Potential Gaps in catabolism of small carbon sources in Limnohabitans parvus II-B4
Found 91 low-confidence and 58 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 | B9Z37_RS10770 | |
| 2-oxoglutarate | Psest_0085: 2-oxoglutarate TRAP transporter, solute receptor component | B9Z37_RS10765 | |
| 4-hydroxybenzoate | ligU: 4-oxalomesaconate tautomerase | | |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| alanine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | B9Z37_RS11950 | |
| alanine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | B9Z37_RS09270 | B9Z37_RS08650 |
| alanine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | B9Z37_RS09280 | B9Z37_RS08660 |
| alanine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | B9Z37_RS09285 | B9Z37_RS10195 |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arabinose | xacB: L-arabinose 1-dehydrogenase | B9Z37_RS11375 | B9Z37_RS12690 |
| arabinose | xacC: L-arabinono-1,4-lactonase | B9Z37_RS06620 | |
| arabinose | xacE: 2-dehydro-3-deoxy-L-arabinonate dehydratase | | |
| arginine | rocE: L-arginine permease | | |
| arginine | rocF: arginase | | |
| asparagine | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | B9Z37_RS12755 | |
| asparagine | aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP | B9Z37_RS12760 | B9Z37_RS06780 |
| asparagine | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | B9Z37_RS12750 | |
| aspartate | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | B9Z37_RS12755 | |
| aspartate | aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP | B9Z37_RS12760 | B9Z37_RS06780 |
| aspartate | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | B9Z37_RS12750 | |
| cellobiose | bgl: cellobiase | | |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | B9Z37_RS06780 | B9Z37_RS12760 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | | |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | | |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
| citrulline | arcC: carbamate kinase | | |
| D-alanine | Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component | B9Z37_RS12745 | |
| D-alanine | Pf6N2E2_5403: ABC transporter for D-Alanine, permease component 2 | B9Z37_RS12750 | |
| D-alanine | Pf6N2E2_5404: ABC transporter for D-Alanine, permease component 1 | B9Z37_RS12755 | |
| D-alanine | Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component | B9Z37_RS12760 | B9Z37_RS06780 |
| 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 | B9Z37_RS12805 | B9Z37_RS04975 |
| deoxyinosine | deoB: phosphopentomutase | B9Z37_RS11745 | |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyinosine | deoD: deoxyinosine phosphorylase | | |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | B9Z37_RS12390 | B9Z37_RS00480 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyribose | deoK: deoxyribokinase | B9Z37_RS02670 | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fructose | frcB: fructose ABC transporter, substrate-binding component FrcB | | |
| fructose | frcC: fructose ABC transporter, permease component FrcC | B9Z37_RS10970 | |
| fructose | scrK: fructokinase | B9Z37_RS10965 | B9Z37_RS02670 |
| fucose | aldA: lactaldehyde dehydrogenase | B9Z37_RS05925 | B9Z37_RS00715 |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | B9Z37_RS07515 | |
| 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 | B9Z37_RS10985 | |
| fumarate | dauA: fumarate transporter DauA | B9Z37_RS13945 | |
| galactose | dgoD: D-galactonate dehydratase | B9Z37_RS02655 | B9Z37_RS02720 |
| galactose | galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) | B9Z37_RS06620 | |
| galactose | galdh: D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) | B9Z37_RS11375 | B9Z37_RS12690 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | uxuL: D-galactaro-1,5-lactonase (UxuL or UxuF) | B9Z37_RS06620 | B9Z37_RS10270 |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | B9Z37_RS05050 | |
| glucosamine | SLC2A2: glucosamine transporter SLC2A2 | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | dctQ: D-glucuronate TRAP transporter, small permease component | | |
| glucuronate | uxuL: D-glucaro-1,5-lactonase UxuL or UxuF | B9Z37_RS06620 | B9Z37_RS10270 |
| glutamate | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | B9Z37_RS12755 | |
| glutamate | aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP | B9Z37_RS12760 | B9Z37_RS06780 |
| glutamate | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | B9Z37_RS12750 | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | B9Z37_RS05785 | |
| glycerol | glpF: glycerol facilitator glpF | | |
