Potential Gaps in catabolism of small carbon sources in Pleomorphomonas diazotrophica R5-392
Found 80 low-confidence and 47 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | CXZ10_RS06180 | |
| 4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | CXZ10_RS17870 | |
| 4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | CXZ10_RS02190 | CXZ10_RS19465 |
| 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 | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | CXZ10_RS02245 | CXZ10_RS02250 |
| alanine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | CXZ10_RS02220 | CXZ10_RS20565 |
| alanine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | CXZ10_RS02230 | CXZ10_RS13695 |
| asparagine | ans: asparaginase | CXZ10_RS04545 | CXZ10_RS21130 |
| citrate | cimH: citrate:H+ symporter CimH | CXZ10_RS05025 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | CXZ10_RS04080 | CXZ10_RS07645 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | CXZ10_RS04075 | CXZ10_RS12885 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | CXZ10_RS04070 | CXZ10_RS03905 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | CXZ10_RS12875 | CXZ10_RS03890 |
| citrulline | arcC: carbamate kinase | | |
| D-alanine | AZOBR_RS08240: D-alanine ABC transporter, permease component 2 | CXZ10_RS02225 | |
| D-alanine | AZOBR_RS08260: D-alanine ABC transporter, substrate-binding component | CXZ10_RS02245 | CXZ10_RS02250 |
| D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | | |
| D-serine | cycA: D-serine:H+ symporter CycA | CXZ10_RS00650 | |
| D-serine | dsdA: D-serine ammonia-lyase | CXZ10_RS06580 | CXZ10_RS06595 |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
| deoxyribonate | aacS: acetoacetyl-CoA synthetase | | |
| deoxyribonate | atoB: acetyl-CoA C-acetyltransferase | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | CXZ10_RS10655 | CXZ10_RS19210 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | CXZ10_RS15815 | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fucose | aldA: lactaldehyde dehydrogenase | CXZ10_RS19950 | CXZ10_RS13775 |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | CXZ10_RS04240 | CXZ10_RS09660 |
| fucose | fucK: L-fuculose kinase FucK | CXZ10_RS04170 | |
| fucose | HSERO_RS05255: ABC transporter for L-fucose, permease component | CXZ10_RS18790 | CXZ10_RS09525 |
| fucose | HSERO_RS05260: ABC transporter for L-fucose, substrate-binding component | CXZ10_RS14275 | |
| fumarate | dctA: fumarate:H+ symporter DctA | | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | uxaC: D-galacturonate isomerase | CXZ10_RS07825 | |
| glucose | mglA: glucose ABC transporter, ATP-binding component (MglA) | CXZ10_RS18795 | CXZ10_RS07200 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | uxaC: D-glucuronate isomerase | CXZ10_RS07825 | |
| glucuronate | uxuB: D-mannonate dehydrogenase | CXZ10_RS07820 | |
| glycerol | glpF: glycerol facilitator glpF | | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | | |
| isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | | |
| isoleucine | fadA: 2-methylacetoacetyl-CoA thiolase | | |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | CXZ10_RS02970 | CXZ10_RS10655 |
| isoleucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| isoleucine | prpB: 2-methylisocitrate lyase | | |
| isoleucine | prpC: 2-methylcitrate synthase | CXZ10_RS18020 | |
| isoleucine | prpD: 2-methylcitrate dehydratase | | |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| L-lactate | lutC: L-lactate dehydrogenase, LutC subunit | CXZ10_RS18525 | |
| leucine | aacS: acetoacetyl-CoA synthetase | | |
| leucine | atoB: acetyl-CoA C-acetyltransferase | | |
| leucine | liuA: isovaleryl-CoA dehydrogenase | | |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | CXZ10_RS16310 | CXZ10_RS06450 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | | |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | | |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| leucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| lysine | hglS: D-2-hydroxyglutarate synthase | | |
| lysine | hisP: L-lysine ABC transporter, ATPase component HisP | CXZ10_RS04080 | CXZ10_RS00845 |
