Spreadsheet: 1b17f2e1-ba7d-4eee-bc44-6c58f61e33e7
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 | SpoIIID BINDING (Electrophoretic Mobility Shift Assay and computational search) | Unnamed: 22 | Unnamed: 23 | Unnamed: 24 | Unnamed: 25 | Unnamed: 26 | GENE.3 | PRESUMED FUNCTION (SubtiList and Swiss-Prot) | Category (SubtiList) | GENE.4 | [NAME] | SEARCH FOR PARALOGS | Unnamed: 33 | GENE.5 | SEARCH FOR ORTHOLOGUES | Unnamed: 36 | Unnamed: 37 | Unnamed: 38 | Unnamed: 39 | Unnamed: 40 | Unnamed: 41 | Unnamed: 42 | GENE.6 | [NAME] SEGMENTS
 |  | -35 | Spacing | -10 | Transcription start | distance to AUG |  | SigE DATA: |  |  | SigE DATA: |  |  | SpoIIID DATA: |  |  | GerR DATA: |  |  |  | Primers used for EMSA | Result EMSA | Binding site | BioProspector/BioOptimizer analysis |  |  |  |  |  |  |  | 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)
 |  | TCATATT | "13-15" | CATANANT | (bold and underlined) | (from last bp of -10) |  | INDUCTION |  |  | Hour 2.5 |  |  | Hour 3.5 |  |  | Hour 3.5 |  |  |  |  |  |  | Sequence of predicted site (location calculated from translational start) |  |  |  |  |  |  |  | BLAST in SUBTILIST | BLAST in SUBTILIST |  | Ames | ATCC 14579 |  | HTE831 | ATCC 824 | str. 13 | LISTILIST | LISTILIST
 |  |  |  |  |  |  |  | sE |  |  | sE |  |  | SpoIIID |  |  | GerR (YlbO) |  |  |  |  |  |  | Site 1 | Site 2 | Site 3 |  |  |  |  |  | E value> 1e-20 | 1e-20> E value> 1e-4
GENES IDENTIFIED BY TRANSCRIPTIONAL PROFILING EXPERIMENTS COMPARING sigE+ TO sigE- STRAINS: |  |  |  |  |  |  |  | Ratio | Score |  | Ratio | Score |  | Ratio | Score |  | Ratio | Score |  |  |  |  |  |  |  |  |  |  |  |  |  | genes indicated in bold characters are mother cell-specific genes
1. sE-CONTROLLED GENES REPRESSED BY SpoIIID:
1.1.  Previously identified sE-controlled genes (with transcription start site mapped by primer extension):
1.1. A. Also identified by overexpression of sE
1.1 A. a) SpoIIID binding confirmed by gel-shift
bofA | bofA | GTCTAAA | 14 | CATAAGCT | TGTACTAGAA | 34 | bofA | 15.10080154164149 | 0.997 |  | 9.61612278383665 | 1 |  | 0.2265524011685087 | 0.002 |  | 1.128843434381079 | 0.852312206492238 |  | bofA | ODR99-100 | shifted | footprint | (-29)TAGAACAAGC(-21) | (+32)TAGGACTGGT(+41) | predicted site not confirmed by footprinting | bofA | inhibition of the pro-sigma-K processing machinery | 1.8 (Sporulation) | bofA | no | no | no | bofA | [NAME] (BA0024) | BC0028 | bofA | bofA (OB0033) | [NAME] (CAC0129) | [NAME] | no | no | bofA | 3 TMs
 |  | GTGGTCTAAAC | 11 | CTCATAAGCTT | BioOptimizer prediction-correct | 33 |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | predicted | (-29)TAGAACAAGC(-21) | not predicted | (-210)TGGAACAGGC(-201)
gerM-rph-ysnA-B | gerM | GTCTATT | 15 | TATACATA | ATAGTACAAA | 30 | gerM | 3.118889584093937 | 0.998 |  | 40.83193863326923 | 1 |  | 0.1792724663990666 | 0 |  | 0.8570386054460668 | 0.191014731501427 |  | gerM | PE784-gerM (RACE 2) | shifted | predicted | (+42)TGAGACAAGT(+33) |  |  | gerM | germination (cortex hydrolysis) and sporulation (stage II, multiple polar septa) | 1.9 (Germination) | gerM | no | no | no | gerM | gerM (BA4716) | BC4495 | gerM | OB2107 | no | no | no | no | gerM | 1 TM (Nter)
 |  | TCGGTCTATTT | 12 | CGTATACATAA | BioOptimizer prediction-correct | 29
 | rph | 110 bp downstream of gerM stop codon |  |  |  |  | rph | 2.027682719521282 | 0.987 |  | 2.26464430759306 | 0.978 |  | 0.511728409860222 | 0.044 |  | 1.075536666094607 | 0.742897162928448 |  | rph |  |  |  |  |  |  | rph | ribonuclease PH (EC 2.7.7.56) | 3.6 (RNA modification) | rph | no | no | pnpA | rph | rph (BA4715) | BC4494 | rph | rph (OB2106) | no [pnpA ([NAME]) (pnpA)] | rnpH (CPE2254) | lmo1238 | lin1201 | rph | 1 TM (mid)
 | ysnA | 12 bp downstream of rph stop codon |  |  |  |  | ysnA | 2.766941645411512 | 0.997 |  | 2.28559880337543 | 0.958 |  | 0.4516365815137037 | 0.02 |  | 0.9191287587809253 | 0.233081348706403 |  | ysnA |  |  |  |  |  |  | ysnA | similar to xanthosine triphosphate pyrophosphatase | 5.2 (From other organisms) | ysnA | no | no | no | ysnA | BA4714 | BC4493 | BH3067 | OB2105 | CAC2665 | CPE2253 | lmo1239 | lin1202 | ysnA | 0 TM
 | ysnB | 10 bp downstream of ysnA stop codon |  |  |  |  | ysnB | 2.398832919019491 | 0.997 |  | 2.046444636724674 | 0.948 |  | 0.3773246289600681 | 0.0105 |  | 1.056081546384562 | 0.670745934979571 |  | ysnB |  |  |  |  |  |  | ysnB | similar to acetyltransferase (calcineurin-like phosphoesterase) | 5.2 (From other organisms) | ysnB | no | no | no | ysnB | BA4713 | BC4492 | BH3066 | OB2104 | CAC2664 | CPE2252 | lmo1240 | lin1203 | ysnB | 0 TM
spoIID | spoIID | TCATATT | 14 | CATAGACT | AGACTAGAGT | 37 | spoIID | 2.432204009073816 | 0.926 |  | 55.20774392807578 | 1 |  | 0.2401082316681688 | 0.003 |  | 0.7382626995841806 | 0.0606984476283506 |  | spoIID | Masaya Fujita | shifted | footprint | (-48)AGGGACAAGC(-57) | (-74)TTGGACAGAA (-83) |  | spoIID | dissolution of the septal cell wall (engulfment and inhibition of septation) | 1.8 (Sporulation) | spoIID | spoIIC | lytB | no | spoIID | spoIID (BA5528) | BC5287 | spoIID | OB2962 | spoIID (CAC2861) and CAC2506 | spoIID (CPE2183) | no | no | spoIID | secreted (pred)
 |  | GAGTCATATTA | 11 | CCCATAGACTA | BioOptimizer prediction-correct | 36 |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | predicted | (-48)AGGGACAAGC(-57) | not predicted
spoIIIAA-AB-AC-AD-AE-AF-AG-AH | spoIIIAA | TCATAAA | 13 | CATACATT | TTAAAGAAGC | 36 | spoIIIAA | 2.735268726306713 | 0.981 |  | 24.21029046736179 | 1 |  | 0.2481774149111892 | 0.003 |  | 0.4466546876562038 | 0.000257855082467784 |  | spoIIIAA | Masaya Fujita | not tested | footprint | (-60)TATGACAAGC(-69) |  |  | spoIIIAA | [NAME] regulation, mutants block sporulation after engulfment | 1.8 (Sporulation) | spoIIIAA | no | no | no | spoIIIAA | spoIIIAA (BA4417) | BC4193 | spoIIIAA | spoIIIAA (OB1894) | CAC2093 | spoIIIAA (CPE1833) | no | no | spoIIIAA | 1 TM (mid)
 |  | TGTTCATAAAT | 12 | GTCATAAAGTC | BioOptimizer-inaccurate | no |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | predicted | (-60)TATGACAAGC(-69)
 | spoIIIAB | 1 bp upstream of spoIIIAA stop codon |  |  |  |  | spoIIIAB | 4.436086439314326 | 0.999 |  | 57.54399373371569 | 1 |  | 0.1949900487235901 | 0.00149999999999995 |  | 0.4958964584293016 | 0.000664037492287384 |  | spoIIIAB |  |  |  |  |  |  | spoIIIAB | [NAME] regulation, mutants block sporulation after engulfment | 1.8 (Sporulation) | spoIIIAB | no | no | no | spoIIIAB | spoIIIAB (BA4416) | BC4192 | spoIIIAB | spoIIIAB (OB1893) | [NAME] | spoIIIAB (CPE1832) | no | no | spoIIIAB | 2 TMs (1 Nter)
 | spoIIIAC | 13 bp downstream |  |  |  |  | spoIIIAC | 4.073802778041128 | 0.997 |  | 9.638290236239706 | 0.984 |  | 0.1494047103427884 | 0.00149999999999995 |  | 0.56686224148655 | 0.0030854016027636 |  | spoIIIAC |  |  |  |  |  |  | spoIIIAC | [NAME] regulation, mutants block sporulation after engulfment | 1.8 (Sporulation) | spoIIIAC | no | no | no | spoIIIAC | spoIIIAC (BA4415) | BC4191 | spoIIIAC | OB1892 | CAC2091 | spoIIIAC (CPE1831) | no | no | spoIIIAC | 2 TMs (1 Nter)
 | spoIIIAD | 22 bp downstream |  |  |  |  | spoIIIAD | 2.910717118066606 | 1 |  | 27.10191631890844 | 0.998 |  | 0.1624164986183673 | 0.002 |  | 0.5834269687298455 | 0.00627780411092671 |  | spoIIIAD |  |  |  |  |  |  | spoIIIAD | [NAME] regulation, mutants block sporulation after engulfment | 1.8 (Sporulation) | spoIIIAD | no | no | no | spoIIIAD | spoIIIAD (BA4414) | BC4190 | spoIIIAD | spoIIIAD (OB1891) | CAC2090 | spoIIIAD (CPE1830) | no | no | spoIIIAD | 3-4 TMs (1 Nter)
 | spoIIIAE | 18 bp downstream |  |  |  |  | spoIIIAE | 2.517676927758856 | 0.995 |  | 32.28494121712635 | 1 |  | 0.1772979705257112 | 0.001 |  | 0.7640384645063978 | 0.0509467919084716 |  | spoIIIAE |  |  |  |  |  |  | spoIIIAE | [NAME] regulation, mutants block sporulation after engulfment | 1.8 (Sporulation) | spoIIIAE | no | no | no | spoIIIAE | spoIIIAE (BA4413) | BC4189 | spoIIIAE | spoIIIAE (OB1890) | CAC2089 | spoIIIAE (CPE1829) | no | no | spoIIIAE | 8 TMs
 | spoIIIAF | overlap |  |  |  |  | spoIIIAF | 2.606153549998896 | 0.998 |  | 47.97334486366894 | 1 |  | 0.2071165080694685 | 0.000499999999999945 |  | 0.733889519919122 | 0.0209107441489649 |  | spoIIIAF |  |  |  |  |  |  | spoIIIAF | [NAME] regulation, mutants block sporulation after engulfment | 1.8 (Sporulation) | spoIIIAF | no | no | no | spoIIIAF | spoIIIAF (BA4412) | BC4188 | spoIIIAF | spoIIIAF (OB1889) | CAC2088 | no? | no | no | spoIIIAF | 2 TMs (1 Nter)
 | spoIIIAG | 2 bp upstream |  |  |  |  | spoIIIAG | 2.716439268839083 | 0.999 |  | 21.13489039836647 | 1 |  | 0.3959931515285581 | 0.03 |  | 0.6704740804206293 | 0.00583040627111331 |  | spoIIIAG |  |  |  |  |  |  | spoIIIAG | [NAME] regulation, mutants block sporulation after engulfment | 1.8 (Sporulation) | spoIIIAG | no | no | no | spoIIIAG | spoIIIAG (BA4411) | BC4187 | spoIIIAG | spoIIIAG (OB1888) | CAC2087 | spoIIIAG (CPE1827) | no | no | spoIIIAG | 1 TM (Nter)
 | spoIIIAH | adjacent |  |  |  |  | spoIIIAH | 2.811900830398941 | 0.999 |  | 8.994975815300352 | 0.999 |  | 0.4176429642650176 | 0.0505 |  | 0.6868166624812966 | 0.011014365862117 |  | spoIIIAH |  |  |  |  |  |  | spoIIIAH | [NAME] regulation, mutants block sporulation after engulfment | 1.8 (Sporulation) | spoIIIAH | no | no | no | spoIIIAH | BA4410 | BC4186 | spoIIIAH | spoIIIAH (OB1887) | CAC2086 | spoIIIAH (CPE1826) | no | no | spoIIIAH | 2 TMs (Nter)
spoIVA | spoIVA-P1 | GAATGAA | 13 | CATACAAA | TAGGGAGAAA (P1) | 158 | spoIVA-P1 | 2.376840286624877 | 0.998 |  | 47.42419852602448 | 1 |  | 0.5044634669517309 | 0.044 |  | 0.7060422524039645 | 0.0194095827346568 |  | spoIVA-P1 | PE815-6 | shifted | predicted | (-255)GGGGACAAAG(-264) | (-227)ACAAACAGGA(-218) | (-208)AAAAACAGGT(-217) | spoIVA-P1 | required for proper spore cortex formation and coat assembly, morphogenetic protein | 1.8 (Sporulation) | spoIVA-P1 | spoVP | no | no | spoIVA-P1 | spoIVA (BA1530) | BC1509 | spoIVA | spoIVA (OB1793) | CAC1713 | spoIVA (CPE1753) | no | no | spoIVA-P1 | 0 TM
 |  | AAGGAATGAAC | 10 | TGCATACAAAT | BioOptimizer prediction-correct | 157
 | spoIVA-P2 | TCATATT | 15 | CATACACA | TATAGTGTCC (P2) | 71
 |  | ATGTCATATTC | 12 | GTCATACACAT | BioOptimizer prediction-correct | 70
spoIVFA-FB | spoIVFA | GAATATT | 14 | CATATGAT | GTACAAAC | 33 | spoIVFA | 3.243396173493493 | 0.997 |  | 20.98939883623525 | 1 |  | 0.1456198956896105 | 0.00149999999999995 |  | 1.099613536073202 | 0.749995253895603 |  | spoIVFA | ODR67-8 | shifted | predicted | (-51)ATGGACAAGA(-42) |  |  | spoIVFA | inhibition of SpoIVFB | 1.8 (Sporulation) | spoIVFA | bofB, spoVL | no | [NAME] | spoIVFA | spoIVFA (BA4679) | BC4441 | spoIVFA | spoIVFA (OB2048) | no | CPE2135 | no | no | spoIVFA | 1 TM (mid)
 |  | ACCGAATATTT | 11 | GACATATGATG | BioOptimizer prediction-correct | 32
 |  | AAGTCATTTTT | 12 | TTAATGTGATA | BioOptimizer-inaccurate | no
 | spoIVFB | 2 bp upstream |  |  |  |  | spoIVFB | 5.623413251903492 | 0.977 |  | 36.05786430216425 | 1 |  | 0.1514052632395501 | 0.000499999999999945 |  | 1.206069577342718 | 0.905043479205742 |  | spoIVFB |  |  |  |  |  |  | spoIVFB | membrane metalloprotease required for the processing of pro-sK to active sK | 1.8 (Sporulation) | spoIVFB | no | no | no | spoIVFB | spoIVFB (BA4678) | BC4440 | spoIVFB | spoIVFB (OB2047) | CAC1253 | CPE2134 | no | no | spoIVFB | 3-4 TMs
[NAME] not included in final total | [NAME] | downstream of spoIVFB (read-through?) |  |  |  |  | [NAME] | 1.85042756115114 | 0.844 |  | 1.960352180115883 | 0.76 |  | 0.4281452550677608 | 0.017 |  | 1.004235481531104 | 0.514431560292054 |  | [NAME]
ysxB not included in final total | ysxB | downstream |  |  |  |  | ysxB | 2.223438673934949 | 0.865 |  | 3.428700099198575 | 0.904 |  | 0.4364621328044681 | 0.013 |  | 1.042210701793399 | 0.642556654409207 |  | ysxB
spoVD | spoVD | [NAME] | 14 | CATAAAAT | GAAACAAG | 32 | spoVD | 3.140508693876217 | 0.998 |  | 43.45102241715716 | 1 |  | 0.2109705653151147 | 0.002 |  | 0.8381497363364021 | 0.2615 |  | spoVD |  |  | footprint | (-48)TTGGACAGGT(-57) | (-33)TGAAACAAGC(-24) |  | spoVD | penicillin-binding protein (spore cortex) | 1.1 (Cell wall) | spoVD | no | pbpB, pbpC, pbpA, pbpI (yrrR), ykuA | ponA, pbpD, pbpF | spoVD | BA4054 | BC3915 | spoVD | spoVD (OB1465) | spoVD (CAC0329) | spoVD ([NAME]) | no [pbpB] | no [pbpB] | spoVD | 3 TMs
 |  | TCGTTCTACCT | 11 | GGCATAAAATG | BioOptimizer prediction-correct | 31 |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | predicted | (-48)TTGGACAGGT(-57) | not predicted
spoVE-murG-B | spoVE | ACATGTT | 13 | CATATGCT | TAAGTAAGGG (P2) | 67 | spoVE | 5.942921586155727 | 0.98 |  | 3.16227766016838 | 0.988 |  | 0.3462749058804098 | 0.006 |  | 0.9181431996143562 | 0.38 |  | spoVE | Masaya Fujita | shifted | footprint | (-205)TTGAACAAGC(-196) | (-57)CAAGACAAGC(-48) |  | spoVE | spore cortex peptidoglycan synthesis | 1.8 (Sporulation) | spoVE | no | ftsW, rodA | no | spoVE | spoVE (BA4050) | BC3911 | spoVE | spoVE (OB1470) | spoVE (CAC2126) | spoVE (CPE1859)/spoVE (CPE2135) | no [lmo1071 (ftsW)] | no [lin1059 (ftsW)] | spoVE | 9 TMs
 |  | GTGACATGTTT | 10 | TGCATATGCTT | BioOptimizer prediction-correct | 66 |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | predicted | (-205)TTGAACAAGC(-196) | (-57)CAAGACAAGC(-48)
 | murG | 122 bp downstream |  |  |  |  | murG | 1.862087136662868 | 0.978 |  | 2.648500138606701 | 0.985 |  | 0.3898319595141425 | 0.0135 |  | 1.370918290265723 | 0.835 |  | murG |  |  |  |  |  |  | murG | UDP-GlcNAc-MurNAc-(pentapeptide) PPi-undecaprenol GlcNAc transferase (EC 2.7.8.13) | 1.1 (Cell wall) | murG | no | no | ugtP, ydhE, yojK, yjiC | murG | murG-1 (BA4049) | BC3910 | murG | murG (OB1093) | murG ([NAME]) | murG (CPE2063) | murG | murG | murG | 2-3 TMs
 | murB | 25 bp downstream |  |  |  |  | murB | 3.258367010020088 | 0.989 |  | 3.09741929921658 | 0.993 |  | 0.4082317114421759 | 0.0145 |  | 1.564945399518519 | 0.891 |  | murB |  |  |  |  |  |  | murB | UDP-N-acetylenolpyruvoylglucosamine reductase | 1.1 (Cell wall) | murB | ylxC | no | no | murB | murB-1 (BA4048)/murB-2 (BA5315) | BC3909 | murB | OB0556 | [NAME] (CAC0510) | murB (CPE0353) | lmo1422 | lin1461 | murB | 1 TM (mid)
divIB not included in final total | divIB | 130 bp downstream of [NAME] (read-through?) |  |  |  |  | divIB | 0.72 | 0.173 |  | 1.66 | 0.884 |  | 0.4199302240671026 | 0.0175 |  | 1.113766411459611 | 0.6475 |  | divIB
ylxW not included in final total | ylxW | overlap |  |  |  |  | ylxW | 0.497737084978936 | 0.039 |  | 2.177709772353159 | 0.961 |  | 0.4564035533452233 | 0.029 |  | 0.9859826610465481 | 0.486 |  | ylxW
ylxX not included in final total | ylxX | 22 bp downstream |  |  |  |  | ylxX | 0.6776415076106751 | 0.138 |  | 1.803017740859569 | 0.949 |  | 0.4982641127678705 | 0.031 |  | 1.011066410410354 | 0.516 |  | ylxX
yabP-Q-divIC | yabP | TTCTAAA | 14 | CATACAAT | GCAGTAATAAT | 44 | yabP | 4.008667176273029 | 0.999 |  | 14.19057521689092 | 1 |  | 0.2740933521899341 | 0.003 |  | 1.078661267801136 | 0.74759769947059 |  | yabP | PE791-2 | shifted | predicted | (-69)TAGAACAAGC(-78) |  |  | yabP | unknown | 1.8 (Sporulation) | yabP | spoVUA | no | no | yabP | BA0057 | BC0063 | BH0074 | OB0068 | CAC3209 | CPE2477 | no | no | yabP | 0 TM
 |  | TTGTTCTAAAA | 11 | CTCATACAATG | BioOptimizer prediction-correct | 43
 | [NAME] | overlap |  |  |  |  | [NAME] | 3.981071705534973 | 0.997 |  | 14.25607593602188 | 1 |  | 0.2440238125254084 | 0.00249999999999995 |  | 1.063627002071858 | 0.680940191201144 |  | [NAME] |  |  |  |  |  |  | [NAME] | spore cortex formation | 1.8 (Sporulation) | [NAME] | spoVUB | no | no | [NAME] | BA0058 | BC0064 | BH0075 | OB0069 | CAC3208 | CPE2476 | no | no | [NAME] | 6 TMs
 | divIC | 17 bp downstream |  |  |  |  | divIC | 2.910717118066606 | 0.993 |  | 9.440608762859235 | 1 |  | 0.259188290670781 | 0.021 |  | 0.9371450152345353 | 0.318897237187948 |  | divIC |  |  |  |  |  |  | divIC | cell-division initiation protein | 1.7 (Cell division) | divIC | no | no | no | divIC | divIC-1 (BA0059)/divIC-2 (BA2853) | BC0065 | divIC | OB0070 | CAC3207 | [NAME] | lmo0219 | [NAME] | divIC | 1 TM
ybaN | ybaN | TTATATT | 14 | [NAME] | GTAAAACAA (5'RACE) | 40 | ybaN | 2.233572222830532 | 0.994 |  | 14.89361077710916 | 0.997 |  | 0.2427355503810915 | 0.002 |  | 1.089072918778418 | 0.76940885416606 |  | ybaN | PE812-ybaN (RACE 4) | shifted | predicted | (-26)ATGGACAAGA(-17) | (-39)TAAAACAAGA(-30) |  | ybaN | polysaccharide deacetylase, similar to YlxY | 2.1.1 (Specific pathways) | ybaN | ybxG | ylxY, yfjS | yjeA, yheN | ybaN | BA0150 | BC0171 | BH0243 | OB0199 | no [CAC2383 (yfjS)] | no [CPE1911] | no [lmo0415 (yjeA)] | no [lin0436 (yjeA)] | ybaN | 1 TM (Nter)
 |  | CGGTTATATTC | 11 | CTCATAAGATG | BioOptimizer prediction-correct | 39
ycgF-G | ycgF | GCATAGC | 14 | AATAAATT | GTACAAGTT (5'RACE) | 34 | ycgF | 2.710191631890843 | 0.994 |  | 7.362070974947363 | 1 |  | 0.08420739769449481 | 0.00849999999999995 |  | 1.247163514103725 | 0.95805405978734 |  | ycgF | PE782-3 | shifted | predicted | (+37)GCAGACAAGG(+46) |  |  | ycgF | putative amino acid transporter (lysine exporter family) | 5.2 (From other organisms) | ycgF | no | no | yisU | ycgF | BA1631 | BC1605 | BH2170 | OB3194 | CAC2593 | CPE2646 | no | no | ycgF | 6 TMs
 |  | TGTGCATAGCT | 11 | CGAATAAATTG | BioOptimizer prediction-correct | 33
 | ycgG | 69 bp downstream |  |  |  |  | ycgG | 4.731512589614805 | 0.971 |  | 11.35010815672315 | 1 |  | 0.189262003225349 | 0.00249999999999995 |  | 0.9833983277420686 | 0.443771749450398 |  | ycgG |  |  |  |  |  |  | ycgG | unknown | 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)
ycgH not included in final total | ycgH | read-through from ycgFG (convergent-31 bp apart)? |  |  |  |  | ycgH | 1.393156802945303 | 0.707 |  | 13.30454417978092 | 0.974 |  | 0.220464521163251 | 0.002 |  | 0.9945802579539613 | 0.481613632189555 |  | ycgH
ykvU-V | ykvU | AAATAAT | 14 | CATATGAT | GTTGGTAGTAC (5'RACE) | 31 | ykvU | 4.027170343254591 | 1 |  | 61.65950018614826 | 1 |  | 0.2131015068906963 | 0.000499999999999945 |  | 1.209106246344164 | 0.888967986622884 |  | ykvU | PE811-ykvU (RACE 2) | shifted | predicted | (-19)AGAGACAAGG(-10) | (-38)TGAGACAAGT(-47) |  | ykvU | similar to spore cortex membrane protein SpoVB | 1.8 (Sporulation) | ykvU | no | spoVB | no | ykvU | no [spoVB (BA4643)] | no [BC4407(spoVB)] | BH0822 | no [spoVB] | CAC1016, CAC1017 | no [spoVB] | no [lmo1624 (ytgP)] | no [lin1665 (ytgP)] | ykvU | 9 TMs
 |  | ATAAAATAATT | 11 | CTCATATGATG | BioOptimizer prediction-correct | 30
 |  | TTTGTCTCAGC | 10 | TTCATATAAAG | BioOptimizer-inaccurate | no
 | ykvV | operon confirmed by RACE (53 bp downstream) |  |  |  |  | ykvV |  |  |  | 6.966265141107687 | 1 |  | 0.3713231724157401 | 0.033 |  | 1.170160461447562 | 0.875966093839972 |  | ykvV |  |  |  |  |  |  | ykvV | sporulation, similar to thioredoxin | 1.4 (Membrane bioenergetics (electron transport chain and ATP synthase)) | ykvV | no | yneN | resA, ykuV, ybdE, trxA | ykvV | BA3674 (yneN/ykvV) | BC3612 (yneN/resA/ykvV) | no [resA] | no [OB0852 (yneN)] | no | no [CPE0741] | no [lmo2830 (trxA)] | no [lin2963 (trxA)] | ykvV | secreted-pred
ylbJ | ylbJ | GTCTAAA | 15 | CGTATATT | AGTACAAAGAAT (5'RACE) | 106 | ylbJ | 2.371373705661656 | 0.995 |  | 31.55004623374628 | 1 |  | 0.2253702538586364 | 0.00149999999999995 |  | 1.479674831704478 | 0.98603904554573 |  | ylbJ | PE804-ylbJ (RACE 2) | shifted | predicted | (-90)GAGGACAGGT(-81) |  |  | ylbJ | sporulation | 5.2 (From other organisms) | ylbJ | no | no | no | ylbJ | [NAME] | BC3928 | BH2588 | OB1452 | CAC1740 | CPE1727 | no | no | ylbJ | 8 TMs
 |  | ATGGTCTAAAC | 12 | CTCGTATATTA | BioOptimizer prediction-correct | 105
 |  | AGGTACTGCTT | 11 | ATCATACATTA | BioOptimizer-inaccurate | no
ylbHI not included in final total | ylbH | read-through from ylbJ (convergent-66bp apart)? |  |  |  |  | ylbH | 0.8649679187756932 | 0.348 |  | 2.884031503126606 | 0.99 |  | 0.4645436432859376 | 0.068 |  | 0.5967604327192868 | 0.187660421874763 |  | ylbH
 | alternative | GTATGGA | 14 | CCTATACA |  | 135
 | ylbI | 10 bp downstream |  |  |  |  | ylbI | 1.253141174941416 | 0.69 |  | 9.61612278383665 | 1 |  | 0.3224869126134487 | 0.005 |  | 1.370281779776615 | 0.984133693587124 |  | ylbI
ypjB | ypjB | GTCTATC | 14 | CATATTCT | GTAAGGAGAGA (5'RACE) | 28 | ypjB | 3.819442708400466 | 0.996 |  | 8.222426499470712 | 0.997 |  | 0.209915680754448 | 0.00149999999999995 |  | 1.175612972334429 | 0.896281073987793 |  | ypjB | PE780-1 | shifted | predicted | (-42)AGGGACAAGG(-51) | (-216)TCAAACAAGT(-207) |  | ypjB | sporulation | 5.2 (From other organisms) | ypjB | no | no | no | ypjB | BA1550 | BC1527 | BH1676 | no | no | no | no | no | ypjB | 2 TMs
 |  | TTGGTCTATCC | 11 | TTCATATTCTG | BioOptimizer prediction-correct | 27
ypjC not included in final total | ypjC | read-through from ypjB? (convergent-41 bp apart) |  |  |  |  | ypjC | 2.466039337234339 | 0.897 |  | 12.97179270983956 | 1 |  | 0.2662177397468626 | 0.006 |  | 1.312250174720532 | 0.962874983778073 |  | ypjC
yqfC-D | yqfC | TGTTAGA | 14 | CATACACA | TGAGATGAAAGGG (5'RACE) | 25 | yqfC | 3.828247433168227 | 0.988 |  | 12.16186000646368 | 1 |  | 0.3780099117236212 | 0.0535 |  | 1.112063089589531 | 0.742252559465573 |  | yqfC | PE803- yqfC (RACE 2) | shifted | predicted | (+34)GCTGACAAGA(+43) |  |  | yqfC | sporulation | 5.2 (From other organisms) | yqfC | no | no | no | yqfC | BA4532 | BC4304 | BH1359 | OB1957 | CAC1290 | CPE2021 | no | no | yqfC | 0 TM
 |  |  |  |  | BioOptimizer-no prediction | no
 | yqfD | 18 bp downstream |  |  |  |  | yqfD | 3.090295432513591 | 0.997 |  | 50.69907082747046 | 1 |  | 0.2317077289476042 | 0.00149999999999995 |  | 0.9660714987862784 | 0.377752885897076 |  | yqfD |  |  |  |  |  |  | yqfD | stage IV sporulation protein (B. megaterium) | 1.8 (Sporulation) | yqfD | no | no | no | yqfD | BA4530 | BC4303 | BH1360 | OB1956 | CAC1291 | spoIV (CPE2020) | no | no | yqfD | 1 TM (mid)
phoH not included in final total | phoH | overlap (read-through?) |  |  |  |  | phoH | 1.438798578255845 | 0.865 |  | 4.385306977749858 | 0.997 |  | 0.4101349056769808 | 0.0225 |  | 0.8616488526913734 | 0.106986390048988 |  | phoH
yqfF not included in final total | yqfF | 78 bp downstream |  |  |  |  | yqfF | 1.227439231158407 | 0.811 |  | 2.018366363681561 | 0.964 |  | 0.499212765396191 | 0.0335 |  | 1.032157243721549 | 0.61578327372882 |  | yqfF
[NAME] | [NAME] | TCATGAA | 14 | CATACTAT | GGTATAAAATTTC (5'RACE) | 32 | [NAME] | 3.213660538640318 | 0.999 |  | 38.01893963205614 | 1 |  | 0.08646571594406308 | 0.000499999999999945 |  | 1.319692235070218 | 0.978964426747126 |  | [NAME] | PE814-yqfZ (RACE 3) | shifted | predicted | (-49)ATGGACAAGC(-40) |  |  | [NAME] | unknown | 5.2 (From other organisms) | [NAME] | no | no | no | [NAME] | BA4501 | BC4275 | BH1402 | OB1935 | no | no | no | no | [NAME] | secreted-pred
 |  | TTGTCATGAAT | 11 | AGCATACTATG | BioOptimizer prediction-correct | 31
 | yqfY | operon confirmed by RACE (121 bp downstream) |  |  |  |  | yqfY | 1.86637969083467 | 0.981 |  | 9.705099672454896 | 0.999 |  | 0.1812537906211763 | 0.001 |  | 0.9322197771087538 | 0.271122747406054 |  | yqfY |  |  |  |  |  |  | yqfY | similar to [NAME]: nonmevalonate pathway to terpenes-isoprenoids | 1.1 (Cell wall) | yqfY | no | no | no | yqfY | [NAME] (BA4502) | BC4276 | gcpE | no? | [NAME] (CAC1797) | gcpE (CPE1692) | lmo1441 | no | yqfY | 2 TMs
1.1 A. b) not tested by gel-shift
[NAME] | [NAME] | TCATATT | 14 | CATAGTTA | TGTAATAACG | 30 | [NAME] | 9.660508789898138 | 1 |  | 16.74942876026438 | 1 |  | 0.1863459445844145 | 0.002 |  | 1.009970628284469 | 0.535139994788268 |  | [NAME] |  |  | predicted | (-23)ACGGACAAGC(-14) | (-37)TGGGACAGGG(-46) |  | [NAME] | N-acetylmuramoyl-L-alanine amidase (sporulation, germination) | 1.1 (Cell wall) | [NAME] | no | lytC | yqiI, yrvJ, cwlC | [NAME] | [NAME] (BA0146) | BC0167 | [NAME] | OB0195 | 231 (CAC3092) | CPE2367 | no [lmo1521(yrvJ)] | no [lin1556 (yrvJ)] | [NAME] | cell wall (secreted)
 |  | TAATCATATTT | 11 | CCCATAGTTAT | BioOptimizer prediction-correct | 29
