Potential Gaps in catabolism of small carbon sources in Flaviramulus ichthyoenteri Th78
Found 101 low-confidence and 39 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | | |
| 4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | | |
| 4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | | |
| 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 | | |
| acetate | actP: cation/acetate symporter ActP | RG22_RS10630 | RG22_RS15110 |
| arabinose | xacB: L-arabinose 1-dehydrogenase | RG22_RS14915 | RG22_RS00320 |
| arabinose | xacC: L-arabinono-1,4-lactonase | | |
| arabinose | xacD: L-arabinonate dehydratase | RG22_RS10975 | RG22_RS14910 |
| arabinose | xacE: 2-dehydro-3-deoxy-L-arabinonate dehydratase | | |
| arginine | rocE: L-arginine permease | | |
| arginine | rocF: arginase | | |
| cellobiose | bgl: cellobiase | RG22_RS07615 | RG22_RS14830 |
| cellobiose | glk: glucokinase | | |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | RG22_RS10040 | RG22_RS01415 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | | |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | | |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
| D-alanine | cycA: D-alanine:H+ symporter CycA | | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | D-LDH: D-lactate dehydrogenase | RG22_RS07435 | RG22_RS01370 |
| D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | | |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| deoxyinosine | deoB: phosphopentomutase | RG22_RS13075 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | RG22_RS03355 | RG22_RS02275 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | garK: glycerate 2-kinase | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoK: deoxyribokinase | | |
| deoxyribose | deoP: deoxyribose transporter | RG22_RS02195 | |
| ethanol | etoh-dh-nad: ethanol dehydrogenase (NAD(P)) | RG22_RS03305 | RG22_RS03255 |
| fructose | 1pfk: 1-phosphofructokinase | | |
| fructose | fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components | | |
| fucose | fucD: L-fuconate dehydratase | | |
| fucose | fucDH: 2-keto-3-deoxy-L-fuconate 4-dehydrogenase | RG22_RS02275 | RG22_RS00320 |
| fucose | fuconolactonase: L-fucono-1,5-lactonase | RG22_RS02225 | |
| galacturonate | exuT: D-galacturonate transporter ExuT | RG22_RS03310 | |
| glucosamine | nagK: N-acetylglucosamine kinase | | |
| glucose | glk: glucokinase | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | RG22_RS03310 | |
| glucuronate | uxuA: D-mannonate dehydratase | RG22_RS14890 | RG22_RS14910 |
| glucuronate | uxuB: D-mannonate dehydrogenase | | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | | |
| glycerol | glpF: glycerol facilitator glpF | RG22_RS01910 | RG22_RS14005 |
| glycerol | glpK: glycerol kinase | | |
| histidine | permease: L-histidine permease | | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | RG22_RS05640 | RG22_RS02810 |
| isoleucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | RG22_RS16905 | RG22_RS05535 |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | RG22_RS04480 | RG22_RS09660 |
| isoleucine | brnQ: L-isoleucine:cation symporter BrnQ/BraZ/BraB | RG22_RS06910 | |
| isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | RG22_RS07780 | RG22_RS12975 |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | RG22_RS03570 | RG22_RS00320 |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | RG22_RS15140 | RG22_RS08620 |
| L-lactate | L-LDH: L-lactate dehydrogenase | RG22_RS07635 | RG22_RS02180 |
| L-malate | sdlC: L-malate:Na+ symporter SdlC | | |
| lactose | glk: glucokinase | | |
| lactose | lacP: lactose permease LacP | | |
| leucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | RG22_RS16905 | RG22_RS05535 |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | RG22_RS04480 | RG22_RS09660 |
| leucine | brnQ: L-leucine:Na+ symporter BrnQ/BraB | RG22_RS06910 | |
| leucine | liuA: isovaleryl-CoA dehydrogenase | RG22_RS05640 | RG22_RS02810 |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | RG22_RS15140 | RG22_RS08620 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | RG22_RS07780 | |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | RG22_RS16470 | RG22_RS15135 |
