Potential Gaps in catabolism of small carbon sources in Streptacidiphilus oryzae TH49
Found 48 low-confidence and 72 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | pcaB: 3-carboxymuconate cycloisomerase | | |
| 4-hydroxybenzoate | pcaI: 3-oxoadipate CoA-transferase subunit A (PcaI) | BS73_RS10025 | |
| 4-hydroxybenzoate | pcaJ: 3-oxoadipate CoA-transferase subunit B (PcaJ) | BS73_RS10020 | |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | BS73_RS06270 | |
| alanine | cycA: L-alanine symporter CycA | BS73_RS16535 | BS73_RS10785 |
| arabinose | xylHsa: L-arabinose ABC transporter, permease component XylH | BS73_RS06550 | BS73_RS07055 |
| arginine | adiA: arginine decarboxylase (AdiA/SpeA) | BS73_RS05790 | |
| arginine | aguB: N-carbamoylputrescine hydrolase | BS73_RS30130 | BS73_RS27285 |
| arginine | patA: putrescine aminotransferase (PatA/SpuC) | BS73_RS14265 | BS73_RS18925 |
| arginine | rocE: L-arginine permease | BS73_RS16535 | BS73_RS10785 |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | BS73_RS15740 | BS73_RS01465 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | BS73_RS15735 | BS73_RS01490 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | BS73_RS15735 | |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
| citrulline | arcC: carbamate kinase | | |
| citrulline | rocA: 1-pyrroline-5-carboxylate dehydrogenase | BS73_RS12295 | BS73_RS24175 |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-serine | cycA: D-serine:H+ symporter CycA | BS73_RS10785 | BS73_RS16535 |
| D-serine | dsdA: D-serine ammonia-lyase | BS73_RS17825 | BS73_RS16930 |
| deoxyinosine | deoB: phosphopentomutase | BS73_RS23610 | BS73_RS22910 |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | BS73_RS15485 | BS73_RS09090 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | BS73_RS27515 | BS73_RS31945 |
| deoxyribonate | garK: glycerate 2-kinase | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | BS73_RS10685 | |
| deoxyribose | deoK: deoxyribokinase | BS73_RS29490 | BS73_RS17345 |
| deoxyribose | deoP: deoxyribose transporter | | |
| fucose | fucDH: 2-keto-3-deoxy-L-fuconate 4-dehydrogenase | BS73_RS15485 | BS73_RS00110 |
| fucose | KDF-hydrolase: 2,4-diketo-3-deoxy-L-fuconate hydrolase | BS73_RS30775 | BS73_RS00400 |
| galactose | galE: UDP-glucose 4-epimerase | BS73_RS17235 | BS73_RS22190 |
| galactose | galP: galactose:H+ symporter GalP | BS73_RS29790 | BS73_RS21860 |
| galacturonate | PS417_04205: D-galacturonate transporter | BS73_RS04730 | |
| galacturonate | uxuL: D-galactaro-1,5-lactonase (UxuL or UxuF) | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | BS73_RS16650 | BS73_RS15815 |
| glucosamine | nagX: transmembrane glucosamine N-acetyltransferase NagX | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | uxuL: D-glucaro-1,5-lactonase UxuL or UxuF | | |
| glutamate | yveA: L-glutamate:H+ symporter YveA | BS73_RS16525 | BS73_RS29095 |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | BS73_RS23040 | BS73_RS10545 |
| histidine | hutG': N-formylglutamate amidohydrolase | | |
| histidine | PA5503: L-histidine ABC transporter, ATPase component | BS73_RS08870 | BS73_RS32880 |
| histidine | PA5504: L-histidine ABC transporter, permease component | BS73_RS35970 | |
| isoleucine | livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | | |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | BS73_RS23635 | BS73_RS25280 |
| lactose | galE: UDP-glucose 4-epimerase | BS73_RS17235 | BS73_RS22190 |
| lactose | lacP: lactose permease LacP | | |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | BS73_RS14910 | BS73_RS33895 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | BS73_RS25285 | BS73_RS00480 |
| leucine | livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | | |
| lysine | cadA: lysine decarboxylase | BS73_RS13335 | BS73_RS03380 |
| lysine | davD: glutarate semialdehyde dehydrogenase | BS73_RS19435 | BS73_RS01225 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | BS73_RS32920 | BS73_RS15390 |
| lysine | lysP: L-lysine:H+ symporter LysP | BS73_RS16535 | BS73_RS10785 |
| lysine | patA: cadaverine aminotransferase | BS73_RS23310 | BS73_RS08925 |
| mannitol | mt2d: mannitol 2-dehydrogenase | BS73_RS07840 | BS73_RS11735 |
| mannitol | mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE | BS73_RS07825 | |
| mannitol | mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) | BS73_RS07830 | BS73_RS30605 |
| mannitol | mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) | BS73_RS07835 | BS73_RS31740 |
| mannitol | mtlK: polyol ABC transporter, ATP component MtlK/SmoG | BS73_RS18100 | BS73_RS14235 |
| mannose | manP: mannose PTS system, EII-CBA components | BS73_RS28560 | |
| myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | BS73_RS11405 | |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | BS73_RS11395 | BS73_RS16635 |
| myoinositol | PGA1_c07300: myo-inositol ABC transport, substrate-binding component | BS73_RS29370 | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | BS73_RS16650 | BS73_RS15815 |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | BS73_RS14910 | BS73_RS20300 |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | BS73_RS05650 | BS73_RS00955 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylacetate | ppa: phenylacetate permease ppa | BS73_RS13175 | BS73_RS06885 |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | BS73_RS16535 | BS73_RS25710 |
| phenylalanine | paaF: 2,3-dehydroadipyl-CoA hydratase | BS73_RS14910 | BS73_RS20300 |
| phenylalanine | paaZ1: oxepin-CoA hydrolase | BS73_RS05650 | BS73_RS00955 |
| phenylalanine | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | pad-dh: phenylacetaldehyde dehydrogenase | BS73_RS27490 | BS73_RS24675 |
| proline | put1: proline dehydrogenase | | |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | BS73_RS23635 | BS73_RS25280 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | BS73_RS14265 | BS73_RS18925 |
| putrescine | potB: putrescine ABC transporter, permease component 1 (PotB/PotH) | BS73_RS14230 | |
| putrescine | potC: putrescine ABC transporter, permease component 2 (PotC/PotI) | BS73_RS14225 | |
| putrescine | potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) | BS73_RS14240 | |
| rhamnose | rhaM: L-rhamnose mutarotase | BS73_RS29745 | |
| ribose | rbsA: D-ribose ABC transporter, ATPase component RbsA | BS73_RS32735 | BS73_RS01755 |
| ribose | rbsB: D-ribose ABC transporter, substrate-binding component RbsB | BS73_RS01760 | BS73_RS13050 |
| ribose | rbsC: D-ribose ABC transporter, permease component RbsC | BS73_RS01760 | BS73_RS13065 |
| ribose | rbsK: ribokinase | BS73_RS29490 | BS73_RS17345 |
| serine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | | |
| serine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | BS73_RS29125 | BS73_RS13625 |
| serine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | BS73_RS29120 | BS73_RS13630 |
| sorbitol | mtlK: ABC transporter for polyols MtlEFGK, permease component MtlK | BS73_RS18100 | BS73_RS14235 |
| sorbitol | sdh: sorbitol dehydrogenase | BS73_RS09090 | BS73_RS31130 |
| sucrose | ams: sucrose hydrolase (invertase) | BS73_RS31275 | BS73_RS04620 |
| threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | | |
| threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | BS73_RS29125 | BS73_RS13625 |
| threonine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | BS73_RS29120 | BS73_RS13630 |
| threonine | pccA: propionyl-CoA carboxylase, alpha subunit | BS73_RS23635 | BS73_RS25280 |
| thymidine | deoA: thymidine phosphorylase DeoA | | |
| thymidine | deoB: phosphopentomutase | BS73_RS23610 | BS73_RS22910 |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | treF: trehalase | BS73_RS04465 | BS73_RS04620 |
| tryptophan | andAa: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa | BS73_RS21365 | BS73_RS33040 |
| tryptophan | andAb: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin subunit AndAb | BS73_RS12335 | BS73_RS21365 |
| tryptophan | andAc: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AndAc | | |
| tryptophan | andAd: athranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AndAd | | |
| tryptophan | mhpD: 2-hydroxypentadienoate hydratase | BS73_RS04080 | BS73_RS37045 |
| tryptophan | mhpE: 4-hydroxy-2-oxovalerate aldolase | BS73_RS11375 | |
| tryptophan | praB: 2-hydroxymuconate 6-semialdehyde dehydrogenase | BS73_RS01225 | BS73_RS23595 |
| tryptophan | praC: 2-hydroxymuconate tautomerase | BS73_RS17890 | BS73_RS04070 |
| tryptophan | praD: 2-oxohex-3-enedioate decarboxylase | BS73_RS04080 | BS73_RS37045 |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | BS73_RS16535 | BS73_RS25710 |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | BS73_RS20300 | BS73_RS14910 |
| valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | BS73_RS29125 | BS73_RS13625 |
| valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | | |
| valine | livM: L-valine ABC transporter, permease component 2 (LivM/BraE) | BS73_RS29120 | BS73_RS13630 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | BS73_RS14210 | BS73_RS27490 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | BS73_RS29620 | BS73_RS32725 |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | BS73_RS23635 | BS73_RS25280 |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | BS73_RS21865 | BS73_RS21860 |
| xylose | xylT: D-xylose transporter | BS73_RS29790 | BS73_RS01090 |
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