Potential Gaps in catabolism of small carbon sources in Dechlorosoma suillum PS
Found 139 low-confidence and 36 medium-confidence steps on the best paths for 62 pathways.
Pathway | Step | Best candidate | 2nd candidate |
2-oxoglutarate | dctP: 2-oxoglutarate TRAP transporter, solute receptor component DctP | Dsui_3155 | |
2-oxoglutarate | dctQ: 2-oxoglutarate TRAP transporter, small permease component DctQ | | |
4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | | |
4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | Dsui_0578 | |
4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
4-hydroxybenzoate | pobA: 4-hydroxybenzoate 3-monooxygenase | | |
4-hydroxybenzoate | praA: protocatechuate 2,3-dioxygenase | | |
4-hydroxybenzoate | xylF: 2-hydroxymuconate semialdehyde hydrolase | | |
alanine | TRIC: TRIC-type L-alanine transporter | Dsui_0014 | Dsui_2676 |
arabinose | araA: L-arabinose isomerase | | |
arabinose | araB: ribulokinase | | |
arabinose | araD: L-ribulose-5-phosphate epimerase | | |
arabinose | araE: L-arabinose:H+ symporter | | |
arginine | rocA: 1-pyrroline-5-carboxylate dehydrogenase | Dsui_0437 | Dsui_1464 |
arginine | rocD: ornithine aminotransferase | Dsui_3250 | Dsui_0023 |
arginine | rocE: L-arginine permease | | |
arginine | rocF: arginase | Dsui_0671 | |
asparagine | ans: asparaginase | | |
cellobiose | cbp: cellobiose phosphorylase | | |
cellobiose | cdt: cellobiose transporter cdt-1/cdt-2 | | |
cellobiose | glk: glucokinase | Dsui_0801 | |
citrate | SLC13A5: citrate:Na+ symporter | | |
citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | Dsui_0638 | Dsui_2068 |
citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | | |
citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | Dsui_0636 | Dsui_0637 |
citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
citrulline | arcC: carbamate kinase | | |
citrulline | rocA: 1-pyrroline-5-carboxylate dehydrogenase | Dsui_0437 | Dsui_1464 |
citrulline | rocD: ornithine aminotransferase | Dsui_3250 | Dsui_0023 |
D-alanine | cycA: D-alanine:H+ symporter CycA | | |
D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | | |
D-serine | cycA: D-serine:H+ symporter CycA | | |
D-serine | dsdA: D-serine ammonia-lyase | Dsui_0728 | |
deoxyinosine | deoB: phosphopentomutase | | |
deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
deoxyinosine | deoD: deoxyinosine phosphorylase | Dsui_2698 | |
deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | Dsui_2312 | Dsui_0676 |
deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
deoxyribose | deoC: deoxyribose-5-phosphate aldolase | | |
deoxyribose | deoK: deoxyribokinase | | |
deoxyribose | deoP: deoxyribose transporter | | |
fructose | 1pfk: 1-phosphofructokinase | | |
fructose | fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components | | |
fucose | aldA: lactaldehyde dehydrogenase | Dsui_1464 | Dsui_0437 |
fucose | fucA: L-fuculose-phosphate aldolase FucA | Dsui_3380 | |
fucose | fucI: L-fucose isomerase FucI | | |
fucose | fucK: L-fuculose kinase FucK | | |
fucose | fucP: L-fucose:H+ symporter FucP | | |
fucose | fucU: L-fucose mutarotase FucU | | |
galactose | galE: UDP-glucose 4-epimerase | Dsui_0398 | Dsui_0083 |
galactose | galK: galactokinase (-1-phosphate forming) | | |
galactose | galP: galactose:H+ symporter GalP | | |
galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
galacturonate | dopDH: 2,5-dioxopentanonate dehydrogenase | Dsui_0437 | Dsui_0105 |
galacturonate | exuT: D-galacturonate transporter ExuT | | |
galacturonate | gci: D-galactarolactone cycloisomerase | | |
galacturonate | gli: D-galactarolactone isomerase | | |
galacturonate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | | |
galacturonate | udh: D-galacturonate dehydrogenase | | |
gluconate | gnd: 6-phosphogluconate dehydrogenase, decarboxylating | | |
gluconate | gntK: D-gluconate kinase | | |
gluconate | gntT: gluconate:H+ symporter GntT | | |
glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | Dsui_1101 | |
glucose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
glucuronate | garL: 5-dehydro-4-deoxy-D-glucarate aldolase | Dsui_1977 | |
glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
glucuronate | udh: D-glucuronate dehydrogenase | | |
glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | | |
glycerol | glpF: glycerol facilitator glpF | | |
glycerol | glpK: glycerol kinase | | |
histidine | hutG: N-formiminoglutamate formiminohydrolase | Dsui_0671 | |
histidine | hutH: histidine ammonia-lyase | | |
histidine | hutI: imidazole-5-propionate hydrolase | | |
histidine | hutU: urocanase | | |
histidine | PA5503: L-histidine ABC transporter, ATPase component | Dsui_0638 | Dsui_2068 |
histidine | PA5504: L-histidine ABC transporter, permease component | Dsui_2067 | |
histidine | PA5505: L-histidine ABC transporter, substrate-binding component | Dsui_2064 | Dsui_2066 |
L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
lactose | galE: UDP-glucose 4-epimerase | Dsui_0398 | Dsui_0083 |
lactose | galK: galactokinase (-1-phosphate forming) | | |
lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
lactose | glk: glucokinase | Dsui_0801 | |
lactose | lacP: lactose permease LacP | | |
lactose | lacZ: lactase (homomeric) | | |
lysine | davT: 5-aminovalerate aminotransferase | Dsui_3250 | Dsui_0023 |
lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | Dsui_0037 | Dsui_1115 |
