Potential Gaps in catabolism of small carbon sources in Laceyella sediminis RHA1
Found 87 low-confidence and 48 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | | |
| 4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | | |
| 4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | CLV36_RS15485 | |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| 4-hydroxybenzoate | pobA: 4-hydroxybenzoate 3-monooxygenase | CLV36_RS15450 | |
| 4-hydroxybenzoate | praA: protocatechuate 2,3-dioxygenase | | |
| 4-hydroxybenzoate | xylF: 2-hydroxymuconate semialdehyde hydrolase | | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| cellobiose | bglG: cellobiose PTS system, EII-BC or EII-BCA components | CLV36_RS04120 | |
| citrate | tctB: citrate/Na+ symporter, small transmembrane component TctB | | |
| citrate | tctC: citrate/Na+ symporter, substrate-binding component TctC | CLV36_RS05410 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | CLV36_RS12700 | CLV36_RS03520 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | CLV36_RS03525 | CLV36_RS02980 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | CLV36_RS12705 | CLV36_RS03525 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | CLV36_RS03530 | CLV36_RS02975 |
| citrulline | arcC: carbamate kinase | | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | D-LDH: D-lactate dehydrogenase | CLV36_RS08235 | CLV36_RS09190 |
| D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | | |
| D-serine | cycA: D-serine:H+ symporter CycA | CLV36_RS12860 | CLV36_RS08665 |
| D-serine | dsdA: D-serine ammonia-lyase | CLV36_RS08880 | CLV36_RS16515 |
| deoxyinosine | bmpA: deoxyinosine ABC transporter, substrate-binding component | CLV36_RS07205 | CLV36_RS07185 |
| deoxyribonate | aacS: acetoacetyl-CoA synthetase | CLV36_RS07430 | CLV36_RS05635 |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | | |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | CLV36_RS03920 | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fucose | aldA: lactaldehyde dehydrogenase | CLV36_RS11570 | CLV36_RS09590 |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | | |
| fucose | fucI: L-fucose isomerase FucI | | |
| fucose | fucK: L-fuculose kinase FucK | | |
| fucose | fucP: L-fucose:H+ symporter FucP | | |
| fucose | fucU: L-fucose mutarotase FucU | | |
| galactose | galK: galactokinase (-1-phosphate forming) | | |
| galactose | galP: galactose:H+ symporter GalP | | |
| galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| galactose | pgmA: alpha-phosphoglucomutase | CLV36_RS15905 | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | kdgK: 2-keto-3-deoxygluconate kinase | CLV36_RS06925 | |
| galacturonate | uxaA: D-altronate dehydratase | | |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | CLV36_RS12640 | CLV36_RS11215 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | CLV36_RS13390 | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | kdgK: 2-keto-3-deoxygluconate kinase | CLV36_RS06925 | |
| glucuronate | uxaC: D-glucuronate isomerase | | |
| glucuronate | uxuB: D-mannonate dehydrogenase | | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | CLV36_RS13250 | CLV36_RS04090 |
| histidine | hutH: histidine ammonia-lyase | CLV36_RS13245 | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | CLV36_RS04005 | CLV36_RS04000 |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | CLV36_RS07570 | CLV36_RS07385 |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | CLV36_RS11055 | CLV36_RS07170 |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | CLV36_RS12475 | CLV36_RS00425 |
| L-lactate | L-LDH: L-lactate dehydrogenase | CLV36_RS06005 | |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| lactose | klh: periplasmic 3'-ketolactose hydrolase | | |
| lactose | lacA': periplasmic lactose 3-dehydrogenase, LacA subunit | | |
| lactose | lacB': periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB) | | |
| lactose | lacC': periplasmic lactose 3-dehydrogenase, LacC subunit | | |
| leucine | aacS: acetoacetyl-CoA synthetase | CLV36_RS07430 | CLV36_RS05635 |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | CLV36_RS07570 | CLV36_RS07385 |
| leucine | liuA: isovaleryl-CoA dehydrogenase | CLV36_RS01015 | CLV36_RS04005 |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | CLV36_RS06640 | CLV36_RS12475 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | CLV36_RS00405 | CLV36_RS12305 |
| lysine | bcd: butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit | CLV36_RS04000 | CLV36_RS04005 |
| lysine | ctfA: butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit | | |
