Potential Gaps in catabolism of small carbon sources in Streptomyces kebangsaanensis SUK12
Found 51 low-confidence and 73 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | RH94_RS11695 | RH94_RS13185 |
| 4-hydroxybenzoate | pcaH: protocatechuate 3,4-dioxygenase, alpha subunit | RH94_RS04405 | RH94_RS04400 |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| arabinose | xacB: L-arabinose 1-dehydrogenase | RH94_RS26255 | RH94_RS33070 |
| arabinose | xacC: L-arabinono-1,4-lactonase | RH94_RS32890 | |
| arabinose | xacD: L-arabinonate dehydratase | RH94_RS35300 | RH94_RS08210 |
| arabinose | xacE: 2-dehydro-3-deoxy-L-arabinonate dehydratase | | |
| arginine | kauB: 4-guanidinobutyraldehyde dehydrogenase | RH94_RS00205 | RH94_RS23895 |
| arginine | rocE: L-arginine permease | RH94_RS03380 | RH94_RS16615 |
| asparagine | ans: asparaginase | RH94_RS26235 | |
| asparagine | glt: aspartate:proton symporter Glt | RH94_RS18945 | RH94_RS23540 |
| aspartate | glt: aspartate:proton symporter Glt | RH94_RS18945 | RH94_RS23540 |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | RH94_RS05215 | RH94_RS35170 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | RH94_RS05210 | RH94_RS07445 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | RH94_RS07445 | RH94_RS05210 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | RH94_RS07450 | |
| citrulline | arcC: carbamate kinase | | |
| citrulline | rocA: 1-pyrroline-5-carboxylate dehydrogenase | RH94_RS12920 | RH94_RS00205 |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | D-LDH: D-lactate dehydrogenase | RH94_RS03330 | RH94_RS12895 |
| D-serine | cycA: D-serine:H+ symporter CycA | RH94_RS03380 | RH94_RS16615 |
| D-serine | dsdA: D-serine ammonia-lyase | RH94_RS03595 | RH94_RS13520 |
| deoxyinosine | bmpA: deoxyinosine ABC transporter, substrate-binding component | RH94_RS22295 | |
| deoxyinosine | deoB: phosphopentomutase | RH94_RS00220 | RH94_RS16250 |
| deoxyinosine | nupB: deoxyinosine ABC transporter, permease component 1 | RH94_RS00105 | |
| deoxyinosine | nupC': deoxyinosine ABC transporter, permease component 2 | RH94_RS00110 | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fucose | fucDH: 2-keto-3-deoxy-L-fuconate 4-dehydrogenase | RH94_RS18480 | RH94_RS29205 |
| fucose | fucP: L-fucose:H+ symporter FucP | | |
| fucose | fucU: L-fucose mutarotase FucU | RH94_RS33560 | |
| fucose | KDF-hydrolase: 2,4-diketo-3-deoxy-L-fuconate hydrolase | RH94_RS37320 | RH94_RS25080 |
| galactose | galE: UDP-glucose 4-epimerase | RH94_RS22900 | RH94_RS06595 |
| galactose | galK: galactokinase (-1-phosphate forming) | | |
| galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | RH94_RS22895 | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | gci: D-galactarolactone cycloisomerase | RH94_RS32815 | RH94_RS18475 |
| 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 | | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | RH94_RS32815 | RH94_RS18475 |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | RH94_RS16595 | RH94_RS01595 |
| histidine | hutG': N-formylglutamate amidohydrolase | | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | PA5503: L-histidine ABC transporter, ATPase component | RH94_RS00340 | RH94_RS35170 |
| histidine | PA5504: L-histidine ABC transporter, permease component | RH94_RS00345 | |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | RH94_RS26770 | RH94_RS09185 |
| isoleucine | livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | RH94_RS35940 | |
| isoleucine | lpd: branched-chain alpha-ketoacid dehydrogenase, E3 component | RH94_RS24415 | RH94_RS04710 |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | RH94_RS07995 | RH94_RS20180 |
| lactose | galE: UDP-glucose 4-epimerase | RH94_RS22900 | RH94_RS06595 |
| lactose | galK: galactokinase (-1-phosphate forming) | | |
| lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | RH94_RS22895 | |
| lactose | lacP: lactose permease LacP | | |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | RH94_RS26770 | RH94_RS09185 |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | RH94_RS07980 | RH94_RS20180 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | RH94_RS12595 | RH94_RS03040 |
| leucine | livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | RH94_RS35940 | |
| leucine | lpd: branched-chain alpha-ketoacid dehydrogenase, E3 component | RH94_RS24415 | RH94_RS04710 |
| lysine | davA: 5-aminovaleramidase | RH94_RS00790 | RH94_RS26805 |
| lysine | davD: glutarate semialdehyde dehydrogenase | RH94_RS37005 | RH94_RS01805 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | RH94_RS20585 | RH94_RS04285 |
| lysine | lysP: L-lysine:H+ symporter LysP | RH94_RS16615 | RH94_RS03380 |
| mannitol | mt2d: mannitol 2-dehydrogenase | RH94_RS35355 | RH94_RS19940 |
| mannitol | PLT5: polyol transporter PLT5 | | |
| mannose | manP: mannose PTS system, EII-CBA components | RH94_RS22560 | |
| myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | RH94_RS19425 | |
| myoinositol | iolE: scyllo-inosose 2-dehydratase | RH94_RS19455 | |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | RH94_RS19435 | RH94_RS34530 |
| myoinositol | PGA1_c07300: myo-inositol ABC transport, substrate-binding component | RH94_RS16760 | |
| myoinositol | PGA1_c07310: myo-inositol ABC transporter, permease component | RH94_RS19445 | RH94_RS16765 |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | RH94_RS12595 | RH94_RS13400 |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | RH94_RS22035 | RH94_RS09950 |
| phenylacetate | ppa: phenylacetate permease ppa | RH94_RS34930 | RH94_RS07565 |
| phenylalanine | livF: L-phenylalanine ABC transporter, ATPase component 1 (LivF) | RH94_RS35960 | RH94_RS13290 |
| phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | RH94_RS35940 | |
| phenylalanine | paaF: 2,3-dehydroadipyl-CoA hydratase | RH94_RS12595 | RH94_RS13400 |
| phenylalanine | paaZ1: oxepin-CoA hydrolase | RH94_RS22035 | RH94_RS09950 |
| phenylalanine | pad-dh: phenylacetaldehyde dehydrogenase | RH94_RS00205 | RH94_RS23895 |
| proline | put1: proline dehydrogenase | | |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | RH94_RS07995 | RH94_RS20180 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | RH94_RS25500 | RH94_RS01895 |
| putrescine | potB: putrescine ABC transporter, permease component 1 (PotB/PotH) | RH94_RS25590 | RH94_RS20885 |
| putrescine | potC: putrescine ABC transporter, permease component 2 (PotC/PotI) | RH94_RS25595 | RH94_RS20890 |
| putrescine | potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) | | |
| rhamnose | rhaB: L-rhamnulokinase | | |
| rhamnose | rhaM: L-rhamnose mutarotase | RH94_RS33560 | |
| rhamnose | rhaP: L-rhamnose ABC transporter, permease component 1 (RhaP) | RH94_RS33575 | RH94_RS33570 |
| rhamnose | rhaQ: L-rhamnose ABC transporter, permease component 2 (RhaQ) | RH94_RS33570 | RH94_RS04600 |
| rhamnose | rhaT': L-rhamnose ABC transporter, ATPase component RhaT | RH94_RS31565 | RH94_RS04605 |
| ribose | rbsA: D-ribose ABC transporter, ATPase component RbsA | RH94_RS32835 | RH94_RS04605 |
| ribose | rbsB: D-ribose ABC transporter, substrate-binding component RbsB | RH94_RS31575 | RH94_RS04610 |
| ribose | rbsC: D-ribose ABC transporter, permease component RbsC | RH94_RS04595 | RH94_RS04600 |
| serine | Ac3H11_1692: L-tyrosine ABC transporter, ATPase component 2 | RH94_RS35960 | RH94_RS13290 |
| serine | Ac3H11_1694: L-tyrosine ABC transporter, permease component 2 | RH94_RS35950 | |
| serine | Ac3H11_2396: L-tyrosine ABC transporter, substrate-binding component component | RH94_RS35940 | |
| sorbitol | mtlF: ABC transporter for polyols MtlEFGK, permease component MtlF | RH94_RS35345 | RH94_RS14995 |
| sorbitol | mtlK: ABC transporter for polyols MtlEFGK, permease component MtlK | RH94_RS27405 | RH94_RS20645 |
| sorbitol | sdh: sorbitol dehydrogenase | RH94_RS33070 | RH94_RS18480 |
| sucrose | ams: sucrose hydrolase (invertase) | RH94_RS31865 | RH94_RS35555 |
| threonine | lpd: dihydrolipoyl dehydrogenase | RH94_RS24415 | RH94_RS04710 |
| thymidine | deoB: phosphopentomutase | RH94_RS00220 | RH94_RS16250 |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | treF: trehalase | RH94_RS01545 | RH94_RS35555 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | RH94_RS15740 | RH94_RS03380 |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | Ac3H11_1692: L-tyrosine ABC transporter, ATPase component 2 | RH94_RS35960 | RH94_RS13290 |
| tyrosine | Ac3H11_1694: L-tyrosine ABC transporter, permease component 2 | RH94_RS35950 | |
| tyrosine | Ac3H11_2396: L-tyrosine ABC transporter, substrate-binding component component | RH94_RS35940 | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | RH94_RS13400 | RH94_RS12595 |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | RH94_RS26770 | RH94_RS09185 |
| valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | RH94_RS35945 | RH94_RS13300 |
| valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | | |
| valine | livM: L-valine ABC transporter, permease component 2 (LivM/BraE) | RH94_RS35950 | RH94_RS13305 |
| valine | lpd: branched-chain alpha-ketoacid dehydrogenase, E3 component | RH94_RS24415 | RH94_RS04710 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | RH94_RS18135 | RH94_RS00205 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | RH94_RS26970 | |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | RH94_RS07995 | RH94_RS20180 |
| xylitol | PS417_12055: xylitol ABC transporter, substrate-binding component | | |
| xylitol | PS417_12065: xylitol ABC transporter, ATPase component | RH94_RS04605 | RH94_RS31565 |
| xylitol | xdhA: xylitol dehydrogenase | RH94_RS35355 | RH94_RS10610 |
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