Potential Gaps in catabolism of small carbon sources in Collimonas arenae Ter10
Found 73 low-confidence and 39 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | pcaC: 4-carboxymuconolactone decarboxylase | CAter10_RS02675 | CAter10_RS13665 |
| 4-hydroxybenzoate | pcaD: 3-oxoadipate enol-lactone hydrolase | CAter10_RS02675 | |
| 4-hydroxybenzoate | pcaH: protocatechuate 3,4-dioxygenase, alpha subunit | CAter10_RS02685 | CAter10_RS02690 |
| 4-hydroxybenzoate | pcaI: 3-oxoadipate CoA-transferase subunit A (PcaI) | CAter10_RS13190 | |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | CAter10_RS05575 | |
| 4-hydroxybenzoate | pobA: 4-hydroxybenzoate 3-monooxygenase | | |
| acetate | dctA: organic acid/proton symporter DctA | CAter10_RS14230 | CAter10_RS06405 |
| alanine | TRIC: TRIC-type L-alanine transporter | CAter10_RS01105 | CAter10_RS05730 |
| arabinose | gguA: L-arabinose ABC transporter, ATPase component GguA | CAter10_RS14380 | CAter10_RS05910 |
| arabinose | xacD: L-arabinonate dehydratase | CAter10_RS12895 | CAter10_RS19065 |
| arginine | rocD: ornithine aminotransferase | CAter10_RS21330 | CAter10_RS16755 |
| arginine | rocE: L-arginine permease | | |
| arginine | rocF: arginase | CAter10_RS21275 | |
| cellobiose | bgl: cellobiase | | |
| cellobiose | glk: glucokinase | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | CAter10_RS00185 | CAter10_RS07860 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | CAter10_RS14915 | CAter10_RS00190 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | CAter10_RS14915 | CAter10_RS00190 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | CAter10_RS04100 | CAter10_RS04105 |
| citrulline | arcC: carbamate kinase | | |
| citrulline | rocD: ornithine aminotransferase | CAter10_RS21330 | CAter10_RS16755 |
| D-alanine | cycA: D-alanine:H+ symporter CycA | | |
| D-lactate | D-LDH: D-lactate dehydrogenase | CAter10_RS06950 | CAter10_RS18180 |
| D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | | |
| D-serine | dsdA: D-serine ammonia-lyase | CAter10_RS13305 | CAter10_RS02845 |
| D-serine | dsdX: D-serine transporter DsdX | CAter10_RS14930 | |
| deoxyinosine | deoB: phosphopentomutase | | |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyinosine | deoD: deoxyinosine phosphorylase | | |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | CAter10_RS05885 | CAter10_RS01150 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | CAter10_RS13675 | CAter10_RS16495 |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fructose | scrK: fructokinase | CAter10_RS14955 | CAter10_RS19685 |
| galacturonate | uxuL: D-galactaro-1,5-lactonase (UxuL or UxuF) | CAter10_RS19125 | CAter10_RS14775 |
| glucosamine | nagK: N-acetylglucosamine kinase | CAter10_RS08450 | |
| glucosamine | nagX: transmembrane glucosamine N-acetyltransferase NagX | | |
| glucosamine | SMc02869: N-acetylglucosamine ABC transporter, ATPase component | CAter10_RS15810 | CAter10_RS08455 |
| glucose | glk: glucokinase | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | uxuL: D-glucaro-1,5-lactonase UxuL or UxuF | CAter10_RS19125 | CAter10_RS14775 |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | | |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| lactose | glk: glucokinase | | |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | | |
| lysine | hglS: D-2-hydroxyglutarate synthase | | |
| lysine | lysN: 2-aminoadipate transaminase | CAter10_RS21330 | CAter10_RS08670 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| maltose | glk: glucokinase | | |
| maltose | susB: alpha-glucosidase (maltase) | | |
| mannitol | mt2d: mannitol 2-dehydrogenase | CAter10_RS15815 | CAter10_RS10730 |
| mannitol | mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE | CAter10_RS15790 | |
| mannitol | mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) | CAter10_RS15795 | |
| mannitol | mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) | CAter10_RS15800 | CAter10_RS08460 |