mmgA-B-C-D-E-yqiQ | mmgA | TCATTCA | 14 | CATACATT | CATAGAAGAC | 56 | mmgA | 2.35504928389601 | 0.995 |  | 53.33348954876212 | 1 |  | 0.4912639007782643 | 0.097 |  | 1.057389241076234 | 0.6933163501653 |  | mmgA |  |  | no prediction |  |  |  | mmgA | acetyl-CoA acetyltransferase | 2.4 (Metabolism of lipids) | mmgA | yqiL, thl | yusK, yhfS | no | mmgA | BA5589 | BC5344 | mmgA | OB3013/OB2632 | CAC2873 | atoB (CPE2125) | lmo1414 | [NAME] | mmgA | 2 TMs
 |  | CATTCATTCAT | 11 | AGCATACATTC | BioOptimizer prediction-correct | 55
 | mmgB | 24 bp downstream |  |  |  |  | mmgB | 2.564484036517718 | 0.995 |  | 27.54228703338167 | 1 |  | 0.5443113783740048 | 0.049 |  | 0.9594889627349312 | 0.351624205391845 |  | mmgB |  |  |  |  |  |  | mmgB | 3-hydroxybutyryl-CoA dehydrogenase | 2.4 (Metabolism of lipids) | mmgB | yqiM | yusL | no | mmgB | BA5588 | BC5343 | mmgB | OB3012 | mmgB (CAC2009) | CPE2297 | no | no | mmgB | 0-1 TM (mid)
 | mmgC | 27 bp downstream |  |  |  |  | mmgC | 2.26464430759306 | 0.997 |  | 67.14288529259524 | 1 |  | 0.5271410235174839 | 0.043 |  | 1.013096410463961 | 0.546908647137834 |  | mmgC |  |  |  |  |  |  | mmgC | acyl-CoA dehydrogenase, similar to AcdA and YngJ | 2.4 (Metabolism of lipids) | mmgC | yqiN, [NAME] | acdA, yngJ, yusJ | ydbM | mmgC | BA5587 | BC5342 | mmgC | OB3011 | bcd (CAC2711) [yngJ,mmgC,acdA] | bcd (CPE2300) | no | no | mmgC | 2 TMs
 | mmgD | 33 bp downstream |  |  |  |  | mmgD | 2.460367604147628 | 0.996 |  | 108.3926914021205 | 1 |  | 0.5100668958122978 | 0.0305 |  | 1.058216466192264 | 0.667306543442287 |  | mmgD |  |  |  |  |  |  | mmgD | citrate synthase III | 2.1.3 (TCA cycle) | mmgD | yqiO | citZ, citA | no | mmgD | BA2348 | BC2285 | mmgD | OB2269 | no | no | no [citZ] | no [citZ] | mmgD | 1 TM (mid)
 | mmgE | 14 bp downstream |  |  |  |  | mmgE | 2.187761623949553 | 0.996 |  | 60.67363295885055 | 1 |  | 0.4628026923978251 | 0.025 |  | 1.010330903337121 | 0.535271544463214 |  | mmgE |  |  |  |  |  |  | mmgE | unknown, possibly involved in propionate catabolism | 4.6 (Miscellaneous) | mmgE | yqiP | no | no | mmgE | BA2349 | BC2286 | BH3923 | OB2268 | no | no | no | no | mmgE | 1 TM (Nter) or 2 TMs
 | yqiQ | 17 bp downstream |  |  |  |  | yqiQ | 1.923091728910158 | 0.987 |  | 9.246981739382225 | 1 |  | 0.4962445681707012 | 0.033 |  | 0.9787166968842962 | 0.424784519673461 |  | yqiQ |  |  |  |  |  |  | yqiQ | phosphoenolpyruvate mutase (carboxyvinyl-carboxyphosphonate phosphorylmutase) | 2.1.1 (Specific pathways) | yqiQ | no | no | no | yqiQ | BA2350 | BC2287 | BH3922 | OB2267 | no | no | lmo0075 | lin0067 | yqiQ | 1 TM (Nter)
phoB-ydhF | phoB | TTCTAAA | 14 | AATAACCA | TTATTTAAGGGTG | 119 | phoB | 2.238721138568339 | 0.981 |  | 29.37649651961531 | 1 |  | 0.5713986974469293 | 0.0555 |  | 0.447918953413681 | 0.00041987325585302 |  | phoB |  |  | no prediction |  |  |  | phoB | alkaline phosphatase III (EC 3.1.3.1) | 2.6 (Metabolism of phosphate) | phoB | phoAIII | phoA | no | phoB | BA4574 | BC4343 | no [BH0874 (phoA)] | no [OB1029 (phoA)] | no | no | no | no | phoB | secreted (pred)-1-2 TMs
 |  | TCGCTCTTTCC | 11 | CTCATAAAAGA | BioOptimizer-inaccurate | no
 | ydhF | 60 bp downstream |  |  |  |  | ydhF | 3.213660538640318 | 0.999 |  | 17.82378767448089 | 1 |  | 0.2476654054781528 | 0.012 |  | 0.4578425039293085 | 0.000406219006439668 |  | ydhF |  |  |  |  |  |  | ydhF | induced by phosphate starvation | 2.6 (Metabolism of phosphate) | ydhF | no | no | yonS | ydhF | no | no | no | no | no | no | no | lin1232 | ydhF | 1 TM (Nter)
yaaH | yaaH | ACATGAT | 14 | CATACATT | GATAGCGATAT | 40 | yaaH | 3.033891184194271 | 0.999 |  | 205.5890595984143 | 1 |  | 0.3311861791935403 | 0.00949999999999995 |  | 1.141098580390048 | 0.790813652546939 |  | yaaH |  |  | predicted | TAAAACAAGG |  |  | yaaH | spore protein required for the L-alanine-stimulated germination pathway, similar to YdhD, similar to spore peptidoglycan hydrolase (sleL) | 1.8 (Sporulation) | yaaH | no | ydhD, yvbX | ykvQ, xlyA, lytF, yojL | yaaH | BA3668 | sleL (BC3607) | BH2292 | OB0024 (yaaH/ydhD) | [NAME] (yaaH/ydhD) | no | no | no | yaaH | 0 TM
 |  | TAAACATGATC | 11 | TTCATACATTG | BioOptimizer prediction-correct | 39
[NAME] (yaaG) not included in final total | [NAME] (yaaG) | downstream (read-through?) |  |  |  |  | [NAME] (yaaG) | 1.481957811543201 | 0.876 |  | 0.9675821770044882 | 0.468 |  | 0.1692046318382371 | 0.0465 |  | 1.291582727767826 | 0.917931470041593 |  | [NAME] (yaaG)
ydcC-alr | ydcC | GCATATT | 14 | CATATATT | TGATAGTGCATT (5'RACE) | 28 | ydcC | 3.221068791283435 | 0.999 |  | 48.64072056914618 | 1 |  | 0.1728668104808115 | 0 |  | 1.030802860122817 | 0.57672364180691 |  | ydcC |  |  | predicted | TCAAACAAGC |  |  | ydcC | unknown | 5.2 (From other organisms) | ydcC | no | no | no | ydcC | BA0251 | BC0263 | BH0519 | OB0621 | CAC0491 | CPE0293 | no | no | ydcC | 1 TM (Nter)
 |  | TCTGCATATTA | 11 | CTCATATATTT | BioOptimizer prediction-correct | 27
 | alr (dal) | 114 bp downstream |  |  |  |  | alr (dal) | 2.824879974915707 | 0.996 |  | 4.456562483975033 | 0.994 |  | 0.3927378390111075 | 0.016 |  | 1.140979606761942 | 0.845382042530147 |  | alr (dal) |  |  |  |  |  |  | alr (dal) | D-alanine racemase (EC 5.1.1.1), similar to yncD | 2.2 (Metabolism of amino acids and related molecules) | alr (dal) | dal | yncD | no | alr (dal) | dal-1 (BA0252) | BC0264 | BH0520 | OB3149/OB3226 | CAC0492 | alr (CPE1061) | dal | lin0885 | alr (dal) | 0 TM
yhaX-hemZ | yhaX | TTCTAAA | 14 | CATATCCT | ATACACAAGTAC (5'RACE) | 37 | yhaX | 2.837919028441556 | 0.989 |  | 22.59435770220979 | 1 |  | 0.3894204560514606 | 0.0105 |  | 0.9526231309616301 | 0.351726005529112 |  | yhaX |  |  | predicted | (-56)AGAGACAGGG(-47) |  |  | yhaX | hydrolase [HAD (haloacid dehalogenase-like hydrolase) superfamily], spore coat protein (inner), PhoP-regulated | 5.1 (From B. subtilis) | yhaX | no | yitU, ycsE, ykrA | ywpJ, yxeH, ywtE | yhaX | BA0870 | BC0886 | BH1151 | no [OB2536 (ycsE)] | no [CAC0698 (yxeH)] | no [CPE1569] | no [lmo0158 (yxeH)] | no [[NAME] (yxeH)] | yhaX | 0 TM
 |  | TTGTTCTAAAC | 11 | GTCATATCCTA | BioOptimizer prediction-correct | 36
 | hemZ (yhaV) | 113 bp downstream |  |  |  |  | hemZ (yhaV) | 2.344228815319922 | 0.995 |  | 6.531305526474723 | 0.999 |  | 0.4802079905624594 | 0.0255 |  | 1.000711442147931 | 0.502369513999267 |  | hemZ (yhaV) |  |  |  |  |  |  | hemZ (yhaV) | coproporphyrinogen III oxidase (heme metabolism) | 2.5 (Metabolism of coenzymes and prosthetic groups) | hemZ (yhaV) | yhaWV | hemN | yqeV | hemZ (yhaV) | BA0871 | BC0889 | BH1152 | no [hemN] | CAC2271 | hemZ (CPE1935) | no [hemN] | no [hemN] | hemZ (yhaV) | 0 TM
yhbH | yhbH | TCAATTA | 14 | CATATGAT | [NAME] (5'RACE) | 93 | yhbH | 2.506109253032114 | 0.99 |  | 42.07266283844444 | 1 |  | 0.4786002156281538 | 0.0315 |  | 0.7096674296686571 | 0.0236775288253044 |  | yhbH |  |  | predicted | TGAAACAAGT |  |  | yhbH | sporulation, PhoP-regulated, putative glycosyltransferase | 5.2 (From other organisms) | yhbH | yzdC | no | no | yhbH | BA0551 | BC0551 | BH1031 | OB2647 | CAC0580 | CPE1333 | no | no | yhbH | 0 TM
 |  | TTTGTCAATTA | 12 | TGCATATGATG | BioOptimizer prediction-correct | 92
 |  | GTTTCATAATC | 11 | GGAATACGTAT | BioOptimizer-inaccurate | no
yjcA (absent from Eichenberger et al., 2003) | yjcA | TCATGAA | 14 | CATATATG | TGAAGGGATCAT | 33 | yjcA |  |  |  | 5.000345349769785 | 0.998 |  | 0.4844112797954764 | 0.0485 |  | 1.470881838471932 | 0.989469104943885 |  | yjcA |  |  | predicted | (-78)CCGGACAAGA(-69) |  |  | yjcA | unknown | 5.1 (From B. subtilis) | yjcA | no | no | yngL | yjcA | BA1235 | BC1219 | BH2840 | no | no | no | no | no | yjcA | 3 TMs
 |  |  |  |  | not included in BioOptimizer list of sequences
yjmC-D-uxuA-yjmF-exuT-R | yjmC | GAATATT | 14 | AATAAAAT | GTGTTTGTAG | 61 | yjmC | 5.420008904016239 | 1 |  | 55.46257129579109 | 1 |  | 0.3911038774729071 | 0.0175 |  | 1.283015773918811 | 0.96597108903221 |  | yjmC |  |  | no prediction |  |  |  | yjmC | hexuronate utilization operon, malate dehydrogenase | 2.1.3 (TCA cycle) | yjmC | ssd | no | no | yjmC | no | no | no | OB2846 | CAC0566 | no | no | no | yjmC | 2 TMs
 |  | AAAGAATATTT | 11 | TAAATAAAATG | BioOptimizer prediction-correct | 60
 | yjmD | 5 bp downstream |  |  |  |  | yjmD | 3.523708710424872 | 0.999 |  | 64.71426157485834 | 1 |  | 0.2710981819507991 | 0.006 |  | 1.43336993509112 | 0.955303415230331 |  | yjmD |  |  |  |  |  |  | yjmD | hexuronate utilization operon, alcohol dehydrogenase | 2.1.1 (Specific pathways) | yjmD | no | gutB, tdh, ydjL, adhB, yycR | yogA, adhA, yhfP | yjmD | no | no | no | no [OB3353 (ydjL)] | no | no | no [lmo0506 (gutB)] | no [lin0506 (gutB)] | yjmD | 1 TM
 | uxuA (yjmE) | 24 bp downstream |  |  |  |  | uxuA (yjmE) | 8.790225168308844 | 0.997 |  | 84.13951416451953 | 1 |  | 0.2413235482645019 | 0.00349999999999995 |  | 1.364279520063677 | 0.963763388002936 |  | uxuA (yjmE) |  |  |  |  |  |  | uxuA (yjmE) | hexuronate utilization operon, D-mannonate hydrolase | 2.1.1 (Specific pathways) | uxuA (yjmE) | yjmE | no | no | uxuA (yjmE) | no | no | BH1063 | OB3411 | [NAME] | CPE0151 | no | no | uxuA (yjmE) | 0 TM
 | yjmF | overlap |  |  |  |  | yjmF | 9.311078754678306 | 0.999 |  | 18.70682140365801 | 0.977 |  | 0.2723916987239573 | 0.005 |  | 1.440692480801756 | 0.952996339945418 |  | yjmF |  |  |  |  |  |  | yjmF | hexuronate utilization operon, D-mannonate oxidoreductase | 2.1.1 (Specific pathways) | yjmF | no | ycdF, ywfD, dhbA, yxbG, gdh, fabG, kduD, yhdF, [NAME] | yhxC, ykuF, yxjF, yoxD, dltE, ywfH, yjdA, yhxD. yvrD, ymfI, yvaG, ykvO, yuxG, ytkK, yqjQ, yusZ, yueD, yusS, fabI | yjmF | no | no | BH1067 | OB3412 | CAC1331 | [NAME] | no [fabG (fabG)] | no [fabG (fabG)] | yjmF | 3 TMs
 | exuT (yjmG) | 47 bp downstream |  |  |  |  | exuT (yjmG) | 8.851156098308355 | 1 |  | 70.95777679633893 | 1 |  | 0.2563103921850079 | 0.004 |  | 1.678925280001886 | 0.98452820447087 |  | exuT (yjmG) |  |  |  |  |  |  | exuT (yjmG) | hexuronate utilization operon, hexuronate transporter | 1.2 (Transport/binding proteins and lipoproteins) | exuT (yjmG) | yjmG | ycbE, yybO, glpT | yceJ, yfmO, yceI, yitG, nasA, yhcA, [NAME], ydhL, yvmA, araE, ycnB, lmrB, ywtG, yyaJ, yqjV, [NAME], ytbD, iolF, ydgK, blt…. | exuT (yjmG) | BA3267 | no | no | no [OB0072 (yhcA)] | no | no [glpT] | no | no | exuT (yjmG) | 8-9 TMs
 | exuR (yjmH) | 87 bp downstream |  |  |  |  | exuR (yjmH) | 2.904022654464451 | 0.989 |  | 15.4170045294956 | 1 |  | 0.2764623239851333 | 0.005 |  | 1.222731956069443 | 0.92754021632341 |  | exuR (yjmH) |  |  |  |  |  |  | exuR (yjmH) | hexuronate utilization operon, transcriptional repressor of the hexuronate utilization operon | 3.5.2 (Regulation) | exuR (yjmH) | yjmH | ccpA, yhjM, degA, rbsR, msmR, yvdE, ykvZ, kdgR, ccpB, lacR | araR, rbsB | exuR (yjmH) | no | no | no [BH3692 (degA)] | no [ccpA (OB2226)] | CAC0693 | no [ccpA] | no [lmo1994 (degA)] | no [lin2102 (degA)] | exuR (yjmH) | 1 TM (mid)
uxaB ([NAME]) not included in final total | uxaB ([NAME]) | downstream of exuR (read-through?) |  |  |  |  | uxaB ([NAME]) |  |  |  | 2.095871731189274 | 0.861 |  | 0.4456303914469224 | 0.018 |  | 1.171544435140154 | 0.83992225558178 |  | uxaB ([NAME])
ykvI | ykvI | TCTTTTC | 13 | CATAGGTT | ATAAAAAGG (5'RACE) | 48 | ykvI | 4.570881896148751 | 1 |  | 40.08667176273029 | 1 |  | 0.190493680239296 | 0.001 |  | 1.163976976241849 | 0.830850896218838 |  | ykvI |  |  | predicted | (-65)TGAGACAAGT(-74) |  |  | ykvI | similar to YyaD | 5.1 (From B. subtilis) | ykvI | no | no | yyaD, yhdH | ykvI | BA2012 | BC2010 | BH4053 (ykvI/yyaD) | OB3223 | CAC3241(ykvI/yyaD) | CPE2559 (ykvI/yyaD) | no | no | ykvI | 10 TMs
 |  | TTCGTCTTTTC | 11 | CTCATAGGTTA | BioOptimizer prediction-correct | 47
yngJ-I-H-G-F-E(-D) | yngJ | GAATGAT | 14 | AATAGGAT | GTTACAAAGATGTGA (5'RACE) | 28 | yngJ | 2.243881923782766 | 0.983 |  | 37.6703798983909 | 1 |  | 0.3438113352608594 | 0.0125 |  | 1.156427390766987 | 0.858762757489692 |  | yngJ |  |  | no prediction |  |  |  | yngJ | butyryl-CoA dehydrogenase, similar to MmgC and AcdA | 2.4 (Metabolism of lipids) | yngJ | no | mmgC, acdA, yusJ | ydbM | yngJ | BA2547 | BC5341 (yngJ/acdA) | BH1130 | OB1695 | bcd (CAC2711) [yngJ,mmgC,acdA] | bcd (CPE2300) | no | no | yngJ | 2 TMs
 |  | AGGGAATGATT | 11 | CTAATAGGATG | BioOptimizer prediction-correct | 27
 |  | ACTGCATGTAT | 12 | CTGATATTATC | BioOptimizer-inaccurate | no
 | yngI | 43 bp downstream |  |  |  |  | yngI | 2.238721138568339 | 0.989 |  | 61.94410750767816 | 1 |  | 0.3457307712192731 | 0.0145 |  | 1.157875848431009 | 0.877613389172158 |  | yngI |  |  |  |  |  |  | yngI | long-chain acyl-CoA synthetase | 2.4 (Metabolism of lipids) | yngI | no | lcfA, yhfL, menE, dhbE, ydaB, acsA, yhfT, ppsB, srfAA, ytcI, pksJ, srfAB, srfAc, pksN, ppsC, dhbF, ppsA, ppsD, dltA | ppsE | yngI | no | no | BH1131 | OB2217 | no | no | no [menE] | no [menE] | yngI | 2 TMs
 | yngH | 9 bp downstream |  |  |  |  | yngH | 2.197859872784825 | 0.994 |  | 57.94286964268813 | 1 |  | 0.3611069426400964 | 0.009 |  | 1.16718945394128 | 0.876205105330895 |  | yngH |  |  |  |  |  |  | yngH | [NAME] | 2.5 (Metabolism of coenzymes and prosthetic groups) | yngH | no | accC, pycA | carB, pyrAB | yngH | BA2548 | BC2484 | BH1132 | OB1696 | no [accC (CAC3570) (accC)] | no [accC (CPE1074)] | no [lmo1357(accC)] | no [lin1394 (accC)] | yngH | 0 TM
 | yngG | 250 bp downstream |  |  |  |  | yngG | 2.192804935350449 | 0.991 |  | 72.61059574351552 | 1 |  | 0.3235240362616038 | 0.014 |  | 1.18329166306667 | 0.875590719522847 |  | yngG |  |  |  |  |  |  | yngG | hydroxymethylglutaryl-CoA lyase | 2.4 (Metabolism of lipids) | yngG | no | no | leuA | yngG | mvaB (BA2550) | BC2486 | BH1133 | OB1343 | no | no | no [leuA] | no [leuA] | yngG | 1 TM (mid)
 | yngF | 20 bp downstream |  |  |  |  | yngF | 2.466039337234339 | 0.997 |  | 35.7272838151929 | 1 |  | 0.3075387949572408 | 0.00749999999999995 |  | 1.329574202445956 | 0.95356227685842 |  | yngF |  |  |  |  |  |  | yngF | 3-hydroxbutyryl-CoA dehydratase | 2.4 (Metabolism of lipids) | yngF | no | ysiB, menB, yhaR | no | yngF | BA2551 | BC2487 | BH1134 | OB1698 | crt (CAC2712) | [NAME] (CPE2301) | no [menB] | no [menB] | yngF | 0-1 TM
 | yngE | 236 bp upstream |  |  |  |  | yngE | 2.35504928389601 | 0.992 |  | 38.63669770540694 | 1 |  | 0.2936493167282286 | 0.006 |  | 1.325046848115029 | 0.97997829476478 |  | yngE |  |  |  |  |  |  | yngE | propionyl-CoA carboxylase | 2.1.1 (Specific pathways) | yngE | no | yqjD | accA, accD | yngE | BA2552 | BC2488 | BH1135 | OB1699 | no | no | no [accD] | no [accD] | yngE | 2 TMs
yngD | yngD | 173 bp downstream of yngE |  |  |  |  | yngD | 2.411476290945105 | 0.981 |  | 2.363068984113916 | 0.962 |  | 0.4265378760947432 | 0.0665 |  | 1.052219905116993 | 0.676006655245972 |  | yngD
yngC not included in final total | yngC | readthrough from yngD (convergent-48 bp apart)? |  |  |  |  | yngC | 1 | 0.501 |  | 5.046612975635284 | 0.953 |  | 0.3695318175968882 | 0.0475 |  | 1.165830175687985 | 0.902139089117236 |  | yngC
"ytrH"-ytrI | "ytrH" | TCATACT | 14 | AATATGAT | ATAAAAGGT (5'RACE) | 21 | "ytrH" | not on the array |  |  | not on the array |  |  | not on the array |  |  | not on the array |  |  | "ytrH" |  |  | predicted | (-37)CAGGACAAGT(-46) |  |  | "ytrH" | sporulation | 5.2 (From other organisms) | "ytrH" | no |  |  | "ytrH" | BA4850 | BC4606 | BH3170 | OB2178 | no | no | no | no | "ytrH" | 3 TMs
 |  |  |  |  | not included in BioOptimizer list
 | ytrI | overlap |  |  |  |  | ytrI | 5.093308710571954 | 0.998 |  | 22.69864851883823 | 1 |  | 0.1750535147016138 | 0.00149999999999995 |  | 1.330345762728396 | 0.977153316484776 |  | ytrI |  |  |  |  |  |  | ytrI | sporulation | 5.2 (From other organisms) | ytrI | no | no | no | ytrI | BA4851 | BC4607 | BH3171 | OB2179 | no | no | no | no | ytrI | 1 TM -Nter
ytvI | ytvI | TCATATT | 13 | AATACATA | TAAAAAATAGG (5'RACE) | 39 | ytvI | 2.004472027365162 | 0.851 |  | 70.30723198838339 | 0.998 |  | 0.1882587699519727 | 0.00249999999999995 |  | 1.267430217436133 | 0.941730145918083 |  | ytvI |  |  | no prediction |  |  |  | ytvI | sporulation (putative permease), similar to YdbI | 5.2 (From other organisms) | ytvI | no | no | yubA, yueF | ytvI | BA4841 | BC4597 | BH0463 | OB2169 | CAC1794 | CPE2648 | no [lmo0584 (yubA)] | no [lin0593 (yubA)] | ytvI | 8 TMs
 |  | TATTCATATTC | 10 | TGAATACATAT | BioOptimizer prediction-correct | 38
ytzA | ytzA | readthrough from ytvI (convergent) |  |  |  |  | ytzA | 1.142009782213101 | 0.651 |  | 1.198558013709047 | 0.572 |  | 0.3572777839762083 | 0.0105 |  | 1.20394157101544 | 0.930477313372523 |  | ytzA
ytxC | ytxC | GTCTATT | 14 | CATATACT | TGTAACAGATG (5'RACE) | 29 | ytxC | 6.591738952443214 | 0.999 |  | 28.24879974915709 | 1 |  | 0.2514576834329591 | 0.00349999999999995 |  | 1.049781837443655 | 0.639363233640095 |  | ytxC |  |  | no prediction |  |  |  | ytxC | unknown | 5.2 (From other organisms) | ytxC | no | no | no | ytxC | BA4821 | BC4577 | BH3142 | OB2155 | CAC2363 | CPE1895 | no | no | ytxC | 0 TM
 |  | TACGTCTATT | 11 | CCCATATACTT | BioOptimizer prediction-correct | 28
 |  | GCTTTCTTTAT | 11 | TGTATATCGTG | BioOptimizer-inaccurate | no
yxjC-scoA-B-yxjF | yxjC | GAATAGT | 14 | CGTACATA | TGGAAAGGGG (5'RACE) | 78 | yxjC | 2.97851642942919 | 0.996 |  | 31.6227766016838 | 1 |  | 0.2377976993964482 | 0.002 |  | 1.213061247298677 | 0.9099760658726 |  | yxjC |  |  | predicted | (-54)GCGGACAGGT(-45) |  |  | yxjC | putative propionate permease | 5.2 (From other organisms) | yxjC | no | no | no | yxjC | BA2221 | BC2175 | BH3897 | OB2630 | no | CPE0772 | no | no | yxjC | 11 TMs
 |  | TCGGAATAGT | 11 | CTCGTACATAT | BioOptimizer prediction-correct | 77
 | scoA (yxjD) | 20 bp downstream |  |  |  |  | scoA (yxjD) | 2.917427014001167 | 0.958 |  | 63.3869711256927 | 0.999 |  | 0.2455163025155847 | 0.00249999999999995 |  | 1.100578940056063 | 0.787046519970543 |  | scoA (yxjD) |  |  |  |  |  |  | scoA (yxjD) | succinyl CoA:3-oxoacid CoA-transferase (subunit A) (EC 2.8.3.5), similar to YodS | 2.4 (Metabolism of lipids) | scoA (yxjD) | yxjD | yodS | no | scoA (yxjD) | no | BC2246 (yodS/scoA) | BH3898 | OB2634 (yodS/scoA) | no | no [CPE0096] | [NAME] | [NAME] | scoA (yxjD) | 1-2 TMs (1 Nter)
 | scoB (yxjE) | overlap |  |  |  |  | scoB (yxjE) | 2.679168324819032 | 0.917 |  | 4.77529273657691 | 0.997 |  | 0.2901143126326725 | 0.00249999999999995 |  | 1.087938962300564 | 0.751938718477098 |  | scoB (yxjE) |  |  |  |  |  |  | scoB (yxjE) | succinyl CoA:3-oxoacid CoA-transferase (subunit B) (EC 2.8.3.5), similar to YodR | 2.4 (Metabolism of lipids) | scoB (yxjE) | yxjE | yodR | no | scoB (yxjE) | no | BC2247 (yodR/scoB) | no | OB2633 (yodR/scoB) | no | no [CPE0096] | no [[NAME] (scoA)] | no [[NAME] (scoA)] | scoB (yxjE) | 0 TM
 | yxjF | 16 bp downstream |  |  |  |  | yxjF | 2.648500138606701 | 0.939 |  | 17.45822152920504 | 0.994 |  | 0.271453947293136 | 0.00349999999999995 |  | 0.925761813881028 | 0.259339640020967 |  | yxjF |  |  |  |  |  |  | yxjF | gluconate 5-dehydrogenase | 2.1.1 (Specific pathways) | yxjF | no | yxgB, ywfD, fabG, kduD, gdh, dhbA, yuxG, ycdF, ywfH, ykuF, ymfI, yvrD, yoxD, fabL, ytkK, yhxC, yhxD, yusZ, yvaG | yhdF, ykvO, ydaD, yqjQ, yjmF, yxnA, yjdA, yusS, pksN, fabI, yusR, dltE, pksJ, pksL, yueD | yxjF | BA4249 | BC4030 | no | OB2631 | no | no [fabG] | no [fabG (fabG)] | no [fabG (fabG)] | yxjF | 1 TM (mid)
yyaD | yyaD | GCATGTT | 14 | TATATAGT | AACAATAACGGG (5'RACE) | 42 | yyaD | 3.404081897010009 | 0.955 |  | 63.24118513762197 | 0.999 |  | 0.1943874577779171 | 0 |  | 1.037399233483034 | 0.58770790159974 |  | yyaD |  |  | predicted | (-180)GCGGACAAAC(-171) | (-33)GGGAACAAGCT(-24) |  | yyaD | similar to YkvI | 5.2 (From other organisms) | yyaD | no | no | ykvI | yyaD | BA2012 (ykvI/yyaD) | BC2010 (ykvI/yyaD) | BH4053 (ykvI/yyaD) | OB3483 | CAC3241(ykvI/yyaD) | CPE2559 (ykvI/yyaD) | no | no | yyaD | 10 TMs
 |  | ATGGCATGTTT | 11 | TTTATATAGTA | BioOptimizer prediction-correct | 41
 | yyaE | 354 bp downstream of yyaD
1.1. B. below cut-off in sigE+ vs. sigE- experiments but identified by overexpression of sE
none
1.1. C. not identified by overexpression of sE
none
1.2. Previously reported sE-controlled genes (but transcription start site has not been mapped):
1.2. A. also identified by overexpression of sE
1.2. A. a) SpoIIID binding confirmed by gel-shift
spoVB | spoVB | TCATGCT | 15 | CATATCTT | not mapped | 44 | spoVB | 2.65460556197554 | 0.994 |  | 15.7398286446622 | 1 |  | 0.1362163836496796 | 0.006 |  |  |  |  | spoVB | PE797-8 | shifted | predicted | (-70)CATGACAAGT(-79) |  |  | spoVB | spore cortex synthesis | 1.8 (Sporulation) | spoVB | spoIIIF | ykvU, ytgP, yabM | yoeA | spoVB | spoVB (BA4643) | BC4407 | spoVB | spoVB (OB2029) | CAC3213 | spoVB ([NAME]) | no [lmo0215 ([NAME])] | no [lin247(yabM)] | spoVB | 13 TMs
 |  | TTGTCATGCTT | 12 | CGCATATCTTT | BioOptimizer-prediction | 43
 |  | ACGACATATAC | 12 | TGTATATGATT | BioOptimizer-prediction
1.2. A. b) not tested by gel-shift
dacB-spmA-B | dacB | TCATAAC | 13 | CATAAACT | not mapped | 31 | dacB | 3.33426412763235 | 0.941 |  | 9.862794856312105 | 0.964 |  | 0.1537192756137975 | 0.00149999999999995 |  | 1.085337110362812 | 0.74232083269989 |  | dacB |  |  | no prediction |  |  |  | dacB | penicillin-binding protein 5* (D-alanyl-D-alanine carboxypeptidase) | 1.1 (Cell wall) | dacB | [NAME]* | dacF, dacA | no | dacB | BA1490 | BC1469 | BH1573 | dacB (OB1826) | dacB ([NAME]) | dacB (CPE1801) | no [[NAME] (dacA)] | no [lin2897(dacA)] | dacB | cell wall (secreted)
 |  | TATTCATAACT | 10 | CGCATAAACTT | BioOptimizer-prediction | 30
 | spmA | 7 bp upstream |  |  |  |  | spmA | 5.7 | 0.992 |  |  |  |  | 0.09394728251372352 | 0.001 |  | 1.23354482887354 | 0.89779357327985 |  | spmA |  |  |  |  |  |  | spmA | spore maturation protein (spore core dehydratation) | 1.8 (Sporulation) | spmA | ypuJ | no | no | spmA | spmA (BA1491) | BC1470 | BH1574 | spmA (OB1825) | spmA (CAC0469) | spmA (CPE2533) | no | no | spmA | 5 TMs
 | spmB | 4 bp downstream |  |  |  |  | spmB | 1.887991349096294 | 0.858 |  | 18.07174126010927 | 0.989 |  | 0.322163233102674 | 0.032 |  | 0.9025141812535344 | 0.276276157463441 |  | spmB |  |  |  |  |  |  | spmB | spore maturation protein (spore core dehydratation) | 1.8 (Sporulation) | spmB | ypuK | no | no | spmB | BA1492 | BC1471 | BH1575 | spmB (OB1824) | spmB (CAC0470) | spmB (CPE2532) | no | no | spmB | 4 TMs
rluB (ypuL) not included in final total | rluB (ypuL) | downstream of spmB (read-through?) |  |  |  |  | rluB (ypuL) | 0.7453335372261958 | 0.328 |  | 1.719607774763449 | 0.883 |  | 0.4824710413631977 | 0.048 |  | 1.021584174945786 | 0.576836867215416 |  | rluB (ypuL)
1.2. B. below cut-off in sigE+ vs. sigE- experiments but identified by overexpression of sE
none
1.2. C. not identified by overexpression of sE
none
1.3. sE-regulated genes with predicted [NAME] promoter (from Eichenberger et al. 2003, JMB):
1.3. A. also identified by overexpression of sE
1.3. A. a) SpoIIID binding confirmed by gel-shift
yitE | yitE | GAGACATAAAT | 10 | CTCATAAAATG | BioOptimizer-prediction | 42 | yitE | 4.77529273657691 | 0.998 |  | 33.65115693754908 | 0.999 |  | 0.1091802058371665 | 0.000499999999999945 |  | 1.409802953717518 | 0.972854674871139 |  | yitE | PE795-6 | shifted | predicted | (-36)GCGGACAAGT(-27) |  |  | yitE | unknown | 5.1 (From B. subtilis) | yitE | no | no | yitT, yxkD, ydeO, yvjA, yqfU | yitE | no [BA5265 (yitT)] | no [BC5018 (yitT)] | no [BH3640 (appD)] | no [OB1770 (ypjC)] | no [CAC0848 (yitT)] | no [CPE0405] | no [lmo2264 (yitT)] | no [lin2365 (yitT)] | yitE | 5 TMs
1.3. A. b) not tested by gel-shift
citH | citH (yxiQ) | TTGGTCTACAT | 11 | GTCATACACAT | BioOptimizer-prediction | 77 | citH (yxiQ) | 3.280952931131191 | 0.997 |  | 62.8058358813318 | 1 |  | 0.3056009618964797 | 0.003 |  | 1.248232872382702 | 0.909413846936564 |  | citH (yxiQ) |  |  | no prediction |  |  |  | citH (yxiQ) | secondary transporter of divalent metal ions/citrate complexes, similar to SpmA | 1.2 (Transport/binding proteins and lipoproteins) | citH (yxiQ) | yxiQ | citM, yraO | spmA, ycgA | citH (yxiQ) | BA0561 | BC0562 | BH0745 | no [OB3255 (citM)] | no | no [CPE0860] | no | no | citH (yxiQ) | 10 TMs
 |  | AGCACATTTAC | 11 | TTCATATAAAC | BioOptimizer-prediction | 133
