Definition of glycerol catabolism
As rules and steps, or see full text
Rules
Overview: Glycerol utilization in GapMind is based on MetaCyc pathways glycerol degradation I via glycerol kinase (link), II via dihydroxyacetone kinase (link), or V via dihydroxyacetone:PEP phosphotransferase (link). Two fermentative pathways are not included because they do not lead to carbon incorporation (link, link).
- all:
- glycerol-transport, glpK, g3p-dehydrogenase and tpi
- or glycerol-transport, dhaD, dhkinase and tpi
- Comment: Pathway I involves glycerol kinase glpK and glycerol-3-phosphate dehydrogenase; the glycerone phosphate can be converted to glyceraldehyde-3-phosphate by triose-phosphate isomerase. In pathways II or V, the dehydrogenase dhaD forms dihydroxyacetone, which is phosphorylated and isomerized to glyceraldehyde 3-phosphate.
- dhkinase:
- dhaK, dhaL and dhaM
- or dhaK'
- Comment: In pathway V, the three-subunit phosphotranfserase dhaKLM phosphorylates dihydroxyacetone, with phosphoenolpyruvate as the donor. In pathway II, a kinase (also known as dhaK, here dhaK') phosphorylates dihydroxyacetone.
- g3p-dehydrogenase:
- glpD
- or glpA, glpB, glpC and glpD
- or glpO
- Comment: Glycerol 3-phosphate dehydrogenase includes EC 1.1.5.3, EC 1.1.1.8, and EC 1.1.1.94. 1.1.5.3 is flavin- or quinone-dependent and may be heteromeric. 1.1.1.8/1.1.1.94 are NAD(P)H dependent and the forward reaction is thermodynamically unfavorable, so they are not included here. An oxygen-dependent enzyme, glycerol-3-phosphate oxidase, can also form glycerone phosphate.
- glycerol-transport:
Steps
glpS: glycerol ABC transporter, ATPase component 1 (GlpS)
- Curated sequence G3LHY8: GlpS, component of Glycerol uptake porter, GlpSTPQV
- Curated sequence Ac3H11_791: ABC transporter for Glycerol, ATPase component 1
- Comment: GlpSTPQV from Rhizobium leguminosarum and a related system from Acidovorax GW101-3H11. GlpS/GlpT are similar to each other; GlpS is more similar to Ac3H11_791 and GlpT to Ac3H11_792.
- Total: 2 characterized proteins
glpT: glycerol ABC transporter, ATPase component 2 (GlpT)
glpP: glycerol ABC transporter, permease component 1 (GlpP)
glpQ: glycerol ABC transporter, permease component 2 (GlpQ)
glpV: glycerol ABC transporter, substrate-binding component GlpV
- Curated sequence G3LHZ3: GlpV, component of Glycerol uptake porter, GlpSTPQV
- Curated sequence Ac3H11_796: ABC transporter for Glycerol, periplasmic substrate-binding component
- Total: 2 characterized proteins
glpF: glycerol facilitator glpF
- Curated sequence CH_024677: aquaglyceroporin. Glycerol uptake facilitator protein; Aquaglyceroporin. Glycerol facilitator, GlpF. Transports various polyols with decreasing rates as size increases (Heller et al. 1980); also transports arsenite (As(III) and antimonite (Sb(III)) (Meng et al., 2004). Oligomerization may play a role in determining the rate of transport. glycerol facilitator. glycerol facilitator
- Curated sequence CH_091207: aquaporin-9. Aquaporin-9; AQP-9; Aquaglyceroporin-9. Aquaporin-9 (Aqp9) (permeable to glycerol, urea, polyols, carbamides, purines, pyrmidines, nucleosides, monocarboxylates, pentavalent methylated arsenicals and the arsenic chemotherapeutic drug, trisenox
