618) | lmo1084 | no | spsL (spsK) | 0 TM
yxeE | yxeE | GTGCCACT | 12 | ACATAAGTT | ATAAGGAATTTCA (5'RACE) | 32 | yxeE | 3.395322495857001 | 0.998819423799673 |  | 6.36795520907916 | 1 |  | 4.725968205245785 | 1 |  | 4.097556024842478 | 0.9995 |  | yxeE | unknown, probable spore coat protein, isolated from yabGD spores | 6 (No similarity) | yxeE | no | no | no | yxeE | BA3589 | BC3534 | no | no | no | no | no | no | yxeE | 0 TM
 |  |  |  |  | BioOptimizer-no prediction | no
2.2. A. 2. not tested by 5'RACE-PCR
none
2.2. B. below cut-off in sigK+ vs. sigK- experiments but identified by overexpression of sK
ykvPQ | ykvP | GTACCGCG | 12 | [NAME] | possible promoter (by visual inspection) | 46 | ykvP | 16.9010372161968 | 0.99904509200541 |  | 1.375937240588283 | 0.84 |  | 16.33789667387247 | 1 |  | 20.4434444867065 | 1 |  | ykvP | unknown, putative spore protein, cell wall binding motif | 5.1 (From B. subtilis) | ykvP | no | no | cgeB, lytF | ykvP | no | no | no (cgeB) | no | no [CAC2177 (cgeB)] | no | no | no | ykvP | 0 TM
 |  |  |  |  | BioOptimizer-no prediction | no
 | ykvQ |  |  |  |  |  | ykvQ | 2.527674029327359 | 0.99096883686359 |  | 1.518295471186137 | 0.91 |  | 2.905243962646911 | 0.9965 |  | 6.431616962816608 | 1 |  | ykvQ | similar to chitinase | 2.1.1 (Specific pathways) | ykvQ | no | no | yvbX, ydhD, yaaH | ykvQ | no | no [BC3607 (yaaH)] | no [BH2292 (yaaH)] | no [OB0024 (yaaH)] | no [CAC2747 (yaaH)] | no | no | no | ykvQ | 0 TM
2.2. C. not identified by overexpression of sK
none
2.2. D. identified neither by overexpression of sK nor in sigK+ vs. sigK-
none
2.3. Newly identified sK-controlled genes:
2.3. A. also identified by overexpression of sK
2.3. A. 1. promoter confirmed by 5'RACE-PCR
yfnHGF | yfnH | TCACCAAG | 12 | TCATATCAT | TACAGTAGATTTT (5'RACE) | 115 | yfnH | 11.27928278126801 | 0.999962487697965 |  | 1.29453843235241 | 0.76 |  | 12.96891414021938 | 0.9995 |  | 16.48518007489147 | 1 |  | yfnH | similar to glucose-1-phosphate cytidylyltransferase | 2.1.1 (Specific pathways) | yfnH | no | no | glgC, spsI, gtaB, yngB, [NAME] | yfnH | no | BC3514 | mpg (spsI/yfnH) | no | no [CAC2981 (glgC)] | no | no | no | yfnH | 0 TM
 |  | TCACC | 15 | TCATATCATTA | BioOptimizer-confirmed by 5'RACE | 113
 | yfnG |  |  |  |  |  | yfnG | 14.11143736014289 | 0.99996976130483 |  | 1.95884467350599 | 0.959 |  | 16.59563224777913 | 1 |  | 22.11515841739273 | 1 |  | yfnG | similar to CDP-glucose 4,6-dehydratase | 1.1 (Cell wall) | yfnG | no | spsJ, ytcB | galE | yfnG | no | BC3359 | no [BH3649 ([NAME])] | no [OB2082 (ytcB)] | no [CAC2334 ([NAME])] | no [rfbB (spsJ)] | no [lmo1083 (spsI)] | no | yfnG | 0 TM
 | [NAME] |  |  |  |  |  | [NAME] | 14.44381691589268 | 0.999974302911222 |  | 2.137962089502232 | 0.971 |  | 9.11202012038511 | 1 |  | 11.02289176609522 | 1 |  | [NAME] | unknown | 5.1 (From B. subtilis) | [NAME] | no | yfnD | no | [NAME] | no | BC3515 | no | no | no | no | no | no | [NAME] | 0 TM
ylbDE | ylbD | GAACACAA | 12 | CGATACATT | GTAGTAGGTACC (5' RACE) | 35 | ylbD | 2.239898568602344 | 0.99032463808709 |  | 5.508076964054035 | 0.986 |  | 2.251217147806942 | 0.994 |  | 1.287453274046055 | 0.8505 |  | ylbD | unknown | 5.1 (From B. subtilis) | ylbD | no | no | no | ylbD | BA4146 | BC3936 | BH2601 | OB1446 | no | no | no | no | ylbD | 0 TM
 |  |  |  |  | BioOptimizer-no prediction | no
 | ylbE |  |  |  |  |  | ylbE | 1.934937898522891 | 0.935358742556953 |  | 4.528975799036209 | 0.991 |  | 2.372577988955975 | 0.988 |  | 1.29852422931643 | 0.826 |  | ylbE | unknown | 5.1 (From B. subtilis) | ylbE | no | no | no | ylbE | BA4145 | BC3935 | BH2600 | OB1447 | no | no | no | no | ylbE | 0 TM
yodHI | yodH | AAACCTAT | 11 | ACATATGAT | AAGGAAAAAGGAGGAT (5'RACE) | 21 | yodH | 3.624221961667014 | 0.99852216322527 |  | 7.906786279998252 | 0.998 |  | 1.676893830150808 | 0.971 |  | 1.824842917985766 | 0.9595 |  | yodH | unknown, similar to methyltransferase | 5.1 (From B. subtilis) | yodH | no | no | no | yodH | BA3641 | BC3583 | BH0821 | no [OB0353 (ycqJ)] | no | no | no | no | yodH | 1 TM (Nter)
 |  | AAACC | 14 | ACATATGATAA | BioOptimizer-confirmed by 5'RACE | 19
 | yodI |  |  |  |  |  | yodI | 1.184266497277666 | 0.777229019824135 |  | 5.847900841444809 | 0.999 |  | 2.169858035650843 | 0.994 |  | 2.844655738449092 | 0.999 |  | yodI | unknown (SAM binding motif) | 6 (No similarity) | yodI | no | no | no | yodI | BA3640 | BC3582 | no | no | no | no | no | no | yodI | 1 TM (Cter)
yodJ (not included in final total) | yodJ | downstream of yodI (convergent), antisense? |  |  |  |  | yodJ | 0.3927442516993018 | 0.00424808817649336 |  |  |  |  | 1.515550627422556 | 0.887 |  | 3.335263456399615 | 0.9985 |  | yodJ |  |  | yodJ |  |  |  | yodJ |  |  |  |  |  |  |  |  | yodJ
2.3. A. 2. not tested by 5'RACE-PCR
yoaI | yoaI | GAACATTG | 12 | TCATGGAAT | preferred predicted promoter | 22 | yoaI | 1.991846934831377 | 0.967121473835035 |  | 2.113489039836647 | 0.977 |  | 3.914863816051634 | 0.9915 |  | 4.680260594930855 | 0.9985 |  | yoaI | similar to 4-hydroxyphenylacetate-3-hydroxylase | 2.1.1 (Specific pathways) | yoaI | no | no | no | yoaI | no | no | BH3836 | OB2872 | no | no | no | no | yoaI | 0-1 TM (mid)
 |  | GAACA | 15 | TCATGGAATGA | BioOptimizer-1st prediction | 22
 |  | AAACA | 14 | ACATGAAATGA | BioOptimizer-2nd prediction | 144
2.3. B. below cut-off in sigK+ vs. sigK- experiments but identified by overexpression of sK
cotQ-yvdQ | cotQ (yvdP) | ATGCGATT | 11 | GCATATTTT | possible promoter (by visual inspection) | 38 | cotQ (yvdP) | 2.484533371682824 | 0.989760857168152 |  | 1.310412912994815 | 0.79 |  | 7.241456289203211 | 1 |  | 8.323607095203025 | 1 |  | cotQ (yvdP) | coat protein-similar to reticuline oxidase, renamed cotQ | 4.2 (Detoxification) | cotQ (yvdP) | yvdP | ygaK | no | cotQ (yvdP) | no | no [BC0412 (ygaK)] | no [BH2730 (ysfC)] | no [OB1259 (ysfC)] | no [CAC2542 (ysfC)] | CPE0406 | no | no | cotQ (yvdP) | 1 TM (mid)
 |  | TCACC | 16 | GCGTATTATAT | BioOptimizer-prediction
 | yvdQ |  |  |  |  |  | yvdQ | 2.704041026962285 | 0.980048716966305 |  | 1.08 | 0.62 |  | 1.601206972860469 | 0.951 |  | 2.291858215876467 | 0.9895 |  | yvdQ | unknown | 5.1 (From B. subtilis) | yvdQ | no | no | no | yvdQ | BA3129 | BC3090 | BH2358 | OB1707 | no | no | no | no | yvdQ | 0 TM
cotR | cotR (yvdO) | ATACAACA | 12 | TCATATACT | possible promoter (by visual inspection) | 28 | cotR (yvdO) | 3.449669919738042 | 0.992411764854275 |  | 0.9261273479116474 | 0.4 |  | 11.53934002008858 | 0.9995 |  | 18.35245370244922 | 1 |  | cotR (yvdO) | coat protein, renamed cotR | 5.2 (From other organisms) | cotR (yvdO) | no | no | no | cotR (yvdO) | no | no | no | no | no | no | no | no | cotR (yvdO) | 1-2 TMs
 |  |  |  |  | not included in BioOptimizer list of sequences | no
kapD | kapD | AAACGAAG | 13 | TCATTATTT | possible promoter (by visual inspection) | 85 | kapD | 2.834217978970114 | 0.976279050909615 |  | 1 | 0.52 |  | 2.132502206690662 | 0.99 |  | 3.835769407182839 | 0.9985 |  | kapD | inhibition of the KinA pathway to sporulation (exonuclease?) | 1.8 (Sporulation) | kapD | yugB | no | no | kapD | kapD (BA5142) | BC4910 | no | no | no [polC (CAC3442)] | no [polC (CPE1691)] | no | no | kapD | 0 TM
 |  |  |  |  | not included in BioOptimizer list of sequences | no
