Potential Gaps in catabolism of small carbon sources in Tistlia consotensis USBA 355
Found 54 low-confidence and 71 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | pcaB: 3-carboxymuconate cycloisomerase | B9O00_RS07275 | B9O00_RS28980 |
| 4-hydroxybenzoate | pcaF: succinyl-CoA:acetyl-CoA C-succinyltransferase | B9O00_RS13575 | B9O00_RS06430 |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| acetate | ybhL: acetate uptake transporter YbhL | B9O00_RS28325 | |
| alanine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | B9O00_RS11400 | B9O00_RS19590 |
| alanine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | B9O00_RS11425 | B9O00_RS18240 |
| alanine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | B9O00_RS11420 | B9O00_RS18235 |
| arabinose | xacC: L-arabinono-1,4-lactonase | B9O00_RS08750 | B9O00_RS08745 |
| arginine | adiA: arginine decarboxylase (AdiA/SpeA) | | |
| arginine | artM: L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) | B9O00_RS08515 | B9O00_RS25795 |
| asparagine | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | B9O00_RS06670 | B9O00_RS30245 |
| asparagine | aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP | B9O00_RS06665 | B9O00_RS30340 |
| aspartate | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | B9O00_RS06670 | B9O00_RS30245 |
| aspartate | aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP | B9O00_RS06665 | B9O00_RS30340 |
| cellobiose | bgl: cellobiase | B9O00_RS18175 | |
| citrate | tctB: citrate/Na+ symporter, small transmembrane component TctB | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | B9O00_RS08530 | B9O00_RS00455 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | B9O00_RS08515 | B9O00_RS25795 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | B9O00_RS08525 | B9O00_RS08535 |
| citrulline | citrullinase: putative citrullinase | B9O00_RS09985 | B9O00_RS13950 |
| citrulline | odc: L-ornithine decarboxylase | B9O00_RS16780 | B9O00_RS17865 |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | B9O00_RS10660 | B9O00_RS21430 |
| deoxyinosine | adh: acetaldehyde dehydrogenase (not acylating) | B9O00_RS05420 | B9O00_RS20310 |
| deoxyinosine | deoB: phosphopentomutase | B9O00_RS14620 | |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyinosine | deoD: deoxyinosine phosphorylase | B9O00_RS18560 | |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | B9O00_RS29460 | |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribose | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribose | drdehyd-alpha: 2-deoxy-D-ribose dehydrogenase, alpha subunit | B9O00_RS26465 | B9O00_RS06075 |
| deoxyribose | drdehyd-beta: 2-deoxy-D-ribose dehydrogenase, beta subunit | B9O00_RS26470 | B9O00_RS10800 |
| deoxyribose | drdehyd-cytc: 2-deoxyribose-D dehydrogenase, cytochrome c component | B9O00_RS25485 | |
| ethanol | adh: acetaldehyde dehydrogenase (not acylating) | B9O00_RS05420 | B9O00_RS20310 |
| fucose | fucD: L-fuconate dehydratase | B9O00_RS01575 | B9O00_RS27415 |
| fucose | fucP: L-fucose:H+ symporter FucP | | |
| fucose | fucU: L-fucose mutarotase FucU | | |
| galactose | dgoD: D-galactonate dehydratase | B9O00_RS28450 | B9O00_RS04150 |
| galactose | galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) | B9O00_RS08745 | B9O00_RS27675 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| gluconate | gntA: gluconate TRAP transporter, small permease component | B9O00_RS25080 | B9O00_RS21635 |
| gluconate | gntB: gluconate TRAP transporter, large permease component | B9O00_RS31065 | B9O00_RS05660 |
| gluconate | gntC: gluconate TRAP transporter, periplasmic solute-binding component | B9O00_RS02415 | B9O00_RS06880 |
| glucosamine | AO353_21710: glucosaminate ABC transporter, substrate-binding component | | |
| glucosamine | AO353_21715: glucosaminate ABC transporter, permease component 1 | B9O00_RS00465 | B9O00_RS11835 |
| glucosamine | AO353_21720: glucosaminate ABC transporter, permease component 2 | B9O00_RS21440 | B9O00_RS11830 |
| glucosamine | AO353_21725: glucosaminate ABC transporter, ATPase component | B9O00_RS00455 | B9O00_RS08530 |
| glucosamine | kdgA: 2-keto-3-deoxygluconate-6-phosphate aldolase EC:4.1.2.14 | B9O00_RS13810 | B9O00_RS09055 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | dctP: D-glucuronate TRAP transporter, solute receptor component | B9O00_RS27400 | B9O00_RS06880 |
| glucuronate | dctQ: D-glucuronate TRAP transporter, small permease component | | |
| glutamate | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | B9O00_RS06670 | B9O00_RS30245 |
| glutamate | aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP | B9O00_RS06665 | B9O00_RS30340 |
