Potential Gaps in catabolism of small carbon sources in Bacillus velezensis CBMB205
Found 58 low-confidence and 45 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | csbX: 2-oxoglutarate permease csbX | AAV34_RS09920 | |
| 4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | | |
| 4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | AAV34_RS06505 | |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| 4-hydroxybenzoate | pobA: 4-hydroxybenzoate 3-monooxygenase | | |
| 4-hydroxybenzoate | praA: protocatechuate 2,3-dioxygenase | | |
| 4-hydroxybenzoate | praB: 2-hydroxymuconate 6-semialdehyde dehydrogenase | AAV34_RS09750 | AAV34_RS05095 |
| 4-hydroxybenzoate | praD: 2-oxohex-3-enedioate decarboxylase | | |
| acetate | dctA: organic acid/proton symporter DctA | AAV34_RS17055 | AAV34_RS14255 |
| cellobiose | bgl: cellobiase | AAV34_RS01120 | AAV34_RS09595 |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | AAV34_RS08140 | AAV34_RS06915 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | AAV34_RS03730 | AAV34_RS08135 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | AAV34_RS17500 | AAV34_RS08135 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | AAV34_RS08130 | AAV34_RS17505 |
| citrulline | arcC: carbamate kinase | | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | D-LDH: D-lactate dehydrogenase | AAV34_RS06295 | AAV34_RS08685 |
| D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | AAV34_RS03335 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | AAV34_RS00185 | AAV34_RS09935 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fucose | aldA: lactaldehyde dehydrogenase | AAV34_RS09750 | AAV34_RS05095 |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | | |
| 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 | | |
| galacturonate | kdgK: 2-keto-3-deoxygluconate kinase | AAV34_RS10295 | AAV34_RS00690 |
| galacturonate | PS417_04205: D-galacturonate transporter | AAV34_RS17755 | AAV34_RS10265 |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | AAV34_RS12475 | AAV34_RS15595 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | AAV34_RS18180 | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | AAV34_RS17755 | |
| glucuronate | kdgK: 2-keto-3-deoxygluconate kinase | AAV34_RS10295 | AAV34_RS00690 |
| glucuronate | uxuB: D-mannonate dehydrogenase | | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | AAV34_RS10080 | AAV34_RS08055 |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | AAV34_RS08115 | AAV34_RS12080 |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | AAV34_RS17910 | AAV34_RS01605 |
| lactose | lacY: lactose:proton symporter LacY | AAV34_RS03170 | |
| lactose | lacZ: lactase (homomeric) | AAV34_RS09595 | AAV34_RS01120 |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | AAV34_RS08115 | AAV34_RS12080 |
| leucine | liuA: isovaleryl-CoA dehydrogenase | AAV34_RS10080 | AAV34_RS08055 |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | AAV34_RS11950 | AAV34_RS07930 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | AAV34_RS10110 | AAV34_RS08160 |
| lysine | cadA: lysine decarboxylase | AAV34_RS03110 | |
| lysine | davD: glutarate semialdehyde dehydrogenase | AAV34_RS17385 | AAV34_RS09750 |
| lysine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | AAV34_RS10105 | AAV34_RS06370 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | | |
| lysine | gcdH: glutaryl-CoA dehydrogenase | AAV34_RS08055 | AAV34_RS10080 |
| lysine | lysP: L-lysine:H+ symporter LysP | AAV34_RS01580 | AAV34_RS00470 |
| lysine | patA: cadaverine aminotransferase | AAV34_RS00465 | AAV34_RS13840 |
| lysine | patD: 5-aminopentanal dehydrogenase | AAV34_RS09750 | AAV34_RS05095 |
| phenylacetate | H281DRAFT_04042: phenylacetate:H+ symporter | AAV34_RS05395 | AAV34_RS18265 |
| 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 | AAV34_RS10105 | AAV34_RS06370 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | AAV34_RS10105 | AAV34_RS06370 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | AAV34_RS04175 | AAV34_RS08045 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | AAV34_RS04175 | AAV34_RS08045 |
| phenylacetate | paaK: phenylacetate-CoA ligase | AAV34_RS14230 | AAV34_RS06360 |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | AAV34_RS06370 | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | AAV34_RS05395 | AAV34_RS18265 |
| phenylalanine | fahA: fumarylacetoacetate hydrolase | AAV34_RS14010 | |
| phenylalanine | hmgA: homogentisate dioxygenase | | |
| phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| phenylalanine | maiA: maleylacetoacetate isomerase | | |
| phenylalanine | PAH: phenylalanine 4-monooxygenase | | |
| phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | AAV34_RS05070 | AAV34_RS05800 |
| propionate | prpE: propionyl-CoA synthetase | AAV34_RS05915 | AAV34_RS05745 |
| propionate | putP: propionate transporter; proline:Na+ symporter | AAV34_RS17725 | AAV34_RS15970 |
| putrescine | gabT: gamma-aminobutyrate transaminase | AAV34_RS17390 | AAV34_RS14730 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | AAV34_RS14730 | AAV34_RS09500 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | AAV34_RS05095 | AAV34_RS09750 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| pyruvate | mctP: pyruvate permease MctP | AAV34_RS09605 | |
| rhamnose | aldA: lactaldehyde dehydrogenase | AAV34_RS09750 | AAV34_RS05095 |
| rhamnose | rhaA: L-rhamnose isomerase | | |
| rhamnose | rhaB: L-rhamnulokinase | | |
| rhamnose | rhaD: rhamnulose 1-phosphate aldolase | | |
| rhamnose | rhaM: L-rhamnose mutarotase | | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsU: probable D-ribose transporter RbsU | AAV34_RS17380 | |
| serine | serP: L-serine permease SerP | AAV34_RS00575 | AAV34_RS18265 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | AAV34_RS02555 | AAV34_RS00665 |
| threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | AAV34_RS07830 | AAV34_RS07825 |
| threonine | ltaE: L-threonine aldolase | AAV34_RS02005 | |
| threonine | serP1: L-threonine uptake transporter SerP1 | AAV34_RS00575 | AAV34_RS05395 |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | AAV34_RS05395 | AAV34_RS16155 |
| tyrosine | fahA: fumarylacetoacetate hydrolase | AAV34_RS14010 | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | AAV34_RS08055 | AAV34_RS10080 |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | AAV34_RS10105 | AAV34_RS05275 |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | AAV34_RS08115 | AAV34_RS12080 |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | AAV34_RS10105 | AAV34_RS06370 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | AAV34_RS12445 | AAV34_RS15420 |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | AAV34_RS02555 | AAV34_RS00665 |
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