kapB not included in final total | kapB | downstream of kapD (convergent), antisense? |  |  |  |  | kapB | 0.6739136070933875 | 0.062758583613747 |  | 1.1 | 0.56 |  | 1.239440963347513 | 0.793 |  | 1.94617551657321 | 0.9945 |  | kapB |  |  | kapB |  |  |  | kapB |  |  |  |  |  |  |  |  | kapB
kinB not included in final total | kinB |  |  |  |  |  | kinB | 0.5878723459461445 | 0.0308537570537528 |  | 0.9 | 0.42 |  | 1.340378404566241 | 0.8375 |  | 2.156464888618014 | 0.991 |  | kinB |  |  | kinB |  |  |  | kinB |  |  |  |  |  |  |  |  | kinB
yclG | yclG | GTTCCATA | 12 | AAATACCTA | possible promoter (by visual inspection) | 158 | yclG | 2.434742264382272 | 0.970908697861605 |  | 0.8 | 0.26 |  | 2.674058606617132 | 0.985 |  | 7.610059473288409 | 1 |  | yclG | unknown | 6 (No similarity) | yclG | no | yorA | yomE | yclG | no | no | no | no | no | no | no | no | yclG | 1 TM (Cter)
 |  |  |  |  | BioOptimizer-no prediction | no
ythC | ythC | AAACGCTA | 12 | GAATAGAGG | possible promoter (by visual inspection) | 45 | ythC | 4.072129480453687 | 0.999275275968796 |  | 0.8647310832770129 | 0.2955 |  | 3.323243142056689 | 0.9995 |  | 5.703647805881546 | 0.9995 |  | ythC | unknown | 6 (No similarity) | ythC | no | no | no | ythC | no | no | no | no | no | no | no | no | ythC | 0-1 TM (mid)
 |  |  |  |  | BioOptimizer-no prediction | no
yycOPQ | yycO | TTACTTTC | 12 | ATATAATGT | possible promoter (by visual inspection) | 48 | yycO | 1.456606869727523 | 0.924207850205738 |  | 1.105892699962818 | 0.64 |  | 2.238993630995336 | 0.9935 |  | 2.606228375336066 | 0.997 |  | yycO | unknown | 5.2 (From other organisms) | yycO | no | no | no | yycO | no | no | no | no | CAC0029 | no | no | no | yycO | 1 TM (Nter)
 |  |  |  |  | not included in BioOptimizer list of sequences | no
 | yycP |  |  |  |  |  | yycP | 2.912551473973582 | 0.956885156799303 |  | 1.353088255575303 | 0.83 |  | 1.989431641593378 | 0.984 |  | 2.127534081077871 | 0.9925 |  | yycP | unknown | 5.2 (From other organisms) | yycP | no | no | no | yycP | no | no | BH3844 | no | no | no | no | no | yycP | secreted
 | yycQ |  |  |  |  |  | yycQ | 1.115236237103127 | 0.687849439641421 |  | 1.138091154913421 | 0.68 |  | 2.610162644182488 | 0.9865 |  | 2.950465927028123 | 0.999 |  | yycQ | unknown | 6 (No similarity) | yycQ |  |  |  | yycQ | no | no | no | no | no | no | no | no | yycQ | 2-3 TMs
2.3. C. not identified by overexpression of sK , but identified in sigK+ vs. sigK- experiment
cotI-ytaB | cotI (ytaA) | AATCATTT | 12 | TCATAAGGT | possible promoter (by visual inspection) | 19 | cotI (ytaA) | 0.7831315357743351 | 0.142630569349394 |  | 2.050695317775173 | 0.95 |  | 15.52097492201263 | 1 |  | 15.97315500581148 | 1 |  | cotI (ytaA) | similar to spore coat protein, renamed cotI | 1.8 (Sporulation) | cotI (ytaA) | ytaA | cotS | yutH | cotI (ytaA) | no | no [BC4954 (yutH)] | BH2306 | no [OB2358 (yutH)] | CAC2906 (cotI/cotS) | CPE2218 (cotS/cotI) | no | no | cotI (ytaA) | 0 TM
 |  |  |  |  | not included in BioOptimizer list of sequences | no
 | ytaB |  |  |  |  |  | ytaB | 1.065732000118119 | 0.597410649349054 |  | 0.8228312965430776 | 0.24 |  | 3.32243426736443 | 0.9985 |  | 5.351071538493173 | 0.9995 |  | ytaB | unknown | 6 (No similarity) | ytaB | no | no | no | ytaB | no | BC3136 | no | no | CA0262 | CPE1985 | no | no | ytaB | 5 TMs
yojBC | yojB | AATCGTTT | 12 | GAATACTTT | possible promoter (by visual inspection) | 32 | yojB | 0.6376302241619314 | 0.124553982983493 |  | 2.606153549998896 | 0.991 |  | 4.10103762125995 | 0.9995 |  | 2.143654664760358 | 0.9885 |  | yojB | unknown | 5.1 (From B. subtilis) | yojB | no | no | no | yojB | no | no | no | no | no | no | no | no | yojB | 2 TMs
 |  |  |  |  | not included in BioOptimizer list of sequences | no
 | yojC |  |  |  |  |  | yojC | 0.4952446459338871 | 0.047682071140994 |  | 4.295364267648873 | 0.995 |  | 1.276127268434816 | 0.7175 |  | 0.8561965921607356 | 0.282 |  | yojC | unknown | 5.1 (From B. subtilis) | yojC | no | no | no | yojC | no | no | no | no | no | no | no | no | yojC | 0 TM
yunC-yunB | [NAME] | CAACAAGC | 11 | TCATAAAGT | possible promoter (by visual inspection) | 23 | [NAME] | 1.71289105486645 | 0.969668381079048 |  | 3.019951720402017 | 0.99 |  | 3.745628432809792 | 0.994 |  | 3.185865618316047 | 0.9975 |  | [NAME] | unknown | 5.1 (From B. subtilis) | [NAME] | no | no | no | [NAME] | BA5208 | BC4976 | BH3452 | OB2372 | no | no | no | no | [NAME] | 0 TM
 |  |  |  |  | not included in BioOptimizer list of sequences | no
 | yunB | TTACTATG | 13 | GCATACATT | possible promoter (by visual inspection) | 23 | yunB | 1.509630882393203 | 0.945368285479956 |  | 1.323046592308434 | 0.7965 |  | 2.276862426980153 | 0.9945 |  | 1.746735167616536 | 0.9845 |  | yunB | sporulation-inactivation results in delayed sK activation | 5.2 (From other organisms) | yunB | no | no | no | yunB | BA5207 | BC4975 | BH1036 | OB2370 | CAC2300 | CPE1961 | no | no | yunB | secreted-pred
 |  |  |  |  | not included in BioOptimizer list of sequences | no
2.3. D. not identified by overexpression of sK and not identified in sigK+ vs. sigK- experiment (either [NAME] is essential for expression or indirect targets)
2.3. D. 1. identified at T5.5 and T6.5
2.3.D.1. 1. ratio in gerE mutant experiment is high (>5)
aprX | aprX | TTACCAAA | 13 | TCATAGAGT | possible promoter (by visual inspection) | 32 | aprX | 0.9603117034021333 | 0.442520537904885 |  | 0.8906581444012822 | 0.34 |  | 21.90212485841261 | 0.9985 |  | 11.34423097368581 | 1 |  | aprX | intracellular alkaline serine protease | 2.2 (Metabolism of amino acids and related molecules) | aprX | no | aprE, epr, bpr, ispA, vpr, wprA |  | aprX | no | no [BC2316 (aprE)] | aprX (BH1930) | OB2375 | [NAME] | aprX (CPE2610) | no | no | aprX | 1-2 TMs
 |  |  |  |  | not included in BioOptimizer list of sequences | no
ppiB | ppiB | no promoter found |  |  |  |  | ppiB | 0.5553114796791268 | 0.0176343652170563 |  | 1 | 0.47 |  | 1.817335353185238 | 0.9745 |  | 5.256014185062785 | 0.99 |  | ppiB | peptidyl-prolyl isomerase (EC 5.2.1.8) | 3.8 (Protein modification) | ppiB | cypBS | no | no | ppiB | BA4283 | BC4061 | BH1545 | ppiB (OB1832) | CAC2769 | CPE2566 | lmo2376 | lin2475 | ppiB | 0 TM
 |  |  |  |  | not included in BioOptimizer list of sequences | no
thyA | thyA | TTGCGATA | 12 | TAATAAATT | possible promoter (by visual inspection) | 40 | thyA | 1.207589079212744 | 0.749759147661663 |  | 1.317331462099345 | 0.794 |  | 8.63953677699754 | 0.9995 |  | 8.439349358663094 | 0.9995 |  | thyA | thymidylate synthase A (EC 2.1.1.45) | 2.3 (Metabolism of nucleotides and nucleic acids) | thyA | no | thyB | no | thyA | thyA (BA2236) | no [BC2191 (thyB)] | no [BH3451 (thyB)] | no [OB1740 (thyB)] | CAC3003 | no | no [lmo1874 (thyB)] | no [lin1988 (thyB)] | thyA | 0 TM
 |  |  |  |  | not included in BioOptimizer list of sequences | no
ygaK | ygaK | GGACTATA | 13 | CAATATTAA | possible promoter (by visual inspection) | 175 | ygaK | 1.238953897292509 | 0.71503637316356 |  | 0.7161421925444392 | 0.12 |  | 3.933790145153707 | 0.9985 |  | 12.95580919042505 | 1 |  | ygaK | similar to reticuline oxidase-similar to coat protein cotQ | 2.1.1 (Specific pathways) | ygaK | no | yvdP | no | ygaK | no | BC0412 | no | no | no | no [CPE0406 (cotQ)] | no | no | ygaK | 2 TMs
 |  |  |  |  | not included in BioOptimizer list of sequences | no