| lysine | hglS: D-2-hydroxyglutarate synthase | | |
| lysine | lat: L-lysine 6-aminotransferase | RG22_RS15250 | RG22_RS05965 |
| lysine | lysN: 2-aminoadipate transaminase | RG22_RS04940 | RG22_RS15250 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | RG22_RS10765 | RG22_RS03180 |
| maltose | glk: glucokinase | | |
| mannitol | mtlA: mannitol phosphotransferase system, EII-CBA components | | |
| mannitol | mtlD: mannitol-1-phosphate 5-dehydrogenase | | |
| mannose | manP: mannose PTS system, EII-CBA components | | |
| 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 | RG22_RS12340 | RG22_RS14865 |
| myoinositol | uxaE: D-tagaturonate epimerase | | |
| myoinositol | uxuA: D-mannonate dehydratase | RG22_RS14890 | RG22_RS14910 |
| myoinositol | uxuB: D-mannonate dehydrogenase | | |
| NAG | nagK: N-acetylglucosamine kinase | | |
| 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 | paaF: 2,3-dehydroadipyl-CoA hydratase | RG22_RS07780 | |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | RG22_RS07780 | |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | RG22_RS12970 | RG22_RS15425 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | RG22_RS12970 | RG22_RS15425 |
| phenylacetate | paaK: phenylacetate-CoA ligase | | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | maiA: maleylacetoacetate isomerase | | |
| phenylalanine | PAH: phenylalanine 4-monooxygenase | RG22_RS04660 | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | | |
| proline | proY: proline:H+ symporter | | |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | RG22_RS15140 | RG22_RS08620 |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | gabD: succinate semialdehyde dehydrogenase | RG22_RS12370 | RG22_RS08970 |
| putrescine | gabT: gamma-aminobutyrate transaminase | RG22_RS10905 | RG22_RS02535 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | RG22_RS02535 | RG22_RS15250 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | RG22_RS12370 | RG22_RS08970 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| pyruvate | actP: large subunit of pyruvate transporter (actP-like) | RG22_RS10630 | RG22_RS15110 |
| pyruvate | yjcH: putative small subunit of pyruvate transporter (yjcH-like) | RG22_RS15105 | RG22_RS10625 |
| rhamnose | rhaB: L-rhamnulokinase | RG22_RS07640 | |
| rhamnose | rhaM: L-rhamnose mutarotase | | |
| ribose | rbsK: ribokinase | | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | snatA: L-serine transporter | RG22_RS15795 | RG22_RS15130 |
| sorbitol | mtlA: PTS system for polyols, EII-CBA components | | |
| sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | RG22_RS00320 | RG22_RS14880 |
| succinate | sdc: succinate:Na+ symporter Sdc | | |
| sucrose | scrK: fructokinase | RG22_RS05410 | |
| sucrose | sut: sucrose:proton symporter SUT/SUC | RG22_RS05415 | |
| threonine | snatA: L-threonine transporter snatA | RG22_RS15795 | RG22_RS15130 |
| thymidine | deoA: thymidine phosphorylase DeoA | RG22_RS01020 | |
| thymidine | deoB: phosphopentomutase | RG22_RS13075 | |
| trehalose | glk: glucokinase | | |
| trehalose | klh: 3-ketotrehalose hydrolase | RG22_RS14540 | RG22_RS10945 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | RG22_RS05640 | RG22_RS02810 |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | RG22_RS07780 | |
| valine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | RG22_RS16905 | RG22_RS05535 |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | RG22_RS04480 | RG22_RS09660 |
| valine | brnQ: L-valine:cation symporter BrnQ/BraZ/BraB | RG22_RS06910 | |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | RG22_RS12370 | |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | | |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | RG22_RS15140 | RG22_RS08620 |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | | |
| xylitol | xdhA: xylitol dehydrogenase | RG22_RS03305 | RG22_RS10325 |
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