| lysine | ctfB: butanoyl-CoA:acetoacetate CoA-transferase, beta subunit | | |
| lysine | etfA: butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit | CLV36_RS05625 | |
| lysine | etfB: butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit | | |
| mannose | manA: mannose-6-phosphate isomerase | CLV36_RS15905 | |
| mannose | manP: mannose PTS system, EII-CBA components | | |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | | |
| myoinositol | iolM: 2-inosose 4-dehydrogenase | | |
| myoinositol | iolN: 2,4-diketo-inositol hydratase | | |
| myoinositol | iolO: 5-dehydro-L-gluconate epimerase | | |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| myoinositol | kdgK: 2-keto-3-deoxygluconate kinase | CLV36_RS06925 | |
| myoinositol | uxaE: D-tagaturonate epimerase | | |
| myoinositol | uxuB: D-mannonate dehydrogenase | | |
| NAG | nagPcb: N-acetylglucosamine phosphotransferase system, EII-CB component NagP | CLV36_RS11215 | CLV36_RS12640 |
| phenylacetate | H281DRAFT_04042: phenylacetate:H+ symporter | CLV36_RS08665 | CLV36_RS12860 |
| phenylacetate | paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C | CLV36_RS09625 | |
| phenylacetate | paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | CLV36_RS07405 | CLV36_RS07410 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | CLV36_RS08665 | CLV36_RS12860 |
| phenylalanine | paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C | CLV36_RS09625 | |
| phenylalanine | paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E | | |
| phenylalanine | paaZ1: oxepin-CoA hydrolase | CLV36_RS07405 | CLV36_RS07410 |
| phenylalanine | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | pad-dh: phenylacetaldehyde dehydrogenase | CLV36_RS11570 | CLV36_RS09590 |
| phenylalanine | PPDCalpha: phenylpyruvate decarboxylase, alpha subunit | CLV36_RS07395 | CLV36_RS12345 |
| phenylalanine | PPDCbeta: phenylpyruvate decarboxylase, beta subunit | CLV36_RS07390 | CLV36_RS12340 |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | CLV36_RS12475 | CLV36_RS00425 |
| propionate | putP: propionate transporter; proline:Na+ symporter | CLV36_RS14680 | |
| putrescine | gabD: succinate semialdehyde dehydrogenase | CLV36_RS11570 | CLV36_RS09590 |
| putrescine | gabT: gamma-aminobutyrate transaminase | CLV36_RS08000 | CLV36_RS03455 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | CLV36_RS01340 | CLV36_RS08000 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | CLV36_RS11570 | CLV36_RS09590 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| rhamnose | aldA: lactaldehyde dehydrogenase | CLV36_RS11570 | CLV36_RS09590 |
| rhamnose | rhaA: L-rhamnose isomerase | | |
| rhamnose | rhaB: L-rhamnulokinase | | |
| rhamnose | rhaD: rhamnulose 1-phosphate aldolase | | |
| rhamnose | rhaM: L-rhamnose mutarotase | | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsA: D-ribose ABC transporter, ATPase component RbsA | CLV36_RS04885 | CLV36_RS07200 |
| ribose | rbsB: D-ribose ABC transporter, substrate-binding component RbsB | CLV36_RS04875 | |
| ribose | rbsC: D-ribose ABC transporter, permease component RbsC | CLV36_RS04880 | |
| serine | serP: L-serine permease SerP | CLV36_RS08665 | CLV36_RS12860 |
| sorbitol | mtlA: PTS system for polyols, EII-CBA components | CLV36_RS12770 | |
| sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | CLV36_RS11055 | CLV36_RS09195 |
| sucrose | ams: sucrose hydrolase (invertase) | CLV36_RS08510 | CLV36_RS10545 |
| threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | CLV36_RS12665 | CLV36_RS12670 |
| trehalose | treF: trehalase | CLV36_RS10545 | CLV36_RS08510 |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aacS: acetoacetyl-CoA synthetase | CLV36_RS07430 | CLV36_RS05635 |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | CLV36_RS08665 | CLV36_RS12860 |
| tyrosine | fahA: fumarylacetoacetate hydrolase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | CLV36_RS04005 | CLV36_RS04000 |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | CLV36_RS03485 | CLV36_RS07405 |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | CLV36_RS07570 | CLV36_RS07385 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | CLV36_RS07930 | CLV36_RS11570 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | CLV36_RS15795 | |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | CLV36_RS12475 | CLV36_RS00425 |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | CLV36_RS08115 | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | | |
| xylose | xylA: xylose isomerase | | |
| xylose | xylB: xylulokinase | CLV36_RS08525 | |
| xylose | xylT: D-xylose transporter | | |
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