yhcJ | yhcJ | CCTTCATT | 13 | TAATAGGAA | possible promoter (by visual inspection) | 140 | yhcJ | 1.451910383610884 | 0.911678322379514 |  | 0.747230807701117 | 0.199 |  | 2.472873462463036 | 0.9955 |  | 4.271685122032483 | 0.999 |  | yhcJ | similar to ABC transporter (binding lipoprotein) | 1.2 (Transport/binding proteins and lipoproteins) | yhcJ | no | yusA | no | yhcJ | BA0314 (yusA/yhcJ) | BC0348 (yhcJ/yusA) | no [BH3479 (yusA)] | OB3165 | no [[NAME] (yusA)] | no | no [lmo0285 (yusA)] | no [lin0313 (yusA)] | yhcJ | 1 TM (Nter)
 |  | TGACA | 14 | GAGTAAGGTAA | BioOptimizer-unlikely | no
yjaU | yjaU | ATTCGTTT | 11 | ACATAAGAT | possible promoter (by visual inspection) | 36 | yjaU | 1.584395118003593 | 0.94158296605197 |  | 1.272154948161562 | 0.79 |  | 5.148711490983786 | 0.999 |  | 7.915856521403453 | 1 |  | yjaU | unknown | 5.1 (From B. subtilis) | yjaU | no | no | no | yjaU | BA1180 | BC1170 | BH2892 | no | no | no | no | no | yjaU | 0 TM
 |  |  |  |  | not included in BioOptimizer list of sequences | no
ymaG | ymaG | GTTCTCTC | 11 | TGATAAGCA | possible promoter (by visual inspection) | 48 | ymaG | 0.7126647791937437 | 0.324693038204495 |  | 1.27309131863115 | 0.78 |  | 5.118550163418451 | 0.9995 |  | 5.037607549741161 | 0.999 |  | ymaG | similar to cell wall protein | 1.1 (Cell wall) | ymaG | no | no | no | ymaG | no | no | no | no | no | no | no | no | ymaG | 1 TM (mid)
 |  | wrong translation start site |  |  | BioOptimizer-no prediction | no
yodN-yozD | yodN | ATGCGAAT | 12 | GCATACGAT | possible promoter (by visual inspection) | 36 | yodN | 1.071388091331387 | 0.588415799071687 |  | 2.305452309107147 | 0.89 |  | 33.44181946102115 | 0.9865 |  | 7.487172409886426 | 1 |  | yodN | unknown | 6 (No similarity) | yodN | no | no | no | yodN | BA2303 | BC2254 | no | no | no | no | no | no | yodN | 1 TM (Nter)
 |  |  |  |  | not included in BioOptimizer list of sequences | no
 | yozD |  |  |  |  |  | yozD | 1.296793167819626 | 0.863103220287436 |  | 0.7 | 0.128 |  |  |  |  | 5.211509873952127 | 0.998 |  | yozD | unknown | 6 (No similarity) | yozD | no | no | no | yozD | BA2305 | BC2256 | no | no | no | no | no | no | yozD | 0 TM
yodU-ypqP | yodU | ATTCGATT | 10 | ACATATGAT | possible promoter (by visual inspection) | 34 | yodU | 0.6185314860951384 | 0.254995526304939 |  | 1.087735204808204 | 0.61 |  | 6.814643460360633 | 0.999 |  | 12.39420917008022 | 1 |  | yodU | putative UDP-Glc isomerase | 4.1 (Adaptation to atypical conditions) | yodU | no | no | yveM (Nter), spsJ, ytcB | yodU | no | no [BC3750 (yveM)] | no [BH3718 (yveM)] | no [OB2896 (yveM)] | no [CAC2194 (yveM)] | no [[NAME] (yveM)] | no | no | yodU | 0-1 TM
 | ypqP | interrupted by SPb in 168, should be next to yodU in PY79 |  |  |  |  | ypqP | 0.8501033861028638 | 0.25148503785802 |  | 1.1 | 0.67 |  | 8.640011394077936 | 0.9985 |  | 14.46113498569673 | 1 |  | ypqP | putative glucosyl-1-P transferase; this ORF is interrupted by insertion of the SPb prophage in strain 168 | 4.1 (Adaptation to atypical conditions) | ypqP | no | yveM (Cter) | no | ypqP | no | no [BC3750 (yveM)] | no [BH3718 (yveM)] | no [OB2896 (yveM)] | no [CAC2194 (yveM)] | no [[NAME] (yveM)] | no | no | ypqP | 0 TM
yubC | yubC | CCTCTAAA | 12 | AAATACCAT | possible promoter (by visual inspection) | 42 | yubC | 1.430825856630935 | 0.838430940049683 |  | 0.9644826946100133 | 0.467 |  | 10.4657223982757 | 1 |  | 9.566690071288015 | 1 |  | yubC | similar to cysteine dioxygenase | 2.2 (Metabolism of amino acids and related molecules) | yubC | no | no | no | yubC | no | no | no | no | no | no | no | no | yubC | 0 TM
 |  |  |  |  | not included in BioOptimizer list of sequences | no
ywhKL | ywhK | AAGCAAAC | 11 | CCATATTCT | possible promoter (by visual inspection) | 45 | ywhK | 0.61327125440635 | 0.0416384541163753 |  | 0.64 | 0.09 |  | 1.843271234192311 | 0.9715 |  | 6.580478387059552 | 0.9995 |  | ywhK | unknown | 5.2 (From other organisms) | ywhK | no | ywhL | no | ywhK | no | no | no | no | no | no | no | no | ywhK | 2 TMs
 |  |  |  |  | not included in BioOptimizer list of sequences | no
 | ywhL |  |  |  |  |  | ywhL | 0.9098542319737799 | 0.424940324868993 |  | 0.57 | 0.08 |  | 1.130284102223568 | 0.6115 |  | 4.268202411422102 | 0.999 |  | ywhL | unknown | 5.2 (From other organisms) | ywhL | no | ywhK | no | ywhL | no | no | no | no | no | no | no | no | ywhL | 2-3 TMs
albG (ywhM) (not included in final total) | albG (ywhM) | downstream of ywhKL (convergent), antisense? |  |  |  |  | albG (ywhM) | 1.235808948283512 | 0.81758529184186 |  | 0.67 | 0.18 |  | 1.340525380180053 | 0.8385 |  | 2.503033283881136 | 0.9685 |  | albG (ywhM) |  |  | albG (ywhM) |  |  |  | albG (ywhM) |  |  |  |  |  |  |  |  | albG (ywhM)
yxkD | yxkD | GGACTGTG | 13 | ACATAGCAG | possible promoter (by visual inspection) | 116 | yxkD | 1.484743872746318 | 0.942597608773043 |  | 0.707062005260252 | 0.13 |  | 2.329252687387243 | 0.99 |  | 5.40382654150459 | 1 |  | yxkD | unknown | 5.2 (From other organisms) | yxkD | no | yqfU, ypjC, yvjA, yitT, ydeO | yitE | yxkD | BA3266 | BC3229 | no [BH1678 (ypjC)] | OB0982 | no [CAC0848 (yjvA)] | no [CPE0298 (yjvA)] | lmo1252 | lin1219 | yxkD | 5 TMs
 |  |  |  |  | not included in BioOptimizer list of sequences | no
GENES IN SECTIONS 2.3.D.1. 2. and 2.3.D.2 ARE NOT INCLUDED IN THE FINAL TOTAL OF SIGK-CONTROLLED GENES
2.3.D.1.2. ratio in gerE mutant experiment is low (thus considered to be an indirect target and not included in final list)
cdd-era-recO | cdd | no promoter found, probably indirect |  |  |  |  | cdd | 1.334063966061935 | 0.88811891207354 |  | 1 | 0.47 |  | 1.820598139979313 | 0.979 |  | 2.326889644663748 | 0.996 |  | cdd |  |  | cdd |  |  |  | cdd |  |  |  |  |  |  |  |  | cdd
 | era (bex) |  |  |  |  |  | era (bex) | 1.42280094763913 | 0.925542940034105 |  | 0.97 | 0.47 |  | 1.651286378646936 | 0.9635 |  | 2.112236851490533 | 0.994 |  | era (bex) |  |  | era (bex) |  |  |  | era (bex) |  |  |  |  |  |  |  |  | era (bex)
 | recO (yqxN) |  |  |  |  |  | recO (yqxN) | 1.72865097510562 | 0.976742670191484 |  | 0.98 | 0.46 |  | 1.448427083597475 | 0.9145 |  | 1.859793535401559 | 0.983 |  | recO (yqxN) |  |  | recO (yqxN) |  |  |  | recO (yqxN) |  |  |  |  |  |  |  |  | recO (yqxN)
[NAME] | hisZ | no promoter found, probably indirect |  |  |  |  | hisZ | 1.44018214494768 | 0.928196669355333 |  | 0.7 | 0.14 |  | 3.560850537637837 | 0.9955 |  | 3.024225787833385 | 0.9915 |  | hisZ |  |  | hisZ |  |  |  | hisZ |  |  |  |  |  |  |  |  | hisZ
 | [NAME] |  |  |  |  |  | [NAME] | 1.948512052414788 | 0.976018505890715 |  | 0.7 | 0.08 |  | 2.619250248203717 | 0.9985 |  | 4.20129647076975 | 1 |  | [NAME] |  |  | [NAME] |  |  |  | [NAME] |  |  |  |  |  |  |  |  | [NAME]
 | [NAME] |  |  |  |  |  | [NAME] | 1.718310196838801 | 0.960978253153696 |  | 0.7 | 0.14 |  | 3.195958431207169 | 0.9975 |  | 3.6865178844217 | 0.996 |  | [NAME] |  |  | [NAME] |  |  |  | [NAME] |  |  |  |  |  |  |  |  | [NAME]
 | hisB |  |  |  |  |  | hisB | 1.311365883779729 | 0.850053527159105 |  | 0.7 | 0.13 |  | 3.502318981878282 | 0.9995 |  | 2.872495670457138 | 0.997 |  | hisB |  |  | hisB |  |  |  | hisB |  |  |  |  |  |  |  |  | hisB
 | [NAME] |  |  |  |  |  | [NAME] | 1.141998765380742 | 0.721496624505341 |  | 0.8 | 0.18 |  | 3.70814855601131 | 0.992 |  | 5.453303554153288 | 1 |  | [NAME] |  |  | [NAME] |  |  |  | [NAME] |  |  |  |  |  |  |  |  | [NAME]
 | [NAME] |  |  |  |  |  | [NAME] | 1.061337777540924 | 0.608148920656578 |  | 0.7 | 0.12 |  | 3.868789954056808 | 0.998 |  | 5.054031456371916 | 0.9995 |  | [NAME] |  |  | [NAME] |  |  |  | [NAME] |  |  |  |  |  |  |  |  | [NAME]
