Genome Property Definition Page
Accession | GenProp0457 | |
Name | rhamnose catabolism | |
Type | SYSTEM | |
Description | L-rhamnose, (aka 6-deoxy-L-mannose) is a common sugar synthesized and utilized in oligosaccharides and glcyolipids by many bacteria [2]. The monosaccharide is available in various environments and thus regulatory, transport and enzymatic systems have also evolved for its breakdown and use as a carbon source. The system modeled here includes specific transporters, ketose-aldose isomerases, kinases, and aldolases which result in the production of lactaldehyde and glycerone-phosphate. As these genes are generally organized into operons, assignments can be made for regulatory components as well as transport and enzymatic components which, by homology alone, cannot be assigned a specific substrate. Certain of the enzymes in this system are similar enough to cognate enzymes in the fucose catabolism system (GenProp0458) as to have caused gene naming errors in the past (i.e. fuculokinase/rhamnokinase). The system in certain rhizobial species [1] has been reported to vary from the canonical pathway in that the sugar may be phosphorylated prior to isomerization (i.e. the rhamnulokinase may in fact be a rhamnokinase and the rhamnose isomerase may be a rhamnose-1-phosphate isomerase), although this has not yet been independantly verified. In addition to the characterized rhamnose:proton symporter [3], rhamnose catabolism operons contain transporters from the ABC, and major facilitator families. Regulators are generally members of the DeoR and AraC [4] families. The product of both rhamnose and fucose catabolism is lactaldehyde, and subsequently alcohol and aldehyde dehydrogenases are often present in those operons to convert it to either 1,2-propane diol or lactate depending on oxidation conditions [5]. Rhamnose operons also often contain an epimerase (mutarotase) enzyme which has been proposed to be essential unly under limiting L-rhamnose conditions [6]. Partial rhamnose catabolism operons have been detected in Thermotoga species which appear to handle the import and cleavage of rhamnose-containing oligosaccharides. | |
JCVI Role | Sugars | |
Parent Property | GenProp0142: catabolism | |
Literature References |
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Web References | KEGG:rhamnose catabolism | |
Gene Ontology Term | GO:0015762: rhamnose transport (biological_process) GO:0019301: rhamnose catabolic process (biological_process) GO:0019301: rhamnose catabolic process (biological_process) GO:0019301: rhamnose catabolic process (biological_process) GO:0043463: regulation of rhamnose catabolic process (biological_process) |
Components
Step Name | Step Num | Required | Evidence (Method) | Evidence Go Terms |
---|---|---|---|---|
clustered alcohol/aldehyde dehydrogenases | ADH | NO | PF00465 (HMM-CLUST): alcohol dehydrogenase, iron-containing PF00171 (HMM-CLUST): aldehyde dehydrogenase (NAD) family protein PF00106 (HMM-CLUST): oxidoreductase, short chain dehydrogenase/reductase family manual (NOCLUST) TIGR02638 (NOCLUST): lactaldehyde reductase | GO:0019301: rhamnose catabolic process GO:0019301: rhamnose catabolic process GO:0019301: rhamnose catabolic process GO:0019301: rhamnose catabolic process GO:0019301: rhamnose catabolic process |
rhamnulose-1-P aldolase (RhaD) | aldolase | YES | TIGR02624 (HMM): rhamnulose-1-phosphate aldolase TIGR02632 (HMM): rhamnulose-1-phosphate aldolase/alcohol dehydrogenase | GO:0019301: rhamnose catabolic process GO:0019301: rhamnose catabolic process |
rhamnose epimerase | epimera | NO | PF05336 (HMM-CLUST): PF05336 domain TIGR02625 (HMM): L-rhamnose mutarotase | GO:0019301: rhamnose catabolic process GO:0019301: rhamnose catabolic process |
L-rhamnose isomerase (RhaA/RhaI) | isomeras | YES | PF06134 (HMM): L-rhamnose isomerase (RhaA) TIGR01748 (HMM): L-rhamnose isomerase TIGR02629 (HMM): L-rhamnose catabolism isomerase TIGR02635 (HMM): L-rhamnose isomerase | GO:0019301: rhamnose catabolic process GO:0019301: rhamnose catabolic process GO:0019301: rhamnose catabolic process GO:0019301: rhamnose catabolic process |
rhamnulokinase (RhaB/RhuK) | kinase | YES | PF00370 (HMM-CLUST): FGGY family of carbohydrate kinases, N-terminal domain TIGR02627 (HMM): rhamnulokinase | GO:0019301: rhamnose catabolic process GO:0019301: rhamnose catabolic process |
