Potential Gaps in catabolism of small carbon sources in Marivita geojedonensis DPG-138
Found 52 low-confidence and 73 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | pcaF: succinyl-CoA:acetyl-CoA C-succinyltransferase | MGEO_RS17560 | MGEO_RS09905 |
| 4-hydroxybenzoate | pcaI: 3-oxoadipate CoA-transferase subunit A (PcaI) | MGEO_RS03530 | MGEO_RS07025 |
| 4-hydroxybenzoate | pcaJ: 3-oxoadipate CoA-transferase subunit B (PcaJ) | MGEO_RS03535 | MGEO_RS07035 |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| acetate | ybhL: acetate uptake transporter YbhL | MGEO_RS15610 | |
| alanine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | MGEO_RS14450 | |
| alanine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | MGEO_RS14465 | MGEO_RS19850 |
| alanine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | MGEO_RS14470 | MGEO_RS19845 |
| arabinose | aldA: (glycol)aldehyde dehydrogenase | MGEO_RS15320 | MGEO_RS17260 |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arabinose | KDG-aldolase: 2-dehydro-3-deoxy-L-arabinonate aldolase | | |
| arabinose | xacD: L-arabinonate dehydratase | MGEO_RS17335 | MGEO_RS01140 |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | MGEO_RS13225 | MGEO_RS08670 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | MGEO_RS13235 | MGEO_RS07800 |
| citrulline | arcC: carbamate kinase | | |
| D-alanine | Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component | MGEO_RS16990 | |
| D-alanine | Pf6N2E2_5403: ABC transporter for D-Alanine, permease component 2 | MGEO_RS16995 | |
| D-alanine | Pf6N2E2_5404: ABC transporter for D-Alanine, permease component 1 | MGEO_RS17000 | MGEO_RS07800 |
| D-alanine | Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component | MGEO_RS17005 | MGEO_RS07775 |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | MGEO_RS12170 | MGEO_RS18545 |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribose | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribose | drdehyd-alpha: 2-deoxy-D-ribose dehydrogenase, alpha subunit | MGEO_RS07545 | MGEO_RS03210 |
| deoxyribose | drdehyd-beta: 2-deoxy-D-ribose dehydrogenase, beta subunit | MGEO_RS07550 | MGEO_RS03215 |
| deoxyribose | drdehyd-cytc: 2-deoxyribose-D dehydrogenase, cytochrome c component | MGEO_RS06505 | |
| fucose | aldA: lactaldehyde dehydrogenase | MGEO_RS07470 | MGEO_RS02095 |
| 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 | dgoD: D-galactonate dehydratase | MGEO_RS17335 | MGEO_RS08380 |
| galactose | dgoK: 2-dehydro-3-deoxygalactonokinase | MGEO_RS13955 | MGEO_RS04970 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| 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) | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | MGEO_RS05715 | |
| 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 | MGEO_RS00820 | MGEO_RS04965 |
| glucuronate | garR: tartronate semialdehyde reductase | MGEO_RS14765 | MGEO_RS13885 |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| glycerol | glpF: glycerol facilitator glpF | | |
| histidine | hisM: L-histidine ABC transporter, permease component 1 (HisM) | MGEO_RS13240 | MGEO_RS07795 |
| histidine | hisQ: L-histidine ABC transporter, permease component 2 (HisQ) | MGEO_RS13235 | MGEO_RS07800 |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| isoleucine | natB: L-isoleucine ABC transporter, substrate-binding component NatB | MGEO_RS14450 | |
| isoleucine | natC: L-isoleucine ABC transporter, permease component 1 (NatC) | MGEO_RS14470 | |
| isoleucine | natD: L-isoleucine ABC transporter, permease component 2 (NatD) | MGEO_RS19850 | MGEO_RS14465 |
| L-lactate | Shew_2731: L-lactate:Na+ symporter, large component | MGEO_RS07640 | |
| L-lactate | Shew_2732: L-lactate:Na+ symporter, small component | MGEO_RS07645 | |
| lactose | dgoD: D-galactonate dehydratase | MGEO_RS17335 | MGEO_RS08380 |
| lactose | dgoK: 2-dehydro-3-deoxygalactonokinase | MGEO_RS13955 | MGEO_RS04970 |
| lactose | lacP: lactose permease LacP | | |
| leucine | natB: L-leucine ABC transporter, substrate-binding component NatB | MGEO_RS14450 | |
| leucine | natC: L-leucine ABC transporter, permease component 1 (NatC) | MGEO_RS14470 | |
| leucine | natD: L-leucine ABC transporter, permease component 2 (NatD) | MGEO_RS14465 | MGEO_RS19850 |