 | hisF |  |  |  |  |  | hisF | 0.8224923842669752 | 0.215017113316961 |  | 0.7 | 0.13 |  | 3.067071563450405 | 0.9985 |  | 3.628070614538188 | 1 |  | hisF |  |  | hisF |  |  |  | hisF |  |  |  |  |  |  |  |  | hisF
yeeK | yeeK | ATACGATC | 12 | TCATACTCT | possible promoter (by visual inspection) | 32 | yeeK | 0.8785090321026862 | 0.278399770136818 |  | 0.797520308879765 | 0.24 |  | 2.734711574617403 | 0.995 |  | 2.690923060306441 | 0.9975 |  | yeeK |  |  | yeeK |  |  |  | yeeK |  |  |  |  |  |  |  |  | yeeK
yhcN | yhcN | false positive? |  |  | sigG and sigF, lacZ fusion expression is sigK independent |  | yhcN | 1.29099672894719 | 0.828539362584957 |  | 1.1 | 0.59 |  | 2.143859864780127 | 0.983 |  | 3.179329905174105 | 0.9895 |  | yhcN |  |  | yhcN |  |  |  | yhcN |  |  |  |  |  |  |  |  | yhcN
yhfC | yhfC | [NAME] | 12 | ACATATGAA | possible promoter (by visual inspection) | 120 | yhfC | 1.078619366461479 | 0.632598409155434 |  | 0.9 | 0.37 |  | 1.858940408355185 | 0.9645 |  | 3.795936866929888 | 0.9995 |  | yhfC |  |  | yhfC |  |  |  | yhfC |  |  |  |  |  |  |  |  | yhfC
yktC | yktC | no promoter found, probably indirect |  |  |  |  | yktC | 0.456442168835356 | 0.0095138539710431 |  | 0.89 | 0.34 |  | 1.851965265628587 | 0.9815 |  | 2.418101652781635 | 0.996 |  | yktC |  |  | yktC |  |  |  | yktC |  |  |  |  |  |  |  |  | yktC
yoaJ | yoaJ | GTTCATTT | 13 | TCATAAGTA | possible promoter (by visual inspection) | 136 | yoaJ | 0.8619223071215919 | 0.277888519045558 |  | 0.8200899652239928 | 0.26 |  | 1.830868544365302 | 0.973 |  | 2.545378877466292 | 0.999 |  | yoaJ |  |  | yoaJ |  |  |  | yoaJ |  |  |  |  |  |  |  |  | yoaJ
yusV | yusV | CTACAATG | 12 | CCATATCAA | possible promoter (by visual inspection) | 109 | yusV | 0.7811121520788789 | 0.140402516944023 |  | 0.9531095739264165 | 0.44 |  | 2.235042482048983 | 0.9895 |  | 2.173498822367288 | 0.9895 |  | yusV |  |  | yusV |  |  |  | yusV |  |  |  |  |  |  |  |  | yusV
yuxJ-pbpD | yuxJ | no promoter found, probably indirect |  |  | divergent from kapD |  | yuxJ | 1.289167995417591 | 0.84893814041169 |  | 1.4 | 0.88 |  | 1.817902072311116 | 0.967 |  | 2.738329373851038 | 0.9975 |  | yuxJ |  |  | yuxJ |  |  |  | yuxJ |  |  |  |  |  |  |  |  | yuxJ
 | pbpD |  |  |  |  |  | pbpD | 0.9608053138694228 | 0.427847615930308 |  | 1.2 | 0.72 |  | 1.007772332523842 | 0.512 |  | 2.046975363439223 | 0.9945 |  | pbpD |  |  | pbpD |  |  |  | pbpD |  |  |  |  |  |  |  |  | pbpD
2.3. D. 2. identified at only one of the two time points and ratios are low (probaly indirect, not included in final list)
ccdA | ccdA |  |  |  |  |  | ccdA | 0.9985799125851275 | 0.498750881901908 |  | 0.8534267327444592 | 0.294 |  | 1.297168691599996 | 0.8435 |  | 2.449046810405985 | 0.9925 |  | ccdA |  |  | ccdA |  |  |  | ccdA |  |  |  |  |  |  |  |  | ccdA
comFA | comFA | GGACAGAA | 13 | GCATACTGT | possible promoter (by visual inspection) | 20 | comFA | 0.7194665076903942 | 0.103176911765647 |  | 0.8 | 0.21 |  | 0.7338601313923223 | 0.1195 |  | 1.667827461713165 | 0.947 |  | comFA |  |  | comFA |  |  |  | comFA |  |  |  |  |  |  |  |  | comFA
deoD | deoD | no promoter found, probably indirect |  |  |  |  | deoD | 0.5120252297231582 | 0.0141281857507749 |  | 1.1 | 0.59 |  | 1.67061664227916 | 0.9615 |  | 2.657551153804401 | 0.9995 |  | deoD |  |  | deoD |  |  |  | deoD |  |  |  |  |  |  |  |  | deoD
pksL | pksL | no promoter found, probably indirect |  |  |  |  | pksL | 1.973056600614678 | 0.98396584270339 |  | 1.177534400521913 | 0.718 |  | 0.5568472894495344 | 0.1125 |  | 2.419356909528531 | 0.958 |  | pksL |  |  | pksL |  |  |  | pksL |  |  |  |  |  |  |  |  | pksL
purEKBCSQLFMNHD | purE | no promoter found, probably indirect |  |  |  |  | purE | 0.9437908114227753 | 0.395786467484533 |  | 1.1 | 0.58 |  |  |  |  | 2.842428966297068 | 0.9965 |  | purE |  |  | purE |  |  |  | purE |  |  |  |  |  |  |  |  | purE
 | purK |  |  |  |  |  | purK | 1.232848633796502 | 0.819549927179185 |  | 1 | 0.54 |  | 0.9555990734606997 | 0.427 |  | 2.509138165039972 | 0.9945 |  | purK |  |  | purK |  |  |  | purK |  |  |  |  |  |  |  |  | purK
 | purB |  |  |  |  |  | purB | 1.869586573506669 | 0.98391609435612 |  | 1.1 | 0.56 |  |  |  |  | 2.347415274254211 | 0.9605 |  | purB |  |  | purB |  |  |  | purB |  |  |  |  |  |  |  |  | purB
 | purC |  |  |  |  |  | purC | 1.818172888716584 | 0.982205025646993 |  | 1 | 0.5 |  | 0.9831663367789926 | 0.4765 |  | 2.348979051627496 | 0.9885 |  | purC |  |  | purC |  |  |  | purC |  |  |  |  |  |  |  |  | purC
 | purS (yexA) |  |  |  |  |  | purS (yexA) | 1.598756720087471 | 0.96463332961543 |  | 0.8879688399159401 | 0.3515 |  | 0.9638274316774668 | 0.4395 |  | 2.384313117584715 | 0.9945 |  | purS (yexA) |  |  | purS (yexA) |  |  |  | purS (yexA) |  |  |  |  |  |  |  |  | purS (yexA)
 | purQ |  |  |  |  |  | purQ | 2.81914555292141 | 0.998068328222612 |  | 1 | 0.54 |  | 0.9433217161250146 | 0.42 |  | 2.368179269262572 | 0.987 |  | purQ |  |  | purQ |  |  |  | purQ |  |  |  |  |  |  |  |  | purQ
 | purL |  |  |  |  |  | purL | 1.672542562335833 | 0.973330431865902 |  | 0.9 | 0.38 |  | 0.9714831261275008 | 0.4495 |  | 2.262554812875706 | 0.988 |  | purL |  |  | purL |  |  |  | purL |  |  |  |  |  |  |  |  | purL
 | purF |  |  |  |  |  | purF | 3.356129596000208 | 0.998867299116648 |  | 1 | 0.51 |  |  |  |  | 2.816917876166694 | 0.9625 |  | purF |  |  | purF |  |  |  | purF |  |  |  |  |  |  |  |  | purF
 | purH |  |  |  |  |  | purH | 2.020822764746162 | 0.982601397038747 |  | 0.9 | 0.4 |  | 1.126082537173055 | 0.683 |  | 2.037973092749988 | 0.977 |  | purH |  |  | purH |  |  |  | purH |  |  |  |  |  |  |  |  | purH
 | purD |  |  |  |  |  | purD | 1.428944471410474 | 0.92637261598101 |  | 0.8480539116570099 | 0.2875 |  | 1.008615079820088 | 0.5155 |  | 2.870158741161263 | 0.978 |  | purD |  |  | purD |  |  |  | purD |  |  |  |  |  |  |  |  | purD
pyrRPBC-AA-AB-KDFE | pyrR | no promoter found, probably indirect |  |  |  |  | pyrR | 0.7272535559435902 | 0.0999659217259669 |  | 1.493874212407876 | 0.8905 |  | 1.042838778258411 | 0.57 |  | 1.662660210644298 | 0.939 |  | pyrR |  |  | pyrR |  |  |  | pyrR |  |  |  |  |  |  |  |  | pyrR
 | pyrP |  |  |  |  |  | pyrP | 1.238432589196133 | 0.822148970982854 |  | 1.234257223020634 | 0.7675 |  | 0.9404589470235265 | 0.391 |  | 1.829999288344508 | 0.9165 |  | pyrP |  |  | pyrP |  |  |  | pyrP |  |  |  |  |  |  |  |  | pyrP
 | pyrB |  |  |  |  |  | pyrB | 0.802790741395168 | 0.169619262628617 |  | 1.303422371223326 | 0.8055 |  | 0.946180729608781 | 0.4065 |  | 2.079590555573658 | 0.9315 |  | pyrB |  |  | pyrB |  |  |  | pyrB |  |  |  |  |  |  |  |  | pyrB
 | pyrC |  |  |  |  |  | pyrC | 0.8020133925658789 | 0.183356753247702 |  | 1.302822604215475 | 0.827 |  | 1.030837232787766 | 0.549 |  | 1.588688510489074 | 0.85 |  | pyrC |  |  | pyrC |  |  |  | pyrC |  |  |  |  |  |  |  |  | pyrC
 | pyrAA |  |  |  |  |  | pyrAA | 0.8136101066230235 | 0.180414703865034 |  | 1.211095086793912 | 0.74 |  | 1.123991041337187 | 0.6595 |  | 2.097484840168863 | 0.953 |  | pyrAA |  |  | pyrAA |  |  |  | pyrAA |  |  |  |  |  |  |  |  | pyrAA
 | pyrAB |  |  |  |  |  | pyrAB | 0.9758879990272565 | 0.458031343554889 |  | 0.9679898712547051 | 0.4525 |  | 1.144102644037397 | 0.711 |  | 1.435218304311274 | 0.9125 |  | pyrAB |  |  | pyrAB |  |  |  | pyrAB |  |  |  |  |  |  |  |  | pyrAB
