Potential Gaps in catabolism of small carbon sources in Amycolatopsis halophila YIM 93223
Found 83 low-confidence and 51 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | | |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | AMYHA_RS13135 | |
| acetate | actP: cation/acetate symporter ActP | AMYHA_RS10755 | AMYHA_RS10735 |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arginine | kauB: 4-guanidinobutyraldehyde dehydrogenase | AMYHA_RS12585 | AMYHA_RS25345 |
| arginine | rocE: L-arginine permease | | |
| asparagine | agcS: Probable asparagine:Na+ symporter AgcS | AMYHA_RS00060 | AMYHA_RS21435 |
| aspartate | glt: aspartate:proton symporter Glt | | |
| cellobiose | MFS-glucose: glucose transporter, MFS superfamily | AMYHA_RS07370 | |
| citrate | SLC13A5: citrate:Na+ symporter | AMYHA_RS03490 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | AMYHA_RS03530 | AMYHA_RS22145 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | | |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | AMYHA_RS03535 | AMYHA_RS22135 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
| citrulline | citrullinase: putative citrullinase | AMYHA_RS23910 | |
| D-alanine | cycA: D-alanine:H+ symporter CycA | | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | D-LDH: D-lactate dehydrogenase | AMYHA_RS03205 | AMYHA_RS20260 |
| 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 | AMYHA_RS05915 | AMYHA_RS01605 |
| deoxyinosine | bmpA: deoxyinosine ABC transporter, substrate-binding component | AMYHA_RS00105 | AMYHA_RS12570 |
| deoxyinosine | deoB: phosphopentomutase | AMYHA_RS25290 | AMYHA_RS12605 |
| deoxyinosine | nupB: deoxyinosine ABC transporter, permease component 1 | AMYHA_RS12560 | AMYHA_RS00095 |
| deoxyinosine | nupC': deoxyinosine ABC transporter, permease component 2 | AMYHA_RS12550 | AMYHA_RS00090 |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | AMYHA_RS13075 | AMYHA_RS23710 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| ethanol | etoh-dh-nad: ethanol dehydrogenase (NAD(P)) | AMYHA_RS23285 | AMYHA_RS08910 |
| fucose | aldA: lactaldehyde dehydrogenase | AMYHA_RS12585 | AMYHA_RS25345 |
| 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 | galP: galactose:H+ symporter GalP | | |
| galactose | pgmA: alpha-phosphoglucomutase | AMYHA_RS09340 | AMYHA_RS25290 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | kdgK: 2-keto-3-deoxygluconate kinase | AMYHA_RS23955 | AMYHA_RS03160 |
| galacturonate | uxaA: D-altronate dehydratase | | |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | AMYHA_RS00010 | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | AMYHA_RS00530 | AMYHA_RS01270 |
| glucose | MFS-glucose: glucose transporter, MFS superfamily | AMYHA_RS07370 | |
| 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 | | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | AMYHA_RS22125 | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| glutamate | gluD: L-glutamate ABC transporter, permease component 2 (GluD) | AMYHA_RS18275 | AMYHA_RS03535 |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | AMYHA_RS10210 | AMYHA_RS25230 |
| histidine | hutG': N-formylglutamate amidohydrolase | | |
| histidine | natB: L-histidine ABC transporter, substrate-binding component NatB | AMYHA_RS16235 | |
| histidine | natC: L-histidine ABC transporter, permease component 1 (NatC) | AMYHA_RS16250 | |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | AMYHA_RS07880 | AMYHA_RS03560 |
| isoleucine | natB: L-isoleucine ABC transporter, substrate-binding component NatB | AMYHA_RS16235 | |
| isoleucine | natC: L-isoleucine ABC transporter, permease component 1 (NatC) | | |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | AMYHA_RS25215 | AMYHA_RS19995 |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | AMYHA_RS13255 | |
| lactose | pgmA: alpha-phosphoglucomutase | AMYHA_RS09340 | AMYHA_RS25290 |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | AMYHA_RS07880 | AMYHA_RS03560 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | AMYHA_RS20710 | AMYHA_RS10445 |
| leucine | natB: L-leucine ABC transporter, substrate-binding component NatB | AMYHA_RS16235 | |
