Genome Property Definition Page

AccessionGenProp0610
Nameendospore formation marker gene set
TypeSYSTEM
DescriptionThe article by Wu, et al. on Carboxydothermus hydrogenoformans Z-2901 describes a minimal set of genes whose phylogenetic profile appears to exactly match the assignment of endospore formation capability. The list corresponds to a fairly small fraction of sporulation and germination-related genes in Bacillus subtilis. This property reflects those genes for which identifying hidden Markov models (HMMs) with appropriate scope are available. Also included in this property, as optional rather than mandatory components, are various classes of small, acid-soluble spore protein, or SASP, where one class may expand into a paralogous family while another class is lost in any given genome.
JCVI RoleSporulation and germination
Parent PropertyGenProp0049: spore formation
Literature References
[ 1 ]Wu M, Ren Q, Durkin AS, Daugherty SC, Brinkac LM, Dodson RJ, Madupu R, Sullivan SA, Kolonay JF, Nelson WC, Tallon LJ, Jones KM, Ulrich LE, Gonzalez JM, Zhulin IB, Robb FT, Eisen JA  Life in Hot Carbon Monoxide: The Complete Genome Sequence of Carboxydothermus hydrogenoformans Z-2901.  PLoS Genet. 2005 Nov 25;1(5):e65.  PMID 16311624

Components
Step NameStep NumRequiredEvidence (Method)Evidence Go Terms
stage 0 sporulation protein A0_AYESTIGR02875 (HMM): sporulation transcription factor Spo0A
dipicolinic acid synthetase, A subunitDipic_ANOTIGR02853 (HMM): dipicolinic acid synthetase, A subunit
dipicolinic acid synthetase, B subunitDipic_BNOTIGR02852 (HMM): dipicolinic acid synthetase, B subunit
germination proteaseGPRYESTIGR01441 (HMM): GPR endopeptidase
stage III sporulation protein AAIII_AAYESTIGR02858 (HMM): stage III sporulation protein AA
stage III sporulation protein ABIII_ABYESTIGR02833 (HMM): stage III sporulation protein AB
stage III sporulation protein ACIII_ACYESTIGR02848 (HMM): stage III sporulation protein AC
stage III sporulation protein ADIII_ADYESTIGR02849 (HMM): stage III sporulation protein AD
stage III sporulation protein AE (TIGR02829)III_AEYESTIGR02829 (HMM): stage III sporulation protein AE
stage III sporulation protein AFIII_AFYESTIGR02896 (HMM): stage III sporulation protein AF
stage III sporulation protein AGIII_AGYESTIGR02830 (HMM): stage III sporulation protein AG
transcriptional regulator SpoIIIDIII_DYESTIGR02844 (HMM): sporulation transcriptional regulator SpoIIID
anti-anti-sigma-FII_AAYESTIGR02886 (HMM): anti-sigma F factor antagonist
anti-sigma-FII_ABYESTIGR01925 (HMM): anti-sigma F factor
sigma-FII_ACYESTIGR02885 (HMM): RNA polymerase sigma-F factor
stage II sporulation protein DII_DYESTIGR02870 (HMM): stage II sporulation protein D
stage II sporulation protein EII_EYESTIGR02865 (HMM): stage II sporulation protein E
sigma-E protease SpoIIGAII_GAYESTIGR02854 (HMM): sigma-E processing peptidase SpoIIGA
stage II sporulation protein MII_MYESTIGR02831 (HMM): stage II sporulation protein M
stage II sporulation protein PII_PYESTIGR02867 (HMM): stage II sporulation protein P
stage II sporulation protein RII_RYESTIGR02837 (HMM): stage II sporulation protein R
stage IV sporulation protein AIV_AYESTIGR02836 (HMM): stage IV sporulation protein A
stage IV sporulation protein BIV_BYESTIGR02860 (HMM): stage IV sporulation protein B
SASP, alpha/beta typeSASP_ABYESPF00269 (HMM): small, acid-soluble spore proteins, alpha/beta type
SASP, gamma typeSASP_GNOTIGR01442 (HMM): small, acid-soluble spore protein, gamma-type
SASP, SspH-typeSASP_HNOTIGR02861 (HMM): small acid-soluble spore protein, H-type
stage VI sporulation protein DVI_DNOTIGR02907 (HMM): stage VI sporulation protein D
stage V sporulation protein ACV_ACYESTIGR02838 (HMM): stage V sporulation protein AC
stage V sporulation protein ADV_ADYESTIGR02845 (HMM): stage V sporulation protein AD
stage V sporulation protein AEV_AEYESTIGR02839 (HMM): stage V sporulation protein AE
stage V sporulation protein BV_BNOTIGR02900 (HMM): stage V sporulation protein B
stage V sporulation protein KV_KNOTIGR02881 (HMM): stage V sporulation protein K
stage V sporulation protein TV_TYESTIGR02851 (HMM): stage V sporulation protein T
germination lipoprotein, YhcN/YlaJ familyYhcNfamNOTIGR02898 (HMM): sporulation lipoprotein, YhcN/YlaJ family
spore coat protein, CotS familycotSNOTIGR02906 (HMM): spore coat protein, CotS family
GerKA-like paralogous familyger(x)AYESPF03323 (HMM): Bacillus/Clostridium GerA spore germination protein
GerKB-like paralogous familyger(x)BYESTIGR00912 (HMM): spore germination protein (amino acid permease)
GerKC-like paralogous familyger(x)CYESTIGR02887 (HMM): germination protein, Ger(x)C family
ATP-dependent protease LonBlonBNOTIGR02902 (HMM): ATP-dependent protease LonB
spore coat assembly protein SafA (yrbB)safANOTIGR02899 (HMM): spore coat assembly protein SafA
sigma-EsigmaEYESTIGR02835 (HMM): RNA polymerase sigma-E factor
sigma-GsigmaGYESTIGR02850 (HMM): RNA polymerase sigma-G factor
sigma-HsigmaHYESTIGR02859 (HMM): RNA polymerase sigma-H factor
sigma-I (heat shock-induced)sigmaINOTIGR02895 (HMM): RNA polymerase sigma-I factor
sigma-KsigmaKYESTIGR02846 (HMM): RNA polymerase sigma-K factor
spore coat assembly protease YabGyabGYESTIGR02855 (HMM): sporulation peptidase YabG
sporulation protein YabPyabPYESTIGR02892 (HMM): sporulation protein YabP
sporulation protein YabQyabQYESTIGR02893 (HMM): spore cortex biosynthesis protein YabQ
sporulation protein YlbJylbJYESTIGR02871 (HMM): sporulation integral membrane protein YlbJ
sporulation protein, YlmC/YmxH familyymxHfamYESTIGR02888 (HMM): sporulation protein, YlmC/YmxH family
germination protein YpeBypeBYESTIGR02889 (HMM): germination protein YpeB
sporulation protein YqfCyqfCYESTIGR02856 (HMM): sporulation protein YqfC
sporulation protein YqfDyqfDYESTIGR02876 (HMM): sporulation protein YqfD
spore coat protein YsxEysxENOTIGR02904 (HMM): spore coat protein YsxE
sporulation protein YtaFytaFYESTIGR02840 (HMM): putative sporulation protein YtaF
sporulation protein YtfJytfJYESTIGR02874 (HMM): sporulation protein YtfJ
sporulation protein YtvIytvIYESTIGR02872 (HMM): sporulation integral membrane protein YtvI
sporulation protein YtxCytxCYESTIGR02834 (HMM): putative sporulation protein YtxC
sporulation protein YunByunBYESTIGR02832 (HMM): sporulation protein YunB
spore coat protein YutHyutHNOTIGR02905 (HMM): spore coat protein YutH
putative sporulation protease YyaCyyaCYESTIGR02841 (HMM): putative sporulation protein YyaC

Parent Properties
AccessionName
GenProp0049spore formation