 | [NAME] |  |  |  |  |  | [NAME] |  |  |  | 1.109943005688452 | 0.6485 |  | 1.019542309049569 | 0.535 |  | 1.626189327045766 | 0.8755 |  | [NAME] |  |  | [NAME] |  |  |  | [NAME] |  |  |  |  |  |  |  |  | [NAME]
 | pyrD |  |  |  |  |  | pyrD | 0.9157836591808645 | 0.345020174042051 |  | 1.032130204251604 | 0.5545 |  | 1.022707290074098 | 0.525 |  | 1.815623755812726 | 0.9525 |  | pyrD |  |  | pyrD |  |  |  | pyrD |  |  |  |  |  |  |  |  | pyrD
 | pyrF |  |  |  |  |  | pyrF | 0.7076408384859924 | 0.0770517418253533 |  | 1.07706327529695 | 0.604 |  | 0.9964166966808954 | 0.494 |  | 1.416881863634663 | 0.7405 |  | pyrF |  |  | pyrF |  |  |  | pyrF |  |  |  |  |  |  |  |  | pyrF
 | pyrE |  |  |  |  |  | pyrE | 0.6145426944355243 | 0.0374354662132871 |  | 1.009386566522808 | 0.516 |  | 1.156252325367765 | 0.693 |  | 1.625561688388732 | 0.9315 |  | pyrE |  |  | pyrE |  |  |  | pyrE |  |  |  |  |  |  |  |  | pyrE
rok (ykuW) | rok (ykuW) | no promoter found, probably indirect |  |  |  |  | rok (ykuW) | 0.6032254458378097 | 0.0291188134183593 |  | 1.1 | 0.67 |  | 1.166121307813001 | 0.709 |  | 2.403470552419675 | 0.995 |  | rok (ykuW) |  |  | rok (ykuW) |  |  |  | rok (ykuW) |  |  |  |  |  |  |  |  | rok (ykuW)
rplJ | rplJ |  |  |  |  |  | rplJ | 1.947401827933326 | 0.985854624588023 |  | 1.037803181073898 | 0.5425 |  | 2.181455416501488 | 0.953 |  | 1.236576590496927 | 0.8305 |  | rplJ |  |  | rplJ |  |  |  | rplJ |  |  |  |  |  |  |  |  | rplJ
ybaS | ybaS | TAACATAC | 13 | TGATATAAT | possible promoter (by visual inspection) | 143 | ybaS | 1.581066061309682 | 0.95927860026454 |  | 0.73 | 0.16 |  | 1.441614670722943 | 0.9085 |  | 2.050776456655141 | 0.948 |  | ybaS |  |  | ybaS |  |  |  | ybaS |  |  |  |  |  |  |  |  | ybaS
ycnKJI | ycnK | TCTCTAAA | 13 | AAATAGATC | possible promoter (by visual inspection) | 20 | ycnK | 1.393095801459938 | 0.909150862732162 |  | 0.913569669196809 | 0.384 |  | 1.114694173345999 | 0.6605 |  | 2.088918260555373 | 0.9955 |  | ycnK |  |  | ycnK |  |  |  | ycnK |  |  |  |  |  |  |  |  | ycnK
 | ycnJ |  |  |  |  |  | ycnJ | 2.919323686037745 | 0.996144199252126 |  | 0.9532064362447424 | 0.429 |  | 1.070963083243584 | 0.608 |  | 1.572476316564868 | 0.964 |  | ycnJ |  |  | ycnJ |  |  |  | ycnJ |  |  |  |  |  |  |  |  | ycnJ
 | ycnI |  |  |  |  |  | ycnI | 1.921577586534552 | 0.980427298732124 |  | 0.8844110377622797 | 0.3275 |  | 1.123258231046482 | 0.688 |  | 1.924814172739035 | 0.984 |  | ycnI |  |  | ycnI |  |  |  | ycnI |  |  |  |  |  |  |  |  | ycnI
yczE | yczE | no promoter found, probably indirect |  |  |  |  | yczE | 0.9966175418108414 | 0.496073623529019 |  | 0.7 | 0.11 |  |  |  |  | 3.222130369156368 | 0.994 |  | yczE |  |  | yczE |  |  |  | yczE |  |  |  |  |  |  |  |  | yczE
yefA | yefA | no promoter found, probably indirect |  |  |  |  | yefA | 1.002169622360238 | 0.504015610070704 |  | 0.87 | 0.32 |  | 1.415865354707423 | 0.8545 |  | 3.045881843490582 | 0.9965 |  | yefA |  |  | yefA |  |  |  | yefA |  |  |  |  |  |  |  |  | yefA
yefB | yefB | downstream of yefA (convergent) |  |  |  |  | yefB | 1.135458822764473 | 0.689687078755993 |  | 1.058581696057618 | 0.5695 |  | 1.13329755240954 | 0.614 |  | 2.690818431303795 | 0.9915 |  | yefB |  |  | yefB |  |  |  | yefB |  |  |  |  |  |  |  |  | yefB
yjzB | yjzB | AAACTATC | 12 | TCATAGAGT | possible promoter (by visual inspection) | 22 | yjzB | 1.34314620454317 | 0.834139509342993 |  | 0.89 | 0.39 |  | 1.407534252240917 | 0.767 |  | 2.75355371195921 | 0.989 |  | yjzB |  |  | yjzB |  |  |  | yjzB |  |  |  |  |  |  |  |  | yjzB
yoeB | yoeB | AATCTATC | 13 | ACATTTGTA | possible promoter (by visual inspection) | 35 | yoeB | 0.8575600046406922 | 0.244098173427812 |  | 1.2 | 0.721 |  | 1.11646106130612 | 0.6625 |  | 1.951527131879795 | 0.9795 |  | yoeB |  |  | yoeB |  |  |  | yoeB |  |  |  |  |  |  |  |  | yoeB
yuaC | yuaC |  |  |  |  |  | yuaC | 1.001471218028111 | 0.501957244228872 |  | 0.6638419568503838 | 0.0935 |  | 1.161599761259195 | 0.6935 |  | 2.10134368164673 | 0.9815 |  | yuaC |  |  | yuaC |  |  |  | yuaC |  |  |  |  |  |  |  |  | yuaC
ywaE | ywaE | GACTCTG | 13 | CATAGCTA | possible promoter (by visual inspection) | 32 | ywaE | 1.253908645668119 | 0.812932618726707 |  | 0.75 | 0.17 |  | 1.537218251395269 | 0.9315 |  | 2.41012438879883 | 0.933 |  | ywaE |  |  | ywaE |  |  |  | ywaE |  |  |  |  |  |  |  |  | ywaE
yxaI | yxaI | no promoter found, probably indirect |  |  |  |  | yxaI | 0.7044113334292783 | 0.183510775504926 |  | 1.1 | 0.61 |  |  |  |  | 2.986672038588624 | 0.99 |  | yxaI |  |  | yxaI |  |  |  | yxaI |  |  |  |  |  |  |  |  | yxaI
3. sK-CONTROLLED GENES UNAFFECTED BY GerE:
3.1. Previously identified sK-controlled genes (with mapped transcription start site):
3.1. A) also identified in overexpression
cotVW | cotV | TTCCGCTC | 12 | GCATTATAT | AGAGTAT (mapped sigK promoter) | 29 | cotV | 5.777539125237064 | 0.999814325366545 |  | 29.44421633798762 | 1 |  | 1.532792018376215 | 0.9455 |  | 1.183764115976995 | 0.7735 |  | cotV | spore coat protein (insoluble fraction) | 1.8 (Sporulation) | cotV | no | no | no | cotV | no | no | no [cotX] | no [OB0575/OB0574 (cotX)] | no | no | no | no | cotV | 1-2 TMs
 |  |  |  |  | BioOptimizer-no prediction | no
 | cotW |  |  |  |  |  | cotW | 7.084503541869169 | 0.999861623047038 |  | 31.47748314101317 | 1 |  | 1.540772068916754 | 0.949 |  | 1.317174988165755 | 0.8565 |  | cotW | spore coat protein (insoluble fraction) | 1.8 (Sporulation) | cotW | no | no | no | cotW | no | no | no | no | no | no | no | no | cotW | 0 TM
gerE | gerE | TCACCTCC | 12 | ACATATGAT | ATCTCGAC (mapped sigK promoter) | 67 | gerE | 3.343194281439543 | 0.998905207194392 |  |  |  |  |  |  |  |  |  |  | gerE | transcriptional regulator required for the expression of late spore coat genes | 3.5.2 (Transcription regulation) | gerE | no | no | degU, yvqC, yhcZ, yocG… | gerE | [NAME] (BA4724) | BC4501 | [NAME] (BH3075) | [NAME] | no [CAC2254 (yfiK)] | no | no [lmo2515 (degU)] | no [lin2625 (degU)] | gerE | 0 TM
 |  | TCACC | 15 | ACATATGATAT | BioOptimizer prediction-correct | 65
ysmB (not included in final total) | ysmB |  |  |  |  |  | ysmB | 1.492677961557602 | 0.940327279258729 |  | 1.142071155322389 | 0.68 |  | 5.985491179461198 | 1 |  | 8.59840271591694 | 1 |  | ysmB |  |  | ysmB |  |  |  | ysmB |  |  |  |  |  |  |  |  | ysmB
racE (not included in final total) | racE |  |  |  |  |  | racE | 0.9747229782060065 | 0.453471482357613 |  | 0.9644918456843863 | 0.45 |  | 7.746551869029809 | 0.9995 |  | 9.819683006748907 | 1 |  | racE |  |  | racE |  |  |  | racE |  |  |  |  |  |  |  |  | racE
spoVIF (yjcC) | spoVIF (yjcC) | GCACATTG | 12 | TCATACAAT | ACCGTATTA | "+17" | spoVIF (yjcC) | 8.039185996828888 | 0.999854624528983 |  | 2.837919028441556 | 0.993 |  | 1.298311094963877 | 0.819 |  | 1.197901666016097 | 0.7865 |  | spoVIF (yjcC) | unknown-stabilization of GerE, renamed [NAME] (Kuwana et al., 2003) | 5.1 (From B. subtilis) | spoVIF (yjcC) | yjcC | no | no | spoVIF (yjcC) | BA1527 | BC1506 | BH1641 | OB1795 | no | no | no | no | spoVIF (yjcC) | 0 TM
 |  |  |  |  | not included in BioOptimizer list of sequences | no