- Curated sequence CH_091783: aquaglyceroporin 1. Aquaporin 1 (permeable to water, glycerol, dihydroxyacetone and urea)
- Curated sequence F9UMX3: Glycerol uptake facilitator protein 4; D/L-lactic acid transporter; Lactic acid channel
- Curated sequence F9UST3: D/L-lactic acid transporter; Lactate racemization operon protein LarD; Lactic acid channel. GlpF1; transports water, dihydroxyacetone and glycerol as well as D,L-lactic acid
- Curated sequence F9USY3: Glycerol uptake facilitator protein 2. GlpF2
- Curated sequence F9UTW9: Glycerol uptake facilitator protein 3. GlpF3
- Curated sequence F9UUB3: Glycerol uptake facilitator protein-like 5. GlpF4. Transports water, dihydroxyacetone and glycerol as well as D,L-lactic acid
- Curated sequence P47862: Aquaporin-3; AQP-3; 31.4 kDa water channel protein; Aquaglyceroporin-3. Aquaporin 3. 95% identical to the human orthologue. Poorly permeable to water, but more permeable to glycerol and arsenic trioxide
- Curated sequence F6QEC2: Aquaporin/glycerol facilitator of 294 aas and 6 TMSs
- Curated sequence P08995: Nodulin-26 aquaporin and glycerol facilitator, NIP (de Paula Santos Martins et al. 2015). Transports NH3 5-fold better than water in Hg2+-sensitive fashion
- Curated sequence P18156: Glycerol facilitator
- Curated sequence P52280: Probable glycerol uptake facilitator protein
- Curated sequence Q6Q1Q6: Major aquaglyceroporin, LmAQP1: transports water, glycerol, methylglyoxal, trivalent metalloids such as arsenite and antimonite, dihydroxyacetone and sugar alcohols. Also takes up the activated form or the drug, pentostam
- Curated sequence Q8WPZ6: Aquaglycerolporin, Aqp (high permeability to ammonium, methylamine, glycerol and water) (Beitz et al., 2004) NH4+/NH3+CH3 transporter
- Curated sequence Q9C4Z5: Hg2+-inhibitable aquaporin, AqpM (transports both water and glycerol as well as CO2) (Kozono et al., 2003; Araya-Secchi et al., 2011). Its 3-d structure has been determined to 1.7 Å. In AqpM, isoleucine replaces a key histidine residue found in the lumen of water channels, which becomes a glycine residue in aquaglyceroporins. As a result of this and other side-chain substituents in the walls of the channel, the channel is intermediate in size and exhibits differentially tuned electrostatics when compared with the other subfamilies
- Ignore hits to O28846 when looking for 'other' hits (MIP family homologue)
- Comment: Ignore an uncharacterized homolog from Archaeoglobus
- Total: 16 characterized proteins
aqp-3: glycerol porter aqp-3
- Curated sequence E3UMZ6: Potato X intrinsic protein, XIP1
- Curated sequence 729057658: Aquaporin-3, Aqp-3 of 271 aas
- Curated sequence E3UMZ5: Morning glory XIP-1-1-α. Transports glycerol, urea and boric acid, but not water
- Curated sequence E3UN01: Tobacco X-intrinsic protein (XIP1-1-β). Transports glycerol, urea and boric acid, but not water
- Total: 4 characterized proteins
stl1: glycerol:H+ symporter Stl1p
- Curated sequence CH_091379: sugar transporter STL1. The glycerol:H+ symporter, Stl1p