patA | patA | AAGGTATGTTT | 10 | CGCATACAATC | BioOptimizer-prediction | 84 | patA | 2.167704104819695 | 0.885 |  | 14.45439770745928 | 0.981 |  | 0.3534055835040974 | 0.01 |  | 0.8676853963018386 | 0.141114133481799 |  | patA |  |  | no prediction |  |  |  | patA | aminotransferase (EC 2.6.1.-), similar to SpsC and YhjL | 2.2 (Metabolism of amino acids and related molecules) | patA | uat | alaT, aspB, ykrV, yhdR, ywfG | patB, ydfD, yisV, ydeF, spsC, hisC | patA | BA4225 | BC4009 | no [BH3350 (alaT)] | OB1391 | patA (CAC0375) | no [aspC (CPE0711)] | lmo1006 | lin1005 | patA | 1 TM (mid)
[NAME] | [NAME] | TTATATA | 14 | ACTATATT | possible promoter | 35 | [NAME] | 1.819700858609984 | 0.98 |  | 12.50259030217721 | 0.999 |  | 0.4164962288889467 | 0.023 |  | 1.335888023779738 | 0.970184238071608 |  | [NAME] |  |  | predicted | (-15)TAGGACAAAC(-24) |  |  | [NAME] | putative permease (similar to YtvI) | 5.2 (From other organisms) | [NAME] | no | no | yubA, yueF, yrrI, ytvI | [NAME] | BA1922 | BC1923 | no [BH2921(yueF)] | no [OB2010 (yrrI)] | CAC2432 | no [CPE0543] | lmo1419 | lin1458 | [NAME] | 6 TMs
yflC-B | yflC | GTATCTT | 14 | AATAAAAT | possible promoter | 53 | yflC |  |  |  | 3.920755857920344 | 0.901 |  |  |  |  |  |  |  | yflC |  |  | no prediction |  |  |  | yflC | unknown |  | yflC |  |  |  | yflC | no | no | no | no | no | no | no | no | yflC
 |  | TCAGCATTTTT | 11 | TTTACAAATGG | BioOptimizer-prediction (unlikely)
 | yflB |  |  |  |  | 187 | yflB | 3.006076302628231 | 0.924 |  | 5.116818355403078 | 0.996 |  | 0.3209941003685116 | 0.01 |  |  |  |  | yflB |  |  | no prediction |  |  |  | yflB | unknown | 5.2 (From other organisms) | yflB | no | no | no | yflB | BA0386 | BC0430 | BH0859 | no | no | no | no | no | yflB | 0 TM
 |  |  |  |  | BioOptimizer-no prediction
yhfN | yhfN | GAATTTG | 13 | AATAGAAG | possible promoter | 29 | yhfN | 2.710191631890843 | 0.997 |  | 14.02813704561959 | 1 |  | 0.2592872269883482 | 0.002 |  | 1.46375155664535 | 0.977401133544536 |  | yhfN |  |  | no prediction |  |  |  | yhfN | similar to metalloendopeptidase (M48 family) | 5.2 (From other organisms) | yhfN | yzoA | no | no | yhfN | [NAME] | BC1123 | no | no | CAC0557 | no | no | no | yhfN | 7 TMs
 |  |  |  |  | BioOptimizer-no prediction
yhfO | yhfO | TGATGAT | 15 | AATAAACT | likely promoter | 52 | yhfO | 2.63633138582538 | 0.991 |  | 2.466039337234339 | 0.975 |  | 0.4053648038323359 | 0.015 |  | 0.851992730837778 | 0.16169247317288 |  | yhfO |  |  | predicted | (+74)ATAGACAGGC(+83) |  |  | yhfO | similar to acetyltransferase ([NAME] family), similar to SpsD | 5.2 (From other organisms) | yhfO | no | no | spsD | yhfO | BA2225 | BC2179 | no | no | no | no [CPE2166] | no | no [lin2807] | yhfO | 0 TM
 |  | TCGTGATATTT | 12 | ATGATAAAAGT | BioOptimizer-prediction (unlikely)
yitC-D (absent from Eichenberger et al., 2003) | yitC | GAACCAT | 14 | [NAME] | TTTTAGCAAAATG (5'RACE) | 37 | yitC |  |  |  | 3.723917062545685 | 0.993 |  | 0.6655462906103197 | 0.1305 |  | 0.7734386208735542 | 0.182460352222982 |  | yitC |  |  | no prediction |  |  |  | yitC | unknown | 5.2 (From other organisms) | yitC | no | no | no | yitC | no | no | no | no | CAC3233 | CPE2556 | no | no | yitC | 0-1 (mid) TM
 |  |  |  |  | not included in BioOptimizer list of sequences
 | yitD | overlap |  |  |  |  | yitD |  |  |  | 19.76969640111862 | 1 |  | 0.2171270937397315 | 0.005 |  | 1.103658402713982 | 0.728996826159636 |  | yitD |  |  |  |  |  |  | yitD | unknown | 5.2 (From other organisms) | yitD | no | no | no | yitD | no | no | no | no | no | no | no | no | yitD | 0 TM
yjbE | yjbE | ATATCATAAAA | 13 | CTCATATAGTA | BioOptimizer-prediction | 38 | yjbE | 2.857590543374947 | 0.994 |  | 19.63360276836047 | 1 |  | 0.1829609175329501 | 0.00149999999999995 |  | 1.23199896317854 | 0.905816830835558 |  | yjbE |  |  | predicted | (-46)TGAGACAGGT(-55) |  |  | yjbE | probable membrane protein, toxic anion resistance (tellurium efflux) | 5.1 (From B. subtilis) | yjbE | no | no | ykoY, yceF | yjbE | BA1201 | BC1189 | BH2860 | OB3167 | CAC1039 | no | no [lmo0991 (ykoY)] | no [lin0990 (ykoY)] | yjbE | 5 TMs
 |  | TATTTCTATTT | 12 | GTCACAAAAGA | BioOptimizer-prediction (unlikely)
yjbD not included in final total | yjbD | downstream (convergent) |  |  |  |  | yjbD | 0.6713349800815469 | 0.196 |  | 1.24763290415434 | 0.697 |  | 0.4386634760005362 | 0.018 |  | 1.118317400186215 | 0.833722919307887 |  | yjbD
yjbC not included in final total | yjbC | downstream (convergent) |  |  |  |  | yjbC | 0.8466319707584548 | 0.272 |  | 1.048102652302304 | 0.554 |  | 0.5284135986861167 | 0.042 |  | 0.8818456895873751 | 0.153771739859284 |  | yjbC
ylaK | ylaK | ACCTTCTATCT | 11 | AACATATATTT | BioOptimizer-prediction | 72 | ylaK | 2.65460556197554 | 0.905 |  | 50.46612975635286 | 0.998 |  | 0.5237352374670672 | 0.0395 |  | 1.084518359005445 | 0.762427657034929 |  | ylaK |  |  | no prediction |  |  |  | ylaK | similar to phosphate starvation inducible protein (PhoH ATPase) | 2.6 (Metabolism of phosphate) | ylaK | no | phoH | no | ylaK | BA4161 | BC3951 | BH2629 | no [OB1955 (phoH)] | no | CPE1665 | lmo1467 | lin1504 | ylaK | 1 TM (mid)
ylaL not included in final total | ylaL | read-through from ylaK? (convergent-3 bp apart) |  |  |  |  | ylaL | 1.874994508067419 | 0.972 |  | 6.561452663029055 | 0.998 |  | 0.5107952857087161 | 0.0405 |  | 1.18581003664409 | 0.912810025224649 |  | ylaL
ylaM | ylaM | TCAAAAT | 14 | CATGAATT | possible promoter (by visual inspection) | 56 | ylaM | 2.66685866452148 | 0.998 |  | 31.6227766016838 | 1 |  | 0.3602770600788222 | 0.01 |  | 1.114904014817285 | 0.826937788095657 |  | ylaM |  |  | predicted | (+57)ACGGACAAGG(+66) |  |  | ylaM | similar to glutaminase | 2.2 (Metabolism of amino acids and related molecules) | ylaM | no | ybgJ | no | ylaM | glsA-1(BA0499) | BC0481 | BH2627 | no [OB0870 (ybgJ] | no | CPE1995 | no | no | ylaM | 2 TMs
 |  | AAATTTG | 15 | CATACGCT | possible promoter (within coding region) | 156
 |  | ATTGCCTTTTA | 11 | CTCATGATATG | BioOptimizer-prediction | 96
 |  | [NAME] | 10 | TGTACAAATTA | BioOptimizer-prediction (unlikely)
ylbK | ylbK | GCATAGG | 14 | CATAGAAT | most likely promoter | 36 | ylbK | 5.260172663907063 | 0.973 |  | 4.159106104940221 | 0.998 |  | 0.5181678848631919 | 0.04 |  | 1.179251097516251 | 0.909354843250972 |  | ylbK |  |  | no prediction |  |  |  | ylbK | similar to papatin-like phospholipase, similar to YqhO | 5.2 (From other organisms) | ylbK | no | no | yqhO | ylbK | BA4137 | BC3927 | BH2587 | no [OB1899 (yqhO)] | CAC2424 | CPE1574 | no | no | ylbK | 1 TM-Nter
 |  |  |  |  | BioOptimizer-no prediction
yloB | yloB | GCATGAA | 14 | AATAAGCA | most likely promoter | 50 | yloB | 4.446312674691088 | 1 |  | 45.08167045414603 | 1 |  | 0.1600342363274415 | 0.00249999999999995 |  | 1.333778113348441 | 0.94847660958481 |  | yloB |  |  | predicted | (+16)TGGGACAAAC(+25) |  |  | yloB | similar to calcium-transporting ATPase, sporulation and germination | 1.2 (Transport/binding proteins and lipoproteins) | yloB | no | ykvW | yvgX, yvgW | yloB | BA4012 | BC3917 | pacL | OB1500 | CAC2137 | CPE2054 | lmo0841 | lin0832 | yloB | 9TMs
 |  | TCTTCCTGCAT | 11 | AGCATGAAATG | BioOptimizer-prediction (unlikely)
ylxY-mlpA | ylxY | GGGTTCTACCT | 11 | TTCATAATGTG | BioOptimizer-prediction | 20 | ylxY | 3.280952931131191 | 0.997 |  | 6.486344335482386 | 1 |  | 0.2708748160860103 | 0.004 |  | 1.129614524776201 | 0.858212528377834 |  | ylxY |  |  | predicted | (-36)AAGGACAAGG(-45) |  |  | ylxY | similar to polysaccharide deacetylase, similar to [NAME] | 2.1.1 (Specific pathways) | ylxY | ymxI | yfjS, ybaN, yjeA | yheN | ylxY | [NAME] | BC3804 | BH2406 | OB1605 | no [CAC2383 (yfjS)] | no [CPE1911] | no [lmo0415 (yjeA)] | no [lin0436 (yjeA)] | ylxY | secreted-pred
 | mlpA (ymxG) | 39 bp downstream |  |  |  |  | mlpA (ymxG) | 3.198895109691398 | 0.998 |  | 11.45512941445536 | 0.999 |  | 0.2619847849354563 | 0.00249999999999995 |  | 0.9994893702930777 | 0.49831037577609 |  | mlpA (ymxG) |  |  |  |  |  |  | mlpA (ymxG) | similar to metalloendopeptidase ([NAME] family) | 3.8 (Protein modification) | mlpA (ymxG) | ymxG | ymfH | ymfG, albF | mlpA (ymxG) | BA3942 | BC3803 | BH2405 | OB1606 | CAC2411 | CPE1924 | no [lmo1393 (ymfH)] | no [lin1429 (ymfG)] | mlpA (ymxG) | 0 TM
yobN | yobN | TCGTGATAGGT | 11 | TGAATATAATG | BioOptimizer-prediction | 128 | yobN | 4.688133821452654 | 0.978 |  | 10.88930093333433 | 1 |  | 0.3658113686300923 | 0.007 |  | 0.574924480804003 | 0.00247883752316869 |  | yobN |  |  | no prediction |  |  |  | yobN | similar to L-amino acid oxidase (flavin containing) | 2.2 (Metabolism of amino acids and related molecules) | yobN | no | no | no | yobN | BA2018 | BC2016 | no | OB1296 | no | no | no | no | yobN | 3 TMs
ypiA | ypiA | TCAAGAT | 13 | AATAAGAC | possible promoter (by visual inspection) | 135 | ypiA | 1.753880501841761 | 0.964 |  | 20.8929613085404 | 1 |  | 0.3205925811924655 | 0.00749999999999995 |  | 0.813122351325921 | 0.0547691503088432 |  | ypiA |  |  | no prediction |  |  |  | ypiA | tetratrico peptide repeat, similar to O-linked GlcNAc transferase (Arabidopsis) | 5.2 (From other organisms) | ypiA | no | no | yrrB, [NAME] | ypiA | BA1541 | BC1519 | BH1669 | OB1779 | no [CAC0045] | no | [NAME] | lin2036 | ypiA | 0 TM
 |  | TCATAAT | 14 | CATAGCTT | possible promoter (not in BioP/BioO sequence) | 278 | initiation codon is more likely ATG (at-78)
 |  | TCTTCCTTTTT | 12 | TCAAGATCTTT | BioOptimizer-prediction (unlikely)
ypiB not included in final total | ypiB | 71 bp downstream |  |  |  |  | ypiB | 1.166809617060963 | 0.713 |  | 2.133044913146577 | 0.97 |  | 0.3549250500305747 | 0.01 |  | 0.8360852720282198 | 0.092575576517492 |  | ypiB
yqeW | yqeW | TTGACATTCTC | 12 | CGAATACACCA | BioOptimizer-prediction | 136 | yqeW | 2.630267991895382 | 0.996 |  | 19.5884467350599 | 0.991 |  | 0.1989254797657894 | 0.001 |  | 1.322064687766121 | 0.96098836220044 |  | yqeW |  |  | predicted | (-21)ATAGACAGGC(-30) |  |  | yqeW | similar to Na+/Pi cotransporter | 1.2 (Transport/binding proteins and lipoproteins) | yqeW | no | no | no | yqeW | BA0785 | BC0803 | BH1353 | OB1933 | no | CPE2368 | lmo0826 | lin0822 | yqeW | 8 TMs pred
 |  | CCGTCATGAGT | 11 | TCTATATAATG | BioOptimizer-prediction | 14 | initiation codon could be at +61 or +91
yqeV not included in final total | yqeV | readthrough from yqeW (convergent)? |  |  |  |  | yqeV | 0.9908319448927675 | 0.492 |  | 2.576321157002575 | 0.981 |  | 0.5402363123446214 | 0.052 |  | 1.074012694299253 | 0.740550211417159 |  | yqeV
yrbG | yrbG | AAATGCA | 14 | CATAAATT | most likely promoter | 40 | yrbG | 11.32400363235557 | 0.994 |  | 14.58814260275349 | 0.998 |  | 0.1820538130383468 | 0.00349999999999995 |  | 1.114672437376995 | 0.786477111853853 |  | yrbG |  |  | no prediction |  |  |  | yrbG | unknown | 5.2 (From other organisms) | yrbG | no | ydfS, ykjA | yetF, ydfR | yrbG | BA4644 | BC4408 | BH1232 | no [OB1377 (ydfS)] | CAC0671 | CPE1348 | no | no | yrbG | 3 TMs
 |  | CTGTTCTTTTT | 10 | GTCAGACATGC | BioOptimizer-prediction (unlikely)
 | alternative | read-through from spoVB? (convergent-3 bp apart)
pbpI (yrrR)-yrrS | pbpI (yrrR) | TCGTGAA | 14 | CATAATAT | most likely promoter | 50 | pbpI (yrrR) | 2.716439268839083 | 0.995 |  | 3.213660538640318 | 0.987 |  | 0.2050841954347022 | 0.001 |  | 1.01471685007667 | 0.55160755465051 |  | pbpI (yrrR) |  |  | no prediction |  |  |  | pbpI (yrrR) | similar to penicillin-binding protein SpoVD | 1.1 (Cell wall) | pbpI (yrrR) | no | spoVD, pbpB | pbpC, ykuA, pbpA, ponA, pbpF | pbpI (yrrR) | BA4606 | BC4372 | no [spoVD] | no [OB1464(pbpB)] | no [CAC0506 (spoVE)] | no [spoVD] | no [pbpB] | no [pbpB] | pbpI (yrrR) | secreted-pred
 |  |  |  |  | BioOptimizer-no prediction
 | yrrS | 64 bp downstream |  |  |  |  | yrrS | 2.051162178825566 | 0.991 |  | 4.731512589614805 | 0.999 |  | 0.1971638242457109 | 0.00149999999999995 |  | 0.7708406978248139 | 0.0409727321265627 |  | yrrS |  |  |  |  |  |  | yrrS | unknown | 5.2 (From other organisms) | yrrS | no | no | no | yrrS | BA4605 | BC4371 | BH1277 | OB2001 | no | no | lmo1496 | lin1531 | yrrS | 1 TM
yrzE | yrzE | [NAME] | 11 | GGAATACATTT | BioOptimizer-prediction | 21 | yrzE | 2.735268726306713 | 0.993 |  | 60.81350012787184 | 1 |  | 0.2871012162607453 | 0.00649999999999995 |  | 0.9322611983450741 | 0.31178267413748 |  | yrzE |  |  | no prediction |  |  |  | yrzE | unknown | 5.2 (From other organisms) | yrzE | no | no | no | yrzE | BA4645 | BC4409 | BH1230 | OB2031 | no | no | no | no | yrzE | 4 TMs
 |  |  |  |  |  |  | initiation codon could be at +64
ytpA-B | ytpA | TGTTCCT | 13 | [NAME] | most likely promoter | 43 | ytpA | 1.472312502432719 | 0.881 |  | 2.964831389524342 | 0.97 |  | 0.7040062485654468 | 0.157 |  | 1.332760413361536 | 0.97494499387764 |  | ytpA |  |  | no prediction |  |  |  | ytpA | similar to triglyceride lipase (lysophospholipase) | 2.4 (Metabolism of lipids) | ytpA | no | no | no | ytpA | BA5009 | BC4753 | BH3288 | OB2431 | no [CAP0133] | pldB | lmo1258 | lin1226 | ytpA | 1 TM (mid)
 |  | TCCTTCTTTCT | 10 | TTCGTATGAGG | BioOptimizer-prediction | 8
 | ytpB | 20 bp downstream |  |  |  |  | ytpB | 1.778279410038923 | 0.961 |  | 3.971915494694403 | 0.997 |  | 0.4635217823563023 | 0.0215 |  | 1.287718555679019 | 0.968224315833428 |  | ytpB |  |  |  |  |  |  | ytpB | unknown | 5.1 (From B. subtilis) | ytpB | no | no | no | ytpB | BA5008 | BC4752 | BH3287 | no | no | no | no | no | ytpB | 1 TM (mid)
ywcB-A | ywcB | AACGCATAAAT | 11 | TACATACCTAT | BioOptimizer-prediction | 46 | ywcB | 4.315190768277652 | 0.999 |  | 20.74913517454911 | 1 |  | 0.2256233221692824 | 0.004 |  | 1.332746754741504 | 0.933970849392927 |  | ywcB |  |  | predicted | (-139)AAAGACAGGC(-148) |  |  | ywcB | unknown | 5.2 (From other organisms) | ywcB | ipa-32r | no | no | ywcB | BA1634 | BC1608 | no | OB2443 | no | no | no | no | ywcB | 2 TMs
 |  | TGTACCTTTTT | 12 | CGAATAAAAGG | BioOptimizer-prediction | 9
 | ywcA | overlap |  |  |  |  | ywcA | 2.897343587701323 | 0.997 |  | 18.79316816803269 | 1 |  | 0.2828651619507628 | 0.001 |  | 1.303043368024369 | 0.952323551531405 |  | ywcA |  |  |  |  |  |  | ywcA | similar to Na+-dependent symport | 1.2 (Transport/binding proteins and lipoproteins) | ywcA | ipa-31r | opuE, ycgO | yhjB, yodF | ywcA | BA1635 | BC1609 | BH3743 | OB2442 | no | no [CPE0186] | no | no | ywcA | 10-11 TMs
ywjF-acdA | ywjF | TGATCATAATC | 12 | TTCATACCGGC | BioOptimizer-prediction | 148 | ywjF | 1.713957307508425 | 0.803 |  | 2.648500138606701 | 0.801 |  | 0.4882600818269067 | 0.0365 |  | 1.107395805008616 | 0.800709211618318 |  | ywjF |  |  | no prediction |  |  |  | ywjF | iron-sulphur-binding reductase | 1.4 (Membrane bioenergetics (electron transport chain and ATP synthase)) | ywjF | no | no | ysfD | ywjF | BA5590 | BC5345 | BH3802 | OB3014 | no | CPE0580 | no | no | ywjF | 6 TMs
 |  | TCATTATTTAT | 12 | CTTATACAGAT | BioOptimizer-prediction | 48
 | acdA | overlap-RACE-operon w/ywjF |  |  |  |  | acdA | 2.66072505979881 | 0.999 |  | 3.647539469256079 | 0.974 |  | 0.5550240936366901 | 0.052 |  | 0.9808232732149207 | 0.430051398418728 |  | acdA |  |  |  |  |  |  | acdA | acyl-CoA dehydrogenase (EC 1.3.99.-), similar to MmgC and YngJ | 2.4 (Metabolism of lipids) | acdA | no | mmgC, yngJ, yusJ | ydbM | acdA | BA5586 | BC5341 (yngJ/acdA) | acdA | acdA (OB3012) | bcd (CAC2711) [yngJ,mmgC,acdA] | bcd (CPE2300) | no | no | acdA | 1-2 TMs
ywlB -C | ywlB | CTGGTCTAAAA | 10 | CTCATAGATTG | BioOptimizer-prediction | 30 | ywlB | 3.515604405282982 | 0.965 |  | 3.483373150360119 | 0.992 |  | 0.3345052980444556 | 0.0125 |  | 0.753411653306031 | 0.0742169706648241 |  | ywlB |  |  | no prediction |  |  |  | ywlB | unknown | 5.1 (From B. subtilis) | ywlB | ipc-28d | no | no | ywlB | BA5569 | BC5326 | BH3772 | no | no | no | no | no | ywlB | 0 TM
 | ywlC | 156 bp downstream |  |  |  |  | ywlC | 1.931968317016924 | 0.886 |  | 3.404081897010009 | 0.997 |  | 0.6580901731833119 | 0.194 |  |  |  |  | ywlC |  |  |  |  |  |  | ywlC | similar to Sua5 (RNA binding protein required for normal growth in yeast) | 5.2 (From other organisms) | ywlC | no | no | no | ywlC | BA5568 | BC5325 | BH3771 | OB2994 | CAC2882 | CPE2200 | lmo2541 | lin2685 | ywlC | 0 TM
1.3. B. below cut-off in sigE+ vs. sigE- experiments but identified by overexpression of sE
none
1.3. C. not identified by overexpression of sE , but down-regulated in the presence of SpoIIID
1.3.C. 1. Genes included in the sE regulon in Eichenberger et al. (2003)
1.3.C.1. a) ratio in sigE+ vs. sigE- experiment is high (>3)
kbaA | kbaA | TTGACATGCTT | 10 | CACATACTTGT | BioOptimizer-prediction | 83 | kbaA | 1.364583136588924 | 0.878 |  | 11.11731727281592 | 1 |  | 0.3170866499125359 | 0.0115 |  | 1.296114510046642 | 0.968069665314731 |  | kbaA |  |  | no prediction |  |  |  | kbaA | activation of KinB | 1.8 (Sporulation) | kbaA | ybaM, ybxC | no | no | kbaA | kbaA (BA0149) | BC0170 | kbaA | OB0198 | no | no | no | no | kbaA | 6 TMs
 |  | TTAATATGATT | 12 | ATTATACATAA | BioOptimizer-prediction | 43
 | alternative | read-through from ybaN (convergent) ?
pepF | pepF (yjbG) | TTGGCATTCGT | 12 | TGCATATGATT | BioOptimizer-prediction | 104 | pepF (yjbG) | 1.333521432163324 | 0.856 |  | 3.647539469256079 | 0.99 |  | 0.5055679673640383 | 0.0345 |  | 1.008086474005972 | 0.517302462310864 |  | pepF (yjbG) |  |  | no prediction |  |  |  | pepF (yjbG) | similar to oligoendopeptidase (M3 family), overexpression inhibits sporulation | 2.2 (Metabolism of amino acids and related molecules) | pepF (yjbG) | yjbG | [NAME] | no | pepF (yjbG) | pepF-1 (BA1206)/pepF-2 (BA3553) | BC1193/BC3484 | BH2856 | OB1216 | no | pepF (CPE1453) | lmo2188 | lin2292 | pepF (yjbG) | 0 TM
yjbH not included in final total | yjbH | readthrough from pepF (convergent) |  |  |  |  | yjbH | 2.29 | 0.94 |  | 4.951950559296893 | 0.999 |  | 1.026977393841978 | 0.5355 |  | 1.169011979657554 | 0.89057602063378 |  | yjbH
ypbG | ypbG | TAATCTA | 13 | AATAAAAT | most likely promoter | 82 | ypbG | 1.729816359215102 | 0.879 |  | 17.13957307508426 | 0.989 |  | 0.1919453683204417 | 0.00149999999999995 |  | 1.080757555945852 | 0.739575984755882 |  | ypbG |  |  | no prediction |  |  |  | ypbG | similar to calcineurin-like phosphoesterase | 5.2 (From other organisms) | ypbG | no | no | ykoQ, ykuE | ypbG | [NAME] (ykuE)] | BC1488 | BH1618 | no [OB0983 (ykuE)] | no [CAC3027 (ykuE)] | no [CPE0391] | no [lmo0763 (ykuE)] | no [lmo0757 (ykuE)] | ypbG | secreted-pred
 |  | AGAGTCTGTTT | 12 | AGCACAAATAT | BioOptimizer-prediction (unlikely)
1.3.C.1. b) ratio in sigE+ vs. sigE- experiment is low (<3)
yyaE | yyaE | TAGTCAAGCAT | 11 | TTCATAAATAG | BioOptimizer-prediction | 46 | yyaE | 1.573982864466219 | 0.874 |  | 2.233572222830532 | 0.952 |  | 0.4702920777110214 | 0.027 |  | 1.020508316122569 | 0.575050402931939 |  | yyaE |  |  | no prediction |  |  |  | yyaE | similar to formate dehydrogenase (molybdopterin oxidoreductase family) | 1.4 (Membrane bioenergetics (electron transport chain and ATP synthase)) | yyaE | no | yoaE, nasC, yjgC, yrhE | narG | yyaE | no | no | no [BH2853 (yoaE)] | no | no | fdh (CPE1548) | no [lmo2586 (yrhE, yjgC] | no [lin2731 (yrhE, yjgC] | yyaE | 0-1 TM
GENES IN SECTIONS  1.3.C. 2. WERE NOT INCLUDED IN THE FINAL TOTAL OF SIGE-CONTROLLED GENES
1.3.C. 2. Genes not included in the sE regulon in Eichenberger et al. (2003)
1.3.C.2. a) ratio in sigE+ vs. sigE- experiment is high (>3)
hit-serC-yhaG | hit | AAATGAG | 14 | CATAACAC | possible promoter (by visual inspection) | 130 | hit | 0.6683439175686146 | 0.127 |  | 2.679168324819032 | 0.976 |  | 0.4865092607423011 | 0.0275 |  | 1.246708507657207 | 0.923071152264423 |  | hit |  |  |  |  |  |  | hit |  |  | hit |  |  |  | hit |  |  |  |  |  |  |  |  | hit
 | serC | 146 bp downstream |  |  |  |  | serC | 0.7870457896950985 | 0.239 |  | 2.157744409152667 | 0.97 |  | 0.8200776298959066 | 0.2895 |  | 1.243810147279942 | 0.922968740912984 |  | serC |  |  |  |  |  |  | serC |  |  | serC |  |  |  | serC |  |  |  |  |  |  |  |  | serC
yhaG | yhaG | ACATTCT | 13 | AATAAATG | possible promoter (by visual inspection) | 49 | yhaG | 1.18032063565173 | 0.71 |  | 5.33334895487621 | 0.994 |  | 0.4125119308066503 | 0.0155 |  | 1.345770322514358 | 0.975121984780234 |  | yhaG |  |  |  |  |  |  | yhaG |  |  | yhaG |  |  |  | yhaG |  |  |  |  |  |  |  |  | yhaG
licB-C-A-H | licB |  |  |  |  |  | licB | 1.001545318312494 | 0.506 |  | 1.830445067350052 | 0.927 |  | 0.1528887106748808 | 0.0175 |  |  |  |  | licB |  |  |  |  |  |  | licB |  |  | licB |  |  |  | licB |  |  |  |  |  |  |  |  | licB
 | licC | no sigE promoter identified |  |  |  |  | licC | 1.124604973966926 | 0.572 |  | 2.360478233180577 | 0.946 |  | 0.4414855478646222 | 0.019 |  | 1.118436473965608 | 0.782067562277732 |  | licC |  |  |  |  |  |  | licC |  |  | licC |  |  |  | licC |  |  |  |  |  |  |  |  | licC
 | licA | 18 bp downstream |  |  |  |  | licA | 1.17489755493953 | 0.736 |  | 3.083187950249355 | 0.97 |  | 0.337517701671559 | 0.0175 |  | 1.000159641782904 | 0.500428620438567 |  | licA |  |  |  |  |  |  | licA |  |  | licA |  |  |  | licA |  |  |  |  |  |  |  |  | licA
 | licH | overlap |  |  |  |  | licH | 1.145512941445536 | 0.595 |  | 3.076096814740708 | 0.996 |  | 0.3760209289964586 | 0.0175 |  | 0.9718878602089479 | 0.400350785008034 |  | licH |  |  |  |  |  |  | licH |  |  | licH |  |  |  | licH |  |  |  |  |  |  |  |  | licH
malL (yvdL)-pgcM (yvdM) | malL (yvdL) | no sigE promoter identified |  |  |  |  | malL (yvdL) | 0.4920395356814509 | 0.152 |  | 7.211074791828997 | 1 |  | 0.3981933806949029 | 0.0205 |  | 1.098709060655665 | 0.774173623530692 |  | malL (yvdL) |  |  |  |  |  |  | malL (yvdL) |  |  | malL (yvdL) |  |  |  | malL (yvdL) |  |  |  |  |  |  |  |  | malL (yvdL)
 | pgcM (yvdM) |  |  |  |  |  | pgcM (yvdM) | 0.5552920144369228 | 0.177 |  | 1.819468746524461 | 0.919 |  | 0.537545344317682 | 0.042 |  | 1.07050325234596 | 0.674042709761763 |  | pgcM (yvdM) |  |  |  |  |  |  | pgcM (yvdM) |  |  | pgcM (yvdM) |  |  |  | pgcM (yvdM) |  |  |  |  |  |  |  |  | pgcM (yvdM)
med | med |  |  |  |  |  | med | 1.049542428652322 | 0.562 |  | 5.533501092157367 | 1 |  | 0.3179645569985397 | 0.00749999999999995 |  | 1.048203062155824 | 0.663514077012588 |  | med |  |  |  |  |  |  | med |  |  | med |  |  |  | med |  |  |  |  |  |  |  |  | med
spoVS-tdh-kbl | spoVS | GAATAGC | 14 | AATATAGT | possible promoter (by visual inspection) | 126 | spoVS |  |  |  | 4.092606597300109 | 0.979 |  | 0.8565455443936643 | 0.3805 |  | 0.866254353778934 | 0.169801622221285 |  | spoVS |  |  |  |  |  |  | spoVS |  |  | spoVS |  |  |  | spoVS |  |  |  |  |  |  |  |  | spoVS
 | tdh | CCATATC | 13 | AATATAAC | possible promoter (by visual inspection) | 25 | tdh | 0.8109610578538407 | 0.228 |  | 5.000345349769785 | 0.997 |  | 0.619488060954144 | 0.16 |  | 0.9674501172727901 | 0.381581571356691 |  | tdh |  |  |  |  |  |  | tdh |  |  | tdh |  |  |  | tdh |  |  |  |  |  |  |  |  | tdh
 | [NAME] | 12 bp downstream |  |  |  |  | [NAME] | 0.7998342550070284 | 0.2 |  | 3.837072454922788 | 0.994 |  | 0.4226727662992993 | 0.019 |  | 0.8869376942604343 | 0.147073054175614 |  | [NAME] |  |  |  |  |  |  | [NAME] |  |  | [NAME] |  |  |  | [NAME] |  |  |  |  |  |  |  |  | [NAME]
yclG | yclG | AACTATT | 15 | AATAAAAT | possible promoter (by visual inspection) | 73 | yclG |  |  |  | 4.764309868054158 | 0.995 |  | 0.4462862918638357 | 0.018 |  | 1.17052964161349 | 0.892718600194152 |  | yclG |  |  |  |  |  |  | yclG |  |  | yclG |  |  |  | yclG |  |  |  |  |  |  |  |  | yclG
yesL-M-N | yesL | TTCTTTC | 13 | CATATTAC | possible promoter (by visual inspection) | 35 | yesL | 1.713957307508425 | 0.819 |  | 1.972422736114854 | 0.948 |  | 0.4810070402549013 | 0.03 |  | 1.190583924788441 | 0.879188689116108 |  | yesL |  |  |  |  |  |  | yesL |  |  | yesL |  |  |  | yesL |  |  |  |  |  |  |  |  | yesL
 | yesM | overlap |  |  |  |  | yesM | 1.475706533275895 | 0.732 |  | 7.379042301291012 | 0.956 |  | 0.6448727549387195 | 0.2005 |  | 1.065125382616318 | 0.686104589514029 |  | yesM |  |  |  |  |  |  | yesM |  |  | yesM |  |  |  | yesM |  |  |  |  |  |  |  |  | yesM
 | yesN | overlap |  |  |  |  | yesN | 1.636816521427809 | 0.794 |  | 15.59552502826954 | 0.992 |  | 0.5531931232260124 | 0.048 |  | 1.069911100984626 | 0.731253605762077 |  | yesN |  |  |  |  |  |  | yesN |  |  | yesN |  |  |  | yesN |  |  |  |  |  |  |  |  | yesN
