Potential Gaps in catabolism of small carbon sources in Caulobacter crescentus NA1000
Found 74 low-confidence and 34 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | pcaI: 3-oxoadipate CoA-transferase subunit A (PcaI) | CCNA_00206 | CCNA_02488 |
| 4-hydroxybenzoate | pcaJ: 3-oxoadipate CoA-transferase subunit B (PcaJ) | CCNA_02489 | CCNA_00207 |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | CCNA_02495 | |
| alanine | snatA: L-alanine symporter SnatA | CCNA_00105 | |
| arabinose | araE: L-arabinose:H+ symporter | CCNA_00857 | |
| arabinose | xacC: L-arabinono-1,4-lactonase | CCNA_00863 | CCNA_01882 |
| arabinose | xacD: L-arabinonate dehydratase | CCNA_01488 | CCNA_00862 |
| arginine | adiA: arginine decarboxylase (AdiA/SpeA) | | |
| arginine | gabT: gamma-aminobutyrate transaminase | CCNA_03233 | CCNA_03245 |
| arginine | puuB: gamma-glutamylputrescine oxidase | CCNA_03229 | |
| arginine | rocE: L-arginine permease | | |
| asparagine | ans: asparaginase | CCNA_00278 | CCNA_00096 |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | CCNA_01506 | CCNA_02751 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | CCNA_01507 | |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | CCNA_01507 | |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | CCNA_01508 | |
| citrulline | citrullinase: putative citrullinase | CCNA_00212 | |
| citrulline | gabT: gamma-aminobutyrate transaminase | CCNA_03233 | CCNA_03245 |
| citrulline | odc: L-ornithine decarboxylase | CCNA_00365 | |
| citrulline | puuB: gamma-glutamylputrescine oxidase | CCNA_03229 | |
| D-alanine | cycA: D-alanine:H+ symporter CycA | | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | D-LDH: D-lactate dehydrogenase | CCNA_03500 | CCNA_03322 |
| 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 | CCNA_02112 | CCNA_03203 |
| deoxyinosine | deoB: phosphopentomutase | CCNA_02347 | |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyinosine | deoD: deoxyinosine phosphorylase | | |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | CCNA_02171 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | CCNA_01892 | CCNA_03172 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | CCNA_02439 | |
| deoxyribonate | garK: glycerate 2-kinase | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fucose | aldA: lactaldehyde dehydrogenase | CCNA_03243 | CCNA_03695 |
| 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 | | |
| galactose | dgoD: D-galactonate dehydratase | CCNA_01488 | CCNA_00862 |
| galactose | galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) | CCNA_00863 | CCNA_01882 |
| galactose | HP1174: Na+-dependent galactose transporter | CCNA_01159 | |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | CCNA_01557 | |
| gluconate | gntK: D-gluconate kinase | CCNA_03103 | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | nagX: transmembrane glucosamine N-acetyltransferase NagX | CCNA_00575 | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | uxaC: D-glucuronate isomerase | CCNA_01557 | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | | |
| glycerol | glpF: glycerol facilitator glpF | CCNA_01572 | |
| isoleucine | Bap2: L-isoleucine permease Bap2 | | |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| leucine | leuT: L-leucine:Na+ symporter LeuT | | |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | CCNA_00500 | |
| lysine | hglS: D-2-hydroxyglutarate synthase | | |
| lysine | lat: L-lysine 6-aminotransferase | CCNA_03233 | CCNA_02326 |
| lysine | lysN: 2-aminoadipate transaminase | CCNA_01603 | CCNA_02244 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | CCNA_03500 | |
| mannitol | mt2d: mannitol 2-dehydrogenase | CCNA_01554 | CCNA_03491 |
| mannitol | PLT5: polyol transporter PLT5 | | |
| mannose | manP: mannose PTS system, EII-CBA components | | |
| 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 | CCNA_00006 | CCNA_02658 |
| phenylacetate | paaK: phenylacetate-CoA ligase | CCNA_01382 | CCNA_03292 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | CCNA_02658 | CCNA_00006 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | | |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | gabT: gamma-aminobutyrate transaminase | CCNA_03233 | CCNA_03245 |
| putrescine | potB: putrescine ABC transporter, permease component 1 (PotB/PotH) | CCNA_03238 | |
| putrescine | potC: putrescine ABC transporter, permease component 2 (PotC/PotI) | CCNA_03236 | |
| putrescine | potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) | CCNA_03239 | |
| putrescine | puuB: gamma-glutamylputrescine oxidase | CCNA_03229 | |
| pyruvate | SLC5A8: sodium-coupled pyruvate transporter | | |
| rhamnose | aldA: lactaldehyde dehydrogenase | CCNA_03243 | CCNA_03695 |
| 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 | | |
| serine | snatA: L-serine transporter | CCNA_00105 | |
| sorbitol | sdh: sorbitol dehydrogenase | CCNA_01892 | CCNA_01345 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
| threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | CCNA_03462 | CCNA_03463 |
| threonine | snatA: L-threonine transporter snatA | CCNA_00105 | |
| thymidine | deoA: thymidine phosphorylase DeoA | | |
| thymidine | deoB: phosphopentomutase | CCNA_02347 | |
| thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | treF: trehalase | CCNA_02368 | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| valine | Bap2: L-valine permease Bap2 | | |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | CCNA_03124 | |
Confidence: high confidence medium confidence low confidence
This GapMind analysis is from Sep 17 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