- Curated sequence CH_122745: glycerol permease. Glycerol uptake permease (Glycerol:H+ symporter) Stl1. (Involved in salt stress relief) (Kayingo et al. 2009) (similar to Stl1 of S. cerevisiae (2.A.1.1.38))
- Curated sequence C4QVV9: Glycerol:H+ symporter of 530 aas and 12 TMSs, GT1
- Total: 3 characterized proteins
glpF': glycerol facilitator-aquaporin
fps1: glycerol uptake/efflux facilitator protein
- Curated sequence CH_091157: glycerol uptake/efflux facilitator protein. Glycerol uptake/efflux facilitator protein. FPS1 glycerol efflux facilitator (important for maintaining osmotic balance during mating-induced yeast cell fusion and for tolerating hypoosmotic shock; also transports arsenite and antimonite). FPS1 is a homotetramer
- Total: 1 characterized proteins
PLT5: glycerol:H+ symporter PLT5
- Curated sequence CH_091483: polyol transporter 5. Polyol transporter 5; Protein POLYOL TRANSPORTER 5; AtPLT5; Sugar-proton symporter PLT5. The broad specificity sugar/sugar alcohol (myo-inositol, glycerol, ribose, sorbitol, mannitol, xylitol, erythritol, etc) H+ symporter, AtPLT5 (transports a wide range of hexoses, pentoses, tetroses, sugar alcohols and a sugar acid, but not disaccharides) (Reinders et al., 2005) (expressed in roots, leaves and floral organs)
- Total: 1 characterized proteins
YFL054C: glycrol facilitator protein
- Curated sequence CH_091497: uncharacterized membrane protein YFL054C. Aquaglycerol porin AQY3; Aquaporin-3. Glycerol facilitator, Yf1054c (70.5 kDa protein)
- Total: 1 characterized proteins
TIPa: glycerol facilitator TIPa
glpK: glycerol kinase
glpD: glycerol 3-phosphate dehydrogenase (monomeric)
- Curated sequence P18158: Aerobic glycerol-3-phosphate dehydrogenase; EC 1.1.5.3
- Curated sequence P13035: glycerol-3-phosphate dehydrogenase [NAD(P)+] (EC 1.1.1.94). glycerol-3-phosphate dehydrogenase; EC 1.1.5.3. aerobic glycerol 3-phosphate dehydrogenase (EC 1.1.5.3). aerobic glycerol 3-phosphate dehydrogenase (EC 1.1.5.3)
- Curated sequence P35571: glycerol-3-phosphate dehydrogenase (EC 1.1.5.3)
- Curated sequence P43304: glycerol-3-phosphate dehydrogenase (EC 1.1.5.3). mitochondrial glycerol-3-phosphate dehydrogenase subunit (EC 1.1.5.3)
- Curated sequence Q06B39: glycerol-3-phosphate dehydrogenase (EC 1.1.5.3)
- Curated sequence Q64521: glycerol-3-phosphate dehydrogenase (EC 1.1.5.3)
- Curated sequence CH_091834: glycerol-3-phosphate dehydrogenase; EC 1.1.5.3
- Curated sequence P32191: Glycerol-3-phosphate dehydrogenase, mitochondrial; GPD-M; GPDH-M; EC 1.1.5.3
- Curated sequence Q8SR40: Probable glycerol-3-phosphate dehydrogenase; GPDH; EC 1.1.5.3
- Curated sequence Q9SS48: Glycerol-3-phosphate dehydrogenase SDP6, mitochondrial; Protein SUGAR-DEPENDENT 6; EC 1.1.5.3. glycerol-3-phosphate dehydrogenase (EC 1.1.5.3)
- Curated sequence CH_122883: glycerol-3-phosphate dehydrogenase, mitochondrial
- UniProt sequence Q92LM5: RecName: Full=Glycerol-3-phosphate dehydrogenase {ECO:0000256|RuleBase:RU361217}; EC=1.1.5.3 {ECO:0000256|RuleBase:RU361217};
- Comment: Fitness data identified SMc02520 (Q92LM5) as the glycerol-3-phosphate dehydrogenase in Sinorhizobium meliloti.