ypbF | ypbF | GTATTAT | 14 | CATATATT | possible promoter (by visual inspection) | 32 | ypbF |  |  |  | 10.18591388054117 | 1 |  | 0.1456751179118389 | 0.000499999999999945 |  | 0.928143027658477 | 0.269230130871482 |  | ypbF |  |  |  |  |  |  | ypbF |  |  | ypbF |  |  |  | ypbF |  |  |  |  |  |  |  |  | ypbF
ytvA | ytvA | ATGTAGA | 13 | CATATGTT | possible promoter (by visual inspection) | 170 | ytvA | 0.6776415076106751 | 0.262 |  | 3.303695410368148 | 0.987 |  | 0.4287627693517361 | 0.0195 |  | 1.14900333357191 | 0.871676918694583 |  | ytvA |  |  |  |  |  |  | ytvA |  |  | ytvA |  |  |  | ytvA |  |  |  |  |  |  |  |  | ytvA
yutH | yutH | TCTTGCG | 15 | AATATGTA | possible promoter (by visual inspection) | 62 | yutH | 1.279381304157525 | 0.715 |  | 12.13388850464978 | 1 |  | 0.4476799444848766 | 0.022 |  | 1.180707751991268 | 0.877117175611676 |  | yutH |  |  |  |  |  |  | yutH |  |  | yutH |  |  |  | yutH |  |  |  |  |  |  |  |  | yutH
 | ywlE | read-through from ywlB? (75 bp downstream of ywlD stop) |  |  |  |  | ywlE | 3.881503659906483 | 0.994 |  | 3.213660538640318 | 0.897 |  | 0.2388768648852412 | 0.001 |  | 1.012205457291187 | 0.532745678806493 |  | ywlE |  |  |  |  |  |  | ywlE |  |  | ywlE |  |  |  | ywlE |  |  |  |  |  |  |  |  | ywlE
ywlF-G | ywlF | GAATATA | 13 | CATATGGT |  | 76 | ywlF | 1.064143018224316 | 0.565 |  | 3.499451670283574 | 0.988 |  | 0.3847132974490868 | 0.0125 |  | 1.081417971301248 | 0.761044821893387 |  | ywlF |  |  |  |  |  |  | ywlF |  |  | ywlF |  |  |  | ywlF |  |  |  |  |  |  |  |  | ywlF
 | ywlG | 12 bp downstream |  |  |  |  | ywlG | 0.3935500754557774 | 0.097 |  | 2.546830252585041 | 0.978 |  | 0.4724030314852459 | 0.03 |  | 1.18878377950523 | 0.913080854645734 |  | ywlG |  |  |  |  |  |  | ywlG |  |  | ywlG |  |  |  | ywlG |  |  |  |  |  |  |  |  | ywlG
1.3.C.2.b) ratio in sigE+ vs. sigE- experiment is low (<3)
manP (yjdD)-manA (yjdE) | manP (yjdD) |  |  |  |  |  | manP (yjdD) | 1.231994686916556 | 0.782 |  | 1.850756571027957 | 0.912 |  | 0.4511352655171652 | 0.0205 |  | 1.18380964245363 | 0.916471966140726 |  | manP (yjdD) |  |  |  |  |  |  | manP (yjdD) |  |  | manP (yjdD) |  |  |  | manP (yjdD) |  |  |  |  |  |  |  |  | manP (yjdD)
 | manA (yjdE) |  |  |  |  |  | manA (yjdE) | 1.134961986070996 | 0.706 |  | 1.55810420628618 | 0.843 |  | 0.4990309793663031 | 0.034 |  | 0.9638620196939441 | 0.389718448080393 |  | manA (yjdE) |  |  |  |  |  |  | manA (yjdE) |  |  | manA (yjdE) |  |  |  | manA (yjdE) |  |  |  |  |  |  |  |  | manA (yjdE)
thyA | thyA | GAATGAA | 14 | CATAAAAA |  | 458 | thyA | 1.757923613958693 | 0.837 |  | 2.269864851883822 | 0.973 |  | 0.5196140889309834 | 0.043 |  | 0.5319296283943779 | 0.00142178731935771 |  | thyA |  |  |  |  |  |  | thyA |  |  | thyA | no |  |  | thyA |  |  |  |  |  |  |  |  | thyA
ugtP (ypfP) | ugtP (ypfP) | GCTTAAC | 14 | AATAATTC |  | 92 | ugtP (ypfP) | 1.264736347471151 | 0.754 |  | 1.986094917357372 | 0.96 |  | 0.4810494309866701 | 0.0455 |  | 0.9495154919562354 | 0.348517862460335 |  | ugtP (ypfP) |  |  |  |  |  |  | ugtP (ypfP) |  |  | ugtP (ypfP) | ypfP |  |  | ugtP (ypfP) |  |  |  |  |  |  |  |  | ugtP (ypfP)
yfnI | yfnI | no sigE promoter identified |  |  |  |  | yfnI | 1.088930093333433 | 0.606 |  | 1.972422736114854 | 0.96 |  | 0.5151607616970951 | 0.0425 |  | 0.9260994347176223 | 0.280016475292168 |  | yfnI |  |  |  |  |  |  | yfnI |  |  | yfnI |  |  |  | yfnI |  |  |  |  |  |  |  |  | yfnI
yvrC-B | yvrC | ACATATA | 13 | [NAME] |  | 262 | yvrC | 1.013911385736679 | 0.52 |  | 2.612161354399207 | 0.99 |  | 0.6918373327540384 | 0.144 |  | 1.166819795285844 | 0.890166912654879 |  | yvrC |  |  |  |  |  |  | yvrC |  |  | yvrC | no |  |  | yvrC |  |  |  |  |  |  |  |  | yvrC
 | yvrB |  |  |  |  |  | yvrB | 0.6353309318517437 | 0.218 |  | 2.805433637951714 | 0.983 |  | 0.5427959468867036 | 0.049 |  | 1.224077052885055 | 0.93782566893318 |  | yvrB |  |  |  |  |  |  | yvrB |  |  | yvrB | no |  |  | yvrB |  |  |  |  |  |  |  |  | yvrB
2. sE-CONTROLLED GENES ACTIVATED BY SpoIIID:
2.1. Previously identified sE-controlled genes (with mapped transcription start site):
2.1. A. Also identified by overexpression of sE
none
2.1. B. below cut-off in mutant vs. [NAME] experiments but identified by overexpression of sK
2.1. B. a) SpoIIID binding confirmed by gel-shift
spoIVCA | spoIVCA | TCATTTG | 15 | CATAGCAT | mapped? | 116 | spoIVCA | 1.870682140365801 | 0.978 |  | 1.193988104464273 | 0.643 |  | 16.36628828352505 | 1 |  | 0.4166105110824919 | 0.000665700710827277 |  | spoIVCA | PE774-5 | shifted | footprint | (-142)TTGGACAAAC(-133) | (+31)AGGAACAAGC(+40) |  | spoIVCA | site-specific DNA recombinase required for creating the sigK gene (excision of the skin element) | 1.8 (Sporulation) | spoIVCA | cisA | no | yokA | spoIVCA | no | no | no [BH2354 (yneB)] | no | no [CAC1956] | no [tnpX] | no [int] | no [int] | spoIVCA | 0 TM
 |  | TTTGCATATTC | 10 | TTAATAACACT | BioOptimizer-inaccurate | no |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | predicted | (-142)TTGGACAAAC(-133) | (+31)AGGAACAAGC(+40)
2.1. B. b) not tested by gel-shift
none
2.1. C. not identified by overexpression of sE
2.1. C. a) SpoIIID binding confirmed by gel-shift
asnO | asnO (yisO) | TCAACTA | 14 | CATAAACT | TACTAAGGTG | 130 | asnO (yisO) | 1.892343618644976 | 0.838 |  | 3.863669770540692 | 0.976 |  | 5.45473749100688 | 0.999 |  | 1.117901251317566 | 0.753784827419713 |  | asnO (yisO) | PE801-2 | shifted | predicted | (-112)TGGGACAGGC(-121) |  |  | 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)
 |  |  |  |  | BioOptimizer-no prediction | no
sigK (spoIVCB-spoIIIC) | spoIVCB (sigK) | ACACAGA | 14 | CATACATT | TACATATAG | 41 | spoIVCB (sigK) | 1.096478196143185 | 0.558 |  | 2.588212915153092 | 0.955 |  | 4.096110636338125 | 0.976 |  | 0.755777949766661 | 0.0996556074407298 |  | spoIVCB (sigK) |  |  | footprint | (-68)ACAGACAGCC(-59) | (+53)AAAGACAAGC(+44) | (+68)AAAAACAATG(+77) | spoIVCB (sigK) | RNA polymerase sporulation mother cell-specific (late) sigma factor (sK N-terminal half) | 3.5.1 (Initiation) | spoIVCB (sigK) | sigK | sigE, sigF, sigG |  | spoIVCB (sigK) | sigK (BA4566) | BC4336 | sigK (BH1285) | sigK (OB1999) | CAC1770 | sigK (CPE1768) | no [rpoD (sigA)] | no [rpoD (sigA)] | spoIVCB (sigK) | 1 TM (prosequence of pro-sigK)
 |  |  |  |  | BioOptimizer-no prediction | no |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | predicted | not predicted | (+53)AAAGACAAGC(+44) | not predicted
 | spoIIIC |  |  |  |  |  | spoIIIC | 1.06 | 0.55 |  |  |  |  | 6.27596242569736 | 0.9665 |  | 0.4574762888951552 | 0.0236476211864544 |  | spoIIIC |  |  |  |  |  |  | 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
 | yqaB | downstream |  |  |  |  | yqaB |  |  |  |  |  |  | 3.162027722680294 | 0.9715 |  | 0.5495176160192459 | 0.00804924791569617 |  | yqaB
2.1. C. b) not tested by gel-shift
cwlJ | cwlJ | TCATCAC | 14 | AATATGAT | GAAAAGAGA | 27 | cwlJ | 1.227439231158407 | 0.645 |  | 2.83139199579938 | 0.976 |  | 2.280273394090698 | 0.986 |  | 1.393234634537823 | 0.95090750574903 |  | cwlJ |  |  | predicted | (-60)AGGGACAGGA(-69) |  |  | cwlJ | cell wall hydrolase, germination | 1.1 (Cell wall) | cwlJ | ycbQ | no | sleB, ykvT | cwlJ | cwlJ-1 (BA2594)/cwlJ-2 (BA5640) | BC2536/BC5390 | cwlJ | OB3024 | no [CAC0686 (sleB)] | no | no | no | cwlJ | 0 TM
 |  | CCATTATGTTT | 12 | TGAATAAATTT | BioOptimizer-inaccurate | no
yknT | yknT | GAATAGC | 13 | CATATTGT | AGTGTTAACATC | 30 | yknT | 1.686553025388741 | 0.957 |  | 53.21082592667943 | 1 |  | 2.563979334127843 | 0.9795 |  | 0.7867435157896215 | 0.160045864661893 |  | yknT |  |  | predicted | (-70)ACAGACAAGC(-79) |  |  | yknT | possible structural component of the spore coat | 1.8 (Sporulation) | yknT | cse15 | no | yttA, yvcE, smc | yknT | no | no | no | no [smc (OB1528)] | no | no | no | no | yknT | 0 TM
 |  |  |  |  | BioOptimizer-no prediction | no
2.1. D. identified neither by overexpression of sE nor in sigE+ vs. sigE- experiments
2.1. D. a) SpoIIID binding confirmed by gel-shift
spoVK | spoVK | GTTTGTC | 15 | AATACAAT | AAGAAATAAA | 136 | spoVK | 1.445439770745927 | 0.729 |  | 5.984115950603198 | 0.943 |  | 4.836099241360541 | 0.998 |  | 0.7301902484814788 | 0.0494748456170849 |  | spoVK | PE799-800 | shifted | predicted | (-157)GTGGACAAAC(-166) |  |  | 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
 |  | ATGGTTTGTCC | 12 | TGAATACAATA | BioOptimizer prediction-correct | 135
2.1. D. b) not tested by gel-shift
none
2.2. Previously reported sE-controlled genes (but transcription start site has not been mapped):
2.2. A. also identified by overexpression of sE
none
2.2. B. below cut-off in mutant vs. [NAME] experiments but identified by overexpression of sE
none
2.2. C. not identified by overexpression of sE
none
2.2. D. identified neither by overexpression of sE nor in sigE+ vs. sigE- experiments
none
2.3. sE-regulated genes with predicted [NAME] promoter (from Eichenberger et al. 2003, JMB):
2.3. A. also identified by overexpression of sE
2.3. A. a) SpoIIID binding confirmed by gel-shift
none
2.3. A. b) not tested by gel-shift
proH-J | proH | TATACATATTT | 11 | ACAATACAAAT | BioOptimizer-prediction | 61 | proH | 7.655966069112565 | 0.982 |  | 5.847900841444809 | 1 |  | 2.605771749408841 | 0.988 |  | 0.9768524871634418 | 0.441908495202522 |  | proH |  |  | no prediction |  |  |  | proH | pyrroline-5-carboxylate reductase (EC 1.5.1.2), similar to ComER | 2.2 (Metabolism of amino acids and related molecules) | proH | yoxE | proI | comER, proG | proH | no | BC4134 (proI/proH) | BH1503 (proI/proH) | OB0013 (proH) | no [proC (CAC3252) (proI)] | no [proC (CPE2633)] | no [proC (lmo0396) (proI)] | no [proC (lin0414) (proI)] | proH | 4 TMs
 |  | AAAAACTGATT | 11 | CTCAGATAATT | BioOptimizer-prediction (unlikely) |  | initiation codon could be wrong
 | proJ | overlap |  |  |  |  | proJ | 1.798870915128788 | 0.964 |  | 7.07945784384138 | 1 |  | 2.326524430596156 | 0.9455 |  | 0.9095119626680124 | 0.269440389720771 |  | proJ |  |  |  |  |  |  | proJ | glutamate 5-kinase | 2.2 (Metabolism of amino acids and related molecules) | proJ | yohA | proB | argB, [NAME], dapG | proJ | no | BC2975 (proB/proJ) | no [BH1505 (proB)] | no [OB1052 (proB)] | no [proB (CAC3253) (proB)] | no [proB (CPE2579)] | no [proB (proB)] | no [proB (proB)] | proJ | 0-1 TM
yhbB | yhbB | GACTAAA | 15 | CATACGTA | possible promoter (by visual inspection) | 58 | yhbB | 2.079696687103696 | 0.996 |  | 8.375292821268829 | 1 |  | 2.042253801379788 | 0.9745 |  | 1.385670590687647 | 0.944548349948616 |  | yhbB |  |  | predicted | (-68)CAGGACAGGC(-77) |  |  | yhbB | spore protein (inner coat) | 5.2 (From other organisms) | yhbB | ygaQ | no | yjcM | yhbB | BA0546 | BC0545 | BH1022 | OB1086 | CAC3320 (yjcM/yhbB) | CPE1404 | no | no | yhbB | 0 TM
 |  |  |  |  | BioOptimizer-no prediction | no | initiation codon probably wrong
2.3. B. below cut-off in mutant vs. [NAME] experiments but identified by overexpression of sE
none
2.3. C. not identified by overexpression of sE , but identified in sigE mutant experiment
2.3. C. a) tested by gel-shift
none
2.3. C. b) not tested by gel-shift
[NAME] (absent from Eichenberger et al., 2003) | [NAME] | TCTTTCT | 14 | CATAAGAA |  | 73 | [NAME] | 1.196740531307243 | 0.739 |  | 3.706807217825761 | 0.997 |  | 3.888427769902099 | 0.9955 |  | 1.614172775080226 | 0.981601407978468 |  | [NAME] |  |  | predicted | (-123)TGGGACAAGG(-114) |  |  | [NAME] | extracellular metalloprotease (EC 3.4.21.-) | 2.2 (Metabolism of amino acids and related molecules) | [NAME] | no | no | no | [NAME] | no | BC0789 | no | no | no | no | no | no | [NAME] | secreted
 |  |  |  |  | BioOptimizer-no prediction | no
ycgM-N (absent from Eichenberger et al., 2003) | ycgM | TTGTCCA | 13 | CATACAAA |  |  | ycgM | 0.7852356346100718 | 0.181 |  | 4.216965034285823 | 0.99 |  | 2.584601224396108 | 0.987 |  | 1.174736592151058 | 0.899201891916866 |  | ycgM |  |  | no prediction |  |  |  | ycgM | proline dehydrogenase (oxidase) | 2.2 (Metabolism of amino acids and related molecules) | ycgM | no | yusM | no | ycgM | BA5253 (ycgM/yusM) | BC5006 (yusM/ycgM) | BH2740 | OB1350 (ycgM/yusM) | no | no | no | no | ycgM | 0 TM
 | ycgN |  |  |  |  |  | ycgN | 0.71 | 0.1 |  | 1.632814317949403 | 0.871 |  | 2.359306011673249 | 0.9875 |  | 1.147204356226823 | 0.792844617944297 |  | ycgN |  |  |  |  |  |  | ycgN | similar to 1-pyrroline-5-carboxylate dehydrogenase | 2.2 (Metabolism of amino acids and related molecules) | ycgN | no | no | no | ycgN | no? | BC0344 (rocA/ycgN) | BH2737/BH3940 | rocA | no | no | no | no | ycgN | 1-2 TMs
yheC-D | yheC | GAATCGT | 14 | AATACCGT |  | 82 | yheC | 1.485935642287007 | 0.759 |  | 4.0179081084894 | 0.892 |  | 5.224452698285227 | 0.998 |  | 1.016425204320551 | 0.558746998068334 |  | yheC |  |  | predicted | (-150)AAGAACAAGC(-141) |  |  | yheC | unknown | 5.1 (From B. subtilis) | yheC | no | no | yheD | yheC | BA0861 | BC0878 | no [BH1145 (yheD), BH1146 (yheD), BH1147 (yheD)] | OB2914 | no | no | no | no | yheC | 0 TM
 |  |  |  |  | BioOptimizer-no prediction | no
 | yheD | RACE-operon w/yheC (5 bp upstream) |  |  |  |  | yheD | 1.713957307508425 | 0.974 |  | 32.13660538640317 | 1 |  | 5.148273701623881 | 0.999 |  | 1.223174431068217 | 0.942362520582616 |  | yheD |  |  |  |  |  |  | yheD | spore coat protein | 5.1 (From B. subtilis) | yheD | no | no | yheC | yheD | BA0860 | BC0877 | BH1146 | OB2913 | no | no | no | no | yheD | 1 TM (mid)
yknU-V | yknU | TTGGCATATCC | 12 | AGCATACAATG | BioOptimizer-prediction | 147 | yknU | 1.442115351524869 | 0.735 |  | 9.660508789898138 | 0.97 |  | 1.864312702123259 | 0.958 |  | 1.328111907310963 | 0.980808121057288 |  | yknU |  |  | no prediction |  |  |  | yknU | similar to ABC transporter (ATP-binding protein) | 1.2 (Transport/binding proteins and lipoproteins) | yknU | no | ygaD, ywjA, yfiC, yknV, yheI, yfiB, yvcC, yheH, cydC, cydD… |  | yknU | no | no | BH1125 | OB1405 | no [[NAME] (ywjA)] | no | lmo0108 | lin0156 | yknU | 5 TMs
 |  | ATTTTCTGTAA | 10 | TACATATGTTA | BioOptimizer-prediction | 115 | initiation codon could be wrong
 | yknV | 11 bp downstream |  |  |  |  | yknV | 1.559552502826954 | 0.913 |  | 10.71519305237607 | 0.999 |  | 1.965077122605425 | 0.9655 |  | 1.324610513546595 | 0.952694369469936 |  | yknV |  |  |  |  |  |  | yknV | similar to ABC transporter (ATP-binding protein) | 1.2 (Transport/binding proteins and lipoproteins) | yknV | no | yfiC, ygaD, ywjA, yknU, yheH, yheI, yvcC, yfiB, cydC, cydB…. |  | yknV | no | no | BH1126 | OB1406 | no [CAC2756 (yheH)] | CPE1525 | lmo0107 | lin0155 | yknV | 6-7 TMs
yqfT (absent from Eichenberger et al., 2003) | yqfT | ACACATT | 13 | CATACATT | possible promoter (by visual inspection) | 22 | yqfT |  |  |  | 3.147748314101316 | 0.973 |  | 2.377262572302845 | 0.987 |  | 1.07054335822194 | 0.66369503599509 |  | yqfT |  |  | no prediction |  |  |  | yqfT | unknown | 5.2 (From other organisms) | yqfT | no | no | no | yqfT | BA4507 | BC4281 | BH1387 | OB1937 | no | no | no | no | yqfT | 0 TM
 |  |  |  |  | BioOptimizer-no prediction | no
2.3. D. not identified by overexpression of sE and not identified in sigE+ vs. sigE- experiment (either SpoIIID is essential for expression or indirect targets)
2.3.D.1. ratio in SpoIIID mutant experiment is high (>3)
2.3. D. 1. a) SpoIIID binding confirmed by gel-shift
cotF (absent from Eichenberger et al., 2003) | cotF | GAACAACA | 11 | GCATATGCT | [NAME] (mapped sigK promoter) | 35 | cotF |  |  |  |  |  |  | 5.218300803085669 | 0.9685 |  | 0.824709927147434 | 0.287283445333352 |  | cotF | PE778-779 | shifted | predicted | (-179)CTAAACAAGA(-170) |  |  | 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
cotT (absent from Eichenberger et al., 2003) | cotT | ACACCCA | 14 | AATATGGT | AAAAGGAT (mapped sigK promoter) | "+33" | cotT |  |  |  | 1.673493384946139 | 0.71 |  | 3.169690189145326 | 0.9915 |  | 0.7770188509398893 | 0.213897188750022 |  | cotT | PE793-794 | shifted | predicted | (+103)TTGAACAAAT(+112) |  |  | 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
 |  |  |  |  | BioOptimizer-not included
2.3. D. 1. b) not tested by gel-shift
cotV-W (absent from Eichenberger et al., 2003) | cotV | TTCCGCT | 14 | CATTATAT | AGAGTAT (mapped sigK promoter) | 29 | cotV | 0.63 | 0.21 |  | 6.496659420499724 | 0.94 |  | 2.972792083163181 | 0.9705 |  | 0.9987276769526988 | 0.498193986321667 |  | cotV |  |  | no prediction |  |  |  | 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-not included
 | cotW |  |  |  |  |  | cotW |  |  |  | 2.284112023911224 | 0.904 |  | 3.684886033572164 | 0.918 |  |  |  |  | cotW |  |  |  |  |  |  | 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
lip (absent from Eichenberger et al., 2003) | lip (lipA) | TACTTAA | 15 | AATACAAT | possible promoter (by visual inspection) | 32 | lip (lipA) |  |  |  | 0.6866670372003321 | 0.137 |  | 3.34732331788157 | 0.9745 |  | 1.345659401770642 | 0.980362997136488 |  | lip (lipA) |  |  | no prediction |  |  |  | lip (lipA) | [NAME] (EC 3.1.1.3) | 2.4 (Metabolism of lipids) | lip (lipA) | lipA | lipB | no | lip (lipA) | no | no | no | no | no | no | no | no | lip (lipA) | 2 TMs
 |  |  |  |  | BioOptimizer-not included
2.3.D. 2. ratio in SpoIIID mutant experiment is low (<3)
ydcI (absent from Eichenberger et al., 2003) | ydcI |  |  |  |  |  | ydcI | 1.11 | 0.59 |  | 1.195428126863015 | 0.667 |  | 2.343971655759669 | 0.986 |  | 1.499321804920123 | 0.989765082221307 |  | ydcI |  |  | no prediction |  |  |  | ydcI | similar to transcription accessory protein (S1 RNA binding domain) | 5.2 (From other organisms) | ydcI | no | no | ypfD, pnpA, yabR, yugI | ydcI | no | BC0267 | BH0531 | OB0632 | no | CPE2168 | lmo0898 | lin0897 | ydcI | 0 TM
yheI-H (absent from Eichenberger et al., 2003) | yheI |  |  |  |  |  | yheI | 1.3 | 0.77 |  | 1.237640264653631 | 0.704 |  | 2.745810596881725 | 0.978 |  | 2.000928911839026 | 0.996992454565535 |  | yheI |  |  | no prediction |  |  |  | yheI | similar to ABC transporter (ATPase), multidrug efflux? | 1.2 (Transport/binding proteins and lipoproteins) | yheI | no | yknU |  | yheI | BA3741 | BC0870 | BH1157 | OB1098 | [NAME] | CPE0527 (yheI/yheH) | lmo1652 | lin1692 | yheI | 5-6 TMs
 | yheH |  |  |  |  |  | yheH | 1.1 | 0.61 |  | 1.203776858061764 | 0.693 |  | 2.356847362295029 | 0.9675 |  | 1.856127276846167 | 0.996063647824236 |  | yheH |  |  |  |  |  |  | yheH | similar to ABC transporter (ATPase), multidrug efflux? | 1.2 (Transport/binding proteins and lipoproteins) | yheH | no | yknV |  | yheH | no [BA2444 (yfiC)] | BC0871 | BH1158 | OB1099 | CAC2756 | CPE0527 (yheI/yheH) | lmo1651 | lin1691 | yheH | 4 TMs
GENES IN SECTIONS   2.4., 2.5.and 2.6. WERE NOT INCLUDED IN THE FINAL TOTAL OF SIGE-CONTROLLED GENES
2.4 Members of the S-box regulon (considered to be indirect targets)
cysK | cysK |  |  |  |  |  | cysK | 0.8 | 0.33 |  | 0.172356949888398 | 0.053 |  | 2.356242641602487 | 0.985 |  | 0.7940612668119469 | 0.0891108460921606 |  | cysK |  |  |  |  |  |  | cysK |  |  | cysK |  |  |  | cysK |  |  |  |  |  |  |  |  | cysK
cysH-P-sat-cysC | cysH |  |  |  |  |  | cysH | 0.97 | 0.47 |  | 0.9544247217208899 | 0.454 |  | 2.412665516804079 | 0.9785 |  | 1.171029524406495 | 0.905638230259488 |  | cysH |  |  |  |  |  |  | cysH |  |  | cysH |  |  |  | cysH |  |  |  |  |  |  |  |  | cysH
 | cysP (ylnA) |  |  |  |  |  | cysP (ylnA) |  |  |  | 1.043130154399943 | 0.551 |  | 2.575022547298558 | 0.9745 |  | 1.407680042113868 | 0.953250464791412 |  | cysP |  |  |  |  |  |  | cysP |  |  | cysP |  |  |  | cysP |  |  |  |  |  |  |  |  | cysP
 | sat (ylnB) |  |  |  |  |  | sat (ylnB) |  |  |  | 0.6969315092086136 | 0.236 |  | 2.287719286678562 | 0.963 |  | 1.027715383653154 | 0.598754720588993 |  | sat |  |  |  |  |  |  | sat |  |  | sat |  |  |  | sat |  |  |  |  |  |  |  |  | sat
 | cysC (ylnC) |  |  |  |  |  | cysC (ylnC) |  |  |  | 0.8464633522280839 | 0.315 |  | 2.126492623862077 | 0.962 |  | 1.017621909431862 | 0.555049925020656 |  | cysC |  |  |  |  |  |  | cysC |  |  | cysC |  |  |  | cysC |  |  |  |  |  |  |  |  | cysC
yoaD-C-B | yoaD |  |  |  |  |  | yoaD | 0.65 | 0.25 |  | 1.34520415477709 | 0.638 |  | 2.439938936062744 | 0.959 |  | 1.378600422097602 | 0.980386644707323 |  | yoaD |  |  |  |  |  |  | yoaD |  |  | yoaD |  |  |  | yoaD |  |  |  |  |  |  |  |  | yoaD
 | yoaC |  |  |  |  |  | yoaC | 0.82 | 0.38 |  | 3.327642788211405 | 0.861 |  | 1.698609467582353 | 0.8525 |  | 1.267202353714376 | 0.95392001785817 |  | yoaC |  |  |  |  |  |  | yoaC |  |  | yoaC |  |  |  | yoaC |  |  |  |  |  |  |  |  | yoaC
 | yoaB |  |  |  |  |  | yoaB |  |  |  | 1.517815906988776 | 0.826 |  | 3.416707437274028 | 0.9895 |  | 1.373774262227722 | 0.984319617633018 |  | yoaB |  |  |  |  |  |  | yoaB |  |  | yoaB |  |  |  | yoaB |  |  |  |  |  |  |  |  | yoaB
yusC-B-A | yusC |  |  |  |  |  | yusC | 1 | 0.49 |  | 2.19188568334146 | 0.974 |  | 2.008081233704474 | 0.933 |  | 1.445210717259763 | 0.989339983527917 |  | yusC |  |  |  |  |  |  | yusC |  |  | yusC |  |  |  | yusC |  |  |  |  |  |  |  |  | yusC
 | yusB |  |  |  |  |  | yusB | 0.82 | 0.3 |  | 1.363305541455516 | 0.781 |  | 1.438640668665423 | 0.8555 |  | 1.420347369525792 | 0.988552189609053 |  | yusB |  |  |  |  |  |  | yusB |  |  | yusB |  |  |  | yusB |  |  |  |  |  |  |  |  | yusB
 | yusA |  |  |  |  |  | yusA | 1.3 | 0.65 |  | 2.901679222700515 | 0.99 |  | 1.430006197598691 | 0.855 |  | 1.34000747426067 | 0.982553823515444 |  | yusA |  |  |  |  |  |  | yusA |  |  | yusA |  |  |  | yusA |  |  |  |  |  |  |  |  | yusA
2.5. Genes repressed in the presence of sigE (considered to be indirect targets, probably repressed by a sigE-controlled gene repressed by SpoIIID)
a) Genes regulated by sigH |  |  |  |  | ratio sigH-T0 | [NAME]
dhbC | dhbC |  |  |  | 1.85 |  | dhbC | 0.6 | 0.21 |  | 0.1117001355140915 | 0.022 |  | 2.763057896524211 | 0.948 |  | 2.106067096826878 | 0.926044406618 |  | dhbC |  |  |  |  |  |  | dhbC |  |  | dhbC |  |  |  | dhbC |  |  |  |  |  |  |  |  | dhbC
fnr | fnr |  |  |  |  | 2.08 | fnr | 1.01 | 0.51 |  | 1.120015801853567 | 0.591 |  | 2.06314936721305 | 0.9585 |  | 1.369982915131576 | 0.959763961461213 |  | fnr |  |  |  |  |  |  | fnr |  |  | fnr |  |  |  | fnr |  |  |  |  |  |  |  |  | fnr
ggt | ggt |  |  |  |  | 2.4 | ggt | 0.56 | 0.12 |  | 0.5321407287078621 | 0.064 |  | 2.57158154779242 | 0.9865 |  | 0.4494020918433939 | 0.00104594577925687 |  | ggt |  |  |  |  |  |  | ggt |  |  | ggt |  |  |  | ggt |  |  |  |  |  |  |  |  | ggt
 | yofA | downstream of ggt (convergent) |  |  |  |  | yofA | 1.11 | 0.57 |  | 0.6677400110759909 | 0.188 |  | 4.025537759045223 | 0.967 |  | 1.509549110363142 | 0.992543787456096 |  | yofA |  |  |  |  |  |  | yofA |  |  | yofA |  |  |  | yofA |  |  |  |  |  |  |  |  | yofA
pksC | pksC |  |  |  |  | 4.35 | pksC | 0.62 | 0.08 |  | 0.4433757131256955 | 0.027 |  | 2.161017452975724 | 0.968 |  | 0.6696077593296395 | 0.0183035746454819 |  | pksC |  |  |  |  |  |  | pksC |  |  | pksC |  |  |  | pksC |  |  |  |  |  |  |  |  | pksC
racA (ywkC) | racA (ywkC) | sigH target |  |  |  | 2.56 | racA (ywkC) |  |  |  | 0.3491647556626531 | 0.015 |  | 2.686660010213404 | 0.9715 |  | 0.9850737561944687 | 0.4600818579732 |  | racA (ywkC) |  |  |  |  |  |  | racA (ywkC) |  |  | racA (ywkC) |  |  |  | racA (ywkC) |  |  |  |  |  |  |  |  | racA (ywkC)
ywcI-sacT | ywcI |  |  |  |  | 11.1 | ywcI |  |  |  | 0.2931053192171502 | 0.007 |  | 12.53167225477574 | 0.9735 |  | 0.07612617584159104 | 4.55703312363109e-06 |  | ywcI |  |  |  |  |  |  | ywcI |  |  | ywcI |  |  |  | ywcI |  |  |  |  |  |  |  |  | ywcI
 | sacT |  |  |  |  | 6.67 | sacT |  |  |  | 0.2359602784521984 | 0.003 |  | 3.559918992223787 | 0.992 |  | 0.07728068934509894 | 2.35073006082942e-06 |  | sacT |  |  |  |  |  |  | sacT |  |  | sacT |  |  |  | sacT |  |  |  |  |  |  |  |  | sacT
skfB (ybcPQ) | skfB (ybcQ) |  |  |  |  | 5.3 | skfB (ybcQ) |  |  |  | 0.3793493986928765 | 0.007 |  | 1.955949991871445 | 0.9545 |  | 0.4016901596337332 | 0.00018017438007456 |  | skfB (ybcQ) |  |  |  |  |  |  | skfB (ybcQ) |  |  | skfB (ybcP) |  |  |  | skfB (ybcQ) |  |  |  |  |  |  |  |  | skfB (ybcQ)
ycdA | ycdA |  |  |  |  | 1.92 | ycdA | 3.9 | 0.94 |  | 1.039743107283437 | 0.539 |  | 3.184936058639249 | 0.963 |  | 2.023359028150177 | 0.997836438781467 |  | ycdA |  |  |  |  |  |  | ycdA |  |  | ycdA |  |  |  | ycdA |  |  |  |  |  |  |  |  | ycdA
