Potential Gaps in catabolism of small carbon sources in Belnapia rosea CPCC 100156
Found 77 low-confidence and 82 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 | BLR02_RS00985 | BLR02_RS13075 |
| 2-oxoglutarate | Psest_0085: 2-oxoglutarate TRAP transporter, solute receptor component | BLR02_RS22645 | |
| 4-hydroxybenzoate | pcaB: 3-carboxymuconate cycloisomerase | BLR02_RS19140 | BLR02_RS19925 |
| 4-hydroxybenzoate | pcaF: succinyl-CoA:acetyl-CoA C-succinyltransferase | BLR02_RS13910 | BLR02_RS00935 |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| alanine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | BLR02_RS12505 | |
| alanine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | BLR02_RS12525 | BLR02_RS19370 |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arabinose | xacB: L-arabinose 1-dehydrogenase | BLR02_RS13095 | BLR02_RS13785 |
| arabinose | xacC: L-arabinono-1,4-lactonase | BLR02_RS16110 | BLR02_RS27415 |
| arginine | braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) | BLR02_RS12525 | BLR02_RS10285 |
| arginine | odc: L-ornithine decarboxylase | BLR02_RS01030 | |
| arginine | patA: putrescine aminotransferase (PatA/SpuC) | BLR02_RS05825 | BLR02_RS13175 |
| arginine | patD: gamma-aminobutyraldehyde dehydrogenase | BLR02_RS07320 | BLR02_RS18460 |
| arginine | rocF: arginase | BLR02_RS05475 | |
| cellobiose | cbp: cellobiose phosphorylase | | |
| cellobiose | cdt: cellobiose transporter cdt-1/cdt-2 | | |
| citrate | tctB: citrate/Na+ symporter, small transmembrane component TctB | | |
| citrate | tctC: citrate/Na+ symporter, substrate-binding component TctC | BLR02_RS20580 | BLR02_RS17655 |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | BLR02_RS02400 | BLR02_RS24955 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | BLR02_RS19470 | BLR02_RS02405 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | BLR02_RS19475 | BLR02_RS10415 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
| citrulline | arcC: carbamate kinase | | |
| citrulline | odc: L-ornithine decarboxylase | BLR02_RS01030 | |
| citrulline | patA: putrescine aminotransferase (PatA/SpuC) | BLR02_RS05825 | BLR02_RS13175 |
| citrulline | patD: gamma-aminobutyraldehyde dehydrogenase | BLR02_RS07320 | BLR02_RS18460 |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | BLR02_RS15635 | BLR02_RS11460 |
| deoxyinosine | adh: acetaldehyde dehydrogenase (not acylating) | BLR02_RS07320 | BLR02_RS18460 |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyinosine | deoD: deoxyinosine phosphorylase | BLR02_RS07410 | |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | BLR02_RS12095 | |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | BLR02_RS22360 | |
| deoxyribose | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | BLR02_RS22360 | |
| deoxyribose | drdehyd-alpha: 2-deoxy-D-ribose dehydrogenase, alpha subunit | BLR02_RS04525 | BLR02_RS22725 |
| deoxyribose | drdehyd-beta: 2-deoxy-D-ribose dehydrogenase, beta subunit | BLR02_RS04520 | BLR02_RS22720 |
| deoxyribose | drdehyd-cytc: 2-deoxyribose-D dehydrogenase, cytochrome c component | | |
| ethanol | adh: acetaldehyde dehydrogenase (not acylating) | BLR02_RS07320 | BLR02_RS18460 |
| fructose | 1pfk: 1-phosphofructokinase | BLR02_RS10215 | |
| fructose | fba: fructose 1,6-bisphosphate aldolase | BLR02_RS17770 | |
| fucose | fucD: L-fuconate dehydratase | BLR02_RS24835 | BLR02_RS03050 |
| fucose | fuconolactonase: L-fucono-1,5-lactonase | | |
| fucose | fucP: L-fucose:H+ symporter FucP | | |
| fucose | fucU: L-fucose mutarotase FucU | | |
| galactose | dgoD: D-galactonate dehydratase | BLR02_RS21720 | BLR02_RS09825 |
| galactose | galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) | BLR02_RS16110 | BLR02_RS27415 |
| galactose | galdh: D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) | BLR02_RS13095 | BLR02_RS13785 |