- Total: 12 characterized proteins
glpA: glycerol 3-phosphate dehydrogenase subunit A
- Curated sequence D4GQU6: Anaerobic glycerol-3-phosphate dehydrogenase subunit A2; G-3-P dehydrogenase A2; G3PDH A2; EC 1.1.5.3
- Curated sequence D4GYI2: Anaerobic glycerol-3-phosphate dehydrogenase subunit A1; G-3-P dehydrogenase A1; G3PDH A1; EC 1.1.5.3
- Curated sequence ANGLYC3PDEHYDROGSUBUNITA-MONOMER: anaerobic glycerol-3-phosphate dehydrogenase subunit A (EC 1.1.5.3). anaerobic glycerol-3-phosphate dehydrogenase subunit A (EC 1.1.5.3)
- Total: 3 characterized proteins
glpB: glycerol 3-phosphate dehydrogenase subunit B
glpC: glycerol 3-phosphate dehydrogenase subunit C
glpO: glycerol 3-phosphate oxidase
tpi: triose-phosphate isomerase
- Curated proteins or TIGRFams with EC 5.3.1.1
- Ignore hits to P85814 when looking for 'other' hits (Triosephosphate isomerase; TIM; Triose-phosphate isomerase; Allergen Pla o 4; EC 5.3.1.1)
- Comment: Ignore a fragmentary (allergen) sequence
- Total: 1 HMMs and 55 characterized proteins
dhaD: glycerol dehydrogenase
dhaK: dihydroxyacetone:PEP phosphotransferase, subunit K
- Curated sequence P76015: glycerone kinase (EC 2.7.1.29). dihydroxyacetone kinase, DhaK subunit; EC 2.7.-.-. PEP-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit DhaK; EC 2.7.1.121. dihydroxyacetone kinase subunit K (EC 2.7.1.121). dihydroxyacetone kinase subunit K
- Curated sequence Q92EU2: PTS-dependent dihydroxyacetone kinase 2, dihydroxyacetone-binding subunit DhaK; EC 2.7.1.121
- Curated sequence Q9CIV8: PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit DhaK; EC 2.7.1.121
- Ignore hits to items matching 2.7.1.121 when looking for 'other' hits
- Ignore hits to A0A1D3TV19 when looking for 'other' hits (glycerone kinase (EC 2.7.1.29))
- Comment: most prokaryotic dihydroxyacetone kinases are heteromeric and use phosophoenolpyruvate rather than ATP as the phosphoryl donor (EC 2.7.1.121) This is a PTS-like system that relies on EI and Hpr proteins to phosphorylate the dhaM subunit The BRENDA entry does not actually seem to be characterized, not clear if it is dhaK or dhaK'
- Total: 3 characterized proteins
dhaL: dihydroxyacetone:PEP phosphotransferase, subunit L
- Curated sequence P76014: glycerone kinase (EC 2.7.1.29). PTS-dependent dihydroxyacetone kinase, DhaL subunit; EC 2.7.-.-; EC 2.7.1.-. PEP-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL; EC 2.7.1.121. dihydroxyacetone kinase subunit L (EC 2.7.1.121). dihydroxyacetone kinase subunit L
- Curated sequence Q92EU3: PEP-dependent dihydroxyacetone kinase 2, ADP-binding subunit DhaL; EC 2.7.1.121
- Curated sequence Q9CIV7: PTS-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL; EC 2.7.1.121
- Ignore hits to items matching 2.7.1.121 when looking for 'other' hits
- Total: 3 characterized proteins
dhaM: dihydroxyacetone:PEP phosphotransferase, subunit M
- Curated sequence Q92ET9: PEP-dependent dihydroxyacetone kinase 2, phosphoryl donor subunit DhaM; PTS system EIIA component; Phosphotransferase enzyme IIA component; EC 2.7.1.121
- Curated sequence Q9CIV6: PTS-dependent dihydroxyacetone kinase, phosphotransferase subunit DhaM; PTS system EIIA component; Phosphotransferase enzyme IIA component; EC 2.7.1.121