yfmI | yfmI |  |  |  |  | 1.85 | yfmI |  |  |  | 0.2239990621432765 | 0.018 |  | 2.274055399974982 | 0.9745 |  | 0.3628346074672876 | 0.00071374534815627 |  | yfmI |  |  |  |  |  |  | yfmI |  |  | yfmI |  |  |  | yfmI |  |  |  |  |  |  |  |  | yfmI
yfjB | yfjB |  |  |  |  | 2.9 | yfjB | 0.97 | 0.47 |  | 0.5346639468581648 | 0.168 |  | 2.182147172219888 | 0.9685 |  | 0.9286392467996337 | 0.280708257632082 |  | yfjB |  |  |  |  |  |  | yfjB |  |  | yfjB |  |  |  | yfjB |  |  |  |  |  |  |  |  | yfjB
yllB-ylxA | yllB |  |  |  |  | 2.04 | yllB | 0.86 | 0.28 |  | 0.3202891301545037 | 0.021 |  | 2.543111127802826 | 0.982 |  | 1.568743700938173 | 0.994280017704082 |  | yllB |  |  |  |  |  |  | yllB |  |  | yllB |  |  |  | yllB |  |  |  |  |  |  |  |  | yllB
 | ylxA |  |  |  |  | 1.5 | ylxA | 0.77 | 0.15 |  | 0.5405464257348988 | 0.055 |  | 2.184083123695494 | 0.9825 |  | 1.58105996671908 | 0.986716595408845 |  | ylxA |  |  |  |  |  |  | ylxA |  |  | ylxA |  |  |  | ylxA |  |  |  |  |  |  |  |  | ylxA
yqxM-sipW | yqxM |  |  |  |  | 2.27 | yqxM | 1.4 | 0.73 |  | 0.6445792191401223 | 0.136 |  | 2.010983469088082 | 0.971 |  | 1.23496114119928 | 0.880509011659641 |  | yqxM |  |  |  |  |  |  | yqxM |  |  | yqxM |  |  |  | yqxM |  |  |  |  |  |  |  |  | yqxM
 | sipW |  |  |  |  | 3.85 | sipW | 2.84 | 0.98 |  | 0.599021347851273 | 0.058 |  | 1.903642633935953 | 0.9505 |  | 1.396816842601547 | 0.979827465787558 |  | sipW |  |  |  |  |  |  | sipW |  |  | sipW |  |  |  | sipW |  |  |  |  |  |  |  |  | sipW
yraI | yraI |  |  |  |  | 2.78 | yraI | 0.76 | 0.22 |  | 0.4063671564574154 | 0.037 |  | 1.796265732533477 | 0.953 |  | 0.5270890389061772 | 0.00275570695843763 |  | yraI |  |  |  |  |  |  | yraI |  |  | yraI |  |  |  | yraI |  |  |  |  |  |  |  |  | yraI
yuaB | yuaB |  |  |  |  | 2.08 | yuaB | 0.86 | 0.4 |  | 0.04109802954302291 | 0.016 |  | 1.961139625284389 | 0.9535 |  | 1.432785810926046 | 0.98418496125457 |  | yuaB |  |  |  |  |  |  | yuaB |  |  | yuaB |  |  |  | yuaB |  |  |  |  |  |  |  |  | yuaB
yvcA-B-yvzA | yvcA |  |  |  |  | 2.22 | yvcA | 1.77 | 0.84 |  | 1.015173258184286 | 0.514 |  | 2.355453554891306 | 0.968 |  | 0.4316161481198433 | 0.000564691889053726 |  | yvcA |  |  |  |  |  |  | yvcA |  |  | yvcA |  |  |  | yvcA |  |  |  |  |  |  |  |  | yvcA
 | yvcB |  |  |  |  | 2.38 | yvcB | 1.19 | 0.65 |  | 0.7845031649198212 | 0.281 |  | 1.735018022455018 | 0.945 |  | 0.4575090087859158 | 0.00173881420581612 |  | yvcB |  |  |  |  |  |  | yvcB |  |  | yvcB |  |  |  | yvcB |  |  |  |  |  |  |  |  | yvcB
 | yvzA |  |  |  |  |  | yvzA |  |  |  | 1.017494386714921 | 0.511 |  | 1.974862438061761 | 0.9665 |  | 0.4556641036670022 | 0.000937738247805076 |  | yvzA |  |  |  |  |  |  | yvzA |  |  | yvzA |  |  |  | yvzA |  |  |  |  |  |  |  |  | yvzA
yvqJ | yvqJ |  |  |  |  | 2.17 | yvqJ | 0.98 | 0.48 |  | 0.5249518855720614 | 0.113 |  | 1.835816039368106 | 0.9575 |  | 1.487002974431125 | 0.991410520296205 |  | yvqJ |  |  |  |  |  |  | yvqJ |  |  | yvqJ |  |  |  | yvqJ |  |  |  |  |  |  |  |  | yvqJ
ywfB-C-D-E-F-G | ywfB | sigH target |  |  |  | 1.8 | ywfB | 0.55 | 0.07 |  | 0.5157239496136923 | 0.06 |  | 2.269199352948366 | 0.963 |  | 0.9731353726363947 | 0.434493971330625 |  | ywfB |  |  |  |  |  |  | ywfB |  |  | ywfB |  |  |  | ywfB |  |  |  |  |  |  |  |  | ywfB
 | ywfC | sigH target |  |  |  | 1.8 | ywfC | 0.85 | 0.4 |  | 0.4999156123863862 | 0.041 |  | 2.072146839187315 | 0.957 |  | 0.9016299076698759 | 0.247934277942157 |  | ywfC |  |  |  |  |  |  | ywfC |  |  | ywfC |  |  |  | ywfC |  |  |  |  |  |  |  |  | ywfC
 | ywfD | sigH target |  |  |  | 1.8 | ywfD | 0.61 | 0.08 |  | 0.4864299421006487 | 0.021 |  | 1.925246393993646 | 0.9395 |  | 0.9619000330983524 | 0.376754526681866 |  | ywfD |  |  |  |  |  |  | ywfD |  |  | ywfD |  |  |  | ywfD |  |  |  |  |  |  |  |  | ywfD
 | ywfE | sigH target |  |  |  | 1.8 | ywfE | 2.21 | 0.9 |  | 0.481232334117534 | 0.018 |  | 1.924804984284238 | 0.9275 |  | 0.8135096769644085 | 0.0879176896070953 |  | ywfE |  |  |  |  |  |  | ywfE |  |  | ywfE |  |  |  | ywfE |  |  |  |  |  |  |  |  | ywfE
 | ywfF | sigH target |  |  |  | 1.8 | ywfF | 0.74 | 0.23 |  | 0.5447623692228898 | 0.265 |  | 1.675551227111801 | 0.9095 |  | 1.097439599776626 | 0.736151742378768 |  | ywfF |  |  |  |  |  |  | ywfF |  |  | ywfF |  |  |  | ywfF |  |  |  |  |  |  |  |  | ywfF
 | ywfG | sigH target |  |  |  | 1.8 | ywfG | 1.08 | 0.55 |  | 0.4760925657936226 | 0.022 |  | 2.045464889631226 | 0.9585 |  | 1.060306961398006 | 0.705561747583937 |  | ywfG |  |  |  |  |  |  | ywfG |  |  | ywfG |  |  |  | ywfG |  |  |  |  |  |  |  |  | ywfG
yxbB-A-yxnB-asnH-yxaM | yxbB |  |  |  |  | 7.69 | yxbB |  |  |  | 0.4103843588757893 | 0.017 |  | 1.916460610973882 | 0.9435 |  | 0.5585379206166421 | 0.0011610912094121 |  | yxbB |  |  |  |  |  |  | yxbB |  |  | yxbB |  |  |  | yxbB |  |  |  |  |  |  |  |  | yxbB
 | yxbA |  |  |  |  | 4.55 | yxbA | 0.51 | 0.13 |  | 0.3214032766456185 | 0.042 |  | 1.549183793941453 | 0.875 |  | 0.6411129080775178 | 0.00698055106541906 |  | yxbA |  |  |  |  |  |  | yxbA |  |  | yxbA |  |  |  | yxbA |  |  |  |  |  |  |  |  | yxbA
 | yxnB |  |  |  |  | 5.88 | yxnB | 0.58 | 0.21 |  | 0.4139178923771777 | 0.009 |  | 2.705061829789915 | 0.9835 |  | 0.5553868214771898 | 0.00151082430462113 |  | yxnB |  |  |  |  |  |  | yxnB |  |  | yxnB |  |  |  | yxnB |  |  |  |  |  |  |  |  | yxnB
 | asnH |  |  |  |  | 6.67 | asnH |  |  |  | 0.4475459176425847 | 0.026 |  | 1.840141920052247 | 0.942 |  | 0.6589960686711968 | 0.0102056389185299 |  | asnH |  |  |  |  |  |  | asnH |  |  | asnH |  |  |  | asnH |  |  |  |  |  |  |  |  | asnH
 | yxaM |  |  |  |  | 3.85 | yxaM | 0.84 | 0.33 |  | 0.4082326160044096 | 0.024 |  | 1.610359306120793 | 0.8905 |  | 0.8004854650094239 | 0.0467454701232047 |  | yxaM |  |  |  |  |  |  | yxaM |  |  | yxaM |  |  |  | yxaM |  |  |  |  |  |  |  |  | yxaM
yybM | yybM |  |  |  |  | 1.72 | yybM | 0.69 | 0.27 |  | 0.1171070659189424 | 0.022 |  | 3.057332709874676 | 0.9615 |  | 0.6056491057865723 | 0.00518653368945643 |  | yybM |  |  |  |  |  |  | yybM |  |  | yybM |  |  |  | yybM |  |  |  |  |  |  |  |  | yybM
b) genes not regulated by sigH
bpr | bpr |  |  |  |  |  | bpr | 0.84 | 0.32 |  | 0.3751052995684228 | 0.018 |  | 2.669225226194304 | 0.9845 |  | 1.076320543369713 | 0.726053754641131 |  | bpr |  |  |  |  |  |  | bpr |  |  | bpr |  |  |  | bpr |  |  |  |  |  |  |  |  | bpr
gbsA | gbsA |  |  |  |  |  | gbsA |  |  |  | 0.4828190531251835 | 0.067 |  | 2.587761665686643 | 0.9805 |  | 1.826760869841226 | 0.99814100963925 |  | gbsA |  |  |  |  |  |  | gbsA |  |  | gbsA |  |  |  | gbsA |  |  |  |  |  |  |  |  | gbsA
spoVAB | spoVAB |  |  |  |  |  | spoVAB |  |  |  | 0.44 | 0.19 |  | 3.707609778470539 | 0.9775 |  | 0.9863526201269834 | 0.452206287098317 |  | spoVAB |  |  |  |  |  |  | spoVAB |  |  | spoVAB |  |  |  | spoVAB |  |  |  |  |  |  |  |  | spoVAB
ykuN-O-P | ykuN |  |  |  |  |  | ykuN | 1.17 | 0.73 |  | 0.2638561370991694 | 0.021 |  | 2.378653166958227 | 0.913 |  | 3.56928210989849 | 0.977073320389817 |  | ykuN |  |  |  |  |  |  | ykuN |  |  | ykuN |  |  |  | ykuN |  |  |  |  |  |  |  |  | ykuN
 | ykuO |  |  |  |  |  | ykuO | 1.11 | 0.65 |  | 0.4292477229329089 | 0.065 |  | 2.801395011262994 | 0.9875 |  | 3.429266552798317 | 0.97809812609642 |  | ykuO |  |  |  |  |  |  | ykuO |  |  | ykuO |  |  |  | ykuO |  |  |  |  |  |  |  |  | ykuO
 | ykuP |  |  |  |  |  | ykuP | 0.98 | 0.47 |  | 0.1700947072094368 | 0.023 |  | 3.608156722183972 | 0.9935 |  | 3.13898878163446 | 0.978261983591892 |  | ykuP |  |  |  |  |  |  | ykuP |  |  | ykuP |  |  |  | ykuP |  |  |  |  |  |  |  |  | ykuP
yufN-O | yufN |  |  |  |  |  | yufN | 0.81 | 0.3 |  | 0.6116265086378266 | 0.075 |  | 2.039571127155702 | 0.9625 |  | 1.502185513494237 | 0.984737051769245 |  | yufN |  |  |  |  |  |  | yufN |  |  | yufN |  |  |  | yufN |  |  |  |  |  |  |  |  | yufN
 | yufO |  |  |  |  |  | yufO |  |  |  | 0.5362956817002723 | 0.049 |  | 5.530096512257009 | 0.968 |  | 1.298301719250627 | 0.950591739127 |  | yufO |  |  |  |  |  |  | yufO |  |  | yufO |  |  |  | yufO |  |  |  |  |  |  |  |  | yufO
yurP-O | yurP |  |  |  |  |  | yurP | 1.1 | 0.58 |  | 0.2296072515456405 | 0.004 |  | 14.99912468881684 | 0.973 |  | 0.9414424733155934 | 0.315822258260023 |  | yurP |  |  |  |  |  |  | yurP |  |  | yurP |  |  |  | yurP |  |  |  |  |  |  |  |  | yurP
 | yurO |  |  |  |  |  | yurO |  |  |  | 0.3162997145649039 | 0.025 |  | 1.746310211281126 | 0.949 |  | 1.102038701791421 | 0.75492662459047 |  | yurO |  |  |  |  |  |  | yurO |  |  | yurO |  |  |  | yurO |  |  |  |  |  |  |  |  | yurO
2.6. Genes from the arginine biosynthesis operon
argC-J-B-D-carA-B-argF-yjzC | argC | no sigE promoter identified, probably indirect |  |  |  |  | argC |  |  |  | 1.83 | 0.93 |  | 2.126240721499996 | 0.963 |  | 1.388241978704835 | 0.980943468696047 |  | argC |  |  |  |  |  |  | argC |  |  | argC |  |  |  | argC |  |  |  |  |  |  |  |  | argC
 | argJ |  |  |  |  |  | argJ |  |  |  | 2.290867652767773 | 0.951 |  | 2.187543020874516 | 0.961 |  | 1.159777852246756 | 0.796573449147693 |  | argJ |  |  |  |  |  |  | argJ |  |  | argJ |  |  |  | argJ |  |  |  |  |  |  |  |  | argJ
 | argB | 14 bp downstream |  |  |  |  | argB |  |  |  | 2.1 | 0.933 |  | 1.250538771829052 | 0.737 |  | 1.146624901514171 | 0.823765144897946 |  | argB |  |  |  |  |  |  | argB |  |  | argB |  |  |  | argB |  |  |  |  |  |  |  |  | argB
argD start and argB stop overlap | argD | overlap |  |  |  |  | argD |  |  |  | 2.38231946935869 | 0.952 |  | 2.32525411904016 | 0.94 |  | 1.05607588443196 | 0.669489173604105 |  | argD |  |  |  |  |  |  | argD |  |  | argD |  |  |  | argD |  |  |  |  |  |  |  |  | argD
carA start is 70 bp downstream of argD stop | carA | 70 bp downstream |  |  |  |  | carA |  |  |  | 12.76438808811344 | 0.985 |  | 1.814164195611521 | 0.9105 |  | 1.111144138168256 | 0.774243741574171 |  | carA |  |  |  |  |  |  | carA |  |  | carA |  |  |  | carA |  |  |  |  |  |  |  |  | carA
carB start is 2 bp upstream of carA stop | carB | 2 bp upstream |  |  |  |  | carB |  |  |  | 3.580964371026361 | 0.986 |  | 1.624954793736074 | 0.844 |  | 1.347218580100564 | 0.977408599020828 |  | carB |  |  |  |  |  |  | carB |  |  | carB |  |  |  | carB |  |  |  |  |  |  |  |  | carB
argF start is 7 bp upstream of carB stop | argF | 7 bp upstream |  |  |  |  | argF |  |  |  | 6.223002851691597 | 0.988 |  | 1.477888019664761 | 0.824 |  | 1.138800133120093 | 0.863021608254663 |  | argF |  |  |  |  |  |  | argF |  |  | argF |  |  |  | argF |  |  |  |  |  |  |  |  | argF
yjzC start is 85 bp downstream of argF stop | yjzC | 85 bp downstream |  |  |  |  | yjzC | 0.5046612975635283 | 0.146 |  | 6.02559586074358 | 0.96 |  |  |  |  |  |  |  | yjzC |  |  |  |  |  |  | yjzC |  |  | yjzC |  |  |  | yjzC |  |  |  |  |  |  |  |  | yjzC
3. sE-CONTROLLED GENES UNAFFECTED BY SpoIIID or GerR:
3.1. Previously identified sE-controlled genes (with mapped transcription start site):
3.1. A) also identified in overexpression
cotE | cotE-P1 | TAAAGTT | 14 | CATACAAT | GGAACAGAAA (P1) | 101 | cotE-P1 | 2.060629913270001 | 0.993 |  | 49.43106869868356 | 0.999 |  | 1.250545060661061 | 0.76 |  | 0.739713144325036 | 0.0677113611806128 |  | cotE-P1 | PE776-7 | not shifted |  |  |  |  | cotE-P1 | spore coat protein (outer), morphogenetic protein | 1.8 (Sporulation) | cotE-P1 | no | no | no | cotE-P1 | cotE (BA3906) | BC3770 | cotE | cotE (OB1630) | no | no | no | no | cotE-P1 | 0 TM
 |  | AAGTAAAGTTT | 11 | TGCATACAATG | BioOptimizer prediction-correct | 100
 | cotE-P2 | GCACACT | 14 | [NAME] | AACACGAAGA (P2) | 31 | cotE-P2 |  |  |  |  |  |  |  |  |  |  |  |  | cotE-P2 |  |  |  |  |  |  | cotE-P2 |  |  | cotE-P2 |  |  |  | cotE-P2 |  |  |  |  |  |  |  |  | cotE-P2
 |  |  |  |  | BioOptimizer-no prediction | no
 |  | TTGGTTTTTCT | 11 | CGTATAAACTT | BioOptimizer-inaccurate | no
 |  | TTTTTATATTT | 12 | TGCACACTAGA | BioOptimizer-inaccurate | no
cotJA-JB-JC-yesJ | cotJA | TCATAAT | 14 | CATACCTA | TTAAGGTCA | 35 | cotJA | 3.749730022454835 | 0.999 |  | 50.81594425605607 | 1 |  | 1.299071116437609 | 0.7885 |  | 1.244926329549738 | 0.934448635017141 |  | cotJA |  |  |  |  |  |  | cotJA | spore coat protein (inner) | 1.8 (Sporulation) | cotJA | no | no | no | cotJA | cotJA (BA0805) | BC0823 | no | no | no | no | no | no | cotJA | 0 TM
 |  | TAGTCATAATC | 11 | [NAME] | BioOptimizer prediction-correct | 34
 | cotJB | overlap |  |  |  |  | cotJB | 8.974287945007486 | 1 |  | 48.86523593428338 | 1 |  | 1.037639722121491 | 0.5495 |  | 1.209947925494865 | 0.89934269930627 |  | cotJB |  |  |  |  |  |  | cotJB | spore coat protein (inner) | 1.8 (Sporulation) | cotJB | no | no | no | cotJB | cotJB (BA0804) | BC0822 | no | no | CAC1337 | no | no | no | cotJB | 0 TM
 | cotJC | 14 bp upstream |  |  |  |  | cotJC | 3.147748314101316 | 0.999 |  | 46.23810213992606 | 1 |  | 0.9387010832705859 | 0.425 |  | 1.142356669922187 | 0.827805358446374 |  | cotJC |  |  |  |  |  |  | cotJC | spore coat protein (inner) | 1.8 (Sporulation) | cotJC | no | ydbD, yjqC | no | cotJC | cotJC (BA0803) | BC0821 | no [BH2190 (yjqC)] | no [OB1667 (yjqC)] | CAC1338 | no | no | no | cotJC | 0 TM
 | yesJ | 123 bp downstream-operon confirmed by RACE |  |  |  |  | yesJ | 4.187935651179184 | 0.999 |  | 29.10717118066606 | 1 |  | 0.8470240414954979 | 0.2995 |  | 1.328716120538818 | 0.965809590726978 |  | yesJ |  |  |  |  |  |  | yesJ | similar to acetyltransferase ([NAME] family) | 5.2 (From other organisms) | yesJ | yeeN, [NAME], yfxD | no | no | yesJ | BA3112 | BC3079 | no | OB0363 | CAC1007 | [NAME] | lmo0652 | lin0655 | yesJ | 0 TM
glgB-C-D-A-P | glgB | GAATAAA | 14 | ACTATGAT | GTCAGAAAGG | 18 | glgB | 2.897343587701323 | 0.976 |  | 2.10862814993329 | 0.963 |  | 1.663475212486651 | 0.9345 |  | 1.082363695595395 | 0.749956530538958 |  | glgB |  |  |  |  |  |  | glgB | 1,4-alpha-glucan branching enzyme | 2.1.1 (Specific pathways) | glgB | no | no | amyX, yvdF, malL, yugT, treA, ycdG | glgB | [NAME] (BA5123) | BC4867 | no | OB0406 | no [CAC2679 (amyX)] | no | no [lmo2126 (yvdF)] | no [lin2231 (yvdF)] | glgB | 0-1 TM
 |  | TTTTTATAAAT | 10 | CTTAGATTTTG | BioOptimizer-inaccurate | no
 |  | TCTCCATATAT | 10 | TTCAGAAAATG | BioOptimizer-inaccurate | no
 |  | AAGGGCTTTTT | 10 | CGAATAAATAC | BioOptimizer-inaccurate | no
 | glgC | overlap |  |  |  |  | glgC | 2.432204009073816 | 0.924 |  | 2.051162178825566 | 0.94 |  | 1.158586666961641 | 0.6195 |  | 1.158245977363129 | 0.883342414889015 |  | glgC |  |  |  |  |  |  | glgC | glucose-1-phosphate adenylyltransferase | 2.1.1 (Specific pathways) | glgC | no | [NAME] | spsI, yfnH, gtaB | glgC | glgC (BA5122) | BC4686 | glgC | OB0407 | glgC (CAC2237-CAC2238) | glgC (CPE0068) | no [lmo1081 (spsI)] | no | glgC | 0 TM
 | [NAME] | 26 bp downstream |  |  |  |  | [NAME] | 2.924152377843336 | 0.993 |  | 2.103778439766475 | 0.96 |  | 1.685000172494353 | 0.9145 |  | 1.285049637612241 | 0.967946785306952 |  | [NAME] |  |  |  |  |  |  | [NAME] | required for glycogen biosynthesis | 2.1.1 (Specific pathways) | [NAME] | no | glgC | no | [NAME] | [NAME] (BA5121) | BC4685 | [NAME] | OB0408 | glgC (CAC2237-CAC2238) | [NAME] (CPE0069) | no | no | [NAME] | 0 TM
 | glgA | overlap |  |  |  |  | glgA | 2.449063241844746 | 0.993 |  | 2.259435770220978 | 0.976 |  | 1.487120100080657 | 0.852 |  | 1.353038002811544 | 0.981078885547519 |  | glgA |  |  |  |  |  |  | glgA | starch (bacterial glycogen) synthase | 2.1.1 (Specific pathways) | glgA | no | no | no | glgA | glgA (BA5120) | BC4684 | glgA | OB0409 | glgA (CAC2239) | glgA (CPE0064) | no | no | glgA | 0 TM
 | glgP | 11 bp upstream |  |  |  |  | glgP | 2.87739841473567 | 0.999 |  | 2.152781734724373 | 0.972 |  | 1.558197244956048 | 0.8665 |  | 1.333994638377111 | 0.98139638244762 |  | glgP |  |  |  |  |  |  | glgP | glycogen phosphorylase | 2.1.1 (Specific pathways) | glgP | no | no | no | glgP | glgP (BA5119) | BC4683 | glgP | OB0410 | glgP (CAC1664) | glgP (CPE0065) | no | no | glgP | 1-2 TM
prkA | prkA | GCATGTA | 14 | CATAGATT | GTATCAAAGT (5'RACE) | 53 | prkA | 2.243881923782766 | 0.995 |  | 8.1846478813479 | 1 |  | 0.8445772907999307 | 0.3 |  | 0.9511217897116484 | 0.371426238941589 |  | prkA |  |  |  |  |  |  | prkA | serine protein kinase, spore coat protein (inner) | 3.8 (Protein modification) | prkA | no | no | no | prkA | BA0550 | BC0548 | prkA | OB2654 | prkA (CAC0579) | prkA (CPE1334) | no | no | prkA | 0 TM
 |  | [NAME] | 11 | GGCATAGATTG | BioOptimizer prediction-correct | 52
safA-coxA | safA (yrbA) | TCATAAC | 14 | CATATGTT | GTGAAGAAA | 61 | safA (yrbA) | 1.770108958317421 | 0.818 |  | 31.76874070649772 | 0.998 |  | 1.152532454996917 | 0.6585 |  | 0.8280041123786996 | 0.0830887033344675 |  | safA (yrbA) |  |  |  |  |  |  | safA (yrbA) | spore coat protein (inner), morphogenetic protein, associated with [NAME] | 1.8 (Sporulation) | safA (yrbA) | yrbA | no | lytF, yojL, yocH | safA (yrbA) | BA4659 | BC4420 | BH1221 | OB2040 | no | CPE2215 | no | no | safA (yrbA) | 0 TM
 |  | TACTCATAACT | 11 | GGCATATGTTG | BioOptimizer prediction-correct | 60
 | coxA (yrbB) | operon identified by Takamatsu H et al. (1998); (228 bp apart) |  |  |  |  | coxA (yrbB) | 3.318944575526104 | 0.995 |  | 3.50751873952568 | 0.977 |  | 1.141776287980102 | 0.659 |  | 0.7666374151530718 | 0.0919959730324524 |  | coxA (yrbB) |  |  |  |  |  |  | coxA (yrbB) | spore cortex protein (sG-regulated) | 1.8 (Sporulation) | coxA (yrbB) | yrbB | no | no | coxA (yrbB) | BA4658 | [NAME] | no | OB2039 | no | no | no | no | coxA (yrbB) | 0 TM
spoVR | spoVR | TCATCTT | 14 | CATACATT | ATAGATAAGTC | 29 | spoVR | 2.477422057633285 | 0.996 |  | 148.2518085145954 | 1 |  | 0.7201290651204972 | 0.1585 |  | 1.097002778520682 | 0.767087789429467 |  | spoVR |  |  |  |  |  |  | spoVR | spore cortex synthesis | 1.8 (Sporulation) | spoVR | no | no | no | spoVR | spoVR (BA 0767) | BC0787 | spoVR | spoVR (OB2646) | spoVR (CAC0581) | spoVR (CPE1332) | no | no | spoVR | 0 TM
 |  | CTATCATCTTT | 11 | CTCATACATTA | BioOptimizer prediction-correct | 28
spoVID-ysxE | [NAME] | TCATATT | 14 | CATACACC | TTTAGTGACA | 47 | [NAME] | 2.07491351745491 | 0.991 |  | 112.2018454301963 | 1 |  | 0.951120811110193 | 0.4445 |  | 0.8921721820400104 | 0.266931627152507 |  | [NAME] |  |  |  |  |  |  | [NAME] | spore coat protein, morphogenetic protein | 1.8 (Sporulation) | [NAME] | no | no | no | [NAME] | BA4692 | BC4467 | [NAME] | [NAME] (OB2064) | no | no | no | no | [NAME] | 0 TM
 |  | CACTCATATTT | 11 | TACATACACCT | BioOptimizer prediction-correct | 46
 | ysxE | 32 bp downstream |  |  |  |  | ysxE | 2.172701178863745 | 0.983 |  | 24.88857318282392 | 1 |  | 0.8803409893169282 | 0.391 |  | 0.8389169057216006 | 0.0815984312993243 |  | ysxE |  |  |  |  |  |  | ysxE | unknown | 5.2 (From other organisms) | ysxE | no | no | no | ysxE | BA4691 | BC4466 | BH3040 | OB2063 | no [CAC2908] | no | no | no | ysxE | 0 TM
ydcA | ydcA | TACTATT | 14 | CATAAACG | TGTTACTATAG (5'RACE) | 41 | ydcA | 2.147830474130534 | 0.983 |  | 4.623810213992605 | 0.998 |  | 0.4605081228885765 | 0.0715 |  |  |  |  | ydcA |  |  |  |  |  |  | ydcA | intramembrane serine protease [rhomboid superfamily (conserved motif WR-N-GASG-H)], growth | 5.1 (From B. subtilis) | ydcA | no | yqgP | no | ydcA | BA0249 | BC0261 | BH0517 | OB0618 | no [CAC0954 (yqgP)] | no [CPE1452 (yqgP)] | no [lmo1337 (yqgP)] | no [lin1374 (yqgP)] | ydcA | 6 TMs (pred)
 |  | ACGTACTATTT | 11 | CTCATAAACGT | BioOptimizer prediction-correct | 40
yjbX | yjbX | TTCTGAT | 14 | CATATAGA | TAGAATATGA (5' RACE) | 23 | yjbX | 2.060629913270001 | 0.944 |  | 34.35579478998747 | 1 |  | 0.7627745616703061 | 0.234 |  | 0.536025745169685 | 0.012483883226216 |  | yjbX |  |  |  |  |  |  | yjbX | glutamic acid rich protein, spore coat protein (outer) | 6 (No similarity) | yjbX | no | no | no | yjbX | BA1233 | BC1217 | no | OB1225 | no | no | no | no | yjbX | 0 TM
 |  | TTCTTCTGATT | 11 | GTCATATAGAT | BioOptimizer prediction-correct | 22
yunB | yunB | TACTATG | 14 | CATACATT | GTGATATGT (5'RACE) | 23 | yunB | 3.273406948788383 | 0.997 |  | 16.25548755750484 | 1 |  | 0.6179952816468353 | 0.094 |  | 1.146286764005547 | 0.796402279078579 |  | yunB |  |  |  |  |  |  | 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
 |  | TATTACTATGT | 11 | AGCATACATTG | BioOptimizer prediction-correct | 22
yuzC | yuzC | TCATATT | 15 | TATACATA | TAGAAACATC (5'RACE) | 30 | yuzC | 5.058246620031141 | 0.986 |  | 25.00345361696431 | 0.999 |  | 1.356022568859051 | 0.8125 |  | 1.998917022527106 | 0.998053677987723 |  | yuzC |  |  |  |  |  |  | yuzC | spore coat protein (inner) | 6 (No similarity) | yuzC | no | no | no | yuzC | no | no | no | no | no | no | no | no | yuzC | 0 TM
 |  | TTGTCATATTC | 12 | TCTATACATAT | BioOptimizer prediction-correct | 29
yuxH not included in final total | yuxH | convergent with yuzC |  |  |  |  | yuxH | 1.3 | 0.86 |  | 14.98004093038383 | 1 |  | 1.421708040173338 | 0.8505 |  | 1.806661882831118 | 0.997563951269846 |  | yuxH |  |  |  |  |  |  | yuxH |  |  | yuxH |  |  |  | yuxH |  |  |  |  |  |  |  |  | yuxH
yybI | yybI | TCTTTGA | 13 | CATATAAT | GATTCATTCA (5'RACE) | 33 | yybI | 2.296148648112362 | 0.994 |  | 10.73989412341245 | 0.999 |  | 1.327142784273901 | 0.7995 |  |  |  |  | yybI |  |  |  |  |  |  | yybI | spore coat protein (inner) | 6 (No similarity) | yybI | no | no | no | yybI | no | no | no | OB2306 | CAC3416 | CPE1622 | no | no | yybI | 0-1 TM
 |  | TATGTCTTTGA | 11 | TGCATATAATG | BioOptimizer prediction-correct | 32
3.1. B) below cut-off in sigE+ vs. sigE- experiments but identified by overexpression of sE
usd-spoIIID-mbl | usd | GCATATT | 14 | AATACACT | GTTACAAAC | 40 | usd |  |  |  | 4.055085354483839 | 0.886 |  |  |  |  | 0.9496918696537813 | 0.324591276323992 |  | usd |  |  |  |  |  |  | usd | translation of spoIIID | 1.8 (Sporulation) | usd | no | no | no | usd | no | no | no | no | no | no | no | no | usd | 0 TM
 |  | TTAGCATATTC | 11 | CTAATACACTG | BioOptimizer prediction-correct | 39
 | spoIIID | 14 bp downstream-gene interrupted by resistance cassette in sigE+ vs sigE- experiment |  |  |  |  | spoIIID | 2.223309890651403 | 0.904 |  |  |  |  |  |  |  | 0.8538710518117143 | 0.133366140348332 |  | spoIIID |  |  |  |  |  |  | spoIIID | transcriptional regulator (DeoR family) | 3.5.2 (Regulation) | spoIIID | no | no | no | spoIIID | spoIIID (BA5521) | BC5282 | spoIIID | OB2959 | spoIIID (CAC2859) | spoIIID (CPE2181) | no | no | spoIIID | 0 TM
 | [NAME] | 164 bp downstream-operon identified by [NAME] and [NAME] (1995), [NAME]. 177, 765- |  |  |  |  | [NAME] | 2.404362800006933 | 0.905 |  | 65.91738952443217 | 0.999 |  | 0.9771993185597798 | 0.4785 |  | 0.9915442022562152 | 0.475139906141911 |  | [NAME] |  |  |  |  |  |  | [NAME] | MreB-like protein | 1.1 (Cell wall) | [NAME] | no | mreB, mreBH | dnaK, ftsA | [NAME] | mbl (BA5520) | BC5281 | [NAME] | OB2958 | CAC2858 | [NAME] (CPE2180) | [NAME] | [NAME] | [NAME] | 0 TM
yteV | yteV | TCATAAC | 14 | AATAGATT | GATAGAG | 24 | yteV | 2.6 | 0.927 |  |  |  |  |  |  |  |  |  |  | yteV |  |  |  |  |  |  | yteV | unknown | 6 (No similarity) | yteV | cse60 | no | no | yteV | BA4965 | no | no | no | no | no | no | no | yteV | 0 TM
 |  |  |  |  | BioOptimizer-no prediction | no
3.1.C) not identified by overexpression
[NAME] | [NAME] (ywdL) | GCATAAT | 14 | CATAAGGT | GAAAGAGATAAAAAT (5'RACE) | 122 | [NAME] (ywdL) | 1.710015315090288 | 0.919 |  | 56.62392890382536 | 1 |  | 1.455310844468855 | 0.8525 |  | 0.787941077903286 | 0.0563868377915069 |  | [NAME] (ywdL) |  |  |  |  |  |  | [NAME] (ywdL) | germination | 5.2 (From other organisms) | [NAME] (ywdL) | no | no | no | [NAME] (ywdL) | BA5641 | BC5391 | BH3827 | OB3025 | no | no | no | no | [NAME] (ywdL) | 0 TM
 |  | TCAGCATAATC | 11 | CTCATAAGGTG | BioOptimizer prediction-correct | 121
3.1.D) not identified by overexpression, nor in sigE+ vs. sigE- experiment
yoaW | yoaW (G4) | GAATATT | 14 | AATACAAT | AAATCGATAGA | 302 | yoaW (G4) | 1.42232878712282 | 0.821 |  | 1.59220872705117 | 0.851 |  | 1.380150271319802 | 0.838 |  | 0.5994656991234124 | 0.00313803877288721 |  | yoaW (G4) |  |  |  |  |  |  | yoaW (G4) | unknown | 6 (No similarity) | yoaW (G4) | G4 | no | no | yoaW (G4) | no | no | no | no | no | no | no | no | yoaW (G4) | secreted-pred