| galactose | galP: galactose:H+ symporter GalP | | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | gci: D-galactarolactone cycloisomerase | BLR02_RS03050 | BLR02_RS00035 |
| galacturonate | gli: D-galactarolactone isomerase | BLR02_RS06440 | BLR02_RS03205 |
| galacturonate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | BLR02_RS02000 | BLR02_RS20920 |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | AO353_21710: glucosaminate ABC transporter, substrate-binding component | | |
| glucosamine | AO353_21715: glucosaminate ABC transporter, permease component 1 | BLR02_RS02410 | BLR02_RS19470 |
| glucosamine | AO353_21720: glucosaminate ABC transporter, permease component 2 | BLR02_RS10410 | BLR02_RS19470 |
| glucosamine | AO353_21725: glucosaminate ABC transporter, ATPase component | BLR02_RS10420 | BLR02_RS02400 |
| glucosamine | gdh: quinoprotein glucose dehydrogenase | BLR02_RS21990 | |
| glucosamine | glucosaminate-lyase: glucosaminate ammonia-lyase | BLR02_RS18980 | |
| glucosamine | kdgA: 2-keto-3-deoxygluconate-6-phosphate aldolase EC:4.1.2.14 | BLR02_RS16045 | BLR02_RS17280 |
| glucose | MFS-glucose: glucose transporter, MFS superfamily | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | dctQ: D-glucuronate TRAP transporter, small permease component | | |
| glucuronate | garL: 5-dehydro-4-deoxy-D-glucarate aldolase | BLR02_RS16825 | BLR02_RS02000 |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | BLR02_RS03050 | BLR02_RS06440 |
| histidine | braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) | BLR02_RS12525 | BLR02_RS10285 |
| histidine | hutG': N-formylglutamate amidohydrolase | BLR02_RS08655 | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | BLR02_RS16555 | BLR02_RS03525 |
| isoleucine | livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) | BLR02_RS12525 | BLR02_RS10285 |
| L-lactate | lutC: L-lactate dehydrogenase, LutC subunit | BLR02_RS08915 | |
| lactose | dgoD: D-galactonate dehydratase | BLR02_RS21720 | BLR02_RS09825 |
| lactose | galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) | BLR02_RS16110 | BLR02_RS27415 |
| lactose | galdh: D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) | BLR02_RS13095 | BLR02_RS13785 |
| lactose | lacP: lactose permease LacP | | |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | BLR02_RS23110 | BLR02_RS05540 |
| leucine | livH: L-leucine ABC transporter, permease component 1 (LivH/BraD) | BLR02_RS12525 | BLR02_RS10285 |
| lysine | davA: 5-aminovaleramidase | BLR02_RS09725 | |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | davT: 5-aminovalerate aminotransferase | BLR02_RS01300 | BLR02_RS12085 |
| lysine | fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase | BLR02_RS03400 | BLR02_RS23340 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| maltose | MAL11: maltose permease | | |
| mannitol | mak: mannose kinase | BLR02_RS06040 | |
| mannitol | mt1d: mannitol 1-dehydrogenase | | |
| mannitol | PLT5: polyol transporter PLT5 | | |
| mannose | manP: mannose PTS system, EII-CBA components | BLR02_RS10220 | |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | BLR02_RS14730 | |
| myoinositol | iolM: 2-inosose 4-dehydrogenase | BLR02_RS03165 | |
| myoinositol | iolN: 2,4-diketo-inositol hydratase | | |
| myoinositol | iolO: 5-dehydro-L-gluconate epimerase | | |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| myoinositol | uxaE: D-tagaturonate epimerase | | |
| myoinositol | uxuA: D-mannonate dehydratase | BLR02_RS03050 | |
| myoinositol | uxuB: D-mannonate dehydrogenase | | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | BLR02_RS07310 | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| 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 | paaF: 2,3-dehydroadipyl-CoA hydratase | BLR02_RS23955 | BLR02_RS09775 |
| phenylacetate | paaH: 3-hydroxyadipyl-CoA dehydrogenase | BLR02_RS03400 | BLR02_RS23340 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | BLR02_RS13910 | BLR02_RS00935 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | BLR02_RS13910 | BLR02_RS00935 |
