Potential Gaps in catabolism of small carbon sources in Halomonas xinjiangensis TRM 0175
Found 75 low-confidence and 62 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | pcaB: 3-carboxymuconate cycloisomerase | JH15_RS07105 | |
| 4-hydroxybenzoate | pcaD: 3-oxoadipate enol-lactone hydrolase | JH15_RS07085 | |
| 4-hydroxybenzoate | pcaF: succinyl-CoA:acetyl-CoA C-succinyltransferase | JH15_RS07090 | JH15_RS15760 |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| acetate | actP: cation/acetate symporter ActP | JH15_RS06410 | |
| arabinose | xacC: L-arabinono-1,4-lactonase | JH15_RS06165 | JH15_RS10355 |
| arginine | gabT: gamma-aminobutyrate transaminase | JH15_RS03040 | JH15_RS04225 |
| asparagine | ans: asparaginase | JH15_RS14455 | JH15_RS01220 |
| aspartate | bgtA: aspartate ABC transporter, ATPase component BgtA | JH15_RS12955 | JH15_RS13610 |
| aspartate | natF: aspartate ABC transporter, substrate-binding component NatF | JH15_RS12970 | |
| aspartate | natG: aspartate ABC transporter, permease component 1 (NatG) | JH15_RS12965 | JH15_RS13615 |
| aspartate | natH: aspartate ABC transporter, permease component 2 (NatH) | JH15_RS12960 | JH15_RS11220 |
| cellobiose | bgl: cellobiase | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | JH15_RS09835 | JH15_RS16045 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | JH15_RS09830 | JH15_RS16055 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | JH15_RS09820 | JH15_RS16050 |
| citrulline | aruF: ornithine/arginine N-succinyltransferase subunit AruAI (AruF) | JH15_RS09235 | JH15_RS09240 |
| citrulline | aruG: ornithine/arginine N-succinyltransferase subunit AruAII (AruG) | JH15_RS09240 | JH15_RS09235 |
| citrulline | astC: succinylornithine transaminase | JH15_RS09230 | JH15_RS04225 |
| citrulline | citrullinase: putative citrullinase | JH15_RS02685 | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-alanine | Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component | JH15_RS12970 | |
| D-alanine | Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component | JH15_RS12955 | JH15_RS13610 |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | JH15_RS10025 | JH15_RS13820 |
| deoxyinosine | deoB: phosphopentomutase | JH15_RS10480 | JH15_RS12400 |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | JH15_RS09280 | JH15_RS15575 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | JH15_RS16010 | |
| deoxyribose | deoK: deoxyribokinase | JH15_RS00495 | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fucose | fdh: L-fucose 1-dehydrogenase | JH15_RS13090 | JH15_RS05320 |
| fucose | fuconolactonase: L-fucono-1,5-lactonase | JH15_RS15405 | |
| fucose | fucP: L-fucose:H+ symporter FucP | | |
| fucose | fucU: L-fucose mutarotase FucU | | |
| galactose | dgoK: 2-dehydro-3-deoxygalactonokinase | JH15_RS06175 | JH15_RS14595 |
| galactose | galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) | JH15_RS06165 | JH15_RS10355 |
| galactose | PfGW456L13_1897: ABC transporter for D-Galactose and D-Glucose, ATPase component | JH15_RS04270 | JH15_RS03500 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | JH15_RS13520 | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | dctP: D-glucuronate TRAP transporter, solute receptor component | JH15_RS11605 | JH15_RS05290 |
| glucuronate | dctQ: D-glucuronate TRAP transporter, small permease component | | |
| glutamate | aapJ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ | JH15_RS12970 | |
| glutamate | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | JH15_RS12960 | JH15_RS13615 |
| glutamate | aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP | JH15_RS12955 | JH15_RS13610 |
| glutamate | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | JH15_RS12965 | |
| histidine | aapJ: L-histidine ABC transporter, substrate-binding component AapJ | JH15_RS12970 | |
| histidine | aapM: L-histidine ABC transporter, permease component 2 (AapM) | JH15_RS12960 | JH15_RS13615 |
| histidine | aapP: L-histidine ABC transporter, ATPase component AapP | JH15_RS12955 | JH15_RS13610 |
| histidine | aapQ: L-histidine ABC transporter, permease component 1 (AapQ) | JH15_RS12965 | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| isoleucine | natB: L-isoleucine ABC transporter, substrate-binding component NatB | JH15_RS14375 | |
