Potential Gaps in catabolism of small carbon sources in Serinicoccus profundi MCCC 1A05965
Found 91 low-confidence and 67 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | GQY_RS0111425 | |
| 4-hydroxybenzoate | adh: acetaldehyde dehydrogenase (not acylating) | GQY_RS0100670 | GQY_RS0105110 |
| 4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | | |
| 4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | GQY_RS17450 | |
| 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 | | |
| acetate | actP: cation/acetate symporter ActP | GQY_RS0103320 | GQY_RS0114140 |
| alanine | alsT: L-alanine symporter AlsT/DagA | GQY_RS0113640 | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | GQY_RS0116450 | |
| arginine | put1: proline dehydrogenase | GQY_RS0110515 | |
| arginine | rocE: L-arginine permease | | |
| asparagine | glt: aspartate:proton symporter Glt | GQY_RS0112055 | |
| aspartate | glt: aspartate:proton symporter Glt | GQY_RS0112055 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | GQY_RS0107955 | GQY_RS0109680 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | GQY_RS0109685 | |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | GQY_RS0107950 | |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | GQY_RS0109690 | |
| citrulline | put1: proline dehydrogenase | GQY_RS0110515 | |
| D-alanine | cycA: D-alanine:H+ symporter CycA | | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | glcE: D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) | GQY_RS0107720 | |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | GQY_RS0111170 | GQY_RS0101640 |
| deoxyinosine | adh: acetaldehyde dehydrogenase (not acylating) | GQY_RS0100670 | GQY_RS0105110 |
| deoxyinosine | deoB: phosphopentomutase | GQY_RS0108885 | GQY_RS0109755 |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | GQY_RS0112020 | GQY_RS0102025 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | garK: glycerate 2-kinase | GQY_RS17605 | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | adh: acetaldehyde dehydrogenase (not acylating) | GQY_RS0100670 | GQY_RS0105110 |
| deoxyribose | deoP: deoxyribose transporter | GQY_RS0103490 | |
| ethanol | adh: acetaldehyde dehydrogenase (not acylating) | GQY_RS0100670 | GQY_RS0105110 |
| fructose | frcA: fructose ABC transporter, ATPase component FrcA | GQY_RS0101930 | GQY_RS0104125 |
| fructose | frcC: fructose ABC transporter, permease component FrcC | GQY_RS0104120 | GQY_RS0101940 |
| fructose | scrK: fructokinase | GQY_RS0109740 | GQY_RS0102585 |
| fucose | aldA: lactaldehyde dehydrogenase | GQY_RS0105110 | GQY_RS0100430 |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | | |
| fucose | fucI: L-fucose isomerase FucI | | |
| fucose | fucK: L-fuculose kinase FucK | | |
| fucose | fucU: L-fucose mutarotase FucU | | |
| galactose | galP: galactose:H+ symporter GalP | GQY_RS0116450 | |
| galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| galacturonate | dopDH: 2,5-dioxopentanonate dehydrogenase | GQY_RS0100670 | GQY_RS0105110 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | garD: meso-galactarate dehydratase (L-threo-forming) GarD | | |
| galacturonate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | | |
| galacturonate | udh: D-galacturonate dehydrogenase | | |
| galacturonate | uxuL: D-galactaro-1,5-lactonase (UxuL or UxuF) | GQY_RS0103865 | |
| gluconate | gntT: gluconate:H+ symporter GntT | GQY_RS0114085 | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | dopDH: 2,5-dioxopentanonate dehydrogenase | GQY_RS0100670 | GQY_RS0105110 |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
| glucuronate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | GQY_RS0107930 | |
| histidine | hutG': N-formylglutamate amidohydrolase | | |
| histidine | natB: L-histidine ABC transporter, substrate-binding component NatB | GQY_RS0112250 | |
| histidine | natC: L-histidine ABC transporter, permease component 1 (NatC) | GQY_RS0112265 | |
| histidine | natD: L-histidine ABC transporter, permease component 2 (NatD) | GQY_RS0112270 | |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | GQY_RS0105830 | GQY_RS0102440 |
| isoleucine | natB: L-isoleucine ABC transporter, substrate-binding component NatB | GQY_RS0112250 | |
| isoleucine | natC: L-isoleucine ABC transporter, permease component 1 (NatC) | GQY_RS0112265 | |
| isoleucine | natD: L-isoleucine ABC transporter, permease component 2 (NatD) | GQY_RS0112270 | GQY_RS0109650 |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | GQY_RS0108870 | |
| L-lactate | lutC: L-lactate dehydrogenase, LutC subunit | | |
| lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | | |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | GQY_RS0105830 | GQY_RS0102440 |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | GQY_RS0108870 | |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | GQY_RS0113400 | GQY_RS0114795 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | GQY_RS0108855 | GQY_RS0113410 |
| leucine | natB: L-leucine ABC transporter, substrate-binding component NatB | GQY_RS0112250 | |
| leucine | natC: L-leucine ABC transporter, permease component 1 (NatC) | GQY_RS0112265 | |
| leucine | natD: L-leucine ABC transporter, permease component 2 (NatD) | GQY_RS0112270 | GQY_RS0109650 |
| lysine | davA: 5-aminovaleramidase | GQY_RS0107030 | |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | davD: glutarate semialdehyde dehydrogenase | GQY_RS0100670 | GQY_RS0100430 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | GQY_RS0103120 | |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| mannitol | mak: mannose kinase | GQY_RS0102585 | GQY_RS0102580 |
| mannitol | mt1d: mannitol 1-dehydrogenase | GQY_RS0102000 | |
| mannitol | PLT5: polyol transporter PLT5 | | |
| 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 | GQY_RS0104515 | |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | GQY_RS21145 | |
| myoinositol | mmsA: malonate-semialdehyde dehydrogenase | GQY_RS0100430 | GQY_RS0115170 |
| myoinositol | SMIT1: myo-inositol:Na+ symporter | GQY_RS0105665 | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | GQY_RS0113400 | GQY_RS0114795 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | GQY_RS0109435 | GQY_RS0113400 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | GQY_RS0115395 | GQY_RS0111685 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | GQY_RS0111685 | GQY_RS0115395 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | GQY_RS0113400 | GQY_RS17365 |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | paaF: 2,3-dehydroadipyl-CoA hydratase | GQY_RS0113400 | GQY_RS0114795 |
| phenylalanine | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | GQY_RS0109435 | GQY_RS0113400 |
| phenylalanine | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | GQY_RS0115395 | GQY_RS0111685 |
| phenylalanine | paaJ2: 3-oxoadipyl-CoA thiolase | GQY_RS0111685 | GQY_RS0115395 |
| phenylalanine | paaZ1: oxepin-CoA hydrolase | GQY_RS0113400 | GQY_RS17365 |
| phenylalanine | pad-dh: phenylacetaldehyde dehydrogenase | GQY_RS0100430 | GQY_RS0115170 |
| proline | put1: proline dehydrogenase | GQY_RS0110515 | |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | GQY_RS0108870 | |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | GQY_RS0105110 | GQY_RS0100430 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| pyruvate | actP: large subunit of pyruvate transporter (actP-like) | GQY_RS0114140 | GQY_RS0103320 |
| pyruvate | yjcH: putative small subunit of pyruvate transporter (yjcH-like) | GQY_RS0114145 | |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | GQY_RS0100435 | GQY_RS0116075 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | | |
| rhamnose | LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase | GQY_RS0100435 | GQY_RS0112020 |
| rhamnose | LRA6: 2,4-diketo-3-deoxyrhamnonate hydrolase | GQY_RS0114625 | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsA: D-ribose ABC transporter, ATPase component RbsA | GQY_RS0105970 | GQY_RS0104125 |
| ribose | rbsB: D-ribose ABC transporter, substrate-binding component RbsB | GQY_RS0104115 | |
| serine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | GQY_RS0112250 | |
| serine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | GQY_RS0112270 | GQY_RS0109650 |
| serine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | GQY_RS0112265 | |
| sorbitol | scrK: fructokinase | GQY_RS0109740 | GQY_RS0102585 |
| sorbitol | sdh: sorbitol dehydrogenase | GQY_RS0100435 | GQY_RS0116335 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | GQY_RS0116450 | |
| threonine | adh: acetaldehyde dehydrogenase (not acylating) | GQY_RS0100670 | GQY_RS0105110 |
| threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | GQY_RS0112250 | |
| threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | GQY_RS0112270 | GQY_RS0109650 |
| threonine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | GQY_RS0112265 | |
| thymidine | adh: acetaldehyde dehydrogenase (not acylating) | GQY_RS0100670 | GQY_RS0105110 |
| thymidine | deoB: phosphopentomutase | GQY_RS0108885 | GQY_RS0109755 |
| trehalose | treF: trehalase | GQY_RS0114095 | GQY_RS0113790 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | hmgA: homogentisate dioxygenase | GQY_RS0108385 | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | GQY_RS0106990 | GQY_RS0113400 |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | GQY_RS0105830 | GQY_RS0102440 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | GQY_RS0100430 | GQY_RS0115170 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | | |
| valine | natB: L-valine ABC transporter, substrate-binding component NatB | GQY_RS0112250 | |
| valine | natC: L-valine ABC transporter, permease component 1 (NatC) | GQY_RS0112265 | |
| valine | natD: L-valine ABC transporter, permease component 2 (NatD) | GQY_RS0112270 | GQY_RS0109650 |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | GQY_RS0108870 | |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | | |
| xylose | xylA: xylose isomerase | | |
| xylose | xylB: xylulokinase | GQY_RS17900 | |
| xylose | xylT: D-xylose transporter | GQY_RS0116450 | |
Confidence: high confidence medium confidence low confidence
This GapMind analysis is from Sep 24 2021. 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