Potential Gaps in catabolism of small carbon sources in Beijerinckia indica ATCC 9039
Found 99 low-confidence and 45 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | | |
| 4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | BIND_RS14270 | BIND_RS02470 |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| 4-hydroxybenzoate | pobA: 4-hydroxybenzoate 3-monooxygenase | | |
| 4-hydroxybenzoate | praA: protocatechuate 2,3-dioxygenase | | |
| 4-hydroxybenzoate | xylF: 2-hydroxymuconate semialdehyde hydrolase | | |
| alanine | snatA: L-alanine symporter SnatA | BIND_RS09515 | |
| arginine | rocE: L-arginine permease | | |
| arginine | rocF: arginase | BIND_RS14185 | |
| asparagine | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | BIND_RS08110 | |
| asparagine | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | BIND_RS08115 | |
| asparagine | ans: asparaginase | | |
| aspartate | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | BIND_RS08110 | |
| aspartate | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | BIND_RS08115 | |
| cellobiose | bgl: cellobiase | | |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | BIND_RS08105 | BIND_RS04215 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | BIND_RS08115 | |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | | |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | BIND_RS09055 | BIND_RS01335 |
| citrulline | arcC: carbamate kinase | | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | | |
| deoxyinosine | deoB: phosphopentomutase | BIND_RS18480 | |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyinosine | deoD: deoxyinosine phosphorylase | BIND_RS00805 | |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | BIND_RS04455 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | BIND_RS01815 | BIND_RS11625 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | BIND_RS15595 | BIND_RS12840 |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | BIND_RS01815 | BIND_RS11625 |
| deoxyribose | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | BIND_RS15595 | BIND_RS12840 |
| deoxyribose | drdehyd-alpha: 2-deoxy-D-ribose dehydrogenase, alpha subunit | BIND_RS17080 | BIND_RS14730 |
| deoxyribose | drdehyd-beta: 2-deoxy-D-ribose dehydrogenase, beta subunit | BIND_RS17075 | |
| deoxyribose | drdehyd-cytc: 2-deoxyribose-D dehydrogenase, cytochrome c component | BIND_RS19290 | BIND_RS17085 |
| deoxyribose | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | BIND_RS05255 | |
| fucose | fucI: L-fucose isomerase FucI | | |
| fucose | fucK: L-fuculose kinase FucK | | |
| fucose | fucP: L-fucose:H+ symporter FucP | BIND_RS16700 | |
| galactose | dgoD: D-galactonate dehydratase | BIND_RS15605 | BIND_RS14225 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | uxaA: D-altronate dehydratase | | |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | BIND_RS09125 | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | uxaC: D-glucuronate isomerase | | |
| glucuronate | uxuA: D-mannonate dehydratase | | |
| glucuronate | uxuB: D-mannonate dehydrogenase | BIND_RS04765 | BIND_RS12435 |
| glutamate | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | BIND_RS08110 | |
| glutamate | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | BIND_RS08115 | |
| histidine | aapM: L-histidine ABC transporter, permease component 2 (AapM) | BIND_RS08110 | |
| histidine | aapQ: L-histidine ABC transporter, permease component 1 (AapQ) | BIND_RS08115 | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| isoleucine | Bap2: L-isoleucine permease Bap2 | | |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | BIND_RS11625 | BIND_RS02160 |
| L-lactate | L-LDH: L-lactate dehydrogenase | BIND_RS18330 | BIND_RS13245 |
| lactose | dgoD: D-galactonate dehydratase | BIND_RS15605 | BIND_RS14225 |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | | |
| leucine | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | BIND_RS08110 | |
| leucine | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | BIND_RS08115 | |
| leucine | liuA: isovaleryl-CoA dehydrogenase | BIND_RS03180 | |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | BIND_RS06690 | BIND_RS19730 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | BIND_RS03165 | BIND_RS08865 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | BIND_RS06685 | |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| lysine | cadA: lysine decarboxylase | BIND_RS09680 | BIND_RS05480 |
| lysine | davT: 5-aminovalerate aminotransferase | BIND_RS14190 | BIND_RS00765 |
| lysine | fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase | BIND_RS08900 | BIND_RS16590 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | BIND_RS11190 | BIND_RS12810 |
| lysine | gcdH: glutaryl-CoA dehydrogenase | BIND_RS08895 | |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| lysine | patA: cadaverine aminotransferase | BIND_RS16295 | BIND_RS14190 |
| lysine | patD: 5-aminopentanal dehydrogenase | BIND_RS16960 | BIND_RS14385 |
| maltose | susB: alpha-glucosidase (maltase) | BIND_RS15260 | |
| myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | | |
| myoinositol | iolC: 5-dehydro-2-deoxy-D-gluconate kinase | | |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | BIND_RS09125 | |
| 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 | BIND_RS03165 | BIND_RS08865 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | BIND_RS03165 | BIND_RS08865 |
| phenylacetate | paaH: 3-hydroxyadipyl-CoA dehydrogenase | BIND_RS08900 | BIND_RS16590 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | BIND_RS15490 | BIND_RS02165 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | BIND_RS02165 | BIND_RS15490 |
| phenylacetate | paaK: phenylacetate-CoA ligase | BIND_RS17440 | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | BIND_RS03165 | BIND_RS08865 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | fahA: fumarylacetoacetate hydrolase | BIND_RS13265 | |
| phenylalanine | hmgA: homogentisate dioxygenase | | |
| phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| phenylalanine | PAH: phenylalanine 4-monooxygenase | | |
| phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | BIND_RS18190 | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | BIND_RS09980 | |
| putrescine | gabT: gamma-aminobutyrate transaminase | BIND_RS06310 | BIND_RS14190 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | BIND_RS16295 | BIND_RS06310 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | BIND_RS14385 | BIND_RS16960 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| rhamnose | rhaA: L-rhamnose isomerase | | |
| rhamnose | rhaB: L-rhamnulokinase | | |
| rhamnose | rhaD: rhamnulose 1-phosphate aldolase | | |
| rhamnose | rhaM: L-rhamnose mutarotase | | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsK: ribokinase | | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | sdaB: L-serine ammonia-lyase | BIND_RS16360 | |
| serine | snatA: L-serine transporter | BIND_RS09515 | |
| sorbitol | sdh: sorbitol dehydrogenase | BIND_RS11835 | BIND_RS19320 |
| threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | BIND_RS03765 | BIND_RS03760 |
| threonine | phtA: L-threonine uptake permease PhtA | BIND_RS17205 | |
| thymidine | deoA: thymidine phosphorylase DeoA | | |
| thymidine | deoB: phosphopentomutase | BIND_RS18480 | |
| thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | treF: trehalase | BIND_RS17180 | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | fahA: fumarylacetoacetate hydrolase | BIND_RS13265 | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | BIND_RS03180 | BIND_RS08895 |
| valine | Bap2: L-valine permease Bap2 | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | BIND_RS03175 | BIND_RS09070 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | BIND_RS00885 | BIND_RS03185 |
| xylitol | PS417_12055: xylitol ABC transporter, substrate-binding component | BIND_RS14240 | BIND_RS13980 |
| xylitol | PS417_12065: xylitol ABC transporter, ATPase component | BIND_RS14235 | BIND_RS14440 |
| xylose | xyrA: xylitol reductase | BIND_RS04445 | BIND_RS16950 |
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