| mannitol | mtlK: polyol ABC transporter, ATP component MtlK/SmoG | CAter10_RS08455 | CAter10_RS15810 |
| mannitol | scrK: fructokinase | CAter10_RS14955 | CAter10_RS19685 |
| mannose | scrK: fructokinase | CAter10_RS14955 | CAter10_RS19685 |
| myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | | |
| myoinositol | iolD: 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase | | |
| NAG | nagK: N-acetylglucosamine kinase | CAter10_RS08450 | |
| NAG | SMc02869: N-acetylglucosamine ABC transporter, ATPase component | CAter10_RS15810 | CAter10_RS08455 |
| phenylacetate | paaA: phenylacetyl-CoA 1,2-epoxidase, subunit A | | |
| phenylacetate | paaB: phenylacetyl-CoA 1,2-epoxidase, subunit B | | |
| phenylacetate | paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C | | |
| phenylacetate | paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E | | |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | CAter10_RS02370 | CAter10_RS03130 |
| phenylacetate | paaH: 3-hydroxyadipyl-CoA dehydrogenase | CAter10_RS06160 | CAter10_RS15290 |
| phenylacetate | paaK: phenylacetate-CoA ligase | CAter10_RS19070 | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | CAter10_RS02370 | CAter10_RS03130 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | | |
| proline | HSERO_RS00900: proline ABC transporter, ATPase component 2 | CAter10_RS06900 | CAter10_RS12275 |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | CAter10_RS16195 | CAter10_RS00210 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | CAter10_RS21305 | CAter10_RS08205 |
| putrescine | potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) | CAter10_RS02965 | |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | CAter10_RS16300 | CAter10_RS07600 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | CAter10_RS16170 | CAter10_RS19065 |
| rhamnose | LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase | CAter10_RS10670 | CAter10_RS05885 |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| serine | Ac3H11_1692: L-tyrosine ABC transporter, ATPase component 2 | CAter10_RS06900 | CAter10_RS12275 |
| sorbitol | scrK: fructokinase | CAter10_RS14955 | CAter10_RS19685 |
| sorbitol | sdh: sorbitol dehydrogenase | CAter10_RS14240 | CAter10_RS15815 |
| sucrose | ams: sucrose hydrolase (invertase) | | |
| sucrose | glk: glucokinase | | |
| threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | CAter10_RS04195 | CAter10_RS04200 |
| threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | CAter10_RS15145 | CAter10_RS06915 |
| threonine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | CAter10_RS15140 | CAter10_RS12280 |
| threonine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | CAter10_RS06905 | CAter10_RS12280 |
| threonine | ltaE: L-threonine aldolase | CAter10_RS15940 | |
| thymidine | deoB: phosphopentomutase | | |
| thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | glk: glucokinase | | |
| trehalose | treF: trehalase | CAter10_RS12685 | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | Ac3H11_1692: L-tyrosine ABC transporter, ATPase component 2 | CAter10_RS06900 | CAter10_RS12275 |
| valine | acdH: isobutyryl-CoA dehydrogenase | CAter10_RS02405 | CAter10_RS15295 |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | CAter10_RS03130 | |
| valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | CAter10_RS15145 | CAter10_RS06915 |
| valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | CAter10_RS04195 | CAter10_RS04200 |
| valine | livM: L-valine ABC transporter, permease component 2 (LivM/BraE) | CAter10_RS15140 | CAter10_RS06910 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | CAter10_RS07655 | CAter10_RS16480 |
| xylitol | PS417_12055: xylitol ABC transporter, substrate-binding component | | |
| xylitol | PS417_12065: xylitol ABC transporter, ATPase component | CAter10_RS12710 | CAter10_RS05910 |
| xylitol | xdhA: xylitol dehydrogenase | CAter10_RS05885 | CAter10_RS18200 |
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