| lysine | davA: 5-aminovaleramidase | MGEO_RS06590 | |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | hisM: L-lysine ABC transporter, permease component 1 (HisM) | MGEO_RS13240 | MGEO_RS07795 |
| mannitol | mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE | MGEO_RS02760 | |
| mannitol | mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) | MGEO_RS02755 | |
| mannitol | mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) | MGEO_RS02750 | |
| mannitol | mtlK: polyol ABC transporter, ATP component MtlK/SmoG | MGEO_RS02745 | MGEO_RS13990 |
| mannose | man-isomerase: D-mannose isomerase | | |
| myoinositol | PS417_11890: myo-inositol ABC transporter, ATPase component | MGEO_RS05035 | MGEO_RS06790 |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | MGEO_RS05715 | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | MGEO_RS17480 | MGEO_RS14005 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | MGEO_RS17560 | MGEO_RS09905 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | MGEO_RS17560 | MGEO_RS09905 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | iorAB: phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB | MGEO_RS11165 | |
| phenylalanine | paaF: 2,3-dehydroadipyl-CoA hydratase | MGEO_RS17480 | MGEO_RS14005 |
| phenylalanine | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | MGEO_RS17560 | MGEO_RS09905 |
| phenylalanine | paaJ2: 3-oxoadipyl-CoA thiolase | MGEO_RS17560 | MGEO_RS09905 |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| rhamnose | aldA: lactaldehyde dehydrogenase | MGEO_RS07470 | MGEO_RS02095 |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | MGEO_RS15495 | MGEO_RS02740 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | | |
| rhamnose | LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase | MGEO_RS04965 | MGEO_RS00820 |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsK: ribokinase | MGEO_RS12785 | MGEO_RS04970 |
| serine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | MGEO_RS14450 | |
| serine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | MGEO_RS14465 | MGEO_RS19850 |
| serine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | MGEO_RS14470 | MGEO_RS19845 |
| threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | MGEO_RS14450 | |
| threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | MGEO_RS14465 | MGEO_RS19850 |
| threonine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | MGEO_RS14470 | MGEO_RS19845 |
| threonine | ltaE: L-threonine aldolase | MGEO_RS04160 | MGEO_RS16680 |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| tryptophan | antA: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA | MGEO_RS03460 | |
| tryptophan | antB: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB | MGEO_RS03465 | |
| tryptophan | antC: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC | MGEO_RS03470 | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | catA: catechol 1,2-dioxygenase | MGEO_RS03510 | MGEO_RS02695 |
| tryptophan | catC: muconolactone isomerase | | |
| tryptophan | kynB: kynurenine formamidase | MGEO_RS15860 | |
| tryptophan | pcaF: succinyl-CoA:acetyl-CoA C-succinyltransferase | MGEO_RS17560 | MGEO_RS09905 |
| tryptophan | pcaI: 3-oxoadipate CoA-transferase subunit A (PcaI) | MGEO_RS03530 | MGEO_RS07025 |
| tryptophan | pcaJ: 3-oxoadipate CoA-transferase subunit B (PcaJ) | MGEO_RS03535 | MGEO_RS07035 |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | MGEO_RS05735 | MGEO_RS13880 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | MGEO_RS13860 | MGEO_RS17260 |
| valine | natB: L-valine ABC transporter, substrate-binding component NatB | MGEO_RS14450 | |
| valine | natC: L-valine ABC transporter, permease component 1 (NatC) | MGEO_RS14470 | |
| valine | natD: L-valine ABC transporter, permease component 2 (NatD) | MGEO_RS19850 | MGEO_RS14465 |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | | |
| xylitol | xdhA: xylitol dehydrogenase | MGEO_RS09275 | MGEO_RS02740 |
| xylose | gtsA: xylose ABC transporter, periplasmic substrate-binding component GtsA | MGEO_RS11970 | |
| xylose | gtsB: xylose ABC transporter, permease component 1 GtsB | MGEO_RS11965 | MGEO_RS00455 |
| xylose | gtsC: xylose ABC transporter, permease component 2 GtsC | MGEO_RS11960 | MGEO_RS00450 |
| xylose | xylA: xylose isomerase | | |
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