Potential Gaps in catabolism of small carbon sources in Amphritea japonica JAMM 1866
Found 107 low-confidence and 31 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | ligA: protocatechuate 4,5-dioxygenase, alpha subunit | G329_RS0107615 | |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| acetate | actP: cation/acetate symporter ActP | G329_RS0115840 | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arginine | astE: succinylglutamate desuccinylase | | |
| aspartate | bgtA: aspartate ABC transporter, ATPase component BgtA | G329_RS0114595 | G329_RS0106215 |
| aspartate | bgtB': aspartate ABC transporter, permease component 1 (BgtB) | G329_RS0114585 | |
| aspartate | natF: aspartate ABC transporter, substrate-binding component NatF | G329_RS0114580 | |
| aspartate | natH: aspartate ABC transporter, permease component 2 (NatH) | G329_RS0114590 | G329_RS0106200 |
| cellobiose | bgl: cellobiase | | |
| cellobiose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | G329_RS0106215 | G329_RS0114595 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | G329_RS0106200 | |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | G329_RS0106205 | G329_RS0106200 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | G329_RS0106210 | |
| citrulline | arcC: carbamate kinase | | |
| citrulline | odc: L-ornithine decarboxylase | G329_RS0103955 | |
| citrulline | patD: gamma-aminobutyraldehyde dehydrogenase | G329_RS0103095 | G329_RS0101520 |
| D-alanine | Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component | G329_RS0114595 | G329_RS0106215 |
| D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | | |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| deoxyinosine | deoB: phosphopentomutase | | |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | | |
| 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 | 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 | G329_RS0101520 | G329_RS0103095 |
| 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 | | |
| fucose | fucU: L-fucose mutarotase FucU | | |
| galactose | galK: galactokinase (-1-phosphate forming) | | |
| galactose | galP: galactose:H+ symporter GalP | | |
| galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | gci: D-galactarolactone cycloisomerase | | |
| galacturonate | gli: D-galactarolactone isomerase | | |
| galacturonate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | G329_RS0108985 | |
| galacturonate | udh: D-galacturonate dehydrogenase | G329_RS0110080 | |
| 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) | G329_RS0107015 | |
| 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 | gci: D-glucaro-1,4-lactone cycloisomerase | | |
| glucuronate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | G329_RS0108985 | |
| glucuronate | udh: D-glucuronate dehydrogenase | G329_RS0110080 | |
| glutamate | aapJ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ | G329_RS0114580 | |
| glutamate | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | G329_RS0114590 | |
| glutamate | aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP | G329_RS0114595 | G329_RS0106215 |
| glutamate | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | G329_RS0114585 | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | | |
| glycerol | glpF: glycerol facilitator glpF | | |
| glycerol | glpK: glycerol kinase | G329_RS0103455 | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| L-lactate | lutC: L-lactate dehydrogenase, LutC subunit | G329_RS0100560 | |
| L-lactate | Shew_2731: L-lactate:Na+ symporter, large component | G329_RS0115840 | |
| lactose | galK: galactokinase (-1-phosphate forming) | | |
| lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| lactose | glk: glucokinase | | |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | | |
| lysine | davA: 5-aminovaleramidase | | |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | davT: 5-aminovalerate aminotransferase | G329_RS0106030 | G329_RS0100460 |
| 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 | G329_RS0110150 | |
| 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 | G329_RS0105535 | |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | G329_RS0107015 | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| propionate | putP: propionate transporter; proline:Na+ symporter | G329_RS0107920 | |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | G329_RS0103095 | G329_RS0101520 |
| pyruvate | dctQ: pyruvate TRAP transporter, small permease component | G329_RS0103015 | G329_RS0107070 |
| rhamnose | aldA: lactaldehyde dehydrogenase | G329_RS0101520 | G329_RS0103095 |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | G329_RS0109870 | G329_RS0110535 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | | |
| rhamnose | LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase | G329_RS0103850 | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsK: ribokinase | | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | G329_RS0113800 | G329_RS0102015 |
| serine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | G329_RS0113790 | G329_RS0103635 |
| sorbitol | mtlA: PTS system for polyols, EII-CBA components | | |
| sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | G329_RS0105920 | G329_RS0109870 |
| sucrose | scrK: fructokinase | | |
| sucrose | SUS: sucrose synthase | | |
| sucrose | sut: sucrose:proton symporter SUT/SUC | | |
| threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | G329_RS0113800 | G329_RS0102015 |
| threonine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | G329_RS0113790 | G329_RS0103635 |
| threonine | ltaE: L-threonine aldolase | G329_RS0101635 | G329_RS0105245 |
| thymidine | deoB: phosphopentomutase | | |
| thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
| trehalose | treF: trehalase | | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | G329_RS0105925 | G329_RS0108885 |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | G329_RS0103745 | G329_RS0102710 |
| 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 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