Potential Gaps in catabolism of small carbon sources in Nocardiopsis baichengensis YIM 90130
Found 49 low-confidence and 70 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| arginine | arcC: carbamate kinase | | |
| arginine | rocE: L-arginine permease | C892_RS0102390 | |
| citrate | tctB: citrate/Na+ symporter, small transmembrane component TctB | | |
| citrate | tctC: citrate/Na+ symporter, substrate-binding component TctC | C892_RS0118780 | C892_RS0118765 |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | C892_RS0107840 | C892_RS0116870 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | C892_RS0116860 | C892_RS0107845 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | C892_RS0107845 | C892_RS0116865 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
| citrulline | arcC: carbamate kinase | | |
| D-alanine | cycA: D-alanine:H+ symporter CycA | C892_RS0102390 | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | glcE: D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) | C892_RS0109980 | |
| D-serine | cycA: D-serine:H+ symporter CycA | C892_RS0102390 | |
| D-serine | dsdA: D-serine ammonia-lyase | C892_RS0100740 | C892_RS0113825 |
| deoxyinosine | deoB: phosphopentomutase | C892_RS0112215 | C892_RS0116540 |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | C892_RS0120830 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | C892_RS0125545 | C892_RS0120415 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | C892_RS0109425 | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fructose | 1pfk: 1-phosphofructokinase | C892_RS0105745 | |
| fructose | fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components | C892_RS0105735 | |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | | |
| fucose | fucI: L-fucose isomerase FucI | | |
| fucose | fucK: L-fuculose kinase FucK | C892_RS0122410 | |
| fucose | fucP: L-fucose:H+ symporter FucP | | |
| fucose | fucU: L-fucose mutarotase FucU | | |
| galactose | pgmA: alpha-phosphoglucomutase | C892_RS0123815 | C892_RS0112215 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | gci: D-galactarolactone cycloisomerase | C892_RS0101000 | |
| galacturonate | gli: D-galactarolactone isomerase | | |
| galacturonate | udh: D-galacturonate dehydrogenase | C892_RS0122295 | C892_RS0122505 |
| gluconate | gntT: gluconate:H+ symporter GntT | C892_RS0127095 | C892_RS0112715 |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | C892_RS0123945 | C892_RS0116550 |
| glucosamine | nagX: transmembrane glucosamine N-acetyltransferase NagX | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | C892_RS0101000 | |
| glucuronate | udh: D-glucuronate dehydrogenase | C892_RS0122295 | C892_RS0122505 |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | C892_RS0116650 | C892_RS0120455 |
| histidine | hutG': N-formylglutamate amidohydrolase | | |
| histidine | PA5503: L-histidine ABC transporter, ATPase component | C892_RS0116870 | C892_RS0109025 |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | C892_RS0109115 | C892_RS0105110 |
| isoleucine | lpd: branched-chain alpha-ketoacid dehydrogenase, E3 component | C892_RS0123470 | C892_RS0114110 |
| isoleucine | natB: L-isoleucine ABC transporter, substrate-binding component NatB | C892_RS0115140 | |
| isoleucine | natC: L-isoleucine ABC transporter, permease component 1 (NatC) | C892_RS0115125 | |
| isoleucine | natD: L-isoleucine ABC transporter, permease component 2 (NatD) | C892_RS0115120 | C892_RS0104280 |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | C892_RS0123485 | C892_RS0127295 |
| L-lactate | lutC: L-lactate dehydrogenase, LutC subunit | | |
| lactose | lacP: lactose permease LacP | | |
| lactose | pgmA: alpha-phosphoglucomutase | C892_RS0123815 | C892_RS0112215 |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | C892_RS0109115 | C892_RS0105110 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | C892_RS0126825 | C892_RS0119610 |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| leucine | lpd: branched-chain alpha-ketoacid dehydrogenase, E3 component | C892_RS0123470 | C892_RS0114110 |
| leucine | natB: L-leucine ABC transporter, substrate-binding component NatB | C892_RS0115140 | |
| leucine | natC: L-leucine ABC transporter, permease component 1 (NatC) | C892_RS0115125 | |
| leucine | natD: L-leucine ABC transporter, permease component 2 (NatD) | C892_RS0115120 | C892_RS0104280 |
| lysine | davD: glutarate semialdehyde dehydrogenase | C892_RS0121440 | C892_RS0126085 |
| lysine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | C892_RS0126825 | C892_RS0118260 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | C892_RS0114505 | C892_RS0124750 |
| lysine | lysP: L-lysine:H+ symporter LysP | C892_RS0102390 | |
| mannitol | mt2d: mannitol 2-dehydrogenase | C892_RS0103360 | C892_RS0113775 |
| mannitol | PLT5: polyol transporter PLT5 | | |
| mannitol | scrK: fructokinase | C892_RS0103380 | C892_RS0103820 |
| mannose | manP: mannose PTS system, EII-CBA components | C892_RS0105735 | |
| myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | C892_RS0103810 | |
| myoinositol | iolE: scyllo-inosose 2-dehydratase | C892_RS0103800 | |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | C892_RS0103825 | C892_RS0117125 |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | C892_RS0103820 | C892_RS0106910 |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | C892_RS0123945 | C892_RS0116550 |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | C892_RS0126825 | C892_RS0127505 |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | C892_RS0103760 | C892_RS0127505 |
| phenylacetate | ppa: phenylacetate permease ppa | C892_RS0105785 | C892_RS0126505 |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | C892_RS0102390 | |
| phenylalanine | paaF: 2,3-dehydroadipyl-CoA hydratase | C892_RS0126825 | C892_RS0127505 |
| phenylalanine | paaZ1: oxepin-CoA hydrolase | C892_RS0103760 | C892_RS0127505 |
| phenylalanine | pad-dh: phenylacetaldehyde dehydrogenase | C892_RS0112195 | C892_RS0105230 |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | C892_RS0123485 | C892_RS0127295 |
| putrescine | gabT: gamma-aminobutyrate transaminase | C892_RS0121435 | C892_RS0108730 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | C892_RS0108730 | C892_RS0108700 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| rhamnose | rhaB: L-rhamnulokinase | C892_RS0122410 | |
| rhamnose | rhaM: L-rhamnose mutarotase | C892_RS0122395 | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | C892_RS0115140 | |
| serine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | C892_RS0115120 | C892_RS0104280 |
| serine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | C892_RS0115125 | C892_RS0110670 |
| sorbitol | mtlF: ABC transporter for polyols MtlEFGK, permease component MtlF | C892_RS0103370 | C892_RS0109005 |
| sorbitol | mtlK: ABC transporter for polyols MtlEFGK, permease component MtlK | C892_RS0124950 | C892_RS0124970 |
| sorbitol | scrK: fructokinase | C892_RS0103380 | C892_RS0103820 |
| sorbitol | sdh: sorbitol dehydrogenase | C892_RS0113925 | C892_RS0120415 |
| sucrose | ams: sucrose hydrolase (invertase) | C892_RS0109915 | C892_RS0126795 |
| threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | C892_RS0115140 | |
| threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | C892_RS0115120 | C892_RS0104280 |
| threonine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | C892_RS0115125 | C892_RS0110670 |
| threonine | lpd: dihydrolipoyl dehydrogenase | C892_RS0123470 | C892_RS0114110 |
| thymidine | deoB: phosphopentomutase | C892_RS0112215 | C892_RS0116540 |
| trehalose | treF: trehalase | C892_RS0109915 | C892_RS0122105 |
| tryptophan | tnaA: tryptophanase | | |
| tryptophan | tnaT: tryptophan:Na+ symporter TnaT | C892_RS0109145 | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | C892_RS0102390 | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | C892_RS0126825 | C892_RS0110920 |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | C892_RS0109115 | C892_RS0105110 |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | C892_RS0126825 | C892_RS0118260 |
| valine | lpd: branched-chain alpha-ketoacid dehydrogenase, E3 component | C892_RS0123470 | C892_RS0114110 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | C892_RS0108545 | C892_RS0105230 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | C892_RS0109730 | C892_RS0109235 |
| valine | natB: L-valine ABC transporter, substrate-binding component NatB | C892_RS0115140 | |
| valine | natC: L-valine ABC transporter, permease component 1 (NatC) | C892_RS0115125 | |
| valine | natD: L-valine ABC transporter, permease component 2 (NatD) | C892_RS0115120 | C892_RS0104280 |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | C892_RS0123485 | C892_RS0127295 |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | C892_RS0105735 | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | C892_RS0103360 | C892_RS0111505 |
| xylose | xylB: xylulokinase | C892_RS0103385 | C892_RS0127260 |
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.
Links
Downloads
Related tools
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