clustered regulatory components | regulat | NO | PF00165 (HMM-CLUST): transcriptional regulator, AraC family PF00455 (HMM-CLUST): DeoR C-terminal sensor domain PF00532 (HMM-CLUST): periplasmic binding proteins and sugar binding domain of the LacI family PF01381 (HMM-CLUST): DNA-binding helix-turn-helix protein PF00356 (HMM-CLUST): transcriptional regulator, LacI family | GO:0043463: regulation of rhamnose catabolic process GO:0019301: rhamnose catabolic process GO:0043463: regulation of rhamnose catabolic process GO:0019301: rhamnose catabolic process GO:0043463: regulation of rhamnose catabolic process GO:0019301: rhamnose catabolic process GO:0043463: regulation of rhamnose catabolic process GO:0019301: rhamnose catabolic process GO:0043463: regulation of rhamnose catabolic process GO:0019301: rhamnose catabolic process |
rhamnose transporters (RhaSTPQ) | transpor | YES | PF07690 (HMM-CLUST): transporter, major facilitator family manual (NOCLUST) PF00083 (HMM-CLUST): transporter, major facilitator superfamily PF06379 (HMM): L-rhamnose-proton symport protein (RhaT) TIGR00776 (HMM): RhaT L-rhamnose-proton symporter family protein PF02653 (HMM-CLUST): branched-chain amino acid ABC transporter, permease protein PF00005 (HMM-CLUST): ABC transporter, ATP-binding protein TIGR02637 (HMM): rhamnose ABC transporter, rhamnose-binding protein | GO:0015762: rhamnose transport GO:0019301: rhamnose catabolic process GO:0015762: rhamnose transport GO:0019301: rhamnose catabolic process GO:0015762: rhamnose transport GO:0019301: rhamnose catabolic process GO:0015762: rhamnose transport GO:0019301: rhamnose catabolic process GO:0015762: rhamnose transport GO:0019301: rhamnose catabolic process GO:0015762: rhamnose transport GO:0019301: rhamnose catabolic process GO:0015762: rhamnose transport GO:0019301: rhamnose catabolic process GO:0015762: rhamnose transport GO:0019301: rhamnose catabolic process |
Parent Properties
Accession | Name |
---|---|
GenProp0142 | catabolism |
Sibling Properties
Accession | Name |
---|---|
GenProp0055 | polyhydroxyalkanoic acids |
GenProp0141 | galactose-6-phosphate degradation via tagatose-6-phosphate |
GenProp0156 | cyanophycin-like storage polymers |
GenProp0168 | glycogen system |
GenProp0210 | phenylacetic acid catabolism |
GenProp0231 | 4-hydroxyphenylacetate degradation |
GenProp0233 | GABA utilization |
GenProp0238 | 2-aminoethylphosphonate catabolism to acetaldehyde |
GenProp0239 | propionyl-CoA catabolism |
GenProp0241 | phosphonate catabolism |
GenProp0271 | trehalose utilization |
GenProp0272 | pyruvate fermentation to acetoin |
GenProp0273 | protocatechuate degradation to beta-ketoadipate |
GenProp0283 | beta-ketoadipate degradation to succinyl-CoA and acetyl-CoA |
GenProp0294 | ethanolamine degradation proteinaceous organelle |
GenProp0458 | fucose catabolism |
GenProp0461 | utilization of deoxynucleosides |
GenProp0653 | ectoine catabolism |
GenProp0674 | malonate decarboxylase |
GenProp0686 | allantoin catabolism to glyoxalate and urea |
GenProp0687 | allantoin catabolism to oxamate and carbamoyl-phosphate |
GenProp0688 | urate catabolism to allantoin |
GenProp0691 | glycolysis |
GenProp0693 | fructose utilization as fructose-1,6-bisphosphate |
GenProp0694 | glucose utilization as fructose-1,6-bisphosphate |
GenProp0700 | purine catabolism via urate, xanthine and allantoin |
GenProp0702 | benzoyl-CoA reductase |
GenProp0703 | 4-hydroxybenzoyl-CoA reductase |
GenProp0706 | cyclohexa-1,5-diene-1-carbonyl-CoA to 3-hydroxypimelyl-CoA, dch/had/oah pathway |
GenProp0708 | catechol meta-cleavage pathway |
GenProp0709 | benzoate catabolism BoxABC pathway |
GenProp0711 | catechol ortho-cleavage upper pathway |
GenProp0714 | galactarate utilization via tartronate semi-aldehyde |
GenProp0715 | galactarate utilization via 2-oxoglutarate semialdehyde |
GenProp0716 | glucarate utilization via tartronate semi-aldehyde |
GenProp0717 | glucarate utilization via 2-oxoglutarate semialdehyde |
GenProp0718 | oxalate degradation |
GenProp0734 | amino acid catabolism |
GenProp0749 | choline sulfate utilization |
GenProp0760 | putrescine degradation to GABA via gamma-glutamylation |
GenProp0763 | nicotinate fermentation to pyruvate and propionate |
GenProp0810 | encapsulin proteinaceous organelle |
GenProp0813 | pyrimidine utilization operon, RutABCDEFGR |
GenProp0902 | quinohemoprotein amine dehydrogenase |
GenProp1071 | myo-inositol catabolism |
GenProp1072 | cyanase system |
GenProp1076 | choline TMA-lyase system |