| leucine | natC: L-leucine ABC transporter, permease component 1 (NatC) | AMYHA_RS16250 | |
| lysine | davD: glutarate semialdehyde dehydrogenase | AMYHA_RS09755 | AMYHA_RS13095 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | AMYHA_RS12685 | AMYHA_RS16450 |
| lysine | gcdH: glutaryl-CoA dehydrogenase | AMYHA_RS24060 | AMYHA_RS09585 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| maltose | thuK: maltose ABC transporter, ATPase component ThuK | AMYHA_RS07215 | AMYHA_RS24840 |
| mannitol | mtlA: mannitol phosphotransferase system, EII-CBA components | | |
| mannitol | mtlD: mannitol-1-phosphate 5-dehydrogenase | | |
| mannose | manP: mannose PTS system, EII-CBA components | AMYHA_RS23550 | |
| 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 | AMYHA_RS08575 | AMYHA_RS18845 |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | | |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | AMYHA_RS00530 | AMYHA_RS01270 |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | AMYHA_RS20710 | AMYHA_RS06590 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | AMYHA_RS24905 | AMYHA_RS15335 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | paaF: 2,3-dehydroadipyl-CoA hydratase | AMYHA_RS20710 | AMYHA_RS06590 |
| phenylalanine | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | AMYHA_RS24905 | AMYHA_RS15335 |
| phenylalanine | pad-dh: phenylacetaldehyde dehydrogenase | AMYHA_RS13095 | AMYHA_RS08895 |
| phenylalanine | PPDCalpha: phenylpyruvate decarboxylase, alpha subunit | AMYHA_RS07890 | AMYHA_RS03550 |
| proline | put1: proline dehydrogenase | | |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | AMYHA_RS25215 | AMYHA_RS19995 |
| propionate | putP: propionate transporter; proline:Na+ symporter | AMYHA_RS16670 | |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | AMYHA_RS13090 | AMYHA_RS15990 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| pyruvate | actP: large subunit of pyruvate transporter (actP-like) | AMYHA_RS10735 | AMYHA_RS10755 |
| pyruvate | yjcH: putative small subunit of pyruvate transporter (yjcH-like) | AMYHA_RS27390 | |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | AMYHA_RS17065 | AMYHA_RS20665 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | | |
| rhamnose | LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase | AMYHA_RS20665 | AMYHA_RS20020 |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | snatA: L-serine transporter | AMYHA_RS24790 | |
| sorbitol | scrK: fructokinase | AMYHA_RS23955 | AMYHA_RS17900 |
| sorbitol | sdh: sorbitol dehydrogenase | AMYHA_RS20020 | AMYHA_RS13075 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
| sucrose | ams: sucrose hydrolase (invertase) | AMYHA_RS21080 | AMYHA_RS07415 |
| threonine | snatA: L-threonine transporter snatA | AMYHA_RS24790 | |
| thymidine | deoB: phosphopentomutase | AMYHA_RS25290 | AMYHA_RS12605 |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | aglF: trehalose ABC transporter, permease component 1 (AglF) | AMYHA_RS24830 | |
| trehalose | aglG: trehalose ABC transporter, permease component 2 (AglG) | AMYHA_RS24825 | AMYHA_RS07420 |
| trehalose | aglK: trehalose ABC trehalose, ATPase component AglK | AMYHA_RS07215 | AMYHA_RS24840 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | | |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | AMYHA_RS07880 | AMYHA_RS03560 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | AMYHA_RS14120 | AMYHA_RS20335 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | AMYHA_RS19775 | AMYHA_RS17060 |
| valine | natB: L-valine ABC transporter, substrate-binding component NatB | AMYHA_RS16235 | |
| valine | natC: L-valine ABC transporter, permease component 1 (NatC) | | |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | AMYHA_RS25215 | AMYHA_RS19995 |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | AMYHA_RS23550 | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | | |
| xylose | xylF: ABC transporter for xylose, substrate binding component xylF | AMYHA_RS17870 | |
| xylose | xylH: ABC transporter for xylose, permease component xylH | AMYHA_RS17860 | AMYHA_RS08565 |
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