| phenylacetate | paaK: phenylacetate-CoA ligase | BLR02_RS03515 | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | BLR02_RS13145 | BLR02_RS02380 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | livH: L-phenylalanine ABC transporter, permease component 1 (LivH) | BLR02_RS12525 | BLR02_RS25435 |
| phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | BLR02_RS12505 | |
| phenylalanine | maiA: maleylacetoacetate isomerase | BLR02_RS22165 | BLR02_RS00400 |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | BLR02_RS21330 | |
| proline | put1: proline dehydrogenase | BLR02_RS10310 | BLR02_RS16755 |
| proline | putA: L-glutamate 5-semialdeyde dehydrogenase | BLR02_RS07320 | BLR02_RS04250 |
| propionate | lctP: propionate permease | BLR02_RS20815 | |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | BLR02_RS05825 | BLR02_RS13175 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | BLR02_RS07320 | BLR02_RS18460 |
| putrescine | potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) | BLR02_RS01710 | |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | BLR02_RS03980 | BLR02_RS25750 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | BLR02_RS24835 | BLR02_RS03050 |
| 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) | BLR02_RS12505 | |
| serine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | BLR02_RS12525 | BLR02_RS19370 |
| sorbitol | scrK: fructokinase | BLR02_RS06040 | BLR02_RS17285 |
| sorbitol | sdh: sorbitol dehydrogenase | BLR02_RS02420 | BLR02_RS03980 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
| sucrose | 1pfk: 1-phosphofructokinase | BLR02_RS10215 | |
| sucrose | ams: sucrose hydrolase (invertase) | BLR02_RS13820 | |
| sucrose | fba: fructose 1,6-bisphosphate aldolase | BLR02_RS17770 | |
| threonine | adh: acetaldehyde dehydrogenase (not acylating) | BLR02_RS07320 | BLR02_RS18460 |
| threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | BLR02_RS12505 | |
| threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | BLR02_RS12525 | BLR02_RS19370 |
| thymidine | adh: acetaldehyde dehydrogenase (not acylating) | BLR02_RS07320 | BLR02_RS18460 |
| thymidine | deoA: thymidine phosphorylase DeoA | | |
| thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
| thymidine | nupC: thymidine permease NupC | BLR02_RS12095 | |
| trehalose | thuE: trehalose ABC transporter, substrate-binding component ThuE | | |
| trehalose | thuF: trehalose ABC transporter, permease component 1 (ThuF) | BLR02_RS27605 | BLR02_RS07865 |
| trehalose | thuG: trehalose ABC transporter, permease component 2 (ThuG) | BLR02_RS27610 | BLR02_RS07860 |
| trehalose | treF: trehalase | BLR02_RS13820 | BLR02_RS20685 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | Ac3H11_1693: L-tyrosine ABC transporter, ATPase component 1 | BLR02_RS12515 | BLR02_RS10295 |
| tyrosine | Ac3H11_1694: L-tyrosine ABC transporter, permease component 2 | BLR02_RS12520 | BLR02_RS25430 |
| tyrosine | Ac3H11_1695: L-tyrosine ABC transporter, permease component 1 | BLR02_RS12525 | BLR02_RS19370 |
| tyrosine | Ac3H11_2396: L-tyrosine ABC transporter, substrate-binding component component | BLR02_RS12505 | |
| tyrosine | maiA: maleylacetoacetate isomerase | BLR02_RS22165 | BLR02_RS00400 |
| valine | acdH: isobutyryl-CoA dehydrogenase | BLR02_RS16555 | BLR02_RS03525 |
| valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | BLR02_RS12525 | BLR02_RS10285 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | BLR02_RS18460 | BLR02_RS04250 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | BLR02_RS01175 | BLR02_RS15295 |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | BLR02_RS10220 | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | BLR02_RS07915 | BLR02_RS21355 |
| xylose | xylC: xylonolactonase | BLR02_RS16110 | BLR02_RS27415 |
| xylose | xylT: D-xylose transporter | | |
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