Potential Gaps in catabolism of small carbon sources in Mesorhizobium ciceri WSM1271
Found 39 low-confidence and 44 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | pcaF: succinyl-CoA:acetyl-CoA C-succinyltransferase | Mesci_1095 | Mesci_1329 |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| alanine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | Mesci_1239 | Mesci_4851 |
| alanine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | Mesci_1234 | Mesci_6236 |
| alanine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | Mesci_1235 | Mesci_6237 |
| arginine | braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) | Mesci_1235 | Mesci_6237 |
| arginine | gbuA: guanidinobutyrase | Mesci_0570 | Mesci_4440 |
| cellobiose | cbp: cellobiose phosphorylase | | |
| citrate | tctB: citrate/Na+ symporter, small transmembrane component TctB | | |
| citrate | tctC: citrate/Na+ symporter, substrate-binding component TctC | Mesci_1768 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | Mesci_0317 | Mesci_2595 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | Mesci_2592 | Mesci_0320 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | Mesci_0319 | Mesci_5618 |
| D-alanine | Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component | Mesci_4657 | Mesci_2581 |
| D-alanine | Pf6N2E2_5403: ABC transporter for D-Alanine, permease component 2 | Mesci_4656 | Mesci_2580 |
| D-alanine | Pf6N2E2_5404: ABC transporter for D-Alanine, permease component 1 | Mesci_4655 | Mesci_2579 |
| 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 | Mesci_4922 | Mesci_0790 |
| deoxyinosine | bmpA: deoxyinosine ABC transporter, substrate-binding component | Mesci_1794 | Mesci_2468 |
| deoxyinosine | nupB: deoxyinosine ABC transporter, permease component 1 | Mesci_2049 | Mesci_1789 |
| deoxyinosine | nupC': deoxyinosine ABC transporter, permease component 2 | Mesci_1099 | Mesci_1788 |
| 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 | Mesci_1336 | Mesci_3778 |
| deoxyribose | drdehyd-beta: 2-deoxy-D-ribose dehydrogenase, beta subunit | Mesci_1337 | |
| deoxyribose | drdehyd-cytc: 2-deoxyribose-D dehydrogenase, cytochrome c component | Mesci_4081 | Mesci_5476 |
| fucose | fucD: L-fuconate dehydratase | Mesci_0298 | Mesci_1686 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | uxaA: D-altronate dehydratase | Mesci_1686 | Mesci_0298 |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | Mesci_1182 | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | nagX: transmembrane glucosamine N-acetyltransferase NagX | | |
| 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 | Mesci_2590 | Mesci_0112 |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | Mesci_1662 | Mesci_0308 |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | Mesci_3403 | Mesci_4845 |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| lactose | lacE: lactose ABC transporter, substrate-binding component | | |
| lactose | lacG: lactose ABC transporter, permease component 2 | Mesci_2353 | Mesci_1566 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | Mesci_6037 | Mesci_1860 |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| lysine | cadA: lysine decarboxylase | Mesci_1913 | Mesci_4422 |
| lysine | fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase | Mesci_1071 | Mesci_6001 |
| lysine | patA: cadaverine aminotransferase | Mesci_5987 | Mesci_3346 |
| mannose | man-isomerase: D-mannose isomerase | Mesci_4925 | |
| 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 | Mesci_6037 | Mesci_4665 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | Mesci_0108 | Mesci_4665 |
| phenylacetate | paaH: 3-hydroxyadipyl-CoA dehydrogenase | Mesci_1071 | Mesci_6001 |
| phenylacetate | paaK: phenylacetate-CoA ligase | Mesci_0122 | Mesci_0716 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | Mesci_6037 | Mesci_4665 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | livH: L-phenylalanine ABC transporter, permease component 1 (LivH) | Mesci_1234 | Mesci_6236 |
| phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | Mesci_1239 | Mesci_4851 |
| phenylalanine | maiA: maleylacetoacetate isomerase | Mesci_3453 | Mesci_4357 |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | Mesci_2598 | |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| serine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | Mesci_1239 | Mesci_4851 |
| serine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | Mesci_1234 | Mesci_6236 |
| serine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | Mesci_1235 | Mesci_6237 |
| threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | Mesci_1239 | Mesci_4851 |
| threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | Mesci_1234 | Mesci_6236 |
| threonine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | Mesci_1235 | Mesci_6237 |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| tryptophan | andAb: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin subunit AndAb | Mesci_2643 | |
| tryptophan | andAc: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AndAc | | |
| tryptophan | andAd: athranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AndAd | | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | kynB: kynurenine formamidase | Mesci_5387 | Mesci_3962 |
| tryptophan | mhpD: 2-hydroxypentadienoate hydratase | Mesci_0681 | |
| tryptophan | xylF: 2-hydroxymuconate semialdehyde hydrolase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | maiA: maleylacetoacetate isomerase | Mesci_3453 | Mesci_4357 |
| valine | acdH: isobutyryl-CoA dehydrogenase | Mesci_3403 | Mesci_4845 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | Mesci_1228 | Mesci_0678 |
| xylitol | xdhA: xylitol dehydrogenase | Mesci_0343 | Mesci_5334 |
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