Potential Gaps in catabolism of small carbon sources in Rhizobium subbaraonis JC85
Found 30 low-confidence and 41 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | CRO48_RS12315 | CRO48_RS07650 |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| alanine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | CRO48_RS14965 | CRO48_RS23625 |
| alanine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | CRO48_RS14940 | CRO48_RS25805 |
| alanine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | CRO48_RS14945 | CRO48_RS25800 |
| asparagine | ans: asparaginase | CRO48_RS16460 | CRO48_RS01555 |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | CRO48_RS25370 | CRO48_RS09105 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | CRO48_RS25355 | CRO48_RS08830 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | CRO48_RS25360 | CRO48_RS08835 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | CRO48_RS08840 | CRO48_RS10365 |
| D-alanine | AZOBR_RS08260: D-alanine ABC transporter, substrate-binding component | CRO48_RS14965 | CRO48_RS23625 |
| 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 | CRO48_RS12735 | CRO48_RS24210 |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | CRO48_RS15665 | CRO48_RS04435 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | CRO48_RS30260 | CRO48_RS20400 |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | CRO48_RS12690 | CRO48_RS24410 |
| deoxyribose | deoP: deoxyribose transporter | | |
| fucose | fdh: L-fucose 1-dehydrogenase | CRO48_RS06815 | CRO48_RS00445 |
| fucose | HSERO_RS05250: ABC transporter for L-fucose, ATPase component | CRO48_RS27860 | CRO48_RS27795 |
| fucose | HSERO_RS05255: ABC transporter for L-fucose, permease component | CRO48_RS03935 | CRO48_RS04945 |
| fucose | HSERO_RS05260: ABC transporter for L-fucose, substrate-binding component | CRO48_RS06805 | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| gluconate | gntC: gluconate TRAP transporter, periplasmic solute-binding component | CRO48_RS20575 | CRO48_RS02480 |
| glucosamine | nagX: transmembrane glucosamine N-acetyltransferase NagX | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | dctQ: D-glucuronate TRAP transporter, small permease component | CRO48_RS03285 | |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | CRO48_RS05745 | CRO48_RS20780 |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | CRO48_RS05405 | CRO48_RS21155 |
| lysine | hisP: L-lysine ABC transporter, ATPase component HisP | CRO48_RS09105 | CRO48_RS25370 |
| mannitol | mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) | CRO48_RS15080 | CRO48_RS04025 |
| myoinositol | PS417_11885: myo-inositol ABC transporter, substrate-binding component | CRO48_RS27805 | CRO48_RS28715 |
| myoinositol | PS417_11895: myo-inositol ABC transporter, permease component | CRO48_RS28720 | CRO48_RS27800 |
| 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 | CRO48_RS07760 | CRO48_RS03545 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | CRO48_RS07760 | CRO48_RS03545 |
| phenylacetate | paaH: 3-hydroxyadipyl-CoA dehydrogenase | CRO48_RS07285 | CRO48_RS25210 |
| phenylacetate | paaK: phenylacetate-CoA ligase | | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | CRO48_RS11970 | CRO48_RS12710 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | livH: L-phenylalanine ABC transporter, permease component 1 (LivH) | CRO48_RS14940 | CRO48_RS25805 |
| phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | CRO48_RS14965 | CRO48_RS23625 |
| phenylalanine | maiA: maleylacetoacetate isomerase | CRO48_RS03230 | CRO48_RS01565 |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | CRO48_RS24670 | |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | CRO48_RS05745 | CRO48_RS20780 |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) | CRO48_RS21865 | CRO48_RS03080 |
| serine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | CRO48_RS14965 | CRO48_RS23625 |
| serine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | CRO48_RS14940 | CRO48_RS25805 |
| serine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | CRO48_RS14945 | CRO48_RS25800 |
| threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | CRO48_RS14965 | CRO48_RS23625 |
| threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | CRO48_RS14940 | CRO48_RS25805 |
| threonine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | CRO48_RS14945 | CRO48_RS25800 |
| 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 | CRO48_RS30045 | CRO48_RS14950 |
| tyrosine | Ac3H11_1695: L-tyrosine ABC transporter, permease component 1 | CRO48_RS14940 | CRO48_RS25805 |
| tyrosine | Ac3H11_2396: L-tyrosine ABC transporter, substrate-binding component component | CRO48_RS14965 | |
| tyrosine | maiA: maleylacetoacetate isomerase | CRO48_RS03230 | CRO48_RS01565 |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | CRO48_RS07770 | CRO48_RS03545 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | CRO48_RS21935 | CRO48_RS18700 |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | CRO48_RS05745 | CRO48_RS20780 |
| xylitol | xdhA: xylitol dehydrogenase | CRO48_RS23655 | CRO48_RS09930 |
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