[NAME] | [NAME] | TAACGAGG | 12 | GCATATATC | ATAAGCGGGGGG | 61 | [NAME] | 16.89733600343608 | 0.999885145502452 |  | 1.914255925021086 | 0.974 |  | 1.370465669797792 | 0.8855 |  | 1.326150251048713 | 0.8825 |  | [NAME] | unknown | 6 (No similarity) | [NAME] | no | no | no | [NAME] | no | no | no | no | no | no | no | no | [NAME] | 0 TM
 |  |  |  |  | not included in BioOptimizer list of sequences | no
3.1. B) below cut-off in sigK+ vs. sigK- experiments but identified by overexpression of sE
none
3.1.C) not identified by overexpression
none
3.1.D) not identified by overexpression, nor in sigK+ vs. sigK- experiment
yjcZ | yjcZ | CCAAGCCG | 13 | ACATAGTGT | ATAGAGAGT | 26 | yjcZ | not on the array |  |  | not on the array |  |  | not on the array |  |  | not on the array |  |  | yjcZ | (Kuwana et al., 2003)-not annotated in SubtiList database |  | yjcZ | no | no | no | yjcZ | no | no | no | no | no | no | no | no | yjcZ | ND
 |  |  |  |  | not included in BioOptimizer list of sequences | no
3.2. Previously reported sK-controlled genes (but transcription start site has not been mapped):
none
3.3. Newly identified sK-controlled genes:
3.3. A. also identified by overexpression of sK
3.3. A. 1. promoter confirmed by 5'RACE-PCR
yfnED | yfnE | AAGCAAGC | 12 | GCATATAAT | TCGAGGAGCGTCTT (5'RACE) | "+33" | yfnE | 12.86383943671061 | 0.999970377286581 |  | 6.934258060165691 | 0.999 |  | 0.9332007220366553 | 0.402 |  | 1.467618522878225 | 0.93 |  | yfnE | similar to glycosyl transferase | 6 (No similarity) | yfnE | no | no | yveR, tuaG, yveo, ggaB, ggaA, yveT, spsA, ywdF | yfnE | no | no | no [BH3713 (tuaG)] | no [OB2922 (tuaG)] | no [CAC2173 (yveO)] | no [[NAME] (yveR)] | no [lmo1091 (yveT)] | no [lin1068 (tagB)] | yfnE | 0 TM
 |  | GCACA | 14 | GCATGAACTGT | BioOptimizer-prediction-ruled out by 5'RACE | 117
 | yfnD |  |  |  |  |  | yfnD | 9.424623700932239 | 0.99974684964548 |  | 6.251726927756859 | 0.996 |  | 0.9349499137544384 | 0.386 |  | 1.371502481369866 | 0.8995 |  | yfnD | unknown | 5.1 (From B. subtilis) | yfnD | no | [NAME] | no | yfnD | no | no | no | no | no | no | no | no | yfnD | 0 TM
yhcOP | yhcO | ACACACTG | 12 | GCATAGAGT | AAAAATAAAAAGGTACAA (5'RACE) | 104 | yhcO | 8.586035534546188 | 0.9997684152935 |  | 2.511886431509581 | 0.993 |  | 0.9133492053944757 | 0.365 |  | 0.66812005499817 | 0.092 |  | yhcO | unknown | 6 (No similarity) | yhcO | no | no | no | yhcO | no | no | no | no | no | no | no | no | yhcO | 1 TM (Nter)
 |  | ACACA | 15 | GCATAGAGTAA | BioOptimizer-confirmed by 5'RACE | 102
 | yhcP |  |  |  |  |  | yhcP | 2.136567175732442 | 0.99286564761723 |  | 2.558585886905646 | 0.984 |  | 0.8305155310125948 | 0.2325 |  | 0.6014258527874882 | 0.0515 |  | yhcP | unknown | 6 (No similarity) | yhcP | no | no | no | yhcP | no | no | no | no | no | no | no | no | yhcP | 0 TM
ypqA | ypqA | TAACAACA | 12 | GCATAATCT | GGTTAAAAAAGGCGG (5'RACE) | 23 | ypqA | 2.302391524615511 | 0.992492874236217 |  | 4.943106869868354 | 0.998 |  | 0.8006731818011077 | 0.2495 |  | 0.704984139971548 | 0.1135 |  | ypqA | unknown | 6 (No similarity) | ypqA | no | no | no | ypqA | no | no | no | no | no | no | no | no | ypqA | 0 TM
 |  | TAACA | 15 | GCATAATCTGG | BioOptimizer-confirmed by 5'RACE | 21
3.3. A. 2. not tested by 5'RACE-PCR
guaC (yumD) | guaC (yumD) | GCACCACA | 12 | TCATAATGT | predicted sigK promoter | 89 | guaC (yumD) | 2.138527664876118 | 0.992590573977322 |  | 2.275097430772071 | 0.982 |  | 0.9497238547140102 | 0.4175 |  | 0.9773212542712502 | 0.471 |  | guaC (yumD) | GMP reductase | 2.3 (Metabolism of nucleotides and nucleic acids) | guaC (yumD) | yumD | guaB | no | guaC (yumD) | guaC (BA5705) | BC5452 | guaB (BH0020) | OB1310 | CAC3471 | CPE2276 | no | no | guaC (yumD) | 1 TM (mid)
 |  | GCACC | 15 | TCATAATGTTT | BioOptimizer-prediction | 87
yrpC | yrpC | [NAME] | 12 | CCATATTAA | possible promoter (by visual inspection) | 91 | yrpC | 2.122613371877438 | 0.979534176732438 |  | 1.99526231496888 | 0.977 |  | 1.086967659409694 | 0.6315 |  | 1.334005473579951 | 0.882 |  | yrpC | similar to glutamate racemase | 2.2 (Metabolism of amino acids and related molecules) | yrpC | no | racE | no | yrpC | racE-2 (BA4717) | BC4496 | no [BH3071(racE)] | no [OB2108(racE)] | CAC3250 | CPE2568 | no [racE ] | no [racE ] | yrpC | 0-1 TM
 |  |  |  |  | BioOptimizer-no prediction | no
[NAME] | ytcA | TCACGAAC | 12 | AAATAGGAT | predicted sigK promoter | 40 | ytcA | 3.25917363704448 | 0.991575665323393 |  | 14.96235656094434 | 1 |  | 1.14647023073436 | 0.707 |  | 0.6396665860162555 | 0.0395 |  | ytcA | similar to NDP-sugar dehydrogenase | 2.1.1 (Specific pathways) | ytcA | no | tuaD, ywqF |  | ytcA | no | no | no [BH3708 (tuaD)] | no [OB2884 (ywqF)] | no | no [CPE0494 (ywqF)] | no | no | ytcA | 1 (Nter)-2 TMs
 |  | TCACG | 14 | TAATAGGATAT | BioOptimizer-prediction | 38
 | ytcB |  |  |  |  |  | ytcB | 6.449340953092757 | 0.999668663385442 |  | 22.49054605835782 | 1 |  | 1.274678541142737 | 0.8205 |  | 0.6979242002895967 | 0.0695 |  | ytcB | similar to NDP-sugar epimerase | 2.1.1 (Specific pathways) | ytcB | no | spsJ, [NAME], yfnG | yodU | ytcB | no | no | BH2304 | OB2082 | CAC0794 | no | no | no | ytcB | 1-2 TMs
 | ytcC |  |  |  |  |  | ytcC | 5.788350138278019 | 0.999819525306795 |  | 16.55769963469529 | 1 |  | 1.264202430976871 | 0.804 |  | 0.6557816108135615 | 0.0495 |  | ytcC | similar to lipopolysaccharide N-acetylglucosaminyltransferase (glycosyl transferase family) | 1.1 (Cell wall) | ytcC | no | cotSA | ypjH, yveN, yqgM, tuaC | ytcC | no | no | BH2305 | no | no [CAC1053 (yqgM)] | no [CPE0498 (cotSA)] | no | no [lin2700 (ypjH)] | ytcC | 0 TM
ywnF | ywnF | GCACCTGC | 12 | ACATATGAT | predicted sigK promoter | 44 | ywnF | 3.986210908905524 | 0.996749286403672 |  | 2.500345361696432 | 0.993 |  | 0.7263291852516698 | 0.143 |  | 0.662190326915392 | 0.0655 |  | ywnF | unknown | 5.1 (From B. subtilis) | ywnF | no | no | no | ywnF | no | no | BH1886 | no | no | no | no | no | ywnF | 2 TMs
 |  | GCACC | 15 | ACATATGATAA | BioOptimizer-prediction | 42
GENES IN SECTIONS 3.3.B) and 3.3.C) ARE NOT INCLUDED IN THE FINAL TOTAL OF SIGK-CONTROLLED GENES
3.3. B) below cut-off in sigK+ vs. sigK- experiments but identified by overexpression of sK
yxeF | yxeF | CTGCGGAT | 11 | TCATAGTGG | possible promoter (by visual inspection) | 143 | yxeF | 1.778263878467954 | 0.97720563894473 |  | 1.702158508394951 | 0.95 |  | 0.9052863291754247 | 0.337 |  | 0.6342461028165352 | 0.162 |  | yxeF |  |  | yxeF |  |  |  | yxeF |  |  |  |  |  |  |  |  | yxeF
 |  |  |  |  | BioOptimizer-no prediction | no
3.3. C) not identified by overexpression of sK
a) ratio in sigK+ vs. sigK- experiment is high (>3)
ycsK | ycsK | TTTCAAGA | 11 | ACATAAGTA | possible promoter (by visual inspection) | 60 | ycsK | 0.4688942729395022 | 0.0116728947390604 |  | 11.8032063565173 | 1 |  | 0.9745481727652849 | 0.465 |  | 1.18439940400739 | 0.768 |  | ycsK |  |  | ycsK |  |  |  | ycsK |  |  |  |  |  |  |  |  | ycsK
yppG | yppG | AAACAATA | 12 | ACATATATA | possible promoter (by visual inspection) | 35 | yppG | 0.6948649389332548 | 0.286074288423587 |  | 5.828608211121999 | 0.9995 |  | 0.8710598049142785 | 0.2935 |  | 0.6041023704572599 | 0.0325 |  | yppG |  |  | yppG |  |  |  | yppG |  |  |  |  |  |  |  |  | yppG
 |  | convergent with ypqA
yqbM | yqbM | inside skin element-no promoter found-start site maybe incorrect |  |  |  |  | yqbM | 1.604180808744712 | 0.943421388174483 |  | 3.539973410834348 | 0.954 |  | 0.988521556679183 | 0.483 |  | 0.7242331641058036 | 0.0875 |  | yqbM |  |  | yqbM |  |  |  | yqbM |  |  |  |  |  |  |  |  | yqbM
