Potential Gaps in catabolism of small carbon sources in Halomonas titanicae BH1
Found 41 low-confidence and 60 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | pcaB: 3-carboxymuconate cycloisomerase | HALTITAN_RS03685 | |
| 4-hydroxybenzoate | pcaD: 3-oxoadipate enol-lactone hydrolase | HALTITAN_RS03665 | HALTITAN_RS16980 |
| 4-hydroxybenzoate | pcaF: succinyl-CoA:acetyl-CoA C-succinyltransferase | HALTITAN_RS03670 | HALTITAN_RS16805 |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| acetate | actP: cation/acetate symporter ActP | HALTITAN_RS13305 | |
| arabinose | xacC: L-arabinono-1,4-lactonase | HALTITAN_RS10390 | |
| arginine | gabT: gamma-aminobutyrate transaminase | HALTITAN_RS00665 | HALTITAN_RS00620 |
| cellobiose | bgl: cellobiase | | |
| citrate | tctB: citrate/Na+ symporter, small transmembrane component TctB | HALTITAN_RS24175 | |
| citrate | tctC: citrate/Na+ symporter, substrate-binding component TctC | HALTITAN_RS02685 | HALTITAN_RS14060 |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | HALTITAN_RS15250 | HALTITAN_RS11450 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | HALTITAN_RS15245 | HALTITAN_RS11440 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | HALTITAN_RS15235 | HALTITAN_RS11445 |
| citrulline | aruF: ornithine/arginine N-succinyltransferase subunit AruAI (AruF) | HALTITAN_RS20110 | HALTITAN_RS20115 |
| citrulline | aruG: ornithine/arginine N-succinyltransferase subunit AruAII (AruG) | HALTITAN_RS20115 | HALTITAN_RS20110 |
| citrulline | astE: succinylglutamate desuccinylase | HALTITAN_RS15255 | |
| D-alanine | dadA: D-alanine dehydrogenase | HALTITAN_RS00795 | |
| D-alanine | Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component | HALTITAN_RS02835 | HALTITAN_RS07485 |
| D-alanine | Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component | HALTITAN_RS02850 | HALTITAN_RS07500 |
| D-serine | cycA: D-serine:H+ symporter CycA | HALTITAN_RS15020 | |
| D-serine | dsdA: D-serine ammonia-lyase | HALTITAN_RS04435 | HALTITAN_RS01110 |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | HALTITAN_RS22580 | HALTITAN_RS15920 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | HALTITAN_RS15745 | HALTITAN_RS03470 |
| deoxyribose | deoK: deoxyribokinase | HALTITAN_RS24160 | HALTITAN_RS10365 |
| deoxyribose | deoP: deoxyribose transporter | | |
| fucose | fdh: L-fucose 1-dehydrogenase | HALTITAN_RS12870 | HALTITAN_RS08065 |
| fucose | fuconolactonase: L-fucono-1,5-lactonase | | |
| fucose | fucP: L-fucose:H+ symporter FucP | | |
| fucose | fucU: L-fucose mutarotase FucU | | |
| galactose | dgoK: 2-dehydro-3-deoxygalactonokinase | HALTITAN_RS10380 | HALTITAN_RS10365 |
| galactose | galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) | HALTITAN_RS10390 | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | udh: D-galacturonate dehydrogenase | | |
| galacturonate | uxuL: D-galactaro-1,5-lactonase (UxuL or UxuF) | HALTITAN_RS10390 | |
| gluconate | gntA: gluconate TRAP transporter, small permease component | HALTITAN_RS11960 | HALTITAN_RS08385 |
| gluconate | gntC: gluconate TRAP transporter, periplasmic solute-binding component | HALTITAN_RS14005 | HALTITAN_RS08380 |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | HALTITAN_RS04115 | HALTITAN_RS21030 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | dctP: D-glucuronate TRAP transporter, solute receptor component | HALTITAN_RS10840 | HALTITAN_RS19995 |
| glucuronate | dctQ: D-glucuronate TRAP transporter, small permease component | | |
| glucuronate | kdgK: 2-keto-3-deoxygluconate kinase | HALTITAN_RS15890 | HALTITAN_RS01140 |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | HALTITAN_RS05565 | |
| histidine | aapM: L-histidine ABC transporter, permease component 2 (AapM) | HALTITAN_RS02845 | HALTITAN_RS07495 |
| histidine | aapP: L-histidine ABC transporter, ATPase component AapP | HALTITAN_RS02850 | HALTITAN_RS07500 |
| histidine | aapQ: L-histidine ABC transporter, permease component 1 (AapQ) | HALTITAN_RS02840 | HALTITAN_RS07490 |
| isoleucine | natB: L-isoleucine ABC transporter, substrate-binding component NatB | HALTITAN_RS19895 | |
| isoleucine | natC: L-isoleucine ABC transporter, permease component 1 (NatC) | | |
| isoleucine | natD: L-isoleucine ABC transporter, permease component 2 (NatD) | HALTITAN_RS19880 | HALTITAN_RS02320 |
| lactose | klh: periplasmic 3'-ketolactose hydrolase | | |
| lactose | lacB': periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB) | | |
| lactose | lacC': periplasmic lactose 3-dehydrogenase, LacC subunit | HALTITAN_RS12975 | |
| leucine | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | HALTITAN_RS02845 | HALTITAN_RS07495 |
| leucine | aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP | HALTITAN_RS02850 | HALTITAN_RS07500 |
| leucine | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | HALTITAN_RS02840 | HALTITAN_RS07490 |
| lysine | davA: