Genome Property Definition Page

Nameradical SAM/SPASM system SynChlorMet
DescriptionThis property features a four-gene cassette that appears to be involved in peptide modification. The system has both a PqqD homolog and two PqqE homologs. The predicted fifth component, putative modification target ScmA, is not identified, but Clim_1912 (YP_001943923.1) from Chlorobium limicola DSM 245 is suggested; homologous ORFs are demonstrated in the cassettes of the other species with the cassette, and their alignment modeled by TIGR04252. Three other species with the cassette are Syntrophobacter fumaroxidans MPOB, Methanocella paludicola SANAE, and delta proteobacterium NaphS2. Regions homologous to Clim_1912 are found in the other three species, and conservation at the amino acid level appears strongest in the reading frame of Clim_1912. The SPASM domain involvement in peptide modification is described in PMID:21478363.
Parent PropertyGenProp0077: natural products biosynthesis
Literature References
[ 1 ]Haft DH, Basu MK  Biological systems discovery in silico: radical S-adenosylmethionine protein families and their target peptides for posttranslational modification.  J Bacteriol. 2011 Jun;193(11):2745-55.  PMID 21478363

Step NameStep NumRequiredEvidence (Method)Evidence Go Terms
putative SynChlorMet system core peptideScmANOTIGR04252 (HMM): SynChlorMet cassette protein ScmA
SynChlorMet cassette protein ScmCScmCYESTIGR04249 (HMM): SynChlorMet cassette protein ScmC
SynChlorMet cassette protein ScmDScmDYESTIGR04248 (HMM): SynChlorMet cassette protein ScmD
SynChlorMet cassette radical SAM/SPASM protein ScmEScmEYESTIGR04250 (HMM): SynChlorMet cassette radical SAM/SPASM protein ScmE
SynChlorMet cassette radical SAM/SPASM protein ScmFScmFYESTIGR04251 (HMM): SynChlorMet cassette radical SAM/SPASM protein ScmF

Parent Properties
GenProp0077natural products biosynthesis

Sibling Properties
GenProp0014polyketide biosynthesis, type I
GenProp0015polyketide biosynthesis, type II
GenProp0040thiotemplate type non-ribosomal peptide biosynthesis
GenProp0169hybrid NRPS-PKS natural pruduct biosynthesis genes
GenProp0724phosphonoacetaldehyde biosynthesis from phosphoenolpyruvate
GenProp0757quorum-sensing, autoinducer-2 system
GenProp0758lycopene biosynthesis from IPP
GenProp0770siderophore biosynthesis
GenProp0807bacteriocin system, heterocycle biosynthesis group
GenProp0808bacteriocin system, TIGR01847 leader group
GenProp0809bacteriocin system, lactococcin 972 group
GenProp0823violacein biosynthesis
GenProp0825bacteriocin system, circular bacteriocin group
GenProp0853lantibiotic system, gallidermin/epidermin family
GenProp0861bacteriocin system, NHLP (nif11/nitrile hydratase leader peptide) transport group
GenProp0901post-ribosomal natural product synthesis system, Burkholderia TOMM-type
GenProp0919SCIFF/radical SAM Clostridial gene pair
GenProp0920radical SAM Y_X(10)_GDL system
GenProp0921radical SAM pair and His-Xaa-Ser repeats peptide
GenProp0936bacteriocin system, sporulation delay protein group
GenProp0945radical SAM maturase bacteriocin system, CLI_3235 type
GenProp0954radical SAM-cylized peptide, Pep1357C family
GenProp0955modified peptide/radical SAM maturase system, YydFG family
GenProp0956radical SAM maturase/selenobacteriocin system
GenProp0962methanobactin biosynthesis, Mb-OB3b family
GenProp0967radical SAM maturase system, CXXX repeats type
GenProp0982radical SAM maturase system, FibroRumin system
GenProp0984radical SAM maturase system, GG-Bacteroidales group
GenProp0990cobaltopeptin biosynthesis
GenProp0991ATP-grasp maturase system, microviridin/marinostatin class
GenProp1000ATP-grasp maturase system, uncharacterized
GenProp1002grasp-with-spasm peptide maturase system
GenProp1003cysteine S-glycopeptide biosynthesis, sublancin family
GenProp1037radical SAM/SPASM system GRRM
GenProp1052geopeptide radical SAM/SPASM maturase system
GenProp1062radical SAM/SPASM system Clo7bot
GenProp1065radical SAM/SPASM TIGR04347/TIGR04031 system
GenProp1078sporulation killing factor system
GenProp1083cyanobactin-like ribosomal natural product biosynthesis
GenProp1084enduracididine biosynthesis
GenProp1090radical SAM/SPASM maturase system XYE
GenProp1097bacimethrin biosynthesis
GenProp10983-methylarginine biosynthesis