b) ratio in sigK+ vs. sigK- experiment is low (thus considered to be an indirect target and not included in final list)
dapF (yutL) | dapF (yutL) | no promoter found |  |  |  |  | dapF (yutL) | 0.6529817693208436 | 0.0456805357872387 |  | 2.259435770220978 | 0.976 |  | 0.7411122584129507 | 0.128 |  | 0.6251230251317724 | 0.0345 |  | dapF (yutL) |  |  | dapF (yutL) |  |  |  | dapF (yutL) |  |  |  |  |  |  |  |  | dapF (yutL)
mtn-yrhA | mtn (yrrU) | no promoter found |  |  |  |  | mtn (yrrU) | 0.8491037788348813 | 0.251646285808395 |  | 1.815515662773136 | 0.966 |  | 0.8747622355019871 | 0.2945 |  | 0.7676632110525494 | 0.152 |  | mtn (yrrU) |  |  | mtn (yrrU) |  |  |  | mtn (yrrU) |  |  |  |  |  |  |  |  | mtn (yrrU)
 | [NAME] | no promoter found |  |  |  |  | [NAME] | 1.306904331903401 | 0.86923278059928 |  | 2.910717118066606 | 0.99 |  | 1.128969078461111 | 0.697 |  | 0.7434463423306058 | 0.14 |  | [NAME] |  |  | [NAME] |  |  |  | [NAME] |  |  |  |  |  |  |  |  | [NAME]
nagP | nagP (yflF) | GTCATTC | 14 | AATAATCT | possible promoter (by visual inspection) | 140 | nagP (yflF) | 1.208403754598209 | 0.710766633828573 |  | 2.792543841237339 | 0.986 |  | 0.7128983532301173 | 0.1095 |  | 0.6626674846471207 | 0.081 |  | nagP (yflF) |  |  | nagP (yflF) |  |  |  | nagP (yflF) |  |  |  |  |  |  |  |  | nagP (yflF)
ribH | ribH | ACAAGC | 14 | CATTTCTA | possible promoter (by visual inspection) | 33 | ribH | 0.5583958432017606 | 0.0865621658794224 |  | 2.890679882365476 | 0.986 |  | 1.206687872378809 | 0.784 |  | 0.9511230664250978 | 0.424 |  | ribH |  |  | ribH |  |  |  | ribH |  |  |  |  |  |  |  |  | ribH
ydfC | ydfC | ATCTTTA | 14 | [NAME] | possible promoter (by visual inspection) | 34 | ydfC | 0.4114206845831545 | 0.0632343766480965 |  | 2.322736796357107 | 0.986 |  | 1.055378624746369 | 0.59 |  | 1.006168451052571 | 0.512 |  | ydfC |  |  | ydfC |  |  |  | ydfC |  |  |  |  |  |  |  |  | ydfC
yebC | yebC | TGCAAAA | 13 | CATACGAT | possible promoter (by visual inspection) | 131 | yebC | 1.730609200536401 | 0.836344075390243 |  | 2.07491351745491 | 0.967 |  | 0.7940324211678376 | 0.1815 |  | 0.6094186899627795 | 0.0325 |  | yebC |  |  | yebC |  |  |  | yebC |  |  |  |  |  |  |  |  | yebC
yhjA | yhjA | AACATGT | 12 | AATAGTGA | possible promoter (by visual inspection) | 127 | yhjA | 0.9540151567798589 | 0.41981150011994 |  | 2.027682719521282 | 0.975 |  | 0.9171577390282424 | 0.371 |  | 0.4948533392809724 | 0.0825 |  | yhjA |  |  | yhjA |  |  |  | yhjA |  |  |  |  |  |  |  |  | yhjA
yppF | yppF | divergent with yppG (no promoter found) |  |  |  |  | yppF | 0.150033566809951 | 0.000830727713379886 |  | 2.910717118066606 | 0.996 |  | 1.019592942788193 | 0.525 |  | 1.06393050841159 | 0.593 |  | yppF |  |  | yppF |  |  |  | yppF |  |  |  |  |  |  |  |  | yppF
ypuBC | ypuB | no promoter found |  |  |  |  | ypuB | 0.5005922491087244 | 0.113449282964302 |  | 2.032357010936222 | 0.977 |  | 0.8856667794066573 | 0.3335 |  | 0.2544535428922138 | 0.0995 |  | ypuB |  |  | ypuB |  |  |  | ypuB |  |  |  |  |  |  |  |  | ypuB
 | ypuC |  |  |  |  |  | ypuC | 0.8610691386935503 | 0.36866266800576 |  | 2.517676927758856 | 0.99 |  | 0.7700281803948834 | 0.153 |  | 0.611513196670199 | 0.048 |  | ypuC |  |  | ypuC |  |  |  | ypuC |  |  |  |  |  |  |  |  | ypuC
4. sE-CONTROLLED GENES turned on by sK overexpression (but not identified in sigK mutant experiment):
cwlJ | cwlJ | TCATCAC | 14 | AATATGAT | GAAAAGAGA (mapped sE promoter) | 27 | cwlJ | 2.765042474739388 | 0.996091600665483 |  | 0.8689671609823547 | 0.3145 |  | 0.9034357607607685 | 0.3595 |  | 0.754079624128685 | 0.1385 |  | cwlJ |  |  | cwlJ |  |  |  | cwlJ |  |  |  |  |  |  |  |  | cwlJ
phoB-ydhF | phoB | TTCTAAA | 14 | AATAACCA | TTATTTAAGGGTG | 119 | phoB | 1.823602626340813 | 0.956316354620766 |  | 0.8014169073772671 | 0.2135 |  | 1.101222987774159 | 0.6415 |  | 1.2257420344461 | 0.8035 |  | phoB |  |  | phoB |  |  |  | phoB |  |  |  |  |  |  |  |  | phoB
 | ydhF |  |  |  |  |  | ydhF | 0.8874429046159431 | 0.347427052141269 |  | 0.893056046093493 | 0.3545 |  | 1.112720976521554 | 0.653 |  | 1.269493222857495 | 0.842 |  | ydhF |  |  | ydhF |  |  |  | ydhF |  |  |  |  |  |  |  |  | ydhF
prkA | prkA | GCATGTA | 14 | CATAGATT | GTATCAAAGT (mapped sE promoter) | 53 | prkA | 1.872704710710592 | 0.97949421481712 |  | 0.8081782651276728 | 0.234 |  | 1.050346166973462 | 0.576 |  | 0.9362021644734794 | 0.373 |  | prkA |  |  | prkA |  |  |  | prkA |  |  |  |  |  |  |  |  | prkA
spoIIM | spoIIM | GCATGTT | 13 | CATACAAT | CTATTAAA | 40 | spoIIM | 2.490479692782924 | 0.98009662420202 |  | 0.7727990528131727 | 0.178 |  | 1.210995559847599 | 0.785 |  | 1.134243227395192 | 0.694 |  | spoIIM |  |  | spoIIM |  |  |  | spoIIM |  |  |  |  |  |  |  |  | spoIIM
spoIIIAA-AB-AC-AD-AE-AF-AG-AH | spoIIIAA | TCATAAA | 13 | CATACATT | TTAAAGAAGC | 36 | spoIIIAA | 1.608493305049751 | 0.963592064491308 |  | 0.9325674294353492 | 0.399 |  | 1.165118560675951 | 0.7165 |  | 1.271115609549833 | 0.8475 |  | spoIIIAA |  |  | spoIIIAA |  |  |  | spoIIIAA |  |  |  |  |  |  |  |  | spoIIIAA
 | spoIIIAB |  |  |  |  |  | spoIIIAB | 2.42774212118266 | 0.99575387966009 |  | 0.9944139427134496 | 0.4905 |  | 1.135320927241805 | 0.6935 |  | 1.354306486581037 | 0.873 |  | spoIIIAB |  |  | spoIIIAB |  |  |  | spoIIIAB |  |  |  |  |  |  |  |  | spoIIIAB
 | spoIIIAC |  |  |  |  |  | spoIIIAC | 2.111635493095896 | 0.991644057404942 |  | 0.8469876190621967 | 0.274 |  | 1.132251445070796 | 0.696 |  | 1.301600588440847 | 0.8545 |  | spoIIIAC |  |  | spoIIIAC |  |  |  | spoIIIAC |  |  |  |  |  |  |  |  | spoIIIAC
 | spoIIIAD |  |  |  |  |  | spoIIIAD | 1.460676254435313 | 0.937924812334092 |  | 0.8374838754137893 | 0.268 |  | 1.186127677307363 | 0.692 |  | 1.277426941774319 | 0.843 |  | spoIIIAD |  |  | spoIIIAD |  |  |  | spoIIIAD |  |  |  |  |  |  |  |  | spoIIIAD
 | spoIIIAE |  |  |  |  |  | spoIIIAE | 1.37598852620521 | 0.73656329559811 |  | 0.9175689742385781 | 0.367 |  | 1.364479756727025 | 0.854 |  | 1.29134915791407 | 0.8615 |  | spoIIIAE |  |  | spoIIIAE |  |  |  | spoIIIAE |  |  |  |  |  |  |  |  | spoIIIAE
spoIIIAF-AG-AH | spoIIIAF | predicted [NAME] promoter (within the spoIIIA operon, Stragier) |  |  |  |  | spoIIIAF | 2.445492446022906 | 0.99508814289921 |  | 0.9987789029329551 | 0.499 |  | 1.180571660160434 | 0.7445 |  | 1.283222269296075 | 0.821 |  | spoIIIAF |  |  | spoIIIAF |  |  |  | spoIIIAF |  |  |  |  |  |  |  |  | spoIIIAF
 | spoIIIAG |  |  |  |  |  | spoIIIAG | 2.189451496463478 | 0.992841436134706 |  | 1.160352599457787 | 0.6955 |  | 1.189726157634983 | 0.763 |  | 1.253544117795463 | 0.816 |  | spoIIIAG |  |  | spoIIIAG |  |  |  | spoIIIAG |  |  |  |  |  |  |  |  | spoIIIAG
 | spoIIIAH |  |  |  |  |  | spoIIIAH | 1.365473775089575 | 0.900478665474851 |  | 0.9357486955667906 | 0.4145 |  | 1.19548843198124 | 0.79 |  | 1.236512005762977 | 0.8155 |  | spoIIIAH |  |  | spoIIIAH |  |  |  | spoIIIAH |  |  |  |  |  |  |  |  | spoIIIAH
spoIVFA-FB | spoIVFA | GAATATT | 14 | CATATGAT | GTACAAAC | 33 | spoIVFA | 1.385332119205973 | 0.91058659487563 |  | 0.9971126900447909 | 0.4955 |  | 1.054063109364227 | 0.5795 |  | 1.273318619632475 | 0.853 |  | spoIVFA |  |  | spoIVFA |  |  |  | spoIVFA |  |  |  |  |  |  |  |  | spoIVFA