| isoleucine | natC: L-isoleucine ABC transporter, permease component 1 (NatC) | | |
| isoleucine | natD: L-isoleucine ABC transporter, permease component 2 (NatD) | JH15_RS14385 | |
| lactose | dgoK: 2-dehydro-3-deoxygalactonokinase | JH15_RS06175 | JH15_RS14595 |
| lactose | galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) | JH15_RS06165 | JH15_RS10355 |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | | |
| leucine | aapJ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ | JH15_RS12970 | |
| leucine | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | JH15_RS12960 | JH15_RS13615 |
| leucine | aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP | JH15_RS12955 | JH15_RS13610 |
| leucine | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | JH15_RS12965 | |
| lysine | argT: L-lysine ABC transporter, substrate-binding component ArgT | JH15_RS16050 | JH15_RS09820 |
| lysine | davA: 5-aminovaleramidase | JH15_RS02685 | |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | hisM: L-lysine ABC transporter, permease component 1 (HisM) | JH15_RS09825 | JH15_RS15195 |
| lysine | hisQ: L-lysine ABC transporter, permease component 2 (HisQ) | JH15_RS09830 | JH15_RS16055 |
| maltose | susB: alpha-glucosidase (maltase) | | |
| mannitol | mt2d: mannitol 2-dehydrogenase | JH15_RS14550 | JH15_RS14530 |
| mannitol | PLT5: polyol transporter PLT5 | | |
| mannose | manA: mannose-6-phosphate isomerase | JH15_RS10645 | |
| mannose | manP: mannose PTS system, EII-CBA components | JH15_RS05180 | |
| 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 | kdgK: 2-keto-3-deoxygluconate kinase | JH15_RS14595 | JH15_RS04925 |
| myoinositol | uxaE: D-tagaturonate epimerase | | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | JH15_RS13520 | |
| 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 | paaK: phenylacetate-CoA ligase | | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | JH15_RS15805 | JH15_RS09270 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | fahA: fumarylacetoacetate hydrolase | JH15_RS10280 | |
| phenylalanine | hmgA: homogentisate dioxygenase | | |
| phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| phenylalanine | maiA: maleylacetoacetate isomerase | | |
| phenylalanine | PAH: phenylalanine 4-monooxygenase | | |
| putrescine | gabT: gamma-aminobutyrate transaminase | JH15_RS03040 | JH15_RS04225 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase | JH15_RS05315 | JH15_RS03910 |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsK: ribokinase | JH15_RS00495 | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | JH15_RS14375 | |
| serine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | JH15_RS14385 | JH15_RS09310 |
| serine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | | |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
| sucrose | ams: sucrose hydrolase (invertase) | | |
| threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | JH15_RS14375 | |
| threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | JH15_RS14385 | JH15_RS09310 |
| threonine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | | |
| thymidine | deoB: phosphopentomutase | JH15_RS10480 | JH15_RS12400 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | fahA: fumarylacetoacetate hydrolase | JH15_RS10280 | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | JH15_RS01460 | JH15_RS15645 |
| valine | natB: L-valine ABC transporter, substrate-binding component NatB | JH15_RS14375 | |
| valine | natC: L-valine ABC transporter, permease component 1 (NatC) | | |
| valine | natD: L-valine ABC transporter, permease component 2 (NatD) | JH15_RS14385 | |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | JH15_RS05180 | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | JH15_RS14530 | |
| xylose | gtsA: xylose ABC transporter, periplasmic substrate-binding component GtsA | JH15_RS04285 | |
| xylose | gtsB: xylose ABC transporter, permease component 1 GtsB | JH15_RS04280 | |
| xylose | gtsD: xylose ABC transporter, ATPase component GtsD | JH15_RS04270 | JH15_RS03500 |
| xylose | gyaR: glyoxylate reductase | JH15_RS14590 | JH15_RS08520 |
| xylose | xdh: D-xylose dehydrogenase | JH15_RS09450 | JH15_RS13090 |
| xylose | xylC: xylonolactonase | JH15_RS06165 | JH15_RS10355 |
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