Potential Gaps in catabolism of small carbon sources in Ochrobactrum rhizosphaerae PR17
Found 54 low-confidence and 37 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | | |
| 4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | CEV32_RS10280 | CEV32_RS08080 |
| 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 | | |
| arabinose | xacD: L-arabinonate dehydratase | CEV32_RS18275 | CEV32_RS14750 |
| asparagine | ans: asparaginase | CEV32_RS22010 | CEV32_RS22440 |
| cellobiose | bgl: cellobiase | | |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | CEV32_RS07440 | CEV32_RS21770 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | CEV32_RS07445 | CEV32_RS00780 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | CEV32_RS02520 | CEV32_RS00785 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | CEV32_RS11040 | CEV32_RS03975 |
| deoxyinosine | deoB: phosphopentomutase | CEV32_RS16260 | |
| deoxyinosine | deoD: deoxyinosine phosphorylase | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | CEV32_RS01915 | CEV32_RS07170 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| galactose | dgoD: D-galactonate dehydratase | CEV32_RS18275 | CEV32_RS14750 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | uxaA: D-altronate dehydratase | CEV32_RS03350 | |
| galacturonate | uxaB: tagaturonate reductase | CEV32_RS03340 | |
| galacturonate | uxaC: D-galacturonate isomerase | | |
| 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 | | |
| glucuronate | uxaC: D-glucuronate isomerase | | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | CEV32_RS13060 | CEV32_RS18875 |
| lactose | dgoD: D-galactonate dehydratase | CEV32_RS18275 | CEV32_RS14750 |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | | |
| lysine | hisP: L-lysine ABC transporter, ATPase component HisP | CEV32_RS07440 | CEV32_RS02145 |
| lysine | lysN: 2-aminoadipate transaminase | CEV32_RS13905 | CEV32_RS13300 |
| lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | CEV32_RS20770 | CEV32_RS06440 |
| maltose | susB: alpha-glucosidase (maltase) | | |
| mannitol | mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE | CEV32_RS01935 | |
| mannitol | mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) | CEV32_RS01930 | CEV32_RS20055 |
| mannitol | mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) | CEV32_RS01925 | CEV32_RS20105 |
| mannitol | mtlK: polyol ABC transporter, ATP component MtlK/SmoG | CEV32_RS01920 | CEV32_RS02050 |
| mannose | man-isomerase: D-mannose isomerase | | |
| myoinositol | PGA1_c07300: myo-inositol ABC transport, substrate-binding component | | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase 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 | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | CEV32_RS07690 | CEV32_RS18700 |
| phenylacetate | paaK: phenylacetate-CoA ligase | | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | CEV32_RS18700 | CEV32_RS07690 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | fahA: fumarylacetoacetate hydrolase | CEV32_RS19910 | |
| phenylalanine | hmgA: homogentisate dioxygenase | | |
| phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| phenylalanine | livH: L-phenylalanine ABC transporter, permease component 1 (LivH) | CEV32_RS16725 | CEV32_RS07575 |
| phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | CEV32_RS18905 | CEV32_RS16700 |
| phenylalanine | maiA: maleylacetoacetate isomerase | CEV32_RS10255 | |
| phenylalanine | PAH: phenylalanine 4-monooxygenase | | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | | |
| putrescine | potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) | CEV32_RS03235 | |
| putrescine | puuB: gamma-glutamylputrescine oxidase | CEV32_RS03195 | CEV32_RS02795 |
| putrescine | puuC: gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase | CEV32_RS19730 | CEV32_RS17870 |
| pyruvate | SLC5A8: sodium-coupled pyruvate transporter | | |
| serine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | CEV32_RS16700 | CEV32_RS18905 |
| serine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | CEV32_RS16725 | CEV32_RS07575 |
| serine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | CEV32_RS16720 | |
| serine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | CEV32_RS16715 | CEV32_RS04135 |
| sorbitol | mtlK: ABC transporter for polyols MtlEFGK, permease component MtlK | CEV32_RS01920 | CEV32_RS02050 |
| sucrose | SUS: sucrose synthase | | |
| threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | CEV32_RS16700 | CEV32_RS18905 |
| threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | CEV32_RS16725 | CEV32_RS07575 |
| threonine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | CEV32_RS16720 | |
| threonine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | CEV32_RS16715 | CEV32_RS04135 |
| thymidine | deoA: thymidine phosphorylase DeoA | | |
| thymidine | deoB: phosphopentomutase | CEV32_RS16260 | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | PsTP: trehalose phosphorylase | | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | CEV32_RS22695 | CEV32_RS22015 |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | CEV32_RS22695 | CEV32_RS22015 |
| tyrosine | fahA: fumarylacetoacetate hydrolase | CEV32_RS19910 | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | CEV32_RS10255 | |
| valine | acdH: isobutyryl-CoA dehydrogenase | CEV32_RS13060 | CEV32_RS07685 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | CEV32_RS16950 | CEV32_RS17870 |
| xylitol | PS417_12055: xylitol ABC transporter, substrate-binding component | | |
| xylitol | PS417_12065: xylitol ABC transporter, ATPase component | CEV32_RS14910 | CEV32_RS01950 |
| xylitol | xdhA: xylitol dehydrogenase | CEV32_RS06880 | CEV32_RS01740 |
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