 | spoIVFB |  |  |  |  |  | spoIVFB | 2.395930016781355 | 0.95389604677716 |  | 0.9479292356063946 | 0.4125 |  | 1.316185413437231 | 0.8465 |  | 1.27977942486195 | 0.844 |  | spoIVFB |  |  | spoIVFB |  |  |  | spoIVFB |  |  |  |  |  |  |  |  | spoIVFB
spoVE | spoVE | ACATGTT | 13 | CATATGCT | TAAGTAAGGG (mapped sE promoter) | 67 | spoVE | 2.765966563611246 | 0.997051576111328 |  | 0.9181431996143562 | 0.38 |  | 1.101358000974237 | 0.648 |  | 1.30372422273989 | 0.8535 |  | spoVE |  |  | spoVE |  |  |  | spoVE |  |  |  |  |  |  |  |  | spoVE
spoVR | spoVR | TCATCTT | 14 | CATACATT | ATAGATAAGTC (mapped sE promoter) | 29 | spoVR | 3.391203358660179 | 0.998677225574323 |  | 1.373700985919722 | 0.812 |  | 0.7237692675829325 | 0.1265 |  | 0.4696238705918999 | 0.005 |  | spoVR |  |  | spoVR |  |  |  | spoVR |  |  |  |  |  |  |  |  | spoVR
ycgF-G | ycgF | GCATAGC | 14 | AATAAATT | GTACAAGTT (5'RACE) | 34 | ycgF | 2.327573860662631 | 0.994785014437455 |  | 0.9216804911964843 | 0.39 |  | 0.9969916569532062 | 0.493 |  | 1.098901712695934 | 0.639 |  | ycgF |  |  | ycgF |  |  |  | ycgF |  |  |  |  |  |  |  |  | ycgF
 | ycgG | probably has its own sK promoter (see above) |  |  |  |  | ycgG | 3.801896960093609 | 0.997631388550004 |  | 2.411843324757608 | 0.985 |  | 0.7521462874338642 | 0.1345 |  | 0.4961843470782044 | 0.0185 |  | ycgG |  |  | ycgG |  |  |  | ycgG |  |  |  |  |  |  |  |  | ycgG
yhbH | yhbH | GTCAATT | 15 | CATATGAT | [NAME] (mapped sE promoter) | 93 | yhbH | 7.49985887571131 | 0.999737297712807 |  | 1.718601579504872 | 0.93 |  | 1.096579220478301 | 0.629 |  | 1.092346080314088 | 0.6375 |  | yhbH |  |  | yhbH |  |  |  | yhbH |  |  |  |  |  |  |  |  | yhbH
yheC-D | yheC | GAATCGT | 14 | AATACCGT | predicted [NAME] promoter | 82 | yheC | 2.010696899859656 | 0.971677351015559 |  | 0.4302449343038013 | 0.0185 |  | 1.112838512943696 | 0.668 |  | 1.295398720232355 | 0.8525 |  | yheC |  |  | yheC |  |  |  | yheC |  |  |  |  |  |  |  |  | yheC
 | yheD |  |  |  |  |  | yheD | 0.9755966453922112 | 0.455409034268483 |  | 0.4834230716945077 | 0.0205 |  | 1.135825815853683 | 0.69 |  | 1.307503894788476 | 0.864 |  | yheD |  |  | yheD |  |  |  | yheD |  |  |  |  |  |  |  |  | yheD
 | yhfN | GAATTTG | 13 | AATAGAAG | predicted [NAME] promoter | 29 | yhfN | 2.246564978827293 | 0.94694093889251 |  | 0.9030258225328149 | 0.362 |  | 1.270336629270868 | 0.8255 |  | 1.285425774586762 | 0.8385 |  | yhfN |  |  | yhfN |  |  |  | yhfN |  |  |  |  |  |  |  |  | yhfN
yisY | yisY | AGATCGT | 14 | [NAME] | predicted [NAME] promoter | 123 | yisY | 3.297665607558412 | 0.998716457014599 |  | 1.719347843111414 | 0.94 |  | 0.6186561273675645 | 0.058 |  | 0.444431378443611 | 0.01 |  | yisY |  |  | yisY |  |  |  | yisY |  |  |  |  |  |  |  |  | yisY
yjmC-D-uxuA-yjmF-exuT-R | yjmC | GAATATT | 14 | AATAAAAT | GTGTTTGTAG | 61 | yjmC | 1.468482443216938 | 0.922491855400221 |  | 0.7494447687602264 | 0.163 |  | 1.243594409814758 | 0.8005 |  | 1.321912355984869 | 0.839 |  | yjmC |  |  | yjmC |  |  |  | yjmC |  |  |  |  |  |  |  |  | yjmC
 | yjmD |  |  |  |  |  | yjmD | 2.200569119839437 | 0.979731428451022 |  | 0.7783266296087579 | 0.204 |  | 1.263300445658882 | 0.82 |  | 1.279242040475504 | 0.828 |  | yjmD |  |  | yjmD |  |  |  | yjmD |  |  |  |  |  |  |  |  | yjmD
 | uxuA (yjmE) |  |  |  |  |  | uxuA (yjmE) | 1.288749160712585 | 0.832115394143006 |  | 0.83158394914452 | 0.2505 |  | 1.175649627597493 | 0.7485 |  | 1.285387971061194 | 0.8485 |  | uxuA (yjmE) |  |  | uxuA (yjmE) |  |  |  | uxuA (yjmE) |  |  |  |  |  |  |  |  | uxuA (yjmE)
 | yjmF |  |  |  |  |  | yjmF | 2.319263853010469 | 0.983681158041708 |  | 0.8705193192420877 | 0.307 |  | 1.172278992956821 | 0.743 |  | 1.175301457439673 | 0.7365 |  | yjmF |  |  | yjmF |  |  |  | yjmF |  |  |  |  |  |  |  |  | yjmF
 | exuT (yjmG) |  |  |  |  |  | exuT (yjmG) | 2.156086826045235 | 0.981370758804688 |  | 0.9279347781796169 | 0.396 |  | 1.144891207785512 | 0.7235 |  | 1.1441188666456 | 0.6865 |  | exuT (yjmG) |  |  | exuT (yjmG) |  |  |  | exuT (yjmG) |  |  |  |  |  |  |  |  | exuT (yjmG)
 | exuR (yjmH) |  |  |  |  |  | exuR (yjmH) | 0.857555378598486 | 0.271935774114505 |  | 0.9687073276286942 | 0.449 |  | 1.041975840595849 | 0.562 |  | 0.9463263668384951 | 0.404 |  | exuR (yjmH) |  |  | exuR (yjmH) |  |  |  | exuR (yjmH) |  |  |  |  |  |  |  |  | exuR (yjmH)
yndA | yndA | TCATAAA | 13 | [NAME] | predicted [NAME] promoter | 112 | yndA | 3.060186634164685 | 0.99677297951793 |  | 1.136958743214401 | 0.662 |  | 0.9453711533353322 | 0.4065 |  | 0.78250033014296 | 0.1515 |  | yndA |  |  | yndA |  |  |  | yndA |  |  |  |  |  |  |  |  | yndA
yngJ-I-H-G-F-E | yngJ | GAATGAT | 14 | AATAGGAT | GTTACAAAGATGTGA (5'RACE) | 28 | yngJ | 2.575906361845513 | 0.995595234423714 |  | 0.6873814019007288 | 0.1305 |  | 1.235345530781831 | 0.8 |  | 0.890786838578833 | 0.316 |  | yngJ |  |  | yngJ |  |  |  | yngJ |  |  |  |  |  |  |  |  | yngJ
 | yngI |  |  |  |  |  | yngI | 3.980500751781994 | 0.99225476034297 |  | 0.786084074144462 | 0.198 |  | 1.267693232827701 | 0.845 |  | 0.8453812542215994 | 0.245 |  | yngI |  |  | yngI |  |  |  | yngI |  |  |  |  |  |  |  |  | yngI
 | yngH |  |  |  |  |  | yngH | 0.7119283292201296 | 0.134953479187332 |  | 0.789840633784455 | 0.2075 |  | 1.142142465525456 | 0.69 |  | 0.8539636192920661 | 0.2455 |  | yngH |  |  | yngH |  |  |  | yngH |  |  |  |  |  |  |  |  | yngH
 | yngG |  |  |  |  |  | yngG | 1.886050334023727 | 0.955899026612152 |  | 0.7567103257649244 | 0.187 |  | 1.153018297834208 | 0.7205 |  | 0.8901143538282907 | 0.326 |  | yngG |  |  | yngG |  |  |  | yngG |  |  |  |  |  |  |  |  | yngG
 | yngF |  |  |  |  |  | yngF | 0.5939642769199147 | 0.0743605598640893 |  | 0.800853811197093 | 0.228 |  | 1.253127096677889 | 0.82 |  | 0.8880199153665983 | 0.303 |  | yngF |  |  | yngF |  |  |  | yngF |  |  |  |  |  |  |  |  | yngF
 | yngE |  |  |  |  |  | yngE | 1.28662434649749 | 0.756525071863542 |  | 0.8815330211017847 | 0.3365 |  | 1.27624551288011 | 0.835 |  | 0.8796936102832225 | 0.2845 |  | yngE |  |  | yngE |  |  |  | yngE |  |  |  |  |  |  |  |  | yngE
yqfT | yqfT | ACACATT | 13 | CATACATT | predicted [NAME] promoter | 22 | yqfT | 2.92647534403842 | 0.99773396773391 |  | 1.4 | 0.87 |  | 0.4642578959970753 | 0.012 |  | 0.3514102073982301 | 0.019 |  | yqfT |  |  | yqfT |  |  |  | yqfT |  |  |  |  |  |  |  |  | yqfT
ysnE | ysnE | TTATATT | 14 | AATATGAT | predicted [NAME] promoter (readthrough from ysnD is also a possibility) | 56 | ysnE | 1.565695738152709 | 0.944608617258872 |  | 1.369152733036665 | 0.8585 |  | 0.9088222624158563 | 0.351 |  | 0.7569603982187889 | 0.1185 |  | ysnE |  |  | ysnE |  |  |  | ysnE |  |  |  |  |  |  |  |  | ysnE
ytbD | ytbD | GCTTACT | 15 | CATACAAC | predicted [NAME] promoter | 23 | ytbD | 1.853028078253765 | 0.980481009244172 |  | 1.262045798985274 | 0.6745 |  |  |  |  | 1.028821279699378 | 0.5415 |  | ytbD |  |  | ytbD |  |  |  | ytbD |  |  |  |  |  |  |  |  | ytbD
yteV | yteV | TCATAAC | 14 | AATAGATT | GATAGAG | 24 | yteV | 1.842166098345338 | 0.97869826490935 |  |  |  |  |  |  |  | 0.529312101205504 | 0.102 |  | yteV |  |  | yteV |  |  |  | yteV |  |  |  |  |  |  |  |  | yteV
yugT | yugT | TGCTGTA | 14 | CATAGGAT | predicted [NAME] promoter | 34 | yugT | 4.910407308070409 | 0.999324906129475 |  | 0.9519125617655467 | 0.4335 |  | 0.6033832635215329 | 0.062 |  | 0.4044870703131724 | 0.01 |  | yugT |  |  | yugT |  |  |  | yugT |  |  |  |  |  |  |  |  | yugT