 |  |  |  |  | BioOptimizer-no prediction | no
spoVM | spoVM | TACTTTT | 14 | CATATTAA | TAATGATAA | 94 | spoVM |  |  |  |  |  |  |  |  |  |  |  |  | spoVM |  |  |  |  |  |  | spoVM | cortex and coat | 1.8 (Sporulation) | spoVM | no | no | no | spoVM | not annotated | not annotated | BH2501 | spoVM (OB1513) | not annotated | not annotated | no | no | spoVM | 0 TM
 |  | AGGTACTTTTT | 11 | GGCATATTAAT | BioOptimizer prediction-correct | 93
rpmB not included in final total | rpmB | convergent |  |  |  |  | rpmB | 0.7798301105232587 | 0.333 |  | 3.126079367123956 | 0.983 |  | 0.8020326045114732 | 0.2375 |  | 1.134359470832695 | 0.847841486779096 |  | rpmB |  |  |  |  |  |  | rpmB |  |  | rpmB |  |  |  | rpmB |  |  |  |  |  |  |  |  | rpmB
yfhS | yfhS | AGTTCTT | 14 | AATAATGG | AATGGCAAG | 27 | yfhS | absent from microarray |  |  |  | absent from microarray |  |  |  | absent from microarray |  |  |  | yfhS |  |  |  |  |  |  | yfhS | unknown | 5.1 (From B. subtilis) | yfhS | no | no | no | yfhS | BA0523 | BC0505 | BH0937 | OB0897 | no | no | no | no | yfhS | 0 TM
 |  |  |  |  | BioOptimizer-no prediction | no
3.2. Previously reported sE-controlled genes (but transcription start site has not been mapped):
3.2. A) also identified in overexpression
ydhD | ydhD | ACATATC | 14 | AATAAGAT | not mapped | 38 | ydhD | 2.223309890651403 | 0.99 |  | 51.40436515824263 | 1 |  | 1.590052092017828 | 0.903 |  | 1.723086921198104 | 0.997355069385656 |  | ydhD |  |  |  |  |  |  | ydhD | spore protein, similar to YaaH | 1.8 (Sporulation) | ydhD | no | yaaH, yvbX | ykvQ, lytF, yojL | ydhD | BA3668 | sleL (BC3607) | BH0693 | OB0024 (yaaH/ydhD) | [NAME] (yaaH/ydhD) | no | no [lmo0105] | no [lin0153] | ydhD | 2 TMs
 |  | TTGGTATTTTT | 12 | CACATATCTAA | BioOptimizer-prediction | 57
3.2. B) below cut-off in sigE+ vs. sigE- experiments but identified by overexpression of sE
none
3.2.C) not identified by overexpression
nucB | nucB | AAATATT | 14 | CATACATT | not mapped | 29 | nucB |  |  |  | 1.931968317016924 | 0.951 |  | 0.8108107766561677 | 0.2465 |  | 1.583688782810813 | 0.983151237955553 |  | nucB |  |  |  |  |  |  | nucB | sporulation-specific extracellular nuclease | 2.3 (Metabolism of nucleotides and nucleic acids) | nucB | no | nucA | no | nucB | no | no [BC4005 (nucA)] | no | no | no | no | no | no | nucB | no (secreted)
 |  | TAAAAATATTC | 11 | CCCATACATTG | BioOptimizer-prediction | 28
3.2.D) not identified by overexpression, nor in mutant experiment
ctpB (absent from Eichenberger et al., 2003) | ctpB (yvjB) | ACATGAA | 14 | CATATACT | not mapped |  | ctpB (yvjB) |  |  |  | 2.67527480806072 | 0.914 |  | 0.6596521109337024 | 0.1975 |  | 0.8506763906178321 | 0.107610755647598 |  | ctpB (yvjB) |  |  |  |  |  |  | ctpB (yvjB) | PDZ-containing serine protease (sigK activation) | 2.2 (Metabolism of amino acids and related molecules) | ctpB (yvjB) | yvjB | ctpA, htrA | spoIVB | ctpB (yvjB) | BA5414 | BC5184 | BH3599 | OB2490 | no [CAC0499 (ctpA)] | no [CPE0301 (ctpA)] | no [lmo1851 (ctpA)] | no [lin1965 (ctpA)] | ctpB (yvjB) | 1 TM (Nter)
3.3. sE-regulated genes with predicted [NAME] promoter (from Eichenberger et al. 2003, JMB):
3.3. A) also identified by overexpression of sE
alkA | alkA | TCTTGATAACT | 10 | CTCATAAATAG | BioOptimizer-prediction | 124 | alkA | 2.218196419800219 | 0.874 |  | 6.165950018614823 | 0.998 |  | 1.004111762523566 | 0.5065 |  | 0.5472164641372481 | 0.00099625625245392 |  | alkA |  |  |  |  |  |  | alkA | DNA-3-methyladenine glycosylase (EC 3.2.2.21)-hydrolysis of alkylated DNA | 3.2 (DNA restriction/modification and repair) | alkA | no | yfjP | no | alkA | alkA (BA3871) | BC3742 | no [BH1749 (yfjP)] | no | no [CAC2707 (ytxB)] | CPE2293 | no | no | alkA | 1 TM (mid)
clsA (ywnE) | clsA (ywnE) | TTATTCTTTTA | 13 | GTTATAATTTG | BioOptimizer-prediction | 79 | clsA (ywnE) | 3.548133892335755 | 0.967 |  | 2.051162178825566 | 0.976 |  | 0.9438754021935508 | 0.448 |  | 1.194340821158561 | 0.929061331765641 |  | clsA (ywnE) |  |  |  |  |  |  | clsA (ywnE) | major cardiolipin synthase (phospholipase D family), similar to YwjE | 2.4 (Metabolism of lipids) | clsA (ywnE) | no | ywiE, ywjE | no | clsA (ywnE) | no [cls-2 (BA1204,ywiE)] | no [BC1191 (ywiE)] | BH2858 (ywiE/ywnE) | OB3045 | no [CAC3316 (ywiE)] | clsD (CPE1430) | [NAME] | lin2646 | clsA (ywnE) | 2-3 TMs
comER | comER | TCGTCATATTT | 14 | CACATATGGTT | BioOptimizer-prediction | 33 | comER | 2.103778439766475 | 0.85 |  | 9.354056741475523 | 0.966 |  | 1.302342715918715 | 0.7855 |  | 0.9644106656437313 | 0.399405047401421 |  | comER |  |  |  |  |  |  | comER | similar to pyrolline-5'-carboxylate reductases (proH) | 2.2 (Metabolism of amino acids and related molecules) | comER | comD,comED | proG | proI, proH | comER | BA4554 | BC4325 | comER | no [OB0013 (proH)] | no [proC (CAC3252) (proI)] | no [proC (CPE2633)] | no [lmo1387(proG)] | no [lin1424 (proG)] | comER | 3 TMs
cotB | cotB | CAACAAA | 13 | TATATATG | CAGTATGT (sigK promoter) | 42 | cotB | 2.460367604147628 | 0.991 |  | 6.151768727098682 | 0.997 |  | 1.607216827219015 | 0.9055 |  | 0.5687262699414578 | 0.00892258556546288 |  | cotB |  |  |  |  |  |  | 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
[NAME] | [NAME] | ATACACT | 13 | CGTACTAT | [NAME] (sigK promoter) | 53 | [NAME] | 3.580964371026361 | 0.984 |  | 5.081594425605605 | 0.993 |  | 1.240628370116169 | 0.7595 |  | 0.7841978707053576 | 0.049372305632583 |  | [NAME] |  |  |  |  |  |  | [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
 |  | CACTTATACAC | 12 | CGCGTACTATG | BioOptimizer-prediction | 52
cotH | cotH | AATCCTC | 14 | TTAAGGAT | GAAGATCCTT (sigK promoter) | 106 | cotH | 3.083187950249355 | 0.993 |  | 9.74989637717387 | 0.999 |  | 1.55202322046007 | 0.894 |  | 0.7457503517832152 | 0.0533179699264404 |  | cotH |  |  |  |  |  |  | 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
cotY-Z | cotY | ACACCAA | 14 | CATATGTT | GTTAAGGACTA (sigK promoter) | 37 | cotY | 2.055890595984142 | 0.867 |  | 6.251726927756859 | 0.997 |  | 0.8645121511980303 | 0.3205 |  | 0.9063025127155022 | 0.25949588654993 |  | cotY |  |  |  |  |  |  | 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
 |  | TTCTTATTTTC | 11 | TGAATATATAG | BioOptimizer-prediction | 85
 | [NAME] |  |  |  |  |  | [NAME] | 9.77237220955811 | 0.997 |  | 7.63835783577691 | 0.999 |  | 0.8574948497081739 | 0.3135 |  | 1.022502680278503 | 0.56399140333143 |  | [NAME] |  |  |  |  |  |  | [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
gerR (ylbO) | gerR (ylbO) | ATAGTCTATCT | 11 | GGCATATGTAT | BioOptimizer-prediction | 34 | gerR (ylbO) | 2.805433637951714 | 0.981 |  | 23.38837238659356 | 1 |  | 1.346090920856259 | 0.819 |  | 2.248527033926052 | 0.994906746811573 |  | gerR (ylbO) |  |  |  |  |  |  | gerR (ylbO) | similar to DNA binding protein ([NAME] family), similar to RsfA (YwfN) | 5.1 (From B. subtilis) | gerR (ylbO) | no | rsfA | no | gerR (ylbO) | BA4061 | BC3922 | BH2581 | OB1457 | no | no | no | no | gerR (ylbO) | 0 TM
glnQ-H-M-P | glnQ | ACATATC | 14 | CATAGACT | most likely promoter (not in BioP/BioO sequence) | 217 | glnQ | 2.546830252585041 | 0.994 |  | 37.6703798983909 | 1 |  | 0.918496487020977 | 0.396 |  | 1.293610469193685 | 0.971648026793787 |  | glnQ |  |  |  |  |  |  | glnQ | glutamine ABC transporter (ATP-binding) | 1.2 (Transport/binding proteins and lipoproteins) | glnQ | no | yqiZ, yckI, ytmN, yxeO | no | glnQ | BA0639 | BC0639 | no [BH1463 (yqiZ)] | OB1006 | glnQ (CAC0112) | no [CPE0602] | no [[NAME] (yqiZ)] | no [lin2353 (yqiZ)] | glnQ | 0 TM
 |  | TGGACATTTTT | 12 | TTCAGAAAAGT | BioOptimizer-prediction (unlikely)
 | glnH | 21 bp downstream |  |  |  |  | glnH | 1.648162391525508 | 0.942 |  | 73.11390834834182 | 1 |  | 0.8779172431492535 | 0.35 |  | 1.041391227891636 | 0.631293658379311 |  | glnH |  |  |  |  |  |  | glnH | glutamine ABC transporter (Gln-binding) | 1.2 (Transport/binding proteins and lipoproteins) | glnH | no | no | yqiX, yxeM, yckK, yckB, ytmK | glnH | BA0640 | BC0640 | no | OB1004 | no | no [CPE0600] | no [lmo1738 (yqiX)] | no [lin0840  (yqiY)] | glnH | 1 TM
 | [NAME] | 60 bp downstream |  |  |  |  | [NAME] | 1.177605973520807 | 0.618 |  | 38.19442708400467 | 0.993 |  | 0.7543762206601559 | 0.2005 |  | 1.385869816845833 | 0.97999127786463 |  | [NAME] |  |  |  |  |  |  | [NAME] | glutamine ABC transporter (membrane) | 1.2 (Transport/binding proteins and lipoproteins) | [NAME] | no | glnP, yckA, yckJ, yqiY, yxeN, ytmL, ytmM | no | [NAME] | BA0641 | BC0641 | no | OB1005 | no [CAC3619 (yqiY)] | no [CPE0601] | no [lmo1240 (ysnB)] | no [lin2352 (yqiY)] | [NAME] | 5 TMs
 | glnP | 16 bp downstream |  |  |  |  | glnP | 6.36795520907916 | 1 |  | 36.22429984166988 | 1 |  | 0.7231222368006079 | 0.169 |  | 1.507152359885197 | 0.991115551072801 |  | glnP |  |  |  |  |  |  | glnP | glutamine ABC transporter (membrane) | 1.2 (Transport/binding proteins and lipoproteins) | glnP | no | [NAME], yckA | yckJ, ytmM, ytml, yqiY, yxeN | glnP | BA0642 | BC0642 | no | OB1005 | CAC0111 | no [CPE0601] | no [lmo1240 (ysnB)] | no [lin2352 (yqiY)] | glnP | 6 TMs
ispE-purR-yabJ | ispE (yabH) | ACTTCAA | 15 | CATACTTA | most likely promoter | 28 | ispE (yabH) | 1.606941253012877 | 0.899 |  | 5.997910762555096 | 0.991 |  | 2.043130943272318 | 0.948 |  | 1.143346791587854 | 0.839059342680238 |  | ispE (yabH) |  |  |  |  |  |  | ispE (yabH) | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (EC 2.7.1.-)-nonmevalonate pathway to terpenes | 2.1.1 (Specific pathways) | ispE (yabH) | yabH | no | no | ispE (yabH) | ispE (BA0043) | BC0050 | BH0061 | OB0055 | CAC2902 | ipk (CPE2212) | lmo0190 | lin0229 | ispE (yabH) | 2 TMs
 |  |  |  |  | BioOptimizer-no prediction | no
 | purR | 55 bp downstream |  |  |  |  | purR | 0.9885530946569387 | 0.484 |  | 4.852885001621212 | 0.998 |  | 1.540232558937758 | 0.8895 |  | 1.207519963494296 | 0.907614678774131 |  | purR |  |  |  |  |  |  | purR | transcriptional repressor of the purine operons | 3.5.2 (Regulation) | purR | yabI | no | xpt, apt, pyrE | purR | purR (BA0044) | BC0051 | purR | OB0056 | purR (CAC3224) | purR (CPE2492) | lmo0192 | lin0231 | purR | 1-2 TMs
 | yabJ | overlap |  |  |  |  | yabJ | 1.432187899273544 | 0.919 |  | 5.97035286583837 | 1 |  | 1.491166604064907 | 0.869 |  | 1.240623890049306 | 0.952311320946395 |  | yabJ |  |  |  |  |  |  | yabJ | similar to translation initiation inhibitor, adenine-mediated repression of purA | 2.3 (Metabolism of nucleotides and nucleic acids) | yabJ | no | no | no | yabJ | BA0046 | BC0052 | BH0063 | OB3060 | CAC1265 | CPE1012 | no | no | yabJ | 0 TM
pucH | pucH (yunH) | TTCTAGC | 14 | AATACGAT | possible promoter | 88 | pucH (yunH) | 2.494594726942955 | 0.987 |  | 7.481695005111545 | 0.999 |  | 1.124311988060535 | 0.607 |  | 1.179064267064457 | 0.866689297772537 |  | pucH (yunH) |  |  |  |  |  |  | pucH (yunH) | allantoinase (purine degradation) | 2.3 (Metabolism of nucleotides and nucleic acids) | pucH (yunH) | yunH | pyrC | ureC, adeC | pucH (yunH) | no | no [BC3888 (pyrC)] | BH2309 | no [pyrC] | no | no [pyrC] | no [pyrC (pyrC)] | no [pyrC (pyrC)] | pucH (yunH) | 0-1 TM
 |  |  |  |  | BioOptimizer-no prediction
sipS | sipS | TTTTTTT | 14 | CATAAATT | possible promoter | 29 | sipS | 2.249054605835781 | 0.932 |  | 3.013006024186121 | 0.99 |  | 0.7055389311815857 | 0.1505 |  | 0.8400241494113805 | 0.0767244925553542 |  | sipS |  |  |  |  |  |  | sipS | signal peptidase I (EC 3.4.21.89) (modulation of the capacity and specificity for protein secretion) | 1.6 (Protein secretion) | sipS | no | sipT, [NAME], [NAME] | no | sipS | no | BC0456 | no | sipS (OB1390) | sipS (CAC2646) | sipS (CPE0597) | lmo1271 | [NAME] | sipS | 1 TM (Nter)
 |  |  |  |  | BioOptimizer-no prediction
spsA-B-C-D-E-F-G-I-J-K-L | spsA | GCGCAAC | 14 | CATAAGAT | AACGATAGTTT (sigK promoter) | 44 | spsA |  |  |  | 3.71799755638099 | 0.909 |  | 1.460556483199402 | 0.7835 |  | 0.9513143714864873 | 0.414000172511835 |  | spsA |  |  |  |  |  |  | spsA |  |  | spsA |  |  |  | spsA |  |  |  |  |  |  |  |  | spsA
(absent from Eichenberger et al., 2003) |  |  |  |  | BioOptimizer-not included
(absent from Eichenberger et al., 2003) | spsB |  |  |  |  |  | spsB | 1.083926914021204 | 0.568 |  | 3.715352290971726 | 0.962 |  | 1.348862455305464 | 0.8265 |  | 1.069875135966959 | 0.628549153454429 |  | spsB |  |  |  |  |  |  | spsB |  |  | spsB |  |  |  | spsB |  |  |  |  |  |  |  |  | spsB
spsC | spsC |  |  |  |  |  | spsC | 2.606153549998896 | 0.926 |  | 2.786121168629771 | 0.984 |  | 1.040973268364289 | 0.549 |  | 1.043988763942513 | 0.598193890561279 |  | spsC |  |  |  |  |  |  | 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)
(absent from Eichenberger et al., 2003) | spsD |  |  |  |  |  | spsD |  |  |  | 4.073802778041128 | 0.99 |  | 1.194908031452531 | 0.7115 |  | 1.136841532051779 | 0.828270906713427 |  | spsD |  |  |  |  |  |  | spsD |  |  | spsD |  |  |  | spsD |  |  |  |  |  |  |  |  | spsD
(absent from Eichenberger et al., 2003) | spsE |  |  |  |  |  | spsE |  |  |  | 4.698941086052156 | 0.999 |  | 1.0016125141631 | 0.502 |  | 1.135423746627264 | 0.784279132542037 |  | spsE |  |  |  |  |  |  | spsE |  |  | spsE |  |  |  | spsE |  |  |  |  |  |  |  |  | spsE
(absent from Eichenberger et al., 2003) | [NAME] |  |  |  |  |  | [NAME] |  |  |  | 3.141519067375362 | 0.937 |  | 0.7213818175140991 | 0.269 |  | 1.173165127652559 | 0.841527478776237 |  | [NAME] |  |  |  |  |  |  | [NAME] |  |  | [NAME] |  |  |  | [NAME] |  |  |  |  |  |  |  |  | [NAME]
spsGIJKL | spsG |  |  |  |  |  | spsG | 7.655966069112565 | 0.99 |  | 6.776415076106751 | 0.999 |  | 0.7472486916405578 | 0.178 |  | 1.02090935472428 | 0.550226653434369 |  | spsG |  |  |  |  |  |  | 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 | 1.706082389003124 | 0.906 |  | 3.723917062545685 | 0.991 |  | 1.523857774081063 | 0.855 |  | 1.03850995848506 | 0.589611676573701 |  | spsI |  |  |  |  |  |  | spsI | spore coat polysaccharide synthesis, similar to sugar-nucleotidylation enzyme | 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 | 3.854783576657718 | 0.997 |  | 19.09853258566238 | 1 |  | 1.104712762445784 | 0.6095 |  | 1.024348222530329 | 0.580898511530572 |  | spsJ |  |  |  |  |  |  | spsJ | spore coat polysaccharide synthesis, UDP-N-acetylglucosamine epimerase | 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 | 3.443499307633386 | 0.987 |  | 7.709034690644301 | 1 |  | 1.011230462015221 | 0.511 |  | 0.9576715300673881 | 0.397132171203489 |  | spsK |  |  |  |  |  |  | spsK | spore coat polysaccharide synthesis, DTDP-L-rhamnose synthetase | 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
(absent from Eichenberger et al., 2003) | spsL |  |  |  |  |  | spsL | 3.443499307633386 | 0.987 |  | 7.709034690644301 | 1 |  | 1.011230462015221 | 0.511 |  | 0.9576715300673881 | 0.397132171203489 |  | spsL |  |  |  |  |  |  | spsL | spore coat polysaccharide synthesis, DTDP-L-rhamnose synthetase | 1.8 (Sporulation) | spsL |  |  |  | spsL | rfbD(BA1231) | BA1215 | [NAME] (BH3365)/rbfC (BH3366) | OB1127 | CAC2315 | [NAME] (CPE0618) | lmo1084 | no | spsL | 0 TM
tmrB | tmrB | ACAACAT | 15 | AATACTTC | possible promoter | 103 | tmrB | 1.945360081622663 | 0.847 |  | 4.139996748197305 | 0.981 |  | 0.6442415799195819 | 0.1995 |  |  |  |  | tmrB |  |  |  |  |  |  | tmrB | tunicamycin resistance (ATP-binding) | 4.2 (Detoxification) | tmrB | no | no | no | tmrB | no | no | no | OB0981 | no | no | no | no | tmrB | 0 TM
 |  |  |  |  | BioOptimizer-no prediction
ycgL | ycgL | GGCTGATAAAT | 12 | CGCATATCATC | BioOptimizer-prediction | 55 | ycgL | 2.032357010936222 | 0.985 |  | 3.723917062545685 | 0.997 |  | 1.349431424774693 | 0.7495 |  | 1.277600845704297 | 0.944184069192927 |  | ycgL |  |  |  |  |  |  | ycgL | unknown | 5.2 (From other organisms) | ycgL | no | no | no | ycgL | BA0363 | BC0397 | no | no | CAC1497 | no | no | no | ycgL | 0 TM
yclF | yclF | ATATAAG | 14 | AATACACT | possible promoter | 24 | yclF | 2.103778439766475 | 0.981 |  | 18.15515662773136 | 1 |  | 0.6422017499476993 | 0.099 |  | 1.426495402012445 | 0.97695637895022 |  | yclF |  |  |  |  |  |  | yclF | di-tripeptide ABC transporter (membrane protein) | 1.2 (Transport/binding proteins and lipoproteins) | yclF | no | no | yvkA, yfmO, nasA | yclF | BA0689 | BC0684 | no | no | [NAME] | CPE0544 | lmo0555 | lin0564 | yclF | 12-13 TMs
 |  |  |  |  | BioOptimizer-no prediction
yeaA-ydjP | yeaA | GGACGAT | 14 | CATATTCT | possible promoter | 155 | yeaA | 2.027682719521282 | 0.985 |  | 5.296634438916579 | 0.999 |  | 1.014829094357672 | 0.515 |  | 1.096762996602392 | 0.714044367274679 |  | yeaA |  |  |  |  |  |  | yeaA | unknown | 6 (No similarity) | yeaA | ydjQ | no | no | yeaA | BA3537 | BC3470 | no | no | no | no | lmo2643 | lin2792 | yeaA | 0 TM
 |  |  |  |  | BioOptimizer-no prediction
 | ydjP | 15 bp downstream |  |  |  |  | ydjP | 2.023019178678271 | 0.99 |  | 6.426877173170197 | 1 |  | 1.335802526651471 | 0.7965 |  | 1.191927238517668 | 0.924005159729874 |  | ydjP |  |  |  |  |  |  | ydjP | similar to chloride peroxidase (a/b hydrolase family), similar to YisY | 4.2 (Detoxification) | ydjP | no | yisY | yvaM, [NAME], ytxM, ybfK, yclE, yraK, yugF | ydjP | no | no [BC3122(yisY)] | no [BH3825 ([NAME])] | OB0990 | no [CAC2688 (yisY)] | no | no [lmo1674 ([NAME])] | no [lin1782 ([NAME])] | ydjP | 2 TMs
yhaS-T | yhaS | GCATATT | 13 | CATAAAGT | possible promoter | 30 | yhaS | 1.025651926251408 | 0.526 |  | 5.902010801718444 | 0.998 |  | 0.7251095432521558 | 0.175 |  | 0.7251095432521558 | 0.175 |  | yhaS |  |  |  |  |  |  | yhaS | unknown | 6 (No similarity) | yhaS | no | no | no | yhaS | no | no | no | no | no | no | no | no | yhaS | 1 TM  (Nter)
 |  |  |  |  | BioOptimizer-no prediction
 | yhaT | 63 bp downstream-RACE-operon w/ yhaS |  |  |  |  | yhaT | 1.807174126010927 | 0.929 |  | 4.954501908047902 | 0.999 |  | 0.785314726504813 | 0.233 |  | 0.785314726504813 | 0.233 |  | yhaT |  |  |  |  |  |  | yhaT | similar to TrkA (K+ channel), NAD-binding component | 5.1 (From B. subtilis) | yhaT | no | yrvC | yuaA, ykqB | yhaT | BA5287 | BC5042 | no | no [OB1407 (ykqB)] | no | no | no | no | yhaT | 0 TM
yhxC | yhxC | TTTCCATATTC | 10 | TACATAGGAAG | BioOptimizer-prediction | 45 | yhxC | 3.443499307633386 | 0.953 |  | 41.68693834703356 | 0.995 |  | 0.7260993614787153 | 0.1585 |  | 1.095955531520237 | 0.734947121909376 |  | yhxC |  |  |  |  |  |  | yhxC | similar to alcohol dehydrogenase (short chain adh family), similar to YkvO | 2.1.1 (Specific pathways) | yhxC | no | ydaD, yhdF, yhxD, yxbG, ycdF, fabG, gdh, ywfD, ymfI, ykvO, ykuF, yoxD, kduD, fabL, [NAME], yjdA, yvrD, [NAME], yjmF, yxjF | yqjQ, yxnA, yusZ, ytkK, ywfH, yusS, yuxG, dltE, fabI, yusR | yhxC | BA0748 | BC0770 | no [BH1511 (yhdF)] | no [OB1186 (yhdF)] | no [CAC1423 (yhdF)] | CPE2598 | no [lmo0669 (yhxD)] | no [lin0679 (yhxD)] | yhxC | 0 TM
yisY | yisY | AGATCGT | 14 | [NAME] | possible promoter | 123 | yisY | 2.08929613085404 | 0.969 |  | 6.982324040771714 | 0.998 |  | 1.151433198578764 | 0.663 |  | 1.238582442448055 | 0.944595747143082 |  | yisY |  |  |  |  |  |  | yisY | similar to chloride peroxidase (a/b hydrolase family), similar to YdjP | 4.2 (Detoxification) | yisY | no | ydjP | yfhM, yvaM, yugF, rsbQ, [NAME], ybfK | yisY | BA5030 | BC3122/BC4774 | no | no | CAC2688 | no | [NAME] | lin2547 | yisY | 1 TM -mid
 |  |  |  |  | BioOptimizer-no prediction
yjaV | yjaV | TAGTCATGAAA | 11 | AGAATATAATG | BioOptimizer-prediction | 70 | yjaV | 3.706807217825761 | 0.999 |  | 13.42764961137864 | 1 |  | 0.5884070279977515 | 0.071 |  | 1.092738394473089 | 0.778897203394708 |  | yjaV |  |  |  |  |  |  | yjaV | similar to UDP-glucose 4-epimerase | 2.1.1 (Specific pathways) | yjaV | no | no | no | yjaV | BA1181 | BC1171 | no [BH2891(ytcB)] | no | no | no | no | no | yjaV | 0 TM
 |  | ATTTCATTTAT | 11 | AGCAGAATTTA | BioOptimizer-prediction (unlikely)
yjaZ | yjaZ | TAATCTT | 14 | CATAATCA | favored predicted promoter | 72 | yjaZ | 1.931968317016924 | 0.894 |  | 6.397348354826484 | 0.993 |  | 0.8019761639427961 | 0.242 |  | 1.369953787519596 | 0.974980272625438 |  | yjaZ |  |  |  |  |  |  | yjaZ | unknown | 5.1 (From B. subtilis) | yjaZ | no | no | yjfC | yjaZ | BA1186 | BC1175 | BH2873 | no | no | no | no | no | yjaZ | 0 TM
yjfA | yjfA | CATGCATGTTT | 10 | TCCATATGATT | BioOptimizer-prediction | 30 | yjfA | 4.285485203974395 | 0.996 |  | 17.17908387157589 | 1 |  | 1.571767532395916 | 0.8895 |  | 1.27263796302966 | 0.9357385354532 |  | yjfA |  |  |  |  |  |  | yjfA | unknown | 6 (No similarity) | yjfA | no | no | no | yjfA | BA3540 | BC3474 | no | no | no | no | no | no | yjfA | secreted-pred
ykoP | ykoP | GAATGTT | 15 | CCTAAAAA | possible promoter | 74 | ykoP | 4.325138310350088 | 0.972 |  | 3.111716337106018 | 0.959 |  | 0.8878243824788741 | 0.4005 |  | 1.202782909871449 | 0.922074520049578 |  | ykoP |  |  |  |  |  |  | ykoP | unknown | 6 (No similarity) | ykoP | no | no | yeeB | ykoP | no | no | no | no | no | no | no | no | ykoP | 0 TM
 |  | CAACTATATTT | 11 | TTCACAAAATA | BioOptimizer-prediction-unlikely
ykrL | ykrL | CTTGCATTTTC | 10 | TTTATAATTTA | BioOptimizer-prediction | 41 | ykrL | 2.228435149270304 | 0.881 |  | 2.060629913270001 | 0.958 |  | 0.6286814529882767 | 0.101 |  | 1.133193790260681 | 0.821271453760382 |  | ykrL |  |  |  |  |  |  | ykrL | similar to heat-shock protein (putative protease) | 4.1 (Adaptation to atypical conditions) | ykrL | no | no | yxkI | ykrL | no | no | BH2702 | OB0156 | no | no | lmo0963 | [NAME] | ykrL | 4 TMs
ykvO | ykvO | TCTTCAAGTAC | 12 | GACATAAAATA | BioOptimizer-prediction | 26 | ykvO | 2.4 | 0.93 |  | 2.211274205976098 | 0.957 |  | 0.8572639356607002 | 0.3785 |  | 0.7860063077703136 | 0.0884470718152316 |  | ykvO |  |  |  |  |  |  | ykvO | similar to glucose 1-dehydrogenase | 2.1.1 (Specific pathways) | ykvO |  |  |  | ykvO | no | no [BC36409(ywfD)] | no [BH3896(fabG)] | no [OB0329(fabG)] | no | no [CPE1070(fabG)] | no [fabG] | no [fabG] | ykvO
 |  | TTTTCATGTCT | 12 | TCCACATTTAT | BioOptimizer-prediction-unlikely
ymaF | ymaF | CGTTCATGTTT | 11 | GTAATAAAGTG | BioOptimizer-prediction | 62 | ymaF | 52.36004365857506 | 1 |  | 30.26913428101307 | 1 |  | 0.9543097850791991 | 0.441 |  | 1.151267904715114 | 0.880923976779487 |  | ymaF |  |  |  |  |  |  | ymaF | unknown | 6 (No similarity) | ymaF | no | no | no | ymaF | no | no | no | no | no | no | no | no | ymaF | 0 TM
yncD | yncD (alr2) | GTTGAATGATT | 11 | TGAATAAAATA | BioOptimizer-prediction | 81 | yncD (alr2) | 2.280342072000418 | 0.994 |  | 14.06047524129914 | 1 |  | 0.8517850019544638 | 0.3195 |  | 1.018554743911824 | 0.563024313014482 |  | yncD (alr2) |  |  |  |  |  |  | yncD (alr2) | similar to Alr, mutant requires exogenous D-Ala for growth | 2.2 (Metabolism of amino acids and related molecules) | yncD (alr2) | alr2 | alr | no | yncD (alr2) | dal-2 (BA2079) | BC2063 | no [BH0520 (alr)] | OB3149/OB3226 | CAC3331 | CPE0868 | no [dal (alr)] | no [lin0885 (alr)] | yncD (alr2) | 2 TMs
yndA | yndA | GATTCATAAAA | 10 | TGAATATAATG | BioOptimizer-prediction | 111 | yndA | 2.716439268839083 | 0.992 |  | 9.397233105646377 | 1 |  | 0.7775447244739675 | 0.3065 |  | 1.107429416008223 | 0.784769427566869 |  | yndA |  |  |  |  |  |  | yndA | unknown | 6 (No similarity) | yndA | no | no | no | yndA | no | no | no | no | no | no | no | no | yndA | secreted-pred
yndB not included in final total | yndB | read-through from yndA (convergent)? |  |  |  |  | yndB | 1.202264434617413 | 0.761 |  | 3.828247433168227 | 0.996 |  | 0.7968661367398643 | 0.2425 |  | 1.229474613049865 | 0.936294505634594 |  | yndB |  |  |  |  |  |  | yndB |  |  | yndB |  |  |  | yndB |  |  |  |  |  |  |  |  | yndB | 0 TM
yngD | yngD | ACATTATGTCA | 12 | TGCATAAAACG | BioOptimizer-prediction | 81 | yngD | 2.409905428686595 | 0.981 |  | 2.360478233180577 | 0.962 |  | 0.4265378760947432 | 0.0665 |  | 1.052219905116993 | 0.676006655245972 |  | yngD |  |  |  |  |  |  | yngD | similar to phosphoesterase (DHH family) | 6 (No similarity) | yngD | no | no | no | yngD | no | no | BH1136 | no | no | no | no | no | yngD | 0 TM
yngK | yngK | TCACCCT | 13 | AATACCGT | AATAGCGAA (sigK promoter) | 44 | yngK | 2.07491351745491 | 0.868 |  | 4.33510878387529 | 0.996 |  | 1.001384453461691 | 0.5025 |  | 1.466081509794105 | 0.993452198331524 |  | yngK |  |  |  |  |  |  | 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)
