Potential Gaps in catabolism of small carbon sources in Ruegeria conchae TW15
Found 48 low-confidence and 58 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | G7G_RS0111655 | G7G_RS0121215 |
| 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 | | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arabinose | xacB: L-arabinose 1-dehydrogenase | G7G_RS0111310 | G7G_RS0100395 |
| arabinose | xacE: 2-dehydro-3-deoxy-L-arabinonate dehydratase | | |
| arginine | bgtB: L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) | G7G_RS0111055 | G7G_RS0111530 |
| cellobiose | glk: glucokinase | G7G_RS23700 | G7G_RS0115580 |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | G7G_RS0105150 | G7G_RS0111050 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | G7G_RS0111530 | G7G_RS0105135 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | G7G_RS0111530 | G7G_RS0105140 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | G7G_RS0105145 | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-alanine | Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component | G7G_RS0100225 | |
| D-alanine | Pf6N2E2_5403: ABC transporter for D-Alanine, permease component 2 | G7G_RS0100230 | |
| D-alanine | Pf6N2E2_5404: ABC transporter for D-Alanine, permease component 1 | G7G_RS0100235 | G7G_RS0111520 |
| D-alanine | Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component | G7G_RS0100240 | G7G_RS0111050 |
| 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 | G7G_RS0112915 | G7G_RS0102515 |
| deoxyinosine | bmpA: deoxyinosine ABC transporter, substrate-binding component | G7G_RS0118045 | |
| deoxyinosine | nupB: deoxyinosine ABC transporter, permease component 1 | G7G_RS0118035 | G7G_RS0100975 |
| deoxyinosine | nupC': deoxyinosine ABC transporter, permease component 2 | G7G_RS0100980 | G7G_RS0118030 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | garK: glycerate 2-kinase | G7G_RS0102040 | G7G_RS0113065 |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | G7G_RS0108590 | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fucose | fucD: L-fuconate dehydratase | G7G_RS0110525 | |
| galactose | dgoD: D-galactonate dehydratase | G7G_RS0111305 | G7G_RS0100630 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | G7G_RS0109625 | |
| gluconate | gntK: D-gluconate kinase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | nagX: transmembrane glucosamine N-acetyltransferase NagX | | |
| glucose | glk: glucokinase | G7G_RS23700 | G7G_RS0115580 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | garK: glycerate 2-kinase | G7G_RS0102040 | G7G_RS0113065 |
| glucuronate | garL: 5-dehydro-4-deoxy-D-glucarate aldolase | G7G_RS0111660 | G7G_RS0100625 |
| glucuronate | garR: tartronate semialdehyde reductase | G7G_RS0109980 | G7G_RS0100580 |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | G7G_RS0106030 | |
| histidine | aapJ: L-histidine ABC transporter, substrate-binding component AapJ | G7G_RS0100225 | |
| histidine | aapM: L-histidine ABC transporter, permease component 2 (AapM) | G7G_RS0100235 | |
| histidine | aapP: L-histidine ABC transporter, ATPase component AapP | G7G_RS0100240 | G7G_RS0111050 |
| histidine | aapQ: L-histidine ABC transporter, permease component 1 (AapQ) | G7G_RS0100230 | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | G7G_RS0106645 | G7G_RS0117695 |
| isoleucine | livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) | G7G_RS0101020 | G7G_RS0115340 |
| isoleucine | livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | | |
| isoleucine | livM: L-isoleucine ABC transporter, permease component 2 (LivM/BraE) | G7G_RS0107135 | G7G_RS0118395 |
| L-lactate | Shew_2731: L-lactate:Na+ symporter, large component | G7G_RS0105940 | |
| L-lactate | Shew_2732: L-lactate:Na+ symporter, small component | G7G_RS0105945 | |
| lactose | dgoD: D-galactonate dehydratase | G7G_RS0111305 | G7G_RS0100630 |
| lactose | glk: glucokinase | G7G_RS23700 | G7G_RS0115580 |
| lactose | lacP: lactose permease LacP | | |
