Potential Gaps in catabolism of small carbon sources in Flavobacterium glycines Gm-149
Found 109 low-confidence and 25 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | BLR17_RS15810 | |
| 4-hydroxybenzoate | pcaI: 3-oxoadipate CoA-transferase subunit A (PcaI) | BLR17_RS02660 | BLR17_RS09290 |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| alanine | cycA: L-alanine symporter CycA | | |
| arabinose | Echvi_1880: L-arabinose:Na+ symporter | BLR17_RS09055 | BLR17_RS08995 |
| arginine | rocE: L-arginine permease | | |
| arginine | rocF: arginase | BLR17_RS15160 | |
| cellobiose | glk: glucokinase | | |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | BLR17_RS12145 | BLR17_RS06945 |
| 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 | BLR17_RS04955 | |
| 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 | BLR17_RS06705 | BLR17_RS06690 |
| deoxyinosine | deoB: phosphopentomutase | BLR17_RS07845 | |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | BLR17_RS09410 | BLR17_RS14060 |
| 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 | BLR17_RS13860 | BLR17_RS03160 |
| ethanol | etoh-dh-nad: ethanol dehydrogenase (NAD(P)) | BLR17_RS03640 | BLR17_RS09060 |
| fucose | fucD: L-fuconate dehydratase | BLR17_RS06410 | |
| fucose | fucDH: 2-keto-3-deoxy-L-fuconate 4-dehydrogenase | BLR17_RS09120 | BLR17_RS14060 |
| fucose | fuconolactonase: L-fucono-1,5-lactonase | BLR17_RS10280 | |
| fumarate | SLC26dg: fumarate transporter SLC26dg | BLR17_RS09740 | |
| gluconate | edd: phosphogluconate dehydratase | BLR17_RS11915 | BLR17_RS13755 |
| gluconate | gntK: D-gluconate kinase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucose | glk: glucokinase | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | uxuB: D-mannonate dehydrogenase | | |
| glutamate | gdhA: glutamate dehydrogenase, NAD-dependent | BLR17_RS03690 | |
| glutamate | gltP: L-glutamate:cation symporter GltP/GltT | BLR17_RS14505 | |
| glycerol | glpF: glycerol facilitator glpF | | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| histidine | permease: L-histidine permease | | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | BLR17_RS11710 | BLR17_RS06975 |
| isoleucine | Bap2: L-isoleucine permease Bap2 | | |
| isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | BLR17_RS02485 | BLR17_RS04170 |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | BLR17_RS06385 | BLR17_RS14060 |
| isoleucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | BLR17_RS04080 | |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| L-lactate | lldG: L-lactate dehydrogenase, LldG subunit | BLR17_RS09465 | |
| L-malate | sdlC: L-malate:Na+ symporter SdlC | | |
| lactose | glk: glucokinase | | |
| lactose | lacP: lactose permease LacP | | |
| leucine | leuT: L-leucine:Na+ symporter LeuT | | |
| leucine | liuA: isovaleryl-CoA dehydrogenase | BLR17_RS06975 | BLR17_RS11710 |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | BLR17_RS04080 | |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | BLR17_RS02485 | |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | BLR17_RS09265 | |
| leucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| lysine | davA: 5-aminovaleramidase | | |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | davD: glutarate semialdehyde dehydrogenase | | |
| lysine | davT: 5-aminovalerate aminotransferase | BLR17_RS15165 | BLR17_RS09610 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | BLR17_RS03135 | |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| maltose | glk: glucokinase | | |
| mannitol | mt2d: mannitol 2-dehydrogenase | BLR17_RS14060 | BLR17_RS01565 |
| mannitol | PLT5: polyol transporter PLT5 | BLR17_RS06000 | BLR17_RS06040 |
| mannose | manA: mannose-6-phosphate isomerase | BLR17_RS10910 | BLR17_RS10395 |
| mannose | manP: mannose PTS system, EII-CBA components | | |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | BLR17_RS01475 | |
| 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 | BLR17_RS10195 | BLR17_RS06040 |
| myoinositol | uxaE: D-tagaturonate epimerase | | |
| myoinositol | uxuB: D-mannonate dehydrogenase | | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| 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 | BLR17_RS02485 | |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | BLR17_RS02485 | |
| 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 | hmgA: homogentisate dioxygenase | | |
| phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| phenylalanine | maiA: maleylacetoacetate isomerase | | |
| phenylalanine | PAH: phenylalanine 4-monooxygenase | | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | | |
| proline | N515DRAFT_2924: proline transporter | BLR17_RS06965 | |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | BLR17_RS04080 | |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | gabD: succinate semialdehyde dehydrogenase | BLR17_RS03500 | |
| putrescine | gabT: gamma-aminobutyrate transaminase | BLR17_RS15165 | BLR17_RS09610 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | BLR17_RS15165 | BLR17_RS09610 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | | |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| pyruvate | SLC5A8: sodium-coupled pyruvate transporter | | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | BLR17_RS09500 | |
| ribose | rbsK: ribokinase | | |
| serine | sdaB: L-serine ammonia-lyase | BLR17_RS06705 | BLR17_RS06690 |
| serine | serP: L-serine permease SerP | | |
| sorbitol | sdh: sorbitol dehydrogenase | BLR17_RS10275 | BLR17_RS08785 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | BLR17_RS06040 | BLR17_RS06000 |
| sucrose | ams: sucrose hydrolase (invertase) | BLR17_RS06005 | BLR17_RS08980 |
| threonine | tdcC: L-threonine:H+ symporter TdcC | | |
| thymidine | deoA: thymidine phosphorylase DeoA | | |
| thymidine | deoB: phosphopentomutase | BLR17_RS07845 | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | glk: glucokinase | | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | BLR17_RS11710 | BLR17_RS06975 |
| valine | Bap2: L-valine permease Bap2 | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | BLR17_RS02485 | |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | BLR17_RS03500 | |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | | |
| valine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | BLR17_RS04080 | |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | BLR17_RS06040 | BLR17_RS10195 |
| xylitol | xdhA: xylitol dehydrogenase | BLR17_RS10275 | BLR17_RS09410 |
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