| histidine | aapM: L-histidine ABC transporter, permease component 2 (AapM) | B9O00_RS06670 | B9O00_RS30245 |
| histidine | aapP: L-histidine ABC transporter, ATPase component AapP | B9O00_RS06665 | B9O00_RS30340 |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| L-malate | dctQ: L-malate TRAP tranpsorter, small permease component DctQ | B9O00_RS00200 | |
| lactose | dgoD: D-galactonate dehydratase | B9O00_RS28450 | B9O00_RS04150 |
| lactose | galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) | B9O00_RS08745 | B9O00_RS27675 |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | | |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | davT: 5-aminovalerate aminotransferase | B9O00_RS06850 | B9O00_RS00755 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | B9O00_RS18960 | B9O00_RS14030 |
| lysine | hisM: L-lysine ABC transporter, permease component 1 (HisM) | B9O00_RS08515 | B9O00_RS25795 |
| lysine | hisP: L-lysine ABC transporter, ATPase component HisP | B9O00_RS08530 | B9O00_RS06665 |
| lysine | hisQ: L-lysine ABC transporter, permease component 2 (HisQ) | B9O00_RS08520 | B9O00_RS25800 |
| maltose | susB: alpha-glucosidase (maltase) | B9O00_RS21700 | |
| mannitol | mt2d: mannitol 2-dehydrogenase | B9O00_RS19815 | B9O00_RS24110 |
| mannitol | mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) | B9O00_RS24120 | B9O00_RS11630 |
| 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 | | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | B9O00_RS24585 | |
| 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 | B9O00_RS13960 | B9O00_RS09170 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | livH: L-phenylalanine ABC transporter, permease component 1 (LivH) | B9O00_RS11425 | B9O00_RS18240 |
| phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | B9O00_RS11400 | B9O00_RS18765 |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | B9O00_RS06120 | |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | potC: putrescine ABC transporter, permease component 2 (PotC/PotI) | B9O00_RS01110 | B9O00_RS15950 |
| putrescine | potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) | B9O00_RS19695 | B9O00_RS15940 |
| pyruvate | dctQ: pyruvate TRAP transporter, small permease component | B9O00_RS10545 | B9O00_RS20285 |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | B9O00_RS14420 | B9O00_RS12565 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | B9O00_RS01575 | B9O00_RS27415 |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| serine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | B9O00_RS11400 | B9O00_RS19590 |
| serine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | B9O00_RS11425 | B9O00_RS18240 |
| serine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | B9O00_RS11420 | B9O00_RS18235 |
| sucrose | ams: sucrose hydrolase (invertase) | B9O00_RS21700 | |
| threonine | adh: acetaldehyde dehydrogenase (not acylating) | B9O00_RS05420 | B9O00_RS20310 |
| threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | B9O00_RS11400 | B9O00_RS19590 |
| threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | B9O00_RS11425 | B9O00_RS18240 |
| threonine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | B9O00_RS11420 | B9O00_RS18235 |
| threonine | ltaE: L-threonine aldolase | B9O00_RS22365 | B9O00_RS11385 |
| thymidine | adh: acetaldehyde dehydrogenase (not acylating) | B9O00_RS05420 | B9O00_RS20310 |
| thymidine | deoA: thymidine phosphorylase DeoA | B9O00_RS15370 | |
| thymidine | deoB: phosphopentomutase | B9O00_RS14620 | |
| thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | treF: trehalase | B9O00_RS09545 | B9O00_RS31295 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | Ac3H11_1692: L-tyrosine ABC transporter, ATPase component 2 | B9O00_RS15725 | B9O00_RS11410 |
| tyrosine | Ac3H11_1693: L-tyrosine ABC transporter, ATPase component 1 | B9O00_RS18235 | B9O00_RS11415 |
| tyrosine | Ac3H11_1694: L-tyrosine ABC transporter, permease component 2 | B9O00_RS11420 | B9O00_RS18235 |
| tyrosine | Ac3H11_1695: L-tyrosine ABC transporter, permease component 1 | B9O00_RS18240 | B9O00_RS11425 |
| tyrosine | Ac3H11_2396: L-tyrosine ABC transporter, substrate-binding component component | B9O00_RS18245 | B9O00_RS11400 |
| valine | livM: L-valine ABC transporter, permease component 2 (LivM/BraE) | B9O00_RS11420 | B9O00_RS18205 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | B9O00_RS16490 | B9O00_RS00790 |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | B9O00_RS09150 | |
| xylose | xdh: D-xylose dehydrogenase | B9O00_RS29730 | B9O00_RS20720 |
| xylose | xylC: xylonolactonase | B9O00_RS08750 | B9O00_RS08745 |
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