Potential Gaps in catabolism of small carbon sources in Marinomonas arctica 328
Found 52 low-confidence and 43 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | Psest_0084: 2-oxoglutarate TRAP transporter, fused 4TM/12TM components | DK187_RS19240 | DK187_RS06330 |
| 2-oxoglutarate | Psest_0085: 2-oxoglutarate TRAP transporter, solute receptor component | DK187_RS12720 | DK187_RS19235 |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| acetate | actP: cation/acetate symporter ActP | DK187_RS13450 | DK187_RS05405 |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | DK187_RS13615 | DK187_RS20495 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | DK187_RS13630 | DK187_RS16320 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | DK187_RS13625 | DK187_RS16320 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | DK187_RS13620 | |
| citrulline | aruG: ornithine/arginine N-succinyltransferase subunit AruAII (AruG) | DK187_RS07635 | DK187_RS07640 |
| citrulline | citrullinase: putative citrullinase | DK187_RS07055 | |
| D-alanine | Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component | DK187_RS03070 | DK187_RS01945 |
| D-alanine | Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component | DK187_RS03055 | DK187_RS01930 |
| D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | | |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| deoxyinosine | bmpA: deoxyinosine ABC transporter, substrate-binding component | DK187_RS16160 | |
| deoxyinosine | deoB: phosphopentomutase | | |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyinosine | deoD: deoxyinosine phosphorylase | | |
| deoxyinosine | nupB: deoxyinosine ABC transporter, permease component 1 | DK187_RS16170 | DK187_RS04040 |
| deoxyinosine | nupC': deoxyinosine ABC transporter, permease component 2 | DK187_RS16175 | DK187_RS04045 |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | DK187_RS15775 | DK187_RS05415 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyribose | deoP: deoxyribose transporter | DK187_RS08940 | DK187_RS15015 |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | DK187_RS10525 | |
| fucose | fucI: L-fucose isomerase FucI | | |
| fucose | fucK: L-fuculose kinase FucK | | |
| galactose | dgoK: 2-dehydro-3-deoxygalactonokinase | DK187_RS11905 | DK187_RS16375 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| gluconate | gntT: gluconate:H+ symporter GntT | DK187_RS10510 | DK187_RS02695 |
| glucosamine | nagK: N-acetylglucosamine kinase | DK187_RS20440 | DK187_RS01540 |
| glucosamine | nagX: transmembrane glucosamine N-acetyltransferase NagX | | |
| glucosamine | SMc02869: N-acetylglucosamine ABC transporter, ATPase component | DK187_RS16415 | DK187_RS02530 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | dctP: D-glucuronate TRAP transporter, solute receptor component | DK187_RS04680 | DK187_RS09270 |
| glucuronate | dctQ: D-glucuronate TRAP transporter, small permease component | | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | DK187_RS15195 | DK187_RS06285 |
| isoleucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | | |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | DK187_RS04985 | DK187_RS12095 |
| isoleucine | livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) | DK187_RS07510 | DK187_RS18835 |
| L-lactate | L-LDH: L-lactate dehydrogenase | DK187_RS04980 | DK187_RS16410 |
| L-lactate | Shew_2731: L-lactate:Na+ symporter, large component | DK187_RS05405 | |
| L-lactate | Shew_2732: L-lactate:Na+ symporter, small component | DK187_RS05400 | |
| L-malate | dctQ: L-malate TRAP tranpsorter, small permease component DctQ | | |
| lactose | dgoK: 2-dehydro-3-deoxygalactonokinase | DK187_RS11905 | DK187_RS16375 |
| lactose | lacP: lactose permease LacP | | |
| leucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | | |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | DK187_RS04985 | DK187_RS12095 |
| leucine | liuA: isovaleryl-CoA dehydrogenase | | |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | DK187_RS09690 | DK187_RS06470 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | DK187_RS04965 | DK187_RS04960 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | | |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| leucine | livH: L-leucine ABC transporter, permease component 1 (LivH/BraD) | DK187_RS07510 | DK187_RS18835 |
| lysine | alr: lysine racemase | DK187_RS19015 | |
| lysine | amaD: D-lysine oxidase | DK187_RS09135 | |
| lysine | hglS: D-2-hydroxyglutarate synthase | | |
| lysine | lysN: 2-aminoadipate transaminase | DK187_RS02410 | DK187_RS06905 |
| mannitol | mt2d: mannitol 2-dehydrogenase | DK187_RS13495 | DK187_RS04655 |
| mannitol | mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE | DK187_RS13515 | |
| mannitol | mtlK: polyol ABC transporter, ATP component MtlK/SmoG | DK187_RS11940 | DK187_RS16415 |
| NAG | nagK: N-acetylglucosamine kinase | DK187_RS20440 | DK187_RS01540 |
| NAG | SMc02869: N-acetylglucosamine ABC transporter, ATPase component | DK187_RS16415 | DK187_RS02530 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylalanine | ARO10: phenylpyruvate decarboxylase | | |
| phenylalanine | livH: L-phenylalanine ABC transporter, permease component 1 (LivH) | DK187_RS07510 | DK187_RS18835 |
| phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | DK187_RS07505 | |
| phenylalanine | pad-dh: phenylacetaldehyde dehydrogenase | DK187_RS01055 | DK187_RS17920 |
| propionate | putP: propionate transporter; proline:Na+ symporter | DK187_RS13450 | |
| putrescine | gabT: gamma-aminobutyrate transaminase | DK187_RS02410 | DK187_RS08575 |
| putrescine | potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) | DK187_RS01040 | |
| putrescine | puuD: gamma-glutamyl-gamma-aminobutyrate hydrolase | | |
| sorbitol | sdh: sorbitol dehydrogenase | DK187_RS09340 | DK187_RS01750 |
| succinate | dctQ: succinate TRAP transporter, small permease component DctQ | | |
| sucrose | ams: sucrose hydrolase (invertase) | DK187_RS03340 | DK187_RS13285 |
| thymidine | deoA: thymidine phosphorylase DeoA | DK187_RS12380 | |
| thymidine | deoB: phosphopentomutase | | |
| thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| 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 | DK187_RS09635 | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | DK187_RS08750 | DK187_RS06285 |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | DK187_RS04960 | |
| valine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | | |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | DK187_RS04985 | DK187_RS12095 |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | DK187_RS04965 | DK187_RS08785 |
| valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | DK187_RS07510 | DK187_RS18835 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | DK187_RS02075 | DK187_RS10550 |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | | |
| xylitol | xdhA: xylitol dehydrogenase | DK187_RS14770 | DK187_RS02445 |
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