| lysine | lat: L-lysine 6-aminotransferase | CXZ10_RS13890 | |
| lysine | lysN: 2-aminoadipate transaminase | CXZ10_RS11020 | CXZ10_RS04540 |
| lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | CXZ10_RS11675 | CXZ10_RS09405 |
| maltose | thuE: maltose ABC transporter, substrate-binding component ThuE | CXZ10_RS06140 | CXZ10_RS17770 |
| myoinositol | PS417_11885: myo-inositol ABC transporter, substrate-binding component | CXZ10_RS18785 | CXZ10_RS05095 |
| myoinositol | PS417_11895: myo-inositol ABC transporter, permease component | CXZ10_RS18790 | CXZ10_RS14285 |
| 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 | | |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | | |
| phenylacetate | paaH: 3-hydroxyadipyl-CoA dehydrogenase | CXZ10_RS16425 | CXZ10_RS10655 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | | |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | | |
| phenylacetate | paaK: phenylacetate-CoA ligase | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aacS: acetoacetyl-CoA synthetase | | |
| phenylalanine | atoB: acetyl-CoA C-acetyltransferase | | |
| phenylalanine | fahA: fumarylacetoacetate hydrolase | CXZ10_RS14265 | |
| phenylalanine | hmgA: homogentisate dioxygenase | | |
| phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| phenylalanine | maiA: maleylacetoacetate isomerase | CXZ10_RS01080 | |
| phenylalanine | PAH: phenylalanine 4-monooxygenase | | |
| phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | | |
| propionate | prpB: 2-methylisocitrate lyase | | |
| propionate | prpC: 2-methylcitrate synthase | CXZ10_RS18020 | |
| propionate | prpD: 2-methylcitrate dehydratase | | |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | gabT: gamma-aminobutyrate transaminase | CXZ10_RS21045 | CXZ10_RS12695 |
| rhamnose | aldA: lactaldehyde dehydrogenase | CXZ10_RS19950 | CXZ10_RS13775 |
| serine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | CXZ10_RS02245 | CXZ10_RS02250 |
| serine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | CXZ10_RS02220 | CXZ10_RS20565 |
| serine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | CXZ10_RS02230 | CXZ10_RS13695 |
| sorbitol | mtlF: ABC transporter for polyols MtlEFGK, permease component MtlF | CXZ10_RS19055 | CXZ10_RS03875 |
| sorbitol | mtlG: ABC transporter for polyols MtlEFGK, permease component MtlG | CXZ10_RS16940 | CXZ10_RS17780 |
| sorbitol | sdh: sorbitol dehydrogenase | CXZ10_RS07210 | CXZ10_RS05070 |
| sucrose | thuE: sucrose ABC transporter, substrate-binding component ThuE | CXZ10_RS06140 | CXZ10_RS17770 |
| threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | CXZ10_RS02245 | CXZ10_RS02250 |
| threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | CXZ10_RS02220 | CXZ10_RS20565 |
| threonine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | CXZ10_RS02230 | CXZ10_RS13695 |
| threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | CXZ10_RS18160 | CXZ10_RS18165 |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | thuK: trehalose ABC transporter, ATPase component ThuK | CXZ10_RS06160 | CXZ10_RS00280 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | CXZ10_RS00650 | |
| tyrosine | aacS: acetoacetyl-CoA synthetase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | CXZ10_RS00650 | |
| tyrosine | atoB: acetyl-CoA C-acetyltransferase | | |
| tyrosine | fahA: fumarylacetoacetate hydrolase | CXZ10_RS14265 | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | CXZ10_RS01080 | |
| valine | acdH: isobutyryl-CoA dehydrogenase | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | | |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | | |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | CXZ10_RS12895 | |
| valine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| valine | prpB: 2-methylisocitrate lyase | | |
| valine | prpC: 2-methylcitrate synthase | CXZ10_RS18020 | |
| valine | prpD: 2-methylcitrate dehydratase | | |
| xylitol | PS417_12055: xylitol ABC transporter, substrate-binding component | CXZ10_RS07190 | CXZ10_RS18785 |
| xylitol | PS417_12065: xylitol ABC transporter, ATPase component | CXZ10_RS19115 | CXZ10_RS11565 |
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