Potential Gaps in catabolism of small carbon sources in Marinobacter guineae M3B
Found 89 low-confidence and 31 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| 4-hydroxybenzoate | praA: protocatechuate 2,3-dioxygenase | CLH62_RS03075 | |
| acetate | actP: cation/acetate symporter ActP | CLH62_RS20085 | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| cellobiose | bgl: cellobiase | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | CLH62_RS07710 | CLH62_RS11910 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | CLH62_RS07720 | CLH62_RS06595 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | CLH62_RS07715 | CLH62_RS11920 |
| citrulline | gabT: gamma-aminobutyrate transaminase | CLH62_RS11925 | CLH62_RS11500 |
| citrulline | odc: L-ornithine decarboxylase | CLH62_RS11085 | |
| citrulline | puuD: gamma-glutamyl-gamma-aminobutyrate hydrolase | CLH62_RS03735 | |
| D-alanine | Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component | CLH62_RS02950 | |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | CLH62_RS13835 | CLH62_RS12020 |
| deoxyinosine | deoB: phosphopentomutase | CLH62_RS07930 | |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyinosine | deoD: deoxyinosine phosphorylase | CLH62_RS03365 | |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | CLH62_RS10280 | CLH62_RS08955 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | garK: glycerate 2-kinase | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyribose | deoK: deoxyribokinase | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fucose | aldA: lactaldehyde dehydrogenase | CLH62_RS15810 | CLH62_RS14090 |
| 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 | galE: UDP-glucose 4-epimerase | CLH62_RS04095 | CLH62_RS02175 |
| galactose | galK: galactokinase (-1-phosphate forming) | | |
| galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | kdgK: 2-keto-3-deoxygluconate kinase | | |
| galacturonate | uxaA: D-altronate dehydratase | | |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | CLH62_RS11670 | |
| glucosamine | SLC2A2: glucosamine transporter SLC2A2 | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | garK: glycerate 2-kinase | | |
| glucuronate | garL: 5-dehydro-4-deoxy-D-glucarate aldolase | CLH62_RS03040 | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| L-lactate | Shew_2731: L-lactate:Na+ symporter, large component | CLH62_RS20085 | |
| L-lactate | Shew_2732: L-lactate:Na+ symporter, small component | CLH62_RS20080 | |
| 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 | | |
| lysine | argT: L-lysine ABC transporter, substrate-binding component ArgT | CLH62_RS07715 | CLH62_RS11920 |
| lysine | cadA: lysine decarboxylase | CLH62_RS10765 | CLH62_RS11085 |
| lysine | hisM: L-lysine ABC transporter, permease component 1 (HisM) | CLH62_RS07725 | CLH62_RS06595 |
| lysine | hisP: L-lysine ABC transporter, ATPase component HisP | CLH62_RS02935 | CLH62_RS07710 |
| lysine | hisQ: L-lysine ABC transporter, permease component 2 (HisQ) | CLH62_RS07720 | CLH62_RS06595 |
| lysine | patA: cadaverine aminotransferase | CLH62_RS11925 | CLH62_RS15685 |
| maltose | susB: alpha-glucosidase (maltase) | | |
| mannitol | mtlA: mannitol phosphotransferase system, EII-CBA components | | |
| mannitol | mtlD: mannitol-1-phosphate 5-dehydrogenase | | |
| mannose | manA: mannose-6-phosphate isomerase | CLH62_RS19130 | CLH62_RS07930 |
| mannose | manP: mannose PTS system, EII-CBA components | CLH62_RS11400 | |
| myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | | |
| myoinositol | iolC: 5-dehydro-2-deoxy-D-gluconate kinase | | |
| myoinositol | iolD: 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase | | |
| myoinositol | iolE: scyllo-inosose 2-dehydratase | | |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | | |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | CLH62_RS06545 | |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | CLH62_RS11670 | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | CLH62_RS15970 | CLH62_RS05465 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylalanine | paaF: 2,3-dehydroadipyl-CoA hydratase | CLH62_RS15970 | CLH62_RS05465 |
| propionate | putP: propionate transporter; proline:Na+ symporter | CLH62_RS03100 | |
| putrescine | gabT: gamma-aminobutyrate transaminase | CLH62_RS11925 | CLH62_RS11500 |
| putrescine | puuD: gamma-glutamyl-gamma-aminobutyrate hydrolase | CLH62_RS03735 | |
| rhamnose | aldA: lactaldehyde dehydrogenase | CLH62_RS15810 | CLH62_RS14090 |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | CLH62_RS03135 | CLH62_RS10265 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | | |
| rhamnose | LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase | CLH62_RS03040 | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsK: ribokinase | | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | CLH62_RS07855 | CLH62_RS05525 |
| serine | sdaB: L-serine ammonia-lyase | CLH62_RS13835 | CLH62_RS12020 |
| sorbitol | mtlA: PTS system for polyols, EII-CBA components | | |
| sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | CLH62_RS03910 | CLH62_RS11700 |
| sucrose | ams: sucrose hydrolase (invertase) | | |
| threonine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | CLH62_RS07855 | CLH62_RS05525 |
| threonine | tdcE: 2-ketobutyrate formate-lyase | | |
| thymidine | deoA: thymidine phosphorylase DeoA | CLH62_RS05080 | |
| thymidine | deoB: phosphopentomutase | CLH62_RS07930 | |
| thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | treF: trehalase | | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | CLH62_RS15975 | CLH62_RS15440 |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | CLH62_RS11400 | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | | |
| xylose | gtsA: xylose ABC transporter, periplasmic substrate-binding component GtsA | CLH62_RS07070 | |
| xylose | gtsB: xylose ABC transporter, permease component 1 GtsB | CLH62_RS07065 | |
| xylose | gtsC: xylose ABC transporter, permease component 2 GtsC | CLH62_RS07060 | |
| xylose | gtsD: xylose ABC transporter, ATPase component GtsD | CLH62_RS07055 | CLH62_RS15845 |
| xylose | xylA: xylose isomerase | | |
| xylose | xylB: xylulokinase | | |
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