 |  |  |  |  | BioOptimizer-no prediction
yocM-L-K | yocM | [NAME] | 12 | CCAATAAATTT | BioOptimizer-prediction | 155 | yocM | 1.717908387157588 | 0.937 |  | 8.090958991783824 | 1 |  | 1.103709147933442 | 0.6195 |  | 1.379102964358491 | 0.986791132079664 |  | yocM |  |  |  |  |  |  | yocM | similar to cotP and cotM (a-crystallin domain of small heat shock proteins) | 4.1 (Adaptation to atypical conditions) | yocM | no | no | cotP | yocM | no | no | no | no | no | no | no | no | yocM | 0 TM
 | yocL | 291 bp downstream |  |  |  |  | yocL | 0.99 | 0.491 |  | 2.99 | 0.992 |  | 0.9049567345995942 | 0.384 |  | 1.276096130298701 | 0.967709866471847 |  | yocL |  |  |  |  |  |  | yocL | unknown | 6 (No similarity) | yocL | no | no | no | yocL | no | no | no | no | no | no | no | no | yocL | 0 TM
 | yocK | 58 bp downstream |  |  |  |  | yocK | 3.311311214825912 | 0.989 |  | 5.445026528424212 | 0.997 |  | 0.7259967151652269 | 0.1695 |  | 1.100462237646717 | 0.801943065845108 |  | yocK |  |  |  |  |  |  | yocK | similar to general stress protein (DskA/TraR C4-type Zn finger family) | 4.1 (Adaptation to atypical conditions) | yocK | no | no | yteA, ylyA | yocK | no | no | no [BH2544 (yteA)] | no [OB2328 (yteA)] | no [CAC2116 (yteA)] | no | no | no | yocK | 0 TM
yodN | yodN | TGCGGATTTTT | 11 | CCCATACCATA | BioOptimizer-prediction | 94 | yodN | 3.341950400261143 | 0.934 |  | 35.64511334262443 | 0.986 |  | 0.5417074629246104 | 0.127 |  | 0.985955345200076 | 0.450558461995239 |  | yodN |  |  |  |  |  |  | yodN | unknown | 6 (No similarity) | yodN | no | no | no | yodN | BA2303 | BC2254 | no | no | no | no | no | no | yodN | 1 TM (Nter)
yodT-S-R-Q-P-kamA | yodT | ACGTCATGCCG | 11 | CTCATACAATA | BioOptimizer-prediction | 27 | yodT | 2.177709772353159 | 0.996 |  | 50.35006087879049 | 1 |  | 0.8112693367985075 | 0.2535 |  | 0.9422667652319326 | 0.29405787232309 |  | yodT |  |  |  |  |  |  | yodT | adenosylmethionine-8-amino-7-oxononanoate aminotransferase | 2.2 (Metabolism of amino acids and related molecules) | yodT | no | yhxA, bioA, argD, gabT, rocD | hemL, gsaB | yodT | BA2294 | BC2245 | BH2260 | no [OB0490 (yhxA)] | no [bioA (CAC1362) (bioA)] | no | no [argD] | no [argD] | yodT | 3 TMs
 | yodS | 6 bp downstream |  |  |  |  | yodS | 2.290867652767773 | 0.989 |  | 20.84490883097289 | 1 |  | 0.6203285156881059 | 0.094 |  | 0.8744431835087918 | 0.13793736664259 |  | yodS |  |  |  |  |  |  | yodS | 3-oxoadipate CoA-transferase, similar to ScoA | 2.4 (Metabolism of lipids) | yodS | no | scoA | no | yodS | atoD (BA2295) | BC2246 (yodS/scoA) | BH2259 | OB2634 (yodS/scoA) | no | no [CPE0096] | no [[NAME] (scoA)] | no [[NAME] (scoA)] | yodS | 1 TM (Nter)
 | yodR | 10 bp upstream |  |  |  |  | yodR | 2.387811282913178 | 0.995 |  | 52.84452517751808 | 1 |  | 0.7121144710017238 | 0.141 |  | 0.82680550595048 | 0.0784001149387568 |  | yodR |  |  |  |  |  |  | yodR | butyrate-acetoacetate CoA-transferase, similar to ScoB | 2.4 (Metabolism of lipids) | yodR | no | scoB | no | yodR | BA2296 | BC2247 (yodR/scoB) | BH2258 | OB2633 (yodR/scoB) | no | no [CPE0096] | no [[NAME] (scoA)] | no [[NAME] (scoA)] | yodR | 1 TM (Nter)
 | yodQ (argE) | 8 bp downstream |  |  |  |  | yodQ (argE) | 2.182729911843002 | 0.992 |  | 7.798301105232591 | 1 |  | 0.8454647828905559 | 0.294 |  | 0.8573520269867723 | 0.108858755741313 |  | yodQ (argE) |  |  |  |  |  |  | yodQ (argE) | succinyl-diaminopimelate desuccinylase | 2.2 (Metabolism of amino acids and related molecules) | yodQ (argE) | argE | ylmB | yqjE, ytjP, rocB | yodQ (argE) | BA2297 | BC2248 | no [BH2678 (ylmB)] | no [OB0705 (ytoP)] | no | no [CPE1211] | lmo0265 | lin0289 | yodQ (argE) | 0 TM
 | yodP | 17 bp upstream |  |  |  |  | yodP | 2.157744409152667 | 0.987 |  | 42.95364267648874 | 1 |  | 0.8398303016099796 | 0.287 |  | 0.9383456666776094 | 0.290044390289287 |  | yodP |  |  |  |  |  |  | yodP | unknown, putative b-Lys-acetyltransferase | 5.2 (From other organisms) | yodP | no | no | no | yodP | BA2298 | BC2249 | BH2257 | no | no | no | no | no | yodP | 1 TM (mid)
 | kamA (yodO) | 28 bp downstream |  |  |  |  | kamA (yodO) | 2.023019178678271 | 0.986 |  | 27.73320104651842 | 1 |  | 0.7698872857886493 | 0.202 |  | 0.7857242299560797 | 0.0598858811769402 |  | kamA (yodO) |  |  |  |  |  |  | kamA (yodO) | lysine 2,3-aminomutase | 2.2 (Metabolism of amino acids and related molecules) | kamA (yodO) | yodO | no | no | kamA (yodO) | kamA (BA2300) | BC2251 | BH2255 | no | no | no | no | no | kamA (yodO) | 0 TM
yozN-yocN | yozN | TTAACATACTT | 10 | AGCATACAACT | BioOptimizer-prediction | 19 | yozN |  |  |  | 8.279421637123345 | 1 |  | 0.9124116669771248 | 0.3865 |  | 1.077910340815936 | 0.746644356886815 |  | yozN |  |  |  |  |  |  | yozN | unknown | 6 (No similarity) | yozN | no | no | yocN | yozN | no | no | no | no | no | no | no | no | yozN | 0 TM
 | yocN | 4 bp downstream |  |  |  |  | yocN | 2.338837238659355 | 0.964 |  | 2.999162518987651 | 0.952 |  | 0.8055353369013065 | 0.321 |  | 1.159807229286841 | 0.887867073750572 |  | yocN |  |  |  |  |  |  | yocN | similar to permease | 1.2 (Transport/binding proteins and lipoproteins) | yocN | no | no | yozN | yocN | no | no | no | no | no | no | no | no | yocN | 0 TM
ypjD-dapB-mgsA-ypjG-H-cca-birA | ypjD | TTTTCCTTCCA | 10 | TTTATATTATA | BioOptimizer-prediction | 94 | ypjD | 2.218196419800219 | 0.973 |  | 6.698846094165265 | 0.999 |  | 0.772991815747357 | 0.1905 |  | 1.23145113252401 | 0.888740787786313 |  | ypjD |  |  |  |  |  |  | ypjD | unknown | 5.2 (From other organisms) | ypjD | jojD | no | yvdC | ypjD | BA1554 | BC1531 | BH1679 | OB1769 | no | no | lmo1908 | lin2022 | ypjD | 0 TM
 | dapB | 11 bp downstream |  |  |  |  | dapB | 1.577611269699349 | 0.944 |  | 3.372873086588689 | 0.997 |  | 0.6094284212236151 | 0.082 |  | 1.320913788339988 | 0.964803082698907 |  | dapB |  |  |  |  |  |  | dapB | dihydro-dipicolinate reductase (EC 1.3.1.26) | 2.2 (Metabolism of amino acids and related molecules) | dapB | no | no | no | dapB | dapB (BA1555) | BC1532 | dapB | dapB (OB1768) | dapB (CAC2379) | dapB (CPE1906) | dapB | dapB | dapB | 0-1 TM
 | mgsA (ypjF) | 15 bp downstream |  |  |  |  | mgsA (ypjF) | 2.63633138582538 | 0.959 |  | 1.59220872705117 | 0.998 |  | 0.6461002990640468 | 0.0945 |  | 1.212815339115355 | 0.93207560934789 |  | mgsA (ypjF) |  |  |  |  |  |  | mgsA (ypjF) | probable methylglyoxal synthase (EC 4.2.99.11) | 2.1.1 (Specific pathways) | mgsA (ypjF) | ypjF, jojF | no | no | mgsA (ypjF) | mgsA (BA1556) | BC1533 | mgsA | OB1767 | CAC1604 | mgsA (CPE1009) | lmo1906 | lin2020 | mgsA (ypjF) | 1 TM (mid)
 | ypjG | 2 bp upstream |  |  |  |  | ypjG | 6.561452663029055 | 0.985 |  | 3.296097121774578 | 0.991 |  | 0.6214491899977981 | 0.0875 |  | 1.346868481986463 | 0.973860719946217 |  | ypjG |  |  |  |  |  |  | ypjG | unknown (LmbE-like) | 5.2 (From other organisms) | ypjG | jojG | no | yvbJ | ypjG | BA1557 | BC1534 | BH1682 | no | no | no | no | no | ypjG | 0 TM
 | ypjH | 31 bp downstream |  |  |  |  | ypjH | 0.3531831697919569 | 0.188 |  | 3.273406948788383 | 0.976 |  | 0.6541577474249083 | 0.0915 |  | 1.157258415439859 | 0.887563945582453 |  | ypjH |  |  |  |  |  |  | ypjH | similar to glycosyl transferase (lipopolysaccharide biosynthesis-related protein) | 1.1 (Cell wall) | ypjH | jojH | no | yveN, tuaC, yqgM, [NAME], tagE, cotSA | ypjH | BA1558 | BC1535 | BH1683 | OB1766 | CAC3052 | no [CPE0479] | no | no | ypjH | 0-1 TM
 | cca (papS) | 4 bp downstream |  |  |  |  | cca (papS) | 1.520547529732496 | 0.878 |  | 4.830588020397728 | 1 |  | 0.5446899630792517 | 0.0505 |  | 1.08881198322977 | 0.762717060480056 |  | cca (papS) |  |  |  |  |  |  | cca (papS) | tRNA nucleotidyltransferase (EC 2.7.7.25) | 3.6 (RNA modification) | cca (papS) | papS, ypjI | no | no | cca (papS) | pcnB (BA1559) | BC1536 | papS | OB1765 | CAC0311 | CPE0022 | cca | cca | cca (papS) | 0-1 TM
 | birA | 10 bp upstream |  |  |  |  | birA | 1.905460717963247 | 0.952 |  | 3.16227766016838 | 0.984 |  | 0.6220487852734249 | 0.0815 |  | 1.036358695349093 | 0.626454137596881 |  | birA |  |  |  |  |  |  | birA | transcriptional regulator and [NAME]-carboxylase synthetase (EC 6.3.4.15) | 3.5.2 (Regulation) | birA | no | no | no | birA | birA (BA1560) | BC1537 | birA | birA (OB1764) | CAC0212 | birA [CPE0673] | birA | birA | birA | 0 TM
yqgT | yqgT | GCTTTCTTTTT | 11 | GTCATATAGTA | BioOptimizer-prediction | 16 | yqgT | 2.013724249862388 | 0.983 |  | 2.716439268839083 | 0.991 |  | 1.459632821992521 | 0.875 |  | 1.279648151753756 | 0.967604755009625 |  | yqgT |  |  |  |  |  |  | yqgT | similar to gamma-D-glutamyl-L-diamino acid endopeptidase I, sporulation specific in B. sphaericus | 1.8 (Sporulation) | yqgT | no | no | yyaH | yqgT | no | no | BH1603 | OB1731 | no | no | no | no | yqgT | 0 TM
yqhO | yqhO | TCCAAAA | 13 | CATAATCA | possible promoter | 129 | yqhO | 2.060629913270001 | 0.995 |  | 4.285485203974395 | 0.989 |  | 1.586120803058765 | 0.9105 |  | 1.261589786508037 | 0.952989396106815 |  | yqhO |  |  |  |  |  |  | yqhO | similar to papatin-like phospholipase, similar to YlbK | 5.2 (From other organisms) | yqhO | no | no | no | yqhO | BA1992 | BC1989 | BH2805 | OB1899 | no | no | no | no | yqhO | 3 TMs
 |  | TAATACG | 14 | CATTCGTT |  | 65
 |  | TTGGTCTATTT | 11 | TTCTTAAAATG | BioOptimizer-prediction-unlikely
yrbD | yrbD | CTCTTCTTATT | 11 | GTCATATAATG | BioOptimizer-prediction | 84 | yrbD | 2.094112455850893 | 0.987 |  | 6.966265141107687 | 0.972 |  | 1.153808625677074 | 0.6745 |  | 1.194487913585086 | 0.903727444675335 |  | yrbD |  |  |  |  |  |  | yrbD | sodium/proton-dependent alanine carrier protein | 1.2 (Transport/binding proteins and lipoproteins) . | yrbD | no | ybgH, alsT, yflA | no | yrbD | BA0638 | BC0638 | no [BH1284 (alsT)] | no [OB2690 (alsT)] | no | no | no | no | yrbD | 10 TMs
ytbD | ytbD | GCTTACT | 15 | CATACAAC | most likely promoter | 23 | ytbD | 2.280342072000418 | 0.953 |  | 4.24619563946313 | 0.998 |  | 0.4660628631248975 | 0.113 |  | 1.025418375561892 | 0.581412322951206 |  | ytbD |  |  |  |  |  |  | ytbD | similar to antibiotic resistance protein (sugar transporter family) | 1.2 (Transport/binding proteins and lipoproteins) | ytbD | no | yfhI, ydhL, ybcL, ywfA | ycnB, yfiU, yceG, ywoG, [NAME], mmr, mdr, yvmA, yusP, bmr… | ytbD | BA5309 | BC5058 | no [BH2116 (ybcL)] | no [OB1281 (yhfI)] | no [thdF (CAC3734)] | no [CPE1238] | lmo0872 | lin0870 | ytbD | 10-11 TMs
 |  | CTTTTATTTCT | 11 | TTCATAATCAC | BioOptimizer-prediction | 94
 |  | TTTTTATTTAT | 11 | GGCAGAATTTC | BioOptimizer-prediction-unlikely
ytvB | ytvB | TCAAGCTTACC | 11 | CACATATAATG | BioOptimizer-prediction | 119 | ytvB | 2.432204009073816 | 0.914 |  | 9.354056741475523 | 0.963 |  | 0.6242538118781278 | 0.089 |  | 1.158037980695777 | 0.884300938409683 |  | ytvB |  |  |  |  |  |  | ytvB | unknown | 6 (No similarity) | ytvB | no | no | no | ytvB | BA2006 | BC2003 | no | no | no | no | no | no | ytvB | 3 TMs
yugT | yugT | TGCTGTA | 14 | CATAGGAT | possible promoter | 34 | yugT | 2.917427014001167 | 0.936 |  | 13.67728825595849 | 0.986 |  | 1.111814789554208 | 0.631 |  | 1.182423902191793 | 0.880841970960855 |  | yugT |  |  |  |  |  |  | yugT | similar to glycosyl hydrolase (exo-alpha-1,4-glucosidase), similar to GlgB | 2.1.1 (Specific pathways) | yugT | no | malL, ycdG, treA | yvdF, amyE, glgB | yugT | no [malL(BA4231)] | BC0413 | BH3868 | OB2556 | no [CAC2686 (yvdF)] | [NAME] | no [lmo0184 (treA, malL)] | no [lin0223] | yugT | 0 TM
 |  |  |  |  | BioOptimizer-no prediction
yumB | yumB | TCAATATATTT | 12 | CCAATAAGCTG | BioOptimizer-prediction | 65 | yumB | 2.606153549998896 | 0.981 |  | 2.483133105295571 | 0.982 |  | 0.7950263820507838 | 0.248 |  | 1.027654199772607 | 0.581899053144814 |  | yumB |  |  |  |  |  |  | yumB | similar to NADH dehydrogenase (pyr redox) | 1.4 (Membrane bioenergetics (electron transport chain and ATP synthase)) | yumB | no | yjlD, yutJ | no | yumB | BA5159 | BC4925 | BH3407 | OB2350 | no | no [narC] | lmo2389 | lin2488 | yumB | 2 TMs
 |  | TCTGAATGTTT | 11 | CGGATAAACAT | BioOptimizer-prediction-unlikely
ywjE | ywjE | TAATGAA | 13 | AATAATTA | possible promoter | 50 | ywjE | 2.582260190634596 | 0.997 |  | 11.77605973520808 | 1 |  | 0.6436314959988806 | 0.0905 |  | 1.13629200223833 | 0.80399132304131 |  | ywjE |  |  |  |  |  |  | ywjE | similar to cardiolipin synthetase (phospholipase D family), similar to YwnE | 2.4 (Metabolism of lipids) | ywjE | no | ywnE, ywiE | no | ywjE | BA2054/BA5591 | BC2039/BC1737 | BH3803 | no [OB3045 (ywnE)] | no [CAC3316 (ywiE)] | no [clsD (CPE1430)] | no [lmo2503 (ywnE)] | no [lin2646 (ywnE)] | ywjE | secreted-pred
 |  |  |  |  | BioOptimizer-no prediction
ywqF | ywqF | TTCGCATTCAT | 11 | CTCATACGATA | BioOptimizer-prediction | 44 | ywqF | 1.909853258566238 | 0.983 |  | 3.784425847170933 | 0.999 |  | 1.605941423707516 | 0.9085 |  | 1.251354853550316 | 0.928450938890247 |  | ywqF |  |  |  |  |  |  | ywqF | similar to NDP-sugar dehydrogenase (UDP-glucose/GDP-mannose dehydrogenase) | 2.1.1 (Specific pathways) | ywqF | no | tuaD, ytcA | no | ywqF | ugd (BA5434) | BC5202 | no | OB2929 | no [CAC3310 (tuaD)] | CPE0494 | no | no | ywqF | 1 TM (Nter)
yxiL -M-deaD | yxiL | TTATATG | 13 | CATATAAA | most likely promoter | 111 | yxiL |  |  |  |  |  |  |  |  |  |  |  |  | yxiL |  |  |  |  |  |  | yxiL | unknown | 6 (No similarity) | yxiL | no | no | no | yxiL | no | no | no | no | no | no | no | no | yxiL | 0 TM
 |  | TTTATATGATT | 10 | CATATAAATAG | BioOptimizer-prediction-shifted
 | yxiM | 182 bp downstream |  |  |  |  | yxiM | 1.976969640111861 | 0.964 |  | 3.758374042884442 | 0.999 |  | 0.5738496008601578 | 0.06 |  | 0.6496165879102622 | 0.00507810340473003 |  | yxiM |  |  |  |  |  |  | yxiM | [NAME] acetylesterase | 2.1.1 (Specific pathways) | yxiM | no | yesY | yesT | yxiM | no | no | no [BH3963 (yesY)] | no [OB2084 (yesT)] | no | no | no | no | yxiM | 1 TM (Nter)
 | deaD | 81 bp downstream |  |  |  |  | deaD | 2.477422057633285 | 0.995 |  | 2.535128630497908 | 0.994 |  | 0.6577857976510715 | 0.114 |  | 0.7447525426022117 | 0.0223762884324696 |  | deaD |  |  |  |  |  |  | deaD | ATP-dependent RNA helicase | 3.6 (RNA modification) | deaD | yxiN | ydbR, yqfR, yfmL | yocI, [NAME], yprA, uvrB, yqhH, [NAME], mfd | deaD | BA5703 | BC5451 | no [BH2384 (ydbR)] | no [OB0609 (ydbR)] | deaD (CAC2748) | deaD (CPE0862) | lmo1246 | lin1214 | deaD | 0 TM
yycN | yycN | TTATGTA | 13 | AATATATG | possible promoter | 13 | yycN | 2.023019178678271 | 0.98 |  | 4.49779854893288 | 0.996 |  | 1.06011973576932 | 0.5665 |  | 0.8085108117520167 | 0.0522808104373588 |  | yycN |  |  |  |  |  |  | yycN | unknown-putative GNAT acetyltransferase | 5.1 (From B. subtilis) | yycN | no | ydgE | ywnH | yycN | BA2069 | BC2051 | no | no [OB0344 (ywnH)] | no | no [CPE1086 (yobR)] | lmo0624 | lin0633 | yycN | 0 TM
 |  |  |  |  | BioOptimizer-no prediction
yycO-P | yycO | ACCTAGT | 15 | CCTAATAT | possible promoter | 53 | yycO | 3.793149849736819 | 0.992 |  | 5.105049999754063 | 0.999 |  | 0.8008080375062772 | 0.259 |  | 0.8023537061423711 | 0.0605367013876704 |  | yycO |  |  |  |  |  |  | yycO | unknown | 5.2 (From other organisms) | yycO | no | no | no | yycO | no | no | no | no | CAC0029 | no | no | no | yycO | 1 TM (Nter)
 |  |  |  |  | BioOptimizer-no prediction
 | yycP | 13 bp downstream |  |  |  |  | yycP | 2.04173794466953 | 0.876 |  | 4.786300923226384 | 0.999 |  | 0.9861449352486579 | 0.4785 |  | 0.7851596889687091 | 0.0424941821114434 |  | yycP |  |  |  |  |  |  | yycP | unknown | 5.2 (From other organisms) | yycP | no | no | no | yycP | no | no | BH3844 | no | no | no | no | no | yycP | secreted
3.3. B) below cut-off in sigE+ vs. sigE- experiments but identified by overexpression of sE
none
3.3. C) not identified by overexpression of sE
3.3.C. 1) Genes included in the sE regulon in Eichenberger et al. (2003)
a) ratio in sigE+ vs. sigE- experiment is high (>3)
lplD | lplD | GGATTTA | 15 | GATACGAT | favored predicted promoter | 144 | lplD | 1.614358556826486 | 0.869 |  | 3.962780342554395 | 0.994 |  | 0.845255618725235 | 0.3035 |  | 1.596572917068804 | 0.997084971358 |  | lplD |  |  |  |  |  |  | lplD | hydrolytic enzyme | 2.1.1 (Specific pathways) | lplD | no | melA, licH, malA | no | lplD | no | no [BC5209 (licH)] | no | no [OB2273 (licH)] | no [glvA ([NAME])] | no [malH (CPE0199)] | no [lmo0521(licH)] | no [lin0526 (licH)] | lplD | 1-2 TMs
phoP-R | phoP | TCGGAATGTCC | 10 | AAAATAAAATC | BioOptimizer-prediction | 70 | phoP | 1.324341535194665 | 0.855 |  | 4.355118736855686 | 1 |  | 0.6993798811725627 | 0.1555 |  | 0.7411312352046868 | 0.0178213404657105 |  | phoP |  |  |  |  |  |  | phoP | two-component response regulator involved in phosphate regulation | 3.5.2 (Regulation) | phoP | no | yycF, resD, ykoG, yclJ, ycbL, yrkP, yvrH, cssR, yxdJ, yvcP, ytsA, [NAME] | spo0F, dctR, spo0A, cheY…. | phoP | phoP (BA4833) | BC4589 | phoP | OB2165 | phoP (CAC1506) | CPE0642 | phoP | phoP | phoP | 0 TM
 |  | TTTTACTATAA | 11 | [NAME] | BioOptimizer-prediction | 139
 | phoR | 2 bp upstream |  |  |  |  | phoR | 1.402813704561958 | 0.88 |  | 4.139996748197305 | 0.997 |  | 0.632472863050465 | 0.0935 |  | 0.8348051431375747 | 0.0767356716010964 |  | phoR |  |  |  |  |  |  | phoR | sensor histidine kinase involved in phosphate regulation | 1.3 (Sensors (signal transduction)) | phoR | no | resE, [NAME], yclK, kinA, kinE, ykoH, kinC, kinB, yvrG, kinD | yvcQ, dctS, cssS, ytsB, ycbM… | phoR | phoR (BA4832) | BC4588 | phoR | OB2164 | phoR ([NAME]) | CPE1757 | phoR | phoR | phoR | 2 TMs
sqhC | sqhC | TAATGGC | 14 | AATATATA | favored predicted promoter | 23 | sqhC | 1.377209468893947 | 0.868 |  | 21.03778439766476 | 0.999 |  | 1.297871599261786 | 0.7815 |  | 1.311704530222623 | 0.96178260646336 |  | sqhC |  |  |  |  |  |  | sqhC | squalene-hopene cyclase (EC 5.4.99.-) | 2.4 (Metabolism of lipids) | sqhC | no | no | no | sqhC | BA3612 | BC3557 | no | no | no | no | no | no | sqhC | 4 TMs
 | sodF |  |  |  |  |  | sodF | 1.37 | 0.68 |  | 12.78933608090806 | 0.97 |  | 1.214658512006042 | 0.7335 |  | 1.14634458633065 | 0.85832897287147 |  | sodF |  |  |  |  |  |  | sodF |  |  | sodF |  |  |  | sodF |  |  |  |  |  |  |  |  | sodF
ybbF-E-D-C | ybbF | ATATAGA | 15 | CATACAAT | favored predicted promoter | 42 | ybbF | 1.552387009958082 | 0.886 |  | 3.380648362059817 | 0.994 |  | 1.008397676338115 | 0.509 |  | 1.745910902306178 | 0.996040739150394 |  | ybbF |  |  |  |  |  |  | ybbF | sucrose phosphotransferase enzyme II | 1.2 (Transport/binding proteins and lipoproteins) | ybbF | no | sacP, sacX, bglP, treP | malP, nagP, gamP, ptsG | ybbF | BA0823 | BC0842 | BH3574 | OB0615 | no [CAC0423 (sacP)] | no [CPE1534] | no [lmo0027 (bglP)] | no [lin0026 (bglP)] | ybbF | 8-9 TMs
 | ybbE | 56 bp downstream |  |  |  |  | ybbE | 1.581248039270383 | 0.923 |  | 4.549880601500487 | 0.999 |  | 1.538608374231311 | 0.904 |  | 1.547558468789576 | 0.993303096688417 |  | ybbE |  |  |  |  |  |  | ybbE | similar to glycosyl hydrolase (beta-lactamase) | 4.2 (Detoxification) | ybbE | no | no | pbpE, pbpX | ybbE | no | no [BC2190 (pbpX)] | no | OB0667 | CAC0181 | no | lmo1916 (pbpX-ybbE) | lin2030 (pbpX-ybbE) | ybbE | secreted-pred
 | ybbD | 27 bp downstream |  |  |  |  | ybbD | 1.432187899273544 | 0.902 |  | 2.97851642942919 | 0.994 |  | 1.011077362988374 | 0.509 |  | 1.378375481194494 | 0.980627506982351 |  | ybbD |  |  |  |  |  |  | ybbD | similar to glycosyl hydrolase (beta-hexosaminidase) | 2.1.1 (Specific pathways) | ybbD | yzbA | no | no | ybbD | no | no | BH0675 | OB1299 | CAC0182 | CPE0266 | lmo2781 | lin1840 | ybbD | 1 TM (Nter)
 | [NAME] | 13 bp downstream |  |  |  |  | [NAME] | 1.435489433353656 | 0.905 |  | 3.026913428101306 | 0.982 |  | 1.642626891745718 | 0.917 |  | 1.260375477238209 | 0.940461283955573 |  | [NAME] |  |  |  |  |  |  | [NAME] | unknown | 5.2 (From other organisms) | [NAME] | yzbB | no | no | [NAME] | no | no | BH0674 | OB1304 | CAC0185 | no | no | no | [NAME] | secreted-pred
yhcO-P | yhcO | ACACACT | 14 | CATAGAGT | AAAAATAAAAAGGTA (5'RACE) | 104 | yhcO | 1.807174126010927 | 0.818 |  | 4.436086439314326 | 0.993 |  | 0.9621237456368773 | 0.4635 |  | 1.022189959757944 | 0.574049226205887 |  | yhcO |  |  |  |  |  |  | yhcO | unknown | 6 (No similarity) | yhcO | no | no | no | yhcO | no | no | no | no | no | no | no | no | yhcO | 1 TM (Nter)
 | yhcP | 4 bp upstream |  |  |  |  | yhcP | 2.07491351745491 | 0.837 |  | 4.073802778041128 | 0.957 |  | 0.6952175230289951 | 0.1375 |  | 0.8951986910741017 | 0.211618966561012 |  | yhcP |  |  |  |  |  |  | yhcP | unknown | 6 (No similarity) | yhcP | no | no | no | yhcP | no | no | no | no | no | no | no | no | yhcP | 0 TM
yuiE | yuiE | TTATACC | 13 | AATACCCA | possible promoter (by visual inspection) | 22 | yuiE | 1.333521432163324 | 0.87 |  | 3.221068791283435 | 0.992 |  | 0.7972297062639527 | 0.253 |  | 1.249906256764897 | 0.95018319492731 |  | yuiE |  |  |  |  |  |  | yuiE | leucyl aminopeptidase | 3.8 (Protein modification) | yuiE | no | no | no | yuiE | pepA (BA5155) | BC4921 | BH3401 | no | no | CPE2501 | no | no | yuiE | 1 TM (mid)
yxiO | yxiO | CCATTCTTTTC | 10 | CTCGTACAATA | BioOptimizer-prediction | 28 | yxiO | 1.485935642287007 | 0.932 |  | 3.890451449942807 | 0.996 |  | 0.9361627716965021 | 0.4125 |  | 1.837589220285074 | 0.996610956392063 |  | yxiO |  |  |  |  |  |  | yxiO | unknown (putative permease) | 5.2 (From other organisms) | yxiO | no | no | ywoG | yxiO | BA0393 | BC0436 | BH2931 | OB1126 | CAC1585 | no [CPE1282] | lmo1417 | lin1456 | yxiO | 11-12 TMs
 |  | AAAGTATGATT | 11 | AACATAAATAT | BioOptimizer-prediction | 82
b) ratio in sigE+ vs. sigE- experiment is low  (<3)
nadA | nadA | TTTTGCA | 15 | AATATAAA | possible promoter | 158 | nadA | 1.717908387157588 | 0.924 |  | 2.409905428686595 | 0.964 |  | 1.631418449596981 | 0.914 |  | 0.9657560964654528 | 0.393973757124686 |  | nadA |  |  |  |  |  |  | nadA | quinolinate synthetase | 2.5 (Metabolism of coenzymes and prosthetic groups) | nadA | no | no | no | nadA | BA4660 | BC4421 | nadA | no | nadA ([NAME]) | nadA (CPE0394) | nadA | nadA | nadA | 0 TM
ygaE | ygaE | CTTGAATATTT | 11 | TGTATATTACT | BioOptimizer-prediction | 75 | ygaE | 1.570362804333552 | 0.853 |  | 2.004472027365162 | 0.955 |  | 1.311753541392576 | 0.805 |  | 1.538883780606929 | 0.992837773963838 |  | ygaE |  |  |  |  |  |  | ygaE | unknown | 5.2 (From other organisms) | ygaE | no | no | no | ygaE | BA0529 | BC0510 | BH0942 | OB2246 | no [CAC2484 (yqjA)] | no [CPE1557] | lmo1686 | lin1794 | ygaE | 4 TMs
ypqA (absent in Eichenberger et al., 2003) | ypqA | TAACAACA | 12 | GCATAATCTG | GTTAAAAAAGGCGG (5'RACE) | 23 | ypqA |  |  |  | 2.047711173230297 | 0.771 |  | 1.329352768219227 | 0.7195 |  | 1.418574169523065 | 0.967352961434106 |  | ypqA |  |  |  |  |  |  | ypqA | unknown | 6 (No similarity) | ypqA | no | no | no | ypqA | no | no | no | no | no | no | no | no | ypqA | 0 TM
yqkF | yqkF | TTCTGTC | 14 | CATACATT | possible promoter | 216 | yqkF | 1.468926277643867 | 0.911 |  | 2.371373705661656 | 0.981 |  | 1.385545959031429 | 0.854 |  | 1.041182846335314 | 0.589086624849399 |  | yqkF |  |  |  |  |  |  | yqkF | similar to oxidoreductase (aldo-keto reductase family) | 2.1.1 (Specific pathways) | yqkF | no | iolS, yccK, yhdN, yrpG | ycsN, yvgN, ytbE | yqkF | iolS (BA4318) | BC4096 | BH1011 | OB1852 | no [CAC3378 (ycsN)] | no | no [lmo0084 (yccK)] | no [lin2113 (yrpG)] | yqkF | 0 TM
ysnE | ysnE | TCTTTATATTT | 11 | GGAATATGATT | BioOptimizer-prediction | 56 | ysnE | 1.706082389003124 | 0.897 |  | 2.818382931264454 | 0.972 |  | 1.448353793744634 | 0.8635 |  | 1.0774019226659 | 0.708527974800943 |  | ysnE |  |  |  |  |  |  | ysnE | similar to acetyltransferase ([NAME] family) | 2.2 (Metabolism of amino acids and related molecules) | ysnE | no | no | yvbK, ybfA | ysnE | no | no [BC2923 (yjcK)] | BH1073 | no | CAC2539 | no | no | no | ysnE | 0 TM
GENES IN SECTIONS 3.3.C. 2) WERE NOT INCLUDED IN THE FINAL TOTAL OF SIGE-CONTROLLED GENES
3.3.C. 2) Genes not included in the sE regulon in Eichenberger et al. (2003)
a) ratio in sigE+ vs. sigE- experiment is high (>3)