| leucine | livH: L-leucine ABC transporter, permease component 1 (LivH/BraD) | G7G_RS0101020 | G7G_RS0115340 |
| leucine | livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | | |
| leucine | livM: L-leucine ABC transporter, permease component 2 (LivM/BraE) | G7G_RS0107135 | G7G_RS0118395 |
| lysine | bgtB: L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) | G7G_RS0111055 | G7G_RS0111530 |
| lysine | hglS: D-2-hydroxyglutarate synthase | | |
| lysine | lysN: 2-aminoadipate transaminase | G7G_RS0104975 | G7G_RS0101615 |
| lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | G7G_RS0112035 | G7G_RS0120340 |
| maltose | glk: glucokinase | G7G_RS23700 | G7G_RS0115580 |
| mannitol | mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE | G7G_RS0120410 | |
| mannitol | mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) | G7G_RS0120415 | G7G_RS0115485 |
| mannitol | mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) | G7G_RS0120420 | G7G_RS0115540 |
| mannitol | mtlK: polyol ABC transporter, ATP component MtlK/SmoG | G7G_RS0120425 | G7G_RS0115470 |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | G7G_RS0116465 | G7G_RS0122460 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylalanine | livH: L-phenylalanine ABC transporter, permease component 1 (LivH) | G7G_RS0101020 | G7G_RS0115340 |
| phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | | |
| phenylalanine | livM: L-phenylalanine ABC transporter, permease component 2 (LivM) | G7G_RS0118395 | G7G_RS0115345 |
| phenylalanine | paaF: 2,3-dehydroadipyl-CoA hydratase | G7G_RS0116465 | G7G_RS0122460 |
| proline | natB: proline ABC transporter, substrate-binding component NatB | G7G_RS0107425 | |
| proline | natC: proline ABC transporter, permease component 1 (NatC) | | |
| proline | natD: proline ABC transporter, permease component 2 (NatD) | G7G_RS0107445 | G7G_RS0107140 |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| rhamnose | aldA: lactaldehyde dehydrogenase | G7G_RS0116915 | G7G_RS0121155 |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | G7G_RS0115690 | G7G_RS0100585 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | G7G_RS0110525 | G7G_RS0100610 |
| rhamnose | LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase | G7G_RS0111660 | G7G_RS0100625 |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| serine | snatA: L-serine transporter | G7G_RS0106075 | G7G_RS0105385 |
| threonine | ltaE: L-threonine aldolase | G7G_RS0112510 | G7G_RS0111845 |
| threonine | snatA: L-threonine transporter snatA | G7G_RS0106075 | G7G_RS0105385 |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | glk: glucokinase | G7G_RS23700 | G7G_RS0115580 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | mhpD: 2-hydroxypentadienoate hydratase | G7G_RS0111655 | G7G_RS0121215 |
| tryptophan | nbaD: 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase | | |
| tryptophan | nbaE: 2-aminomuconate 6-semialdehyde dehydrogenase | G7G_RS0111640 | G7G_RS0120200 |
| tryptophan | nbaF: 2-aminomuconate deaminase | G7G_RS0109455 | G7G_RS0100965 |
| tryptophan | nbaG: 2-oxo-3-hexenedioate decarboxylase | G7G_RS0121215 | G7G_RS0111655 |
| tryptophan | sibC: L-kynurenine 3-monooxygenase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | G7G_RS0117695 | G7G_RS0106645 |
| valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | G7G_RS0101020 | G7G_RS0115340 |
| valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | | |
| valine | livM: L-valine ABC transporter, permease component 2 (LivM/BraE) | G7G_RS0107135 | G7G_RS0118395 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | G7G_RS0106675 | G7G_RS0111640 |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | | |
| xylitol | xdhA: xylitol dehydrogenase | G7G_RS0116430 | G7G_RS0120430 |
| xylose | xylF: ABC transporter for xylose, substrate binding component xylF | G7G_RS0115585 | |
| xylose | xylG: ABC transporter for xylose, ATP-binding component xylG | G7G_RS0100415 | G7G_RS0100435 |
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