| histidine | aapP: L-histidine ABC transporter, ATPase component AapP | B9Z37_RS12760 | B9Z37_RS06780 |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| L-malate | sdlC: L-malate:Na+ symporter SdlC | | |
| lactose | klh: periplasmic 3'-ketolactose hydrolase | | |
| lactose | lacA': periplasmic lactose 3-dehydrogenase, LacA subunit | | |
| lactose | lacB': periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB) | B9Z37_RS13585 | |
| lactose | lacC': periplasmic lactose 3-dehydrogenase, LacC subunit | | |
| lysine | davD: glutarate semialdehyde dehydrogenase | B9Z37_RS11445 | B9Z37_RS07645 |
| lysine | davT: 5-aminovalerate aminotransferase | B9Z37_RS09810 | B9Z37_RS00710 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| lysine | patA: cadaverine aminotransferase | B9Z37_RS09810 | B9Z37_RS00710 |
| lysine | patD: 5-aminopentanal dehydrogenase | B9Z37_RS11445 | B9Z37_RS06135 |
| maltose | susB: alpha-glucosidase (maltase) | | |
| mannitol | mt2d: mannitol 2-dehydrogenase | B9Z37_RS12650 | B9Z37_RS02600 |
| mannitol | PLT5: polyol transporter PLT5 | | |
| mannitol | scrK: fructokinase | B9Z37_RS10965 | B9Z37_RS02670 |
| mannose | manA: mannose-6-phosphate isomerase | | |
| mannose | manP: mannose PTS system, EII-CBA components | | |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | | |
| myoinositol | iolM: 2-inosose 4-dehydrogenase | | |
| 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 | uxuB: D-mannonate dehydrogenase | B9Z37_RS12650 | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | B9Z37_RS05050 | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylalanine | iorAB: phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB | B9Z37_RS07030 | |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | gabT: gamma-aminobutyrate transaminase | B9Z37_RS00710 | B9Z37_RS06015 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | B9Z37_RS00710 | B9Z37_RS06015 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | B9Z37_RS00715 | B9Z37_RS05925 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| pyruvate | dctM: pyruvate TRAP transporter, large permease component | B9Z37_RS03275 | B9Z37_RS10085 |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | B9Z37_RS01605 | B9Z37_RS02600 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | B9Z37_RS12660 | B9Z37_RS10310 |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsA: D-ribose ABC transporter, ATPase component RbsA | B9Z37_RS03475 | |
| ribose | rbsB: D-ribose ABC transporter, substrate-binding component RbsB | B9Z37_RS10975 | |
| ribose | rbsK: ribokinase | B9Z37_RS02670 | |
| serine | sdaB: L-serine ammonia-lyase | B9Z37_RS12805 | B9Z37_RS04975 |
| sorbitol | scrK: fructokinase | B9Z37_RS10965 | B9Z37_RS02670 |
| sorbitol | sdh: sorbitol dehydrogenase | B9Z37_RS12695 | B9Z37_RS09565 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
| succinate | dauA: succinate:H+ symporter DauA | B9Z37_RS13945 | |
| sucrose | ams: sucrose hydrolase (invertase) | | |
| threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | B9Z37_RS11950 | |
| threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | B9Z37_RS09270 | B9Z37_RS08650 |
| threonine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | B9Z37_RS09280 | B9Z37_RS08660 |
| threonine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | B9Z37_RS09285 | B9Z37_RS10195 |
| threonine | tdcE: 2-ketobutyrate formate-lyase | | |
| thymidine | deoA: thymidine phosphorylase DeoA | B9Z37_RS07680 | B9Z37_RS03025 |
| thymidine | deoB: phosphopentomutase | B9Z37_RS11745 | |
| thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | treF: trehalase | | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | B9Z37_RS14155 | B9Z37_RS13395 |
| valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | B9Z37_RS11950 | |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | B9Z37_RS06540 | B9Z37_RS06135 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | B9Z37_RS07625 | B9Z37_RS06075 |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | | |
| xylose | DKDP-dehydrog: D-2-keto-3-deoxypentoate dehydrogenase | B9Z37_RS12690 | B9Z37_RS00480 |
| xylose | gtsA: xylose ABC transporter, periplasmic substrate-binding component GtsA | B9Z37_RS08260 | |
| xylose | gtsB: xylose ABC transporter, permease component 1 GtsB | B9Z37_RS08265 | B9Z37_RS13745 |
| xylose | gtsC: xylose ABC transporter, permease component 2 GtsC | B9Z37_RS08270 | |
| xylose | gtsD: xylose ABC transporter, ATPase component GtsD | B9Z37_RS08275 | B9Z37_RS13735 |
| xylose | xad: D-xylonate dehydratase | B9Z37_RS02655 | B9Z37_RS02630 |
| xylose | xdh: D-xylose dehydrogenase | B9Z37_RS02600 | B9Z37_RS12390 |
| xylose | xylC: xylonolactonase | B9Z37_RS06620 | |
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