Potential Gaps in catabolism of small carbon sources in Thioclava dalianensis DLFJ1-1
Found 44 low-confidence and 49 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| alanine | snatA: L-alanine symporter SnatA | DL1_RS06400 | |
| arginine | artM: L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) | DL1_RS06155 | DL1_RS01475 |
| arginine | artP: L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA | DL1_RS06170 | DL1_RS04395 |
| arginine | artQ: L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) | DL1_RS01475 | DL1_RS07755 |
| citrate | tctB: citrate/Na+ symporter, small transmembrane component TctB | DL1_RS13035 | |
| citrulline | arcC: carbamate kinase | | |
| citrulline | PS417_17590: ABC transporter for L-Citrulline, periplasmic substrate-binding component | DL1_RS06165 | DL1_RS01470 |
| citrulline | PS417_17595: ABC transporter for L-Citrulline, permease component 1 | DL1_RS07755 | DL1_RS01475 |
| citrulline | PS417_17600: ABC transporter for L-Citrulline, permease component 2 | DL1_RS06155 | DL1_RS01475 |
| citrulline | PS417_17605: ABC transporter for L-Citrulline, ATPase component | DL1_RS06170 | DL1_RS12415 |
| D-alanine | cycA: D-alanine:H+ symporter CycA | | |
| D-alanine | dadA: D-alanine dehydrogenase | DL1_RS20020 | |
| 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 | DL1_RS03640 | |
| deoxyinosine | bmpA: deoxyinosine ABC transporter, substrate-binding component | DL1_RS13290 | |
| deoxyinosine | nupB: deoxyinosine ABC transporter, permease component 1 | DL1_RS13300 | |
| deoxyinosine | nupC': deoxyinosine ABC transporter, permease component 2 | DL1_RS08125 | DL1_RS13305 |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | DL1_RS03170 | DL1_RS01330 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | garK: glycerate 2-kinase | DL1_RS04565 | |
| deoxyribose | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | DL1_RS03170 | DL1_RS01330 |
| deoxyribose | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribose | garK: glycerate 2-kinase | DL1_RS04565 | |
| 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 | DL1_RS19795 | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | gli: D-galactarolactone isomerase | | |
| glucosamine | nagX: transmembrane glucosamine N-acetyltransferase NagX | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glutamate | aspA: L-aspartate ammonia-lyase | DL1_RS00215 | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| histidine | hutV: L-histidine ABC transporter, ATPase component HutV | DL1_RS14115 | DL1_RS15640 |
| histidine | hutX: L-histidine ABC transporter, substrate-binding component HutX | DL1_RS14105 | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | DL1_RS01635 | DL1_RS03415 |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | DL1_RS01330 | DL1_RS12245 |
| isoleucine | livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) | DL1_RS09650 | DL1_RS11165 |
| isoleucine | livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | | |
| isoleucine | livM: L-isoleucine ABC transporter, permease component 2 (LivM/BraE) | DL1_RS09655 | DL1_RS07590 |
| L-lactate | Shew_2731: L-lactate:Na+ symporter, large component | DL1_RS09905 | |
| L-lactate | Shew_2732: L-lactate:Na+ symporter, small component | DL1_RS09910 | |
| lactose | lacP: lactose permease LacP | | |
| leucine | aapJ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ | DL1_RS04380 | |
| leucine | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | DL1_RS04390 | DL1_RS07755 |
| leucine | aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP | DL1_RS04395 | DL1_RS03645 |
| leucine | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | DL1_RS04385 | DL1_RS07755 |
| lysine | fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase | DL1_RS09670 | DL1_RS08390 |
| lysine | hisM: L-lysine ABC transporter, permease component 1 (HisM) | DL1_RS06155 | DL1_RS01475 |
| lysine | hisP: L-lysine ABC transporter, ATPase component HisP | DL1_RS04395 | DL1_RS06170 |
| lysine | hisQ: L-lysine ABC transporter, permease component 2 (HisQ) | DL1_RS07755 | DL1_RS01475 |
| lysine | patA: cadaverine aminotransferase | DL1_RS02455 | DL1_RS05075 |
| lysine | patD: 5-aminopentanal dehydrogenase | DL1_RS03800 | DL1_RS04745 |
| myoinositol | PGA1_c07300: myo-inositol ABC transport, substrate-binding component | DL1_RS12530 | |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | DL1_RS07215 | DL1_RS09635 |
| phenylacetate | paaH: 3-hydroxyadipyl-CoA dehydrogenase | DL1_RS09670 | DL1_RS08390 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylalanine | ARO10: phenylpyruvate decarboxylase | | |
| phenylalanine | livG: L-phenylalanine ABC transporter, ATPase component 2 (LivG) | DL1_RS09660 | DL1_RS07575 |
| phenylalanine | livH: L-phenylalanine ABC transporter, permease component 1 (LivH) | DL1_RS09650 | DL1_RS00275 |
| phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | | |
| phenylalanine | livM: L-phenylalanine ABC transporter, permease component 2 (LivM) | DL1_RS09655 | DL1_RS07590 |
| phenylalanine | paaF: 2,3-dehydroadipyl-CoA hydratase | DL1_RS07215 | DL1_RS09635 |
| phenylalanine | paaH: 3-hydroxyadipyl-CoA dehydrogenase | DL1_RS09670 | DL1_RS08390 |
| propionate | putP: propionate transporter; proline:Na+ symporter | DL1_RS18285 | |
| putrescine | potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) | DL1_RS02780 | |
| putrescine | puuC: gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase | DL1_RS04745 | DL1_RS03800 |
| ribose | rbsK: ribokinase | DL1_RS08595 | |
| serine | snatA: L-serine transporter | DL1_RS06400 | |
| threonine | snatA: L-threonine transporter snatA | DL1_RS06400 | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | Ac3H11_1693: L-tyrosine ABC transporter, ATPase component 1 | DL1_RS09660 | DL1_RS07575 |
| tyrosine | Ac3H11_1694: L-tyrosine ABC transporter, permease component 2 | DL1_RS07590 | DL1_RS09655 |
| tyrosine | Ac3H11_1695: L-tyrosine ABC transporter, permease component 1 | DL1_RS09650 | |
| tyrosine | Ac3H11_2396: L-tyrosine ABC transporter, substrate-binding component component | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | DL1_RS07035 | |
| valine | acdH: isobutyryl-CoA dehydrogenase | DL1_RS03415 | DL1_RS01635 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | DL1_RS09340 | DL1_RS04745 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | DL1_RS01445 | DL1_RS00155 |
| valine | natB: L-valine ABC transporter, substrate-binding component NatB | DL1_RS00290 | |
| valine | natC: L-valine ABC transporter, permease component 1 (NatC) | | |
| valine | natD: L-valine ABC transporter, permease component 2 (NatD) | DL1_RS00275 | DL1_RS09650 |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | | |
| xylitol | xdhA: xylitol dehydrogenase | DL1_RS04040 | DL1_RS15075 |
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