- Curated sequence P37349: glycerone kinase (EC 2.7.1.29). PEP-dependent dihydroxyacetone kinase, phosphoryl donor subunit DhaM; Dihydroxyacetone kinase subunit M; EC 2.7.1.121. dihydroxyacetone kinase subunit M. dihydroxyacetone kinase subunit M
- Curated sequence CH_000735: PTS-dependent dihydroxyacetone kinase, DhaM subunit; EC 2.7.1.-
- Curated sequence A0A0H3H456: PEP-dependent dihydroxyacetone kinase, phosphoryl donor subunit DhaM; Dihydroxyacetone kinase subunit M; EC 2.7.1.121
- Curated sequence D4GL26: PEP-dependent dihydroxyacetone kinase, phosphoryl donor subunit DhaM; Dihydroxyacetone kinase subunit M; EC 2.7.1.121
- Curated sequence P0DN88: PEP-dependent dihydroxyacetone kinase, phosphoryl donor subunit DhaM; Dihydroxyacetone kinase subunit M; EC 2.7.1.121
- Ignore hits to items matching 2.7.1.121 when looking for 'other' hits
- Total: 7 characterized proteins
dhaK': dihydroxyacetone kinase, ATP dependent (monomeric)
- Curated sequence P43550: glycerone kinase (EC 2.7.1.29). dihydroxyacetone kinase 2 (EC 2.7.1.29)
- Curated sequence P54838: glycerone kinase (EC 2.7.1.29). Dihydroxyacetone kinase 1; DHA kinase 1; Glycerone kinase 1; Triokinase 1; Triose kinase 1; EC 2.7.1.28; EC 2.7.1.29. dihydroxyacetone kinase 1 (EC 2.7.1.29)
- Curated sequence Q3LXA3: triokinase (EC 2.7.1.28); glycerone kinase (EC 2.7.1.29); FAD-AMP lyase (cyclizing) (EC 4.6.1.15). Triokinase/FMN cyclase; Bifunctional ATP-dependent dihydroxyacetone kinase/FAD-AMP lyase (cyclizing); EC 2.7.1.28; EC 2.7.1.29; EC 4.6.1.15
- Curated sequence CH_008528: glycerone kinase; EC 2.7.1.29. Dihydroxyacetone kinase; DHA kinase; Glycerone kinase; EC 2.7.1.29
- Curated sequence CH_124545: dihydroxyacetone kinase Dak1; EC 2.7.1.29. glycerone kinase (EC 2.7.1.29)
- Curated sequence F1RKQ4: Triokinase/FMN cyclase; Bifunctional ATP-dependent dihydroxyacetone kinase/FAD-AMP lyase (cyclizing); EC 2.7.1.28; EC 2.7.1.29; EC 4.6.1.15
- Curated sequence Q4KLZ6: Triokinase/FMN cyclase; Bifunctional ATP-dependent dihydroxyacetone kinase/FAD-AMP lyase (cyclizing); EC 2.7.1.28; EC 2.7.1.29; EC 4.6.1.15. bifunctional ATP-dependent dihydroxyacetone kinase/FAD-AMP lyase (cyclizing) (EC 2.7.1.29; EC 4.6.1.15)
- Curated sequence MONOMER-13163: dihydroxyacetone kinase subunit (EC 2.7.1.29)
- Curated sequence MONOMER-16996: dihydroxyacetone kinase 2 (EC 2.7.1.29)
- Ignore hits to items matching 2.7.1.29 when looking for 'other' hits
- Comment: These dihydroxyacetone kinases utilize ATP directly; these are mostly eukaryotic, but also include a system from Citrobacter (also known as dhaK)
- Total: 9 characterized proteins
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Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using
ublast (a fast alternative to protein BLAST)
against a database of manually-curated proteins (most of which are experimentally characterized) or by using
HMMer with enzyme models (usually from
TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").
Otherwise, a candidate is "medium confidence" if either:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps."
For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways.
For diverse bacteria and archaea that can utilize a carbon source, there is a complete
high-confidence catabolic pathway (including a transporter) just 38% of the time, and
there is a complete medium-confidence pathway 63% of the time.
Gaps may be due to:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory