Potential Gaps in catabolism of small carbon sources in Nocardiopsis gilva YIM 90087
Found 61 low-confidence and 67 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| arabinose | araE: L-arabinose:H+ symporter | CDO52_RS15385 | CDO52_RS07205 |
| arabinose | xacB: L-arabinose 1-dehydrogenase | CDO52_RS13580 | CDO52_RS11130 |
| arabinose | xacC: L-arabinono-1,4-lactonase | | |
| arabinose | xacD: L-arabinonate dehydratase | CDO52_RS20460 | CDO52_RS15320 |
| arabinose | xacE: 2-dehydro-3-deoxy-L-arabinonate dehydratase | | |
| arginine | arcC: carbamate kinase | | |
| arginine | rocE: L-arginine permease | CDO52_RS15070 | CDO52_RS05495 |
| citrate | tctB: citrate/Na+ symporter, small transmembrane component TctB | | |
| citrate | tctC: citrate/Na+ symporter, substrate-binding component TctC | CDO52_RS23810 | CDO52_RS23825 |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | CDO52_RS08200 | CDO52_RS20590 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | CDO52_RS08205 | |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | CDO52_RS05705 | CDO52_RS08205 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
| citrulline | arcC: carbamate kinase | | |
| D-alanine | cycA: D-alanine:H+ symporter CycA | CDO52_RS05495 | CDO52_RS15070 |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | glcE: D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) | CDO52_RS09915 | |
| D-lactate | glcF: D-lactate dehydrogenase, FeS subunit GlcF | CDO52_RS09910 | |
| D-serine | cycA: D-serine:H+ symporter CycA | CDO52_RS05495 | CDO52_RS15070 |
| D-serine | dsdA: D-serine ammonia-lyase | CDO52_RS17305 | CDO52_RS14725 |
| deoxyinosine | bmpA: deoxyinosine ABC transporter, substrate-binding component | CDO52_RS21120 | |
| deoxyinosine | deoB: phosphopentomutase | CDO52_RS21155 | CDO52_RS25060 |
| deoxyinosine | nupB: deoxyinosine ABC transporter, permease component 1 | | |
| deoxyinosine | nupC': deoxyinosine ABC transporter, permease component 2 | CDO52_RS21135 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | CDO52_RS09535 | CDO52_RS07220 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | garK: glycerate 2-kinase | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fructose | scrK: fructokinase | CDO52_RS22090 | CDO52_RS05430 |
| fucose | aldA: lactaldehyde dehydrogenase | CDO52_RS21175 | CDO52_RS14780 |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | CDO52_RS03545 | |
| 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 | galK: galactokinase (-1-phosphate forming) | CDO52_RS24645 | |
| galactose | galP: galactose:H+ symporter GalP | CDO52_RS07205 | CDO52_RS15385 |
| galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| galactose | pgmA: alpha-phosphoglucomutase | CDO52_RS24225 | CDO52_RS21155 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | gci: D-galactarolactone cycloisomerase | | |
| galacturonate | gli: D-galactarolactone isomerase | | |
| galacturonate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | CDO52_RS20715 | |
| galacturonate | udh: D-galacturonate dehydrogenase | CDO52_RS13580 | |
| gluconate | gntT: gluconate:H+ symporter GntT | CDO52_RS10715 | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | CDO52_RS24085 | CDO52_RS25050 |
| 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 | | |
| glucuronate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | CDO52_RS20715 | |
| glucuronate | udh: D-glucuronate dehydrogenase | CDO52_RS13580 | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | CDO52_RS24930 | CDO52_RS23420 |
| histidine | hutG': N-formylglutamate amidohydrolase | | |
| histidine | PA5503: L-histidine ABC transporter, ATPase component | CDO52_RS19395 | CDO52_RS05715 |
| isoleucine | Bap2: L-isoleucine permease Bap2 | CDO52_RS15070 | CDO52_RS05495 |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | CDO52_RS03640 | CDO52_RS19570 |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | CDO52_RS24535 | CDO52_RS21065 |
| lactose | galK: galactokinase (-1-phosphate forming) | CDO52_RS24645 | |
| lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | CDO52_RS20930 | CDO52_RS06830 |
| lactose | pgmA: alpha-phosphoglucomutase | CDO52_RS24225 | CDO52_RS21155 |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | CDO52_RS03640 | CDO52_RS19570 |
| leucine | leuT: L-leucine:Na+ symporter LeuT | CDO52_RS15475 | |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | CDO52_RS22645 | CDO52_RS23745 |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | CDO52_RS12620 | |
| lysine | davD: glutarate semialdehyde dehydrogenase | CDO52_RS01405 | CDO52_RS03550 |
| lysine | lysP: L-lysine:H+ symporter LysP | CDO52_RS05495 | CDO52_RS15070 |
| mannitol | mt2d: mannitol 2-dehydrogenase | CDO52_RS17250 | CDO52_RS17480 |
| mannitol | mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE | CDO52_RS17255 | |
| mannitol | mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) | CDO52_RS17260 | CDO52_RS20065 |
| mannitol | mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) | CDO52_RS17265 | CDO52_RS16285 |
| mannitol | mtlK: polyol ABC transporter, ATP component MtlK/SmoG | CDO52_RS13845 | CDO52_RS13825 |
| mannitol | scrK: fructokinase | CDO52_RS22090 | CDO52_RS05430 |
| mannose | scrK: fructokinase | CDO52_RS22090 | CDO52_RS05430 |
| myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | CDO52_RS05440 | |
| myoinositol | iolE: scyllo-inosose 2-dehydratase | CDO52_RS05455 | |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | CDO52_RS05430 | |
| myoinositol | iolT: myo-inositol:H+ symporter | CDO52_RS15385 | CDO52_RS07205 |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | CDO52_RS24085 | CDO52_RS25050 |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | CDO52_RS22645 | CDO52_RS06140 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | CDO52_RS07695 | CDO52_RS13230 |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | CDO52_RS01700 | CDO52_RS05490 |
| phenylacetate | ppa: phenylacetate permease ppa | CDO52_RS23060 | CDO52_RS18770 |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | CDO52_RS15070 | CDO52_RS05495 |
| phenylalanine | paaF: 2,3-dehydroadipyl-CoA hydratase | CDO52_RS22645 | CDO52_RS06140 |
| phenylalanine | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | CDO52_RS07695 | CDO52_RS13230 |
| phenylalanine | paaZ1: oxepin-CoA hydrolase | CDO52_RS01700 | CDO52_RS05490 |
| phenylalanine | pad-dh: phenylacetaldehyde dehydrogenase | CDO52_RS21175 | CDO52_RS14780 |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | CDO52_RS24535 | CDO52_RS21065 |
| putrescine | gabT: gamma-aminobutyrate transaminase | CDO52_RS05530 | CDO52_RS01410 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | CDO52_RS19160 | CDO52_RS05530 |
| putrescine | potB: putrescine ABC transporter, permease component 1 (PotB/PotH) | CDO52_RS05550 | |
| putrescine | potC: putrescine ABC transporter, permease component 2 (PotC/PotI) | CDO52_RS05555 | CDO52_RS05775 |
| putrescine | potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) | CDO52_RS05545 | |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | CDO52_RS21950 | CDO52_RS11130 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | | |
| rhamnose | LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase | CDO52_RS17250 | CDO52_RS11130 |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| serine | serP: L-serine permease SerP | CDO52_RS05495 | |
| sorbitol | mtlF: ABC transporter for polyols MtlEFGK, permease component MtlF | CDO52_RS17260 | CDO52_RS20065 |
| sorbitol | mtlK: ABC transporter for polyols MtlEFGK, permease component MtlK | CDO52_RS13845 | CDO52_RS13825 |
| sorbitol | scrK: fructokinase | CDO52_RS22090 | CDO52_RS05430 |
| sorbitol | sdh: sorbitol dehydrogenase | CDO52_RS11130 | CDO52_RS03370 |
| sucrose | ams: sucrose hydrolase (invertase) | CDO52_RS09975 | CDO52_RS13800 |
| sucrose | scrK: fructokinase | CDO52_RS22090 | CDO52_RS05430 |
| threonine | RR42_RS28305: L-threonine:H+ symporter | CDO52_RS05495 | CDO52_RS15070 |
| thymidine | deoB: phosphopentomutase | CDO52_RS21155 | CDO52_RS25060 |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | treF: trehalase | CDO52_RS09975 | CDO52_RS13800 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | CDO52_RS15070 | CDO52_RS05495 |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | CDO52_RS05495 | CDO52_RS15070 |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | Bap2: L-valine permease Bap2 | CDO52_RS15070 | CDO52_RS05495 |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | CDO52_RS23440 | |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | CDO52_RS03640 | CDO52_RS19570 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | CDO52_RS09015 | CDO52_RS05450 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | CDO52_RS20160 | |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | CDO52_RS24535 | CDO52_RS21065 |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | CDO52_RS15385 | |
| xylitol | xdhA: xylitol dehydrogenase | CDO52_RS02195 | CDO52_RS11130 |
| xylose | xylT: D-xylose transporter | CDO52_RS15385 | CDO52_RS07205 |
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