comFA | comFA | TTATTTT | 15 | AATATTCA | possible promoter (by visual inspection) | 34 | comFA | 0.5662392890382533 | 0.199 |  | 5.445026528424212 | 0.948 |  | 1.598907589316682 | 0.8365 |  | 1.188259449299821 | 0.854345293145517 |  | comFA |  |  |  |  |  |  | comFA |  |  | comFA |  |  |  | comFA |  |  |  |  |  |  |  |  | comFA
cotI (ytaA) | cotI (ytaA) | CAATCCA | 15 | CATAAGGT | possible promoter (by visual inspection) | 19 | cotI (ytaA) |  |  |  | 3.033891184194271 | 0.975 |  | 0.7068101960517708 | 0.23 |  | 1.068063731262719 | 0.727123885983261 |  | cotI (ytaA) |  |  |  |  |  |  | cotI (ytaA) |  |  | cotI (ytaA) |  |  |  | cotI (ytaA) |  |  |  |  |  |  |  |  | cotI (ytaA)
cotM | cotM | TCACCCA | 14 | CATATGAT | GTAAAGCAA (sigK promoter) | 16 | cotM | 0.7227698036021702 | 0.278 |  | 6.918309709189367 | 0.957 |  | 0.4506375411365067 | 0.074 |  |  |  |  | cotM |  |  |  |  |  |  | cotM |  |  | cotM |  |  |  | cotM |  |  |  |  |  |  |  |  | cotM
cotR (yvdO) | cotR (yvdO) | ATACAAC | 14 | CATATACT | possible promoter (by visual inspection) | 28 | cotR (yvdO) |  |  |  | 10.2093948370768 | 0.999 |  | 0.7261979263179666 | 0.265 |  | 1.417167036204871 | 0.98502664943933 |  | cotR (yvdO) |  |  |  |  |  |  | cotR (yvdO) |  |  | cotR (yvdO) |  |  |  | cotR (yvdO) |  |  |  |  |  |  |  |  | cotR (yvdO)
cotX | cotX | CAGTCAA | 15 | CATTTAAT | AACAGTAA (sigK promoter) | 27 | cotX |  |  |  | 4.931738039549359 | 0.991 |  | 1.022027746054888 | 0.5145 |  |  |  |  | cotX |  |  |  |  |  |  | cotX |  |  | cotX |  |  |  | cotX |  |  |  |  |  |  |  |  | cotX
degQ-comQ-X-P | degQ | AAATACC | 14 | CATACACA | possible promoter (by visual inspection) | 36 | degQ |  |  |  |  |  |  |  |  |  |  |  |  | degQ |  |  |  |  |  |  | degQ |  |  | degQ |  |  |  | degQ |  |  |  |  |  |  |  |  | degQ
 | comQ | 184 bp downstream |  |  |  |  | comQ | 0.9638290236239705 | 0.439 |  | 4.216965034285823 | 0.998 |  | 1.028716237519433 | 0.5435 |  | 0.9920586136159416 | 0.4725605109854 |  | comQ |  |  |  |  |  |  | comQ |  |  | comQ |  |  |  | comQ |  |  |  |  |  |  |  |  | comQ
 | comX | 7 bp upstream |  |  |  |  | comX | 0.4139996748197304 | 0.105 |  | 2.642408757321947 | 0.955 |  | 0.6426483680885048 | 0.107 |  | 0.9926329718571132 | 0.480581671305408 |  | comX |  |  |  |  |  |  | comX |  |  | comX |  |  |  | comX |  |  |  |  |  |  |  |  | comX
 | comP | 14 bp downstream |  |  |  |  | comP | 0.8790225168308843 | 0.306 |  | 3.040885025676279 | 0.993 |  | 0.7313824845956016 | 0.181 |  | 1.025903222807788 | 0.563963298457494 |  | comP |  |  |  |  |  |  | comP |  |  | comP |  |  |  | comP |  |  |  |  |  |  |  |  | comP
des (yocE)-yocF-G | des (yocE) | TGACAAA | 14 | CATGATGT | possible promoter (by visual inspection) | 69 | des (yocE) | 0.95 | 0.47 |  | 1.976724750104291 | 0.964 |  | 1.104246431314968 | 0.6165 |  | 0.9544005864899182 | 0.358282905491271 |  | des (yocE) |  |  |  |  |  |  | des (yocE) |  |  | des (yocE) |  |  |  | des (yocE) |  |  |  |  |  |  |  |  | des (yocE)
 | yocF |  |  |  |  |  | yocF | 1.16 | 0.61 |  | 3.543795073010359 | 0.994 |  | 0.9251327891180566 | 0.408 |  | 0.9642086773583223 | 0.372388816583984 |  | yocF |  |  |  |  |  |  | yocF |  |  | yocF |  |  |  | yocF |  |  |  |  |  |  |  |  | yocF
 | yocG |  |  |  |  |  | yocG |  |  |  | 5.634299125513188 | 0.998 |  | 0.7018165455441517 | 0.236 |  | 1.104229722852799 | 0.74858007682365 |  | yocG |  |  |  |  |  |  | yocG |  |  | yocG |  |  |  | yocG |  |  |  |  |  |  |  |  | yocG
gapB | gapB | TTATAAT | 14 | AATATGTA | possible promoter (by visual inspection) | 81 | gapB | 0.8241381150130023 | 0.255 |  | 3.013006024186121 | 0.988 |  | 1.692937675611425 | 0.911 |  | 0.9439951756720042 | 0.345579285347112 |  | gapB |  |  |  |  |  |  | gapB |  |  | gapB |  |  |  | gapB |  |  |  |  |  |  |  |  | gapB
mcpB | mcpB | no promoter found |  |  |  |  | mcpB | 0.61 | 0.22 |  | 16.71440803376619 | 0.993 |  | 0.5999416539890399 | 0.068 |  | 1.217064913191455 | 0.89691539284126 |  | mcpB |  |  |  |  |  |  | mcpB |  |  | mcpB |  |  |  | mcpB |  |  |  |  |  |  |  |  | mcpB
ndhF | ndhF | TGATAGG | 15 | AATAAAAA | possible promoter (by visual inspection) | 304 | ndhF |  |  |  | 8.298507675144227 | 0.964 |  | 1.256541496328321 | 0.67 |  |  |  |  | ndhF |  |  |  |  |  |  | ndhF |  |  | ndhF |  |  |  | ndhF |  |  |  |  |  |  |  |  | ndhF
pucK (yunK) | pucK (yunK) | no promoter found |  |  |  |  | pucK (yunK) |  |  |  | 6.770334090317946 | 0.99 |  | 1.274937740630572 | 0.6915 |  | 1.557676601227482 | 0.973025468853425 |  | pucK (yunK) |  |  |  |  |  |  | pucK (yunK) |  |  | pucK (yunK) |  |  |  | pucK (yunK) |  |  |  |  |  |  |  |  | pucK (yunK)
spoVFA-B | spoVFA | TCACCGG | 14 | [NAME] | GAAGGGGA (sigK promoter) | 56 | spoVFA | 1.339676687425935 | 0.765 |  | 3.104559588128356 | 0.964 |  | 0.9424661087801356 | 0.4505 |  | 0.6113896812975677 | 0.121213986002501 |  | spoVFA |  |  |  |  |  |  | spoVFA |  |  | spoVFA |  |  |  | spoVFA |  |  |  |  |  |  |  |  | spoVFA
 | spoVFB |  |  |  |  |  | spoVFB | 1.140249787561169 | 0.579 |  | 3.206269324505466 | 0.979 |  | 1.003165316731155 | 0.503 |  | 0.5836602165185338 | 0.07154347721165 |  | spoVFB |  |  |  |  |  |  | spoVFB |  |  | spoVFB |  |  |  | spoVFB |  |  |  |  |  |  |  |  | spoVFB
trpB | trpB | no promoter found |  |  |  |  | trpB | 1.68 | 0.78 |  | 3.989934810226652 | 0.992 |  | 0.7334340721820227 | 0.169 |  | 1.187852874297871 | 0.903712674005904 |  | trpB |  |  |  |  |  |  | trpB |  |  | trpB |  |  |  | trpB |  |  |  |  |  |  |  |  | trpB
yesQ-R | yesQ | TCATTGT | 15 | CATATTGT | possible promoter (by visual inspection) | 49 | yesQ | 1.11 | 0.56 |  | 2.499857193882846 | 0.961 |  | 0.7385777844129066 | 0.285 |  | 1.078051464589583 | 0.691479657971658 |  | yesQ |  |  |  |  |  |  | yesQ |  |  | yesQ |  |  |  | yesQ |  |  |  |  |  |  |  |  | yesQ
 | yesR |  |  |  |  |  | yesR | 1.3 | 0.69 |  | 3.654610519766674 | 0.991 |  | 0.6696311187333398 | 0.111 |  | 1.206716342432825 | 0.916985821041016 |  | yesR |  |  |  |  |  |  | yesR |  |  | yesR |  |  |  | yesR |  |  |  |  |  |  |  |  | yesR
yfkA | yfkA | ACATGTC | 14 | AATAATCA | possible promoter (by visual inspection) | 179 | yfkA | 0.7798301105232587 | 0.334 |  | 3.311311214825912 | 0.963 |  | 0.5445375319981072 | 0.1175 |  | 1.608557949323738 | 0.977536911888669 |  | yfkA |  |  |  |  |  |  | yfkA |  |  | yfkA |  |  |  | yfkA |  |  |  |  |  |  |  |  | yfkA
yfnA | yfnA | ATATAAT | 13 | CATATAAT | possible promoter (by visual inspection) | 38 | yfnA |  |  |  | 4.415704473533126 | 0.968 |  | 1.06015261294398 | 0.5425 |  | 1.710962503959129 | 0.991790912125653 |  | yfnA |  |  |  |  |  |  | yfnA |  |  | yfnA |  |  |  | yfnA |  |  |  |  |  |  |  |  | yfnA
yhaL | yhaL | ACATAAC | 14 | CATATGGT | possible promoter (by visual inspection) | 36 | yhaL | 1.870682140365801 | 0.838 |  | 6.531305526474723 | 0.998 |  | 0.681876607197576 | 0.2245 |  | 0.9870012555563559 | 0.455258488307916 |  | yhaL |  |  |  |  |  |  | yhaL |  |  | yhaL |  |  |  | yhaL |  |  |  |  |  |  |  |  | yhaL
yjbB | yjbB | TCATAGA | 15 | CATTTACA |  | 29 | yjbB | 0.74 | 0.28 |  | 8.591844335351498 | 0.985 |  | 0.6166310925381352 | 0.082 |  | 1.252236978093773 | 0.955792608948864 |  | yjbB |  |  |  |  |  |  | yjbB |  |  | yjbB |  |  |  | yjbB |  |  |  |  |  |  |  |  | yjbB
yjbJ | yjbJ | GTTTCAG | 14 | AATATACA | possible promoter (by visual inspection) | 54 | yjbJ | 0.4775292736576908 | 0.135 |  | 3.126079367123956 | 0.981 |  | 0.9206709097326613 | 0.422 |  | 1.339870235999288 | 0.960828738142056 |  | yjbJ |  |  |  |  |  |  | yjbJ |  |  | yjbJ |  |  |  | yjbJ |  |  |  |  |  |  |  |  | yjbJ
yjbO | yjbO | no promoter found |  |  |  |  | yjbO | 1.04 | 0.52 |  | 8.239559609248913 | 0.976 |  | 0.9886688562794904 | 0.4915 |  | 1.172279007493404 | 0.89235144444448 |  | yjbO |  |  |  |  |  |  | yjbO |  |  | yjbO |  |  |  | yjbO |  |  |  |  |  |  |  |  | yjbO
yjdH | yjdH | GTATGTC | 14 | AATATGTA | possible promoter (by visual inspection) | 150 | yjdH | 0.9057326008982002 | 0.441 |  | 7.06317554262962 | 0.997 |  | 1.385772006154368 | 0.834 |  | 0.8091545127251939 | 0.101345919305546 |  | yjdH |  |  |  |  |  |  | yjdH |  |  | yjdH |  |  |  | yjdH |  |  |  |  |  |  |  |  | yjdH
ykoN | ykoN | AAATCGG | 13 | CATATGGA | possible promoter (by visual inspection) | 109 | ykoN |  |  |  | 4.677351412871984 | 0.994 |  | 0.9086618086545618 | 0.3815 |  | 1.114351470403647 | 0.808655749392718 |  | ykoN |  |  |  |  |  |  | ykoN |  |  | ykoN |  |  |  | ykoN |  |  |  |  |  |  |  |  | ykoN
ynzB-yndD-E-F | ynzB | TAATAAC | 15 | CATAGCGT | possible promoter (by visual inspection) | 232 | ynzB | 1.694337800447329 | 0.814 |  | 9.33254300796991 | 0.989 |  | 0.8494957275265953 | 0.3755 |  | 0.9410790518223148 | 0.351086888948038 |  | ynzB |  |  |  |  |  |  | ynzB |  |  | ynzB |  |  |  | ynzB |  |  |  |  |  |  |  |  | ynzB
 | yndD | CGTTAGT | 14 | CATATGTA | possible promoter (by visual inspection) | 43 | yndD |  |  |  | 3.341950400261143 | 0.956 |  | 0.9820688651954174 | 0.4745 |  | 0.931311567689471 | 0.264449950492459 |  | yndD |  |  |  |  |  |  | yndD |  |  | yndD |  |  |  | yndD |  |  |  |  |  |  |  |  | yndD
 | yndE |  |  |  |  |  | yndE |  |  |  | 1.85 | 0.883 |  | 0.7542832750307458 | 0.208 |  | 0.9722872314898995 | 0.411391707503775 |  | yndE |  |  |  |  |  |  | yndE |  |  | yndE |  |  |  | yndE |  |  |  |  |  |  |  |  | yndE
 | yndF | 5 bp upstream |  |  |  |  | yndF |  |  |  | 2.070141348791042 | 0.957 |  | 1.112563018306477 | 0.6275 |  | 0.5548752443831393 | 0.00274155914224028 |  | yndF |  |  |  |  |  |  | yndF |  |  | yndF |  |  |  | yndF |  |  |  |  |  |  |  |  | yndF
yoaQ | yoaQ | TAATATT | 14 | AATAGTAA | possible promoter (by visual inspection) | 25 | yoaQ |  |  |  | 3.614098626396133 | 0.971 |  | 1.384885097612729 | 0.8355 |  | 1.238933376464909 | 0.948332728150103 |  | yoaQ |  |  |  |  |  |  | yoaQ |  |  | yoaQ |  |  |  | yoaQ |  |  |  |  |  |  |  |  | yoaQ
yobW | yobW | TACTATT | 14 | CATACACT | TCTCAACGGA (sigK promoter) | 24 | yobW |  |  |  | 11.37627285823431 | 0.999 |  | 0.540765610528601 | 0.116 |  | 1.042723203415963 | 0.592571363090403 |  | yobW |  |  |  |  |  |  | yobW |  |  | yobW |  |  |  | yobW |  |  |  |  |  |  |  |  | yobW
yocR | yocR | TCATAAC | 14 | AATAATTT | possible promoter (by visual inspection) | 136 | yocR | 1.258925411794167 | 0.737 |  | 6.180164001384161 | 0.999 |  | 0.8311955235760279 | 0.272 |  | 1.261017778861705 | 0.916573796144447 |  | yocR |  |  |  |  |  |  | yocR |  |  | yocR |  |  |  | yocR |  |  |  |  |  |  |  |  | yocR
 | alternative | read-through from sqhC (convergent) ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | alternative |  |  | alternative |  |  |  | alternative |  |  |  |  |  |  |  |  | alternative
yozD-yodM | yozD | GTATAAT | 14 | CATAAAAC | possible promoter (by visual inspection) | 23 | yozD |  |  |  | 20.60629913270001 | 0.992 |  |  |  |  |  |  |  | yozD |  |  |  |  |  |  | yozD |  |  | yozD |  |  |  | yozD |  |  |  |  |  |  |  |  | yozD
 | yodM | 77 bp downstream |  |  |  |  | yodM |  |  |  | 3.483373150360119 | 0.971 |  | 0.5957876581465099 | 0.1605 |  | 0.8505525656418098 | 0.154456476542573 |  | yodM |  |  |  |  |  |  | yodM |  |  | yodM |  |  |  | yodM |  |  |  |  |  |  |  |  | yodM
ypzC | ypzC | AAATATT | 15 | CATAATTC | possible promoter (by visual inspection) | 81 | ypzC |  |  |  | 5.847900841444809 | 0.961 |  | 0.9494233391289313 | 0.435 |  |  |  |  | ypzC |  |  |  |  |  |  | ypzC |  |  | ypzC |  |  |  | ypzC |  |  |  |  |  |  |  |  | ypzC
yrrI | yrrI | GACTGAC | 15 | AATAATTC | favored predicted promoter | 38 | yrrI | 1.636816521427809 | 0.774 |  | 3.926449353995999 | 0.993 |  | 1.641406814723821 | 0.8085 |  | 1.275366651003683 | 0.96765435837122 |  | yrrI |  |  |  |  |  |  | yrrI |  |  | yrrI |  |  |  | yrrI |  |  |  |  |  |  |  |  | yrrI
ythP-Q | ythP | GGATTAC | 15 | AATATTAT | possible promoter (by visual inspection) | 56 | ythP |  |  |  | 3.793149849736819 | 0.999 |  | 0.5675715932706328 | 0.0585 |  | 1.549709640183257 | 0.995662834667957 |  | ythP |  |  |  |  |  |  | ythP |  |  | ythP |  |  |  | ythP |  |  |  |  |  |  |  |  | ythP
 | ythQ |  |  |  |  |  | ythQ |  |  |  | 3.741105882720533 | 0.993 |  | 0.4855903310062601 | 0.0905 |  |  |  |  | ythQ |  |  |  |  |  |  | ythQ |  |  | ythQ |  |  |  | ythQ |  |  |  |  |  |  |  |  | ythQ
yxdM | yxdM | no promoter found |  |  |  |  | yxdM | 1.37 | 0.7 |  | 3.372668061779853 | 0.996 |  | 0.5571800545897728 | 0.1375 |  | 1.315678933653359 | 0.897652214514942 |  | yxdM |  |  |  |  |  |  | yxdM |  |  | yxdM |  |  |  | yxdM |  |  |  |  |  |  |  |  | yxdM
yxiJ-K | yxiJ | TGATCCG | 15 | AATAAATG | possible promoter (by visual inspection) | 28 | yxiJ | 0.88 | 0.42 |  | 2.914288214500293 | 0.946 |  | 0.589729363145749 | 0.151 |  |  |  |  | yxiJ |  |  |  |  |  |  | yxiJ |  |  | yxiJ |  |  |  | yxiJ |  |  |  |  |  |  |  |  | yxiJ
 | yxiK |  |  |  |  |  | yxiK | 1.14 | 0.6 |  | 3.438301050984164 | 0.979 |  | 0.4375964118085492 | 0.075 |  |  |  |  | yxiK |  |  |  |  |  |  | yxiK |  |  | yxiK |  |  |  | yxiK |  |  |  |  |  |  |  |  | yxiK
yybC | yybC | no promoter found |  |  |  |  | yybC | 0.93 | 0.46 |  | 6.703601662561124 | 0.957 |  | 1.179651288636216 | 0.6195 |  | 1.218920801862045 | 0.94288647946361 |  | yybC |  |  |  |  |  |  | yybC |  |  | yybC |  |  |  | yybC |  |  |  |  |  |  |  |  | yybC
b) ratio in sigE+  vs. sigE- experiment is low
bglC | bglC |  |  |  |  |  | bglC | 0.9 | 0.4 |  | 2.332231194975292 | 0.973 |  | 1.124510944983603 | 0.6545 |  | 1.49176695691694 | 0.988877353510699 |  | bglC |  |  |  |  |  |  | bglC |  |  | bglC |  |  |  | bglC |  |  |  |  |  |  |  |  | bglC
ctpA | ctpA |  |  |  |  |  | ctpA | 1.22 | 0.74 |  | 1.897477784865362 | 0.976 |  | 0.9884322228119465 | 0.4875 |  | 0.5645941939402546 | 0.00424085784661588 |  | ctpA |  |  |  |  |  |  | ctpA |  |  | ctpA |  |  |  | ctpA |  |  |  |  |  |  |  |  | ctpA
dapA | dapA |  |  |  |  |  | dapA | 0.83 | 0.3 |  | 2.677448955924408 | 0.981 |  | 0.7346583096419216 | 0.169 |  | 0.9503028522589378 | 0.320945248994665 |  | dapA |  |  |  |  |  |  | dapA |  |  | dapA |  |  |  | dapA |  |  |  |  |  |  |  |  | dapA
dnaX-yaaK | dnaX |  |  |  |  |  | dnaX | 1.14 | 0.71 |  | 2.077595519348543 | 0.973 |  | 0.7189181385565826 | 0.175 |  | 0.8489358903978983 | 0.108512745673433 |  | dnaX |  |  |  |  |  |  | dnaX |  |  | dnaX |  |  |  | dnaX |  |  |  |  |  |  |  |  | dnaX
 | yaaK |  |  |  |  |  | yaaK | 1.12 | 0.69 |  | 2.505544958756841 | 0.966 |  | 0.7736270476361777 | 0.23 |  | 0.7689117033367954 | 0.0399241560379292 |  | yaaK |  |  |  |  |  |  | yaaK |  |  | yaaK |  |  |  | yaaK |  |  |  |  |  |  |  |  | yaaK
gid | gid |  |  |  |  |  | gid | 1.786487574852051 | 0.838 |  | 2.728977782808041 | 0.972 |  | 1.26699376162585 | 0.763 |  | 0.9622701008394503 | 0.365688120257985 |  | gid |  |  |  |  |  |  | gid |  |  | gid |  |  |  | gid |  |  |  |  |  |  |  |  | gid
glpK | glpK |  |  |  |  |  | glpK | 0.88 | 0.31 |  | 1.933034476828417 | 0.956 |  | 0.8926547396507345 | 0.371 |  | 1.134713013141969 | 0.854276902663863 |  | glpK |  |  |  |  |  |  | glpK |  |  | glpK |  |  |  | glpK |  |  |  |  |  |  |  |  | glpK
kinC | kinC |  |  |  |  |  | kinC | 0.86 | 0.28 |  | 2.567666411602202 | 0.98 |  | 1.172132464443073 | 0.683 |  | 1.69931646589357 | 0.997731772193684 |  | kinC |  |  |  |  |  |  | kinC |  |  | kinC |  |  |  | kinC |  |  |  |  |  |  |  |  | kinC
nhaC (yheL) | nhaC (yheL) |  |  |  |  |  | nhaC (yheL) | 1.39 | 0.8 |  | 2.296769434931138 | 0.967 |  | 1.154507673091369 | 0.6795 |  | 1.09943999584026 | 0.781593417389073 |  | nhaC (yheL) |  |  |  |  |  |  | nhaC (yheL) |  |  | nhaC (yheL) |  |  |  | nhaC (yheL) |  |  |  |  |  |  |  |  | nhaC (yheL)
rocR | rocR |  |  |  |  |  | rocR | 1.01 | 0.52 |  | 2.449069444946765 | 0.985 |  | 0.6700902951786204 | 0.1205 |  | 1.168702654263701 | 0.895774268060199 |  | rocR |  |  |  |  |  |  | rocR |  |  | rocR |  |  |  | rocR |  |  |  |  |  |  |  |  | rocR
spoIISA | spoIISA |  |  |  |  |  | spoIISA |  |  |  | 2.671853858545538 | 0.985 |  | 1.459914960064536 | 0.864 |  | 1.2345456193132 | 0.926619482105834 |  | spoIISA |  |  |  |  |  |  | spoIISA |  |  | spoIISA |  |  |  | spoIISA |  |  |  |  |  |  |  |  | spoIISA
ydeF | ydeF |  |  |  |  |  | ydeF | 1.42 | 0.82 |  | 2.023917939991029 | 0.969 |  | 1.568354252928393 | 0.8825 |  | 0.5126879147344304 | 0.0015236082542921 |  | ydeF |  |  |  |  |  |  | ydeF |  |  | ydeF |  |  |  | ydeF |  |  |  |  |  |  |  |  | ydeF
yfiB-C | yfiB |  |  |  |  |  | yfiB | 1.15 | 0.6 |  | 2.965995583438885 | 0.873 |  | 1.096456836937515 | 0.578 |  | 1.15657484128344 | 0.838552865104238 |  | yfiB |  |  |  |  |  |  | yfiB |  |  | yfiB |  |  |  | yfiB |  |  |  |  |  |  |  |  | yfiB
 | yfiC |  |  |  |  |  | yfiC | 1.3 | 0.77 |  | 2.793493724064339 | 0.978 |  | 0.8731363659073101 | 0.3515 |  | 1.354955802339503 | 0.971067908027263 |  | yfiC |  |  |  |  |  |  | yfiC |  |  | yfiC |  |  |  | yfiC |  |  |  |  |  |  |  |  | yfiC
yhaN-M | yhaN |  |  |  |  |  | yhaN | 1.28 | 0.77 |  | 2.368900938523277 | 0.965 |  | 1.249559321769113 | 0.7445 |  | 1.081473571828773 | 0.691397060570435 |  | yhaN |  |  |  |  |  |  | yhaN |  |  | yhaN |  |  |  | yhaN |  |  |  |  |  |  |  |  | yhaN
 | yhaM |  |  |  |  |  | yhaM | 0.98 | 0.46 |  | 2.394418724198603 | 0.945 |  | 1.217775751920307 | 0.7285 |  | 1.056248166948368 | 0.686048828637968 |  | yhaM |  |  |  |  |  |  | yhaM |  |  | yhaM |  |  |  | yhaM |  |  |  |  |  |  |  |  | yhaM
ykrA | ykrA |  |  |  |  |  | ykrA | 1.08 | 0.58 |  | 2.069953073627084 | 0.948 |  | 0.686335999997438 | 0.2125 |  | 1.287151434162749 | 0.921818392483105 |  | ykrA |  |  |  |  |  |  | ykrA |  |  | ykrA |  |  |  | ykrA |  |  |  |  |  |  |  |  | ykrA
ykoW | ykoW |  |  |  |  |  | ykoW | 1.1 | 0.6 |  | 1.814912534244177 | 0.957 |  | 0.8304835835645228 | 0.282 |  | 1.307269931358686 | 0.974802251251346 |  | ykoW |  |  |  |  |  |  | ykoW |  |  | ykoW |  |  |  | ykoW |  |  |  |  |  |  |  |  | ykoW
ykuI | ykuI |  |  |  |  |  | ykuI | 1.778279410038923 | 0.812 |  | 2.564484036517718 | 0.982 |  | 0.7143161716784305 | 0.1355 |  | 1.516128014316762 | 0.914776646589145 |  | ykuI |  |  |  |  |  |  | ykuI |  |  | ykuI |  |  |  | ykuI |  |  |  |  |  |  |  |  | ykuI
ypdP | ypdP |  |  |  |  |  | ypdP | 1.465547840955912 | 0.831 |  | 2.564484036517718 | 0.966 |  | 1.337809830079653 | 0.8115 |  | 1.111329389692043 | 0.779304258125852 |  | ypdP |  |  |  |  |  |  | ypdP |  |  | ypdP |  |  |  | ypdP |  |  |  |  |  |  |  |  | ypdP
ypeP | ypeP |  |  |  |  |  | ypeP |  |  |  | 2.839002009971199 | 0.975 |  | 1.116908200794117 | 0.6355 |  | 1.032349458285499 | 0.602788697418637 |  | ypeP |  |  |  |  |  |  | ypeP |  |  | ypeP |  |  |  | ypeP |  |  |  |  |  |  |  |  | ypeP
ypiP | ypiP |  |  |  |  |  | ypiP | 0.94 | 0.46 |  | 2.258895810774775 | 0.969 |  | 1.238081368900485 | 0.7405 |  | 1.282070482154123 | 0.954986731516611 |  | ypiP |  |  |  |  |  |  | ypiP |  |  | ypiP |  |  |  | ypiP |  |  |  |  |  |  |  |  | ypiP
yqjX | yqjX |  |  |  |  |  | yqjX |  |  |  | 2.845940394756175 | 0.954 |  | 0.7370743182388867 | 0.267 |  |  |  |  | yqjX |  |  |  |  |  |  | yqjX |  |  | yqjX |  |  |  | yqjX |  |  |  |  |  |  |  |  | yqjX
yuaE | yuaE |  |  |  |  |  | yuaE | 0.94 | 0.44 |  | 2.978475279988264 | 0.987 |  |  |  |  | 1.03617601656945 | 0.594778304967464 |  | yuaE |  |  |  |  |  |  | yuaE |  |  | yuaE |  |  |  | yuaE |  |  |  |  |  |  |  |  | yuaE
yvfL | yvfL |  |  |  |  |  | yvfL | 0.46 | 0.05 |  | 2.289533487237313 | 0.952 |  | 1.095372625090183 | 0.618 |  | 1.179286084380047 | 0.866768550407397 |  | yvfL |  |  |  |  |  |  | yvfL |  |  | yvfL |  |  |  | yvfL |  |  |  |  |  |  |  |  | yvfL
ywnH | ywnH |  |  |  |  |  | ywnH | 1.57 | 0.79 |  | 2.32142309090906 | 0.987 |  | 0.950950642202269 | 0.4365 |  | 1.180695418863158 | 0.843556892493294 |  | ywnH |  |  |  |  |  |  | ywnH |  |  | ywnH |  |  |  | ywnH |  |  |  |  |  |  |  |  | ywnH
4. sE-CONTROLLED GENES UNAFFECTED BY SpoIIID AND REPRESSED BY GerR (YlbO):
4.1. Previously identified sE-controlled genes (with mapped transcription start site):
4.1. A) also identified by overexpression of sE
spoIIM | spoIIM | GCATGTT | 13 | CATACAAT | CTATTAAA | 40 | spoIIM | 4.634469197362881 | 0.998 |  | 4.139996748197305 | 0.998 |  | 1.299267103074169 | 0.784 |  | 0.1867385426815137 | 8.53958826829704e-06 |  | spoIIM |  |  |  |  |  |  | spoIIM | dissolution of the septal cell wall (engulfment and inhibition of septation) | 1.8 (Sporulation) | spoIIM | no | no | no | spoIIM | spoIIM (BA4314) | BC4092 | spoIIM | spoIIM (OB1850) | CAC2068 | spoIIM (CPE1809) | no | no | spoIIM | 5 TMs
 |  | AGGGCATGTTT | 10 | TTCATACAATC | BioOptimizer prediction-correct | 39
4.1. B) identified neither by overexpression of sE nor in sigE+ vs. sigE- experiment
spoIIP | spoIIP | TTCTACT | 14 | CATAGAGT | AATTACTAGA | 29 | spoIIP | 1.914255925021086 | 0.842 |  | 1.566751070108149 | 0.699 |  | 0.9644008928521577 | 0.454 |  | 0.5008160728709437 | 0.000699701486444382 |  | spoIIP |  |  |  |  |  |  | spoIIP | required for dissolution of the septal cell wall (engulfment and inhibition of septation) | 1.8 (Sporulation) | spoIIP | no | no | no | spoIIP | BA2068/BA3102 | BC2050/BC2058 | spoIIP | spoIIP (OB1974) | spoIIP (CAC1276) | spoIIP (CPE2040) | no | no | spoIIP | 1 TM
 |  | CAGTTCTACTT | 11 | TTCATAGAGTA | BioOptimizer prediction-correct | 28
4.2. sE-regulated genes with predicted [NAME] promoter (from Eichenberger et al. 2003, JMB):
4.2. A) also identified by overexpression of sE
cypA | cypA | TCCTGATTTTA | 12 | ATCATAACCTT | BioOptimizer-prediction | 21 | cypA | 4.027170343254591 | 0.997 |  | 24.04362800006934 | 1 |  | 1.469359448939227 | 0.8475 |  | 0.2987451668334044 | 7.41150295899828e-05 |  | cypA |  |  |  |  |  |  | cypA | cytochrome P450-like enzyme | 4.2 (Detoxification) | cypA | yrdE | [NAME], bioI, yjiB, cypX | yrhJ, yetO | cypA | cypA (BA2627) | BC2609 | no [BH0579 (yrhJ)] | no | no | no | no | no | cypA | 0-1 TM
kapD | kapD | AAATGTC | 13 | GATATACT | possible promoter (by visual inspection) | 44 | kapD | 3.019951720402017 | 0.936 |  | 11.32400363235557 | 1 |  | 0.6504838609333118 | 0.0925 |  | 0.4650840761956583 | 0.000576088529937402 |  | kapD |  |  |  |  |  |  | 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
 |  | CCTTACTAATT | 12 | TTCACAATTTA | BioOptimizer-prediction (unlikely)
yfnE-D | yfnE | AAGCAAG | 14 | CATATAAT | TCGAGGAGC (sigK promoter) | "+33" | yfnE | 2.187761623949553 | 0.987 |  | 2.904022654464451 | 0.945 |  | 0.8358901964516451 | 0.3645 |  | 0.2939770842335416 | 0.00015276066825487 |  | yfnE |  |  |  |  |  |  | yfnE | unknown | 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 (yveT)] | yfnE | 0 TM
 |  |  |  |  | BioOptimizer-no prediction
 | yfnD | adjacent |  |  |  |  | yfnD | 1.729816359215102 | 0.965 |  | 2.128139045982712 | 0.954 |  | 1.16661802964798 | 0.6185 |  | 0.4904188129240016 | 0.00208979384389651 |  | yfnD |  |  |  |  |  |  | yfnD | unknown | 5.1 (From B. subtilis) | yfnD | no | [NAME] | no | yfnD | no | no | no | no | no | no | no | no | yfnD | 0 TM
yhjL | yhjL | TTTTGCTATTT | 11 | GGCATATTTTC | BioOptimizer-prediction | 97 | yhjL | 3.184197521726125 | 0.935 |  | 20.84490883097289 | 0.992 |  | 1.194875534038585 | 0.7125 |  | 0.476853201391584 | 0.00051373166430313 |  | yhjL |  |  |  |  |  |  | yhjL | similar to DegT/DnrJ/EryC1/StrS aminotransferase, similar to SpsC and PatA | 1.3 (Sensors (signal transduction)) | yhjL | no | spsC, yvfE | alaT, patA, speA, aspB | yhjL | no | no | no | no [OB2893 (yvfE)] | no [CAC2260 (spsC)] | no [CPE0464] | no [lmo1006 (patA)] | no [lin1005 (patA)] | yhjL | 1 TM (mid)
yqhV | yqhV | CAAGACTACTT | 14 | AGCATATCATA | BioOptimizer-prediction | 28 | yqhV | 3.443499307633386 | 0.991 |  | 8.356030182312482 | 0.965 |  | 0.5939603358659956 | 0.187 |  | 0.2779749682462297 | 3.31425680395459e-05 |  | yqhV |  |  |  |  |  |  | yqhV | unknown | 5.2 (From other organisms) | yqhV | yqgE | no | no | yqhV | BA4418 | BC4194 | BH2798 | no | no | no | no | no | yqhV | 3 TMs
4.2. B) not identified by overexpression of sE
ybaS | ybaS | GAGAAATTTTA | 12 | TGCATATGATG | BioOptimizer-prediction | 101 | ybaS | 1.651961798229015 | 0.886 |  | 2.805433637951714 | 0.979 |  | 0.6997811333922529 | 0.243 |  | 0.3956649450119942 | 0.000585849615715395 |  | ybaS |  |  |  |  |  |  | ybaS | sodium dependent transporter | 1.2 (Transport/binding proteins and lipoproteins) | ybaS | no | no | yocS | ybaS | no [BA1907 (arsB)] | no [BC1834 (arsB)] | BH0489 | no [OB0994 (yocS)] | no | no | no | no | ybaS | 8 TMs