lysine | lysP: L-lysine:H+ symporter LysP | | |
lysine | patA: cadaverine aminotransferase | Dsui_3250 | Dsui_0023 |
lysine | patD: 5-aminopentanal dehydrogenase | Dsui_0437 | Dsui_1464 |
maltose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
maltose | susB: alpha-glucosidase (maltase) | | |
mannitol | mtlA: mannitol phosphotransferase system, EII-CBA components | | |
mannitol | mtlD: mannitol-1-phosphate 5-dehydrogenase | | |
mannose | manA: mannose-6-phosphate isomerase | Dsui_0087 | |
mannose | manP: mannose PTS system, EII-CBA components | | |
myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | | |
myoinositol | iolC: 5-dehydro-2-deoxy-D-gluconate kinase | | |
myoinositol | iolD: 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase | | |
myoinositol | iolE: scyllo-inosose 2-dehydratase | | |
myoinositol | iolG: myo-inositol 2-dehydrogenase | | |
myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | Dsui_0050 | |
myoinositol | iolT: myo-inositol:H+ symporter | | |
myoinositol | mmsA: malonate-semialdehyde dehydrogenase | Dsui_0437 | Dsui_0105 |
NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | Dsui_1101 | |
NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
phenylacetate | paaA: phenylacetyl-CoA 1,2-epoxidase, subunit A | | |
phenylacetate | paaB: phenylacetyl-CoA 1,2-epoxidase, subunit B | | |
phenylacetate | paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C | | |
phenylacetate | paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E | | |
phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | Dsui_0502 | Dsui_1378 |
phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | Dsui_0317 | Dsui_3239 |
phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | Dsui_0317 | Dsui_3239 |
phenylacetate | paaZ1: oxepin-CoA hydrolase | Dsui_0502 | Dsui_1378 |
phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
phenylacetate | ppa: phenylacetate permease ppa | Dsui_0522 | Dsui_0290 |
phenylalanine | fahA: fumarylacetoacetate hydrolase | | |
phenylalanine | hmgA: homogentisate dioxygenase | | |
phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
phenylalanine | maiA: maleylacetoacetate isomerase | Dsui_1815 | |
phenylalanine | PAH: phenylalanine 4-monooxygenase | | |
phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | Dsui_3224 | |
proline | put1: proline dehydrogenase | | |
proline | putA: L-glutamate 5-semialdeyde dehydrogenase | Dsui_0437 | Dsui_1464 |
propionate | mctC: propionate:H+ symporter | Dsui_0290 | Dsui_0522 |
putrescine | gabT: gamma-aminobutyrate transaminase | Dsui_3250 | Dsui_0023 |
putrescine | patA: putrescine aminotransferase (PatA/SpuC) | Dsui_3250 | Dsui_0023 |
putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | Dsui_0105 | Dsui_1464 |
putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
rhamnose | aldA: lactaldehyde dehydrogenase | Dsui_1464 | Dsui_0437 |
rhamnose | LRA1: L-rhamnofuranose dehydrogenase | Dsui_2448 | Dsui_2538 |
rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
rhamnose | LRA3: L-rhamnonate dehydratase | | |
rhamnose | LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase | | |
rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
ribose | rbsK: ribokinase | | |
ribose | rbsU: probable D-ribose transporter RbsU | | |
serine | sdaB: L-serine ammonia-lyase | Dsui_0728 | |
sorbitol | scrK: fructokinase | Dsui_0801 | |
sorbitol | sdh: sorbitol dehydrogenase | Dsui_2448 | Dsui_2538 |
sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
sucrose | scrK: fructokinase | Dsui_0801 | |
sucrose | SUS: sucrose synthase | | |
sucrose | sut: sucrose:proton symporter SUT/SUC | | |
threonine | ltaE: L-threonine aldolase | Dsui_1265 | Dsui_2254 |
threonine | phtA: L-threonine uptake permease PhtA | Dsui_3451 | |
thymidine | deoA: thymidine phosphorylase DeoA | Dsui_3246 | |
thymidine | deoB: phosphopentomutase | | |
thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
thymidine | nupG: thymidine permease NupG/XapB | | |
trehalose | glk: glucokinase | Dsui_0801 | |
trehalose | PsTP: trehalose phosphorylase | | |
trehalose | TRET1: facilitated trehalose transporter Tret1 | | |
tryptophan | aroP: tryptophan:H+ symporter AroP | | |
tryptophan | tnaA: tryptophanase | | |
tyrosine | fahA: fumarylacetoacetate hydrolase | | |
tyrosine | hmgA: homogentisate dioxygenase | | |
tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
tyrosine | maiA: maleylacetoacetate isomerase | Dsui_1815 | |
valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | Dsui_1378 | Dsui_0502 |
valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | Dsui_0629 | Dsui_2060 |
valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | Dsui_0630 | Dsui_2061 |
valine | livM: L-valine ABC transporter, permease component 2 (LivM/BraE) | Dsui_0628 | Dsui_2059 |
valine | mmsA: methylmalonate-semialdehyde dehydrogenase | Dsui_0437 | Dsui_0105 |
valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | Dsui_3436 | Dsui_3438 |
xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | | |
xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | | |
xylose | xylA: xylose isomerase | | |
xylose | xylB: xylulokinase | | |
xylose | xylT: D-xylose transporter | | |
Confidence: high confidence medium confidence low confidence
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
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About GapMind
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