Potential Gaps in catabolism of small carbon sources in Halomonas desiderata SP1
Found 55 low-confidence and 54 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | fcbT1: tripartite 4-hydroxybenzoate transporter, substrate-binding component FcbT1 | BZY95_RS16000 | BZY95_RS01830 |
| 4-hydroxybenzoate | fcbT2: tripartite 4-hydroxybenzoate transporter, small DctQ-like component FcbT2 | BZY95_RS15995 | |
| 4-hydroxybenzoate | pcaB: 3-carboxymuconate cycloisomerase | BZY95_RS03585 | |
| 4-hydroxybenzoate | pcaD: 3-oxoadipate enol-lactone hydrolase | BZY95_RS03565 | |
| 4-hydroxybenzoate | pcaF: succinyl-CoA:acetyl-CoA C-succinyltransferase | BZY95_RS06835 | BZY95_RS03570 |
| acetate | actP: cation/acetate symporter ActP | BZY95_RS03245 | |
| arabinose | xacC: L-arabinono-1,4-lactonase | BZY95_RS16655 | BZY95_RS16570 |
| asparagine | ans: asparaginase | BZY95_RS06040 | BZY95_RS09260 |
| cellobiose | bgl: cellobiase | | |
| citrate | tctB: citrate/Na+ symporter, small transmembrane component TctB | | |
| citrate | tctC: citrate/Na+ symporter, substrate-binding component TctC | BZY95_RS08755 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | BZY95_RS02060 | BZY95_RS02565 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | BZY95_RS02055 | BZY95_RS02050 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | BZY95_RS02040 | BZY95_RS02045 |
| citrulline | arcC: carbamate kinase | | |
| citrulline | gabT: gamma-aminobutyrate transaminase | BZY95_RS10460 | BZY95_RS15480 |
| citrulline | odc: L-ornithine decarboxylase | | |
| D-alanine | dadA: D-alanine dehydrogenase | BZY95_RS19365 | |
| D-alanine | Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component | BZY95_RS06440 | |
| D-alanine | Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component | BZY95_RS02565 | BZY95_RS12910 |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | BZY95_RS13015 | BZY95_RS11575 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribose | deoK: deoxyribokinase | BZY95_RS18425 | BZY95_RS07810 |
| deoxyribose | deoP: deoxyribose transporter | | |
| fucose | fdh: L-fucose 1-dehydrogenase | BZY95_RS11780 | BZY95_RS18525 |
| fucose | fuconolactonase: L-fucono-1,5-lactonase | | |
| fucose | fucP: L-fucose:H+ symporter FucP | | |
| fucose | fucU: L-fucose mutarotase FucU | | |
| galactose | galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) | BZY95_RS16655 | BZY95_RS16570 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| gluconate | gntA: gluconate TRAP transporter, small permease component | BZY95_RS04840 | |
| gluconate | gntB: gluconate TRAP transporter, large permease component | BZY95_RS16160 | BZY95_RS12010 |
| gluconate | gntC: gluconate TRAP transporter, periplasmic solute-binding component | BZY95_RS12945 | BZY95_RS20685 |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| histidine | aapM: L-histidine ABC transporter, permease component 2 (AapM) | BZY95_RS06450 | BZY95_RS12915 |
| histidine | aapP: L-histidine ABC transporter, ATPase component AapP | BZY95_RS02565 | BZY95_RS12910 |
| histidine | aapQ: L-histidine ABC transporter, permease component 1 (AapQ) | BZY95_RS06445 | |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | BZY95_RS18770 | BZY95_RS09725 |
| isoleucine | natB: L-isoleucine ABC transporter, substrate-binding component NatB | BZY95_RS14935 | |
| isoleucine | natC: L-isoleucine ABC transporter, permease component 1 (NatC) | | |
| isoleucine | natD: L-isoleucine ABC transporter, permease component 2 (NatD) | BZY95_RS14925 | |
| lactose | galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) | BZY95_RS16655 | BZY95_RS16570 |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | | |
| leucine | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | BZY95_RS06450 | BZY95_RS12915 |
| leucine | aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP | BZY95_RS02565 | BZY95_RS12910 |
| leucine | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | BZY95_RS06445 | |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | BZY95_RS18770 | BZY95_RS09725 |
| lysine | davA: 5-aminovaleramidase | BZY95_RS02275 | BZY95_RS05890 |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| mannitol | mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE | BZY95_RS17260 | |
| mannitol | mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) | BZY95_RS17255 | BZY95_RS16610 |
| mannitol | mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) | BZY95_RS17250 | |
| mannose | manA: mannose-6-phosphate isomerase | | |
| mannose | manP: mannose PTS system, EII-CBA components | BZY95_RS07790 | |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | BZY95_RS03490 | |
| myoinositol | iolM: 2-inosose 4-dehydrogenase | BZY95_RS06260 | |
| myoinositol | iolN: 2,4-diketo-inositol hydratase | | |
| myoinositol | iolO: 5-dehydro-L-gluconate epimerase | | |
| myoinositol | iolT: myo-inositol:H+ symporter | BZY95_RS16640 | |
| myoinositol | kdgK: 2-keto-3-deoxygluconate kinase | BZY95_RS16175 | BZY95_RS07810 |
| myoinositol | uxaE: D-tagaturonate epimerase | | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylalanine | ARO10: phenylpyruvate decarboxylase | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | pad-dh: phenylacetaldehyde dehydrogenase | BZY95_RS10455 | BZY95_RS11785 |
| putrescine | gabT: gamma-aminobutyrate transaminase | BZY95_RS10460 | BZY95_RS15480 |
| putrescine | potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) | BZY95_RS10500 | |
| rhamnose | aldA: lactaldehyde dehydrogenase | BZY95_RS10455 | BZY95_RS07130 |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | BZY95_RS06205 | BZY95_RS21330 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | BZY95_RS14785 | BZY95_RS06130 |
| rhamnose | LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase | BZY95_RS06135 | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsK: ribokinase | BZY95_RS18425 | BZY95_RS07810 |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | BZY95_RS14935 | |
| serine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | BZY95_RS14925 | BZY95_RS14710 |
| serine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | | |
| sorbitol | sdh: sorbitol dehydrogenase | BZY95_RS17045 | BZY95_RS17225 |
| sucrose | ams: sucrose hydrolase (invertase) | BZY95_RS11675 | BZY95_RS11685 |
| threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | BZY95_RS14935 | |
| threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | BZY95_RS14925 | BZY95_RS14710 |
| threonine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | | |
| threonine | ltaE: L-threonine aldolase | BZY95_RS13805 | BZY95_RS07965 |
| trehalose | treF: trehalase | BZY95_RS11685 | BZY95_RS11675 |
| tryptophan | antA: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA | BZY95_RS21650 | BZY95_RS06270 |
| tryptophan | antB: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB | | |
| tryptophan | antC: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC | BZY95_RS21530 | BZY95_RS07140 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | catA: catechol 1,2-dioxygenase | BZY95_RS21655 | BZY95_RS08310 |
| tryptophan | pcaD: 3-oxoadipate enol-lactone hydrolase | BZY95_RS03565 | |
| tryptophan | pcaF: succinyl-CoA:acetyl-CoA C-succinyltransferase | BZY95_RS06835 | BZY95_RS03570 |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | BZY95_RS09135 | BZY95_RS09860 |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | BZY95_RS18770 | BZY95_RS09725 |
| valine | natB: L-valine ABC transporter, substrate-binding component NatB | BZY95_RS14935 | |
| valine | natC: L-valine ABC transporter, permease component 1 (NatC) | | |
| valine | natD: L-valine ABC transporter, permease component 2 (NatD) | BZY95_RS14925 | |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | BZY95_RS07790 | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | BZY95_RS16145 | |
| xylose | gyaR: glyoxylate reductase | BZY95_RS06210 | BZY95_RS01720 |
| xylose | xdh: D-xylose dehydrogenase | BZY95_RS16600 | BZY95_RS04820 |
| xylose | xylC: xylonolactonase | BZY95_RS16570 | BZY95_RS16655 |
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