Potential Gaps in catabolism of small carbon sources in Chryseobacterium angstadtii KM
Found 95 low-confidence and 47 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | | |
| 4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | | |
| 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 | cycA: L-alanine symporter CycA | ACM46_RS20800 | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arginine | rocE: L-arginine permease | ACM46_RS20800 | |
| arginine | rocF: arginase | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | ACM46_RS06830 | ACM46_RS09635 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | | |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | | |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
| D-alanine | cycA: D-alanine:H+ symporter CycA | ACM46_RS20800 | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | D-LDH: D-lactate dehydrogenase | ACM46_RS04955 | ACM46_RS14515 |
| D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | | |
| D-serine | cycA: D-serine:H+ symporter CycA | ACM46_RS20800 | |
| D-serine | dsdA: D-serine ammonia-lyase | ACM46_RS17595 | |
| deoxyinosine | deoB: phosphopentomutase | ACM46_RS12570 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | ACM46_RS03525 | ACM46_RS02755 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | garK: glycerate 2-kinase | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoK: deoxyribokinase | ACM46_RS06915 | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fructose | fruP: fructose porter FruP | ACM46_RS00050 | ACM46_RS17930 |
| fructose | scrK: fructokinase | ACM46_RS18140 | ACM46_RS06915 |
| fucose | aldA: lactaldehyde dehydrogenase | ACM46_RS05760 | ACM46_RS19960 |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | | |
| fucose | fucI: L-fucose isomerase FucI | | |
| fucose | fucK: L-fuculose kinase FucK | | |
| fucose | fucP: L-fucose:H+ symporter FucP | ACM46_RS17930 | |
| fucose | fucU: L-fucose mutarotase FucU | | |
| galactose | galK: galactokinase (-1-phosphate forming) | ACM46_RS05580 | |
| galacturonate | eda: 2-keto-3-deoxygluconate 6-phosphate aldolase | | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | kdgK: 2-keto-3-deoxygluconate kinase | | |
| galacturonate | uxaA: D-altronate dehydratase | | |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | | |
| gluconate | gntK: D-gluconate kinase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| 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 | ACM46_RS05760 | ACM46_RS19960 |
| 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 | | |
| glutamate | gltP: L-glutamate:cation symporter GltP/GltT | ACM46_RS11445 | ACM46_RS14650 |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | ACM46_RS01020 | |
| histidine | permease: L-histidine permease | ACM46_RS20800 | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | ACM46_RS17335 | ACM46_RS12875 |
| isoleucine | Bap2: L-isoleucine permease Bap2 | ACM46_RS20800 | |
| isoleucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | ACM46_RS15815 | ACM46_RS17390 |
| isoleucine | bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit | ACM46_RS07330 | ACM46_RS17390 |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | ACM46_RS12205 | ACM46_RS15820 |
| isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | ACM46_RS04995 | ACM46_RS00315 |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | ACM46_RS03525 | ACM46_RS21200 |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | ACM46_RS19135 | |
| L-lactate | lctO: L-lactate oxidase or 2-monooxygenase | | |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| lactose | galK: galactokinase (-1-phosphate forming) | ACM46_RS05580 | |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | ACM46_RS00870 | ACM46_RS05590 |
| leucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | ACM46_RS15815 | ACM46_RS17390 |
| leucine | bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit | ACM46_RS07330 | ACM46_RS17390 |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | ACM46_RS12205 | ACM46_RS15820 |
| leucine | leuT: L-leucine:Na+ symporter LeuT | | |
| leucine | liuA: isovaleryl-CoA dehydrogenase | ACM46_RS17335 | ACM46_RS12875 |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | ACM46_RS19135 | |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | ACM46_RS04995 | ACM46_RS00325 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | ACM46_RS22070 | |
| lysine | hglS: D-2-hydroxyglutarate synthase | | |
| lysine | lysN: 2-aminoadipate transaminase | ACM46_RS15480 | ACM46_RS19150 |
| lysine | lysP: L-lysine:H+ symporter LysP | ACM46_RS20800 | |
| lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | | |
| mannitol | PLT5: polyol transporter PLT5 | | |
| mannitol | scrK: fructokinase | ACM46_RS18140 | ACM46_RS06915 |
| mannose | gluP: mannose:Na+ symporter | ACM46_RS17930 | ACM46_RS00050 |
| mannose | manA: mannose-6-phosphate isomerase | ACM46_RS03800 | ACM46_RS03360 |
| 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 | | |
| myoinositol | iolT: myo-inositol:H+ symporter | ACM46_RS12000 | |
| myoinositol | mmsA: malonate-semialdehyde dehydrogenase | ACM46_RS05760 | ACM46_RS19960 |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagP: N-acetylglucosamine transporter NagP | | |
| phenylacetate | H281DRAFT_04042: phenylacetate:H+ symporter | ACM46_RS20800 | |
| phenylacetate | paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C | ACM46_RS00345 | |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | ACM46_RS04995 | ACM46_RS00325 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | ACM46_RS00325 | ACM46_RS04995 |
| phenylalanine | ARO10: phenylpyruvate decarboxylase | | |
| phenylalanine | paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C | ACM46_RS00345 | |
| phenylalanine | paaF: 2,3-dehydroadipyl-CoA hydratase | ACM46_RS04995 | ACM46_RS00325 |
| phenylalanine | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | ACM46_RS00325 | ACM46_RS04995 |
| phenylalanine | pad-dh: phenylacetaldehyde dehydrogenase | ACM46_RS12150 | ACM46_RS05760 |
| proline | proY: proline:H+ symporter | ACM46_RS20800 | |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | ACM46_RS19135 | |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | gabT: gamma-aminobutyrate transaminase | ACM46_RS16210 | ACM46_RS14005 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | ACM46_RS07295 | ACM46_RS19150 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | ACM46_RS05760 | ACM46_RS19960 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| pyruvate | ybdD: small subunit of pyruvate transporter (YbdD) | | |
| rhamnose | aldA: lactaldehyde dehydrogenase | ACM46_RS05760 | ACM46_RS19960 |
| rhamnose | rhaA: L-rhamnose isomerase | | |
| rhamnose | rhaB: L-rhamnulokinase | | |
| rhamnose | rhaD: rhamnulose 1-phosphate aldolase | | |
| rhamnose | rhaM: L-rhamnose mutarotase | | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsK: ribokinase | ACM46_RS06915 | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | serP: L-serine permease SerP | ACM46_RS20800 | |
| sorbitol | scrK: fructokinase | ACM46_RS18140 | ACM46_RS06915 |
| sorbitol | sdh: sorbitol dehydrogenase | ACM46_RS18155 | ACM46_RS03525 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | ACM46_RS12000 | |
| sucrose | ams: sucrose hydrolase (invertase) | | |
| threonine | RR42_RS28305: L-threonine:H+ symporter | ACM46_RS20800 | |
| thymidine | deoA: thymidine phosphorylase DeoA | ACM46_RS15635 | |
| thymidine | deoB: phosphopentomutase | ACM46_RS12570 | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | ACM46_RS17335 | ACM46_RS12875 |
| valine | Bap2: L-valine permease Bap2 | ACM46_RS20800 | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | ACM46_RS00325 | |
| valine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | ACM46_RS15815 | ACM46_RS17390 |
| valine | bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit | ACM46_RS07330 | ACM46_RS17390 |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | ACM46_RS12205 | ACM46_RS15820 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | ACM46_RS05760 | ACM46_RS19960 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | ACM46_RS16400 | |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | ACM46_RS19135 | |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | | |
| xylose | xylA: xylose isomerase | | |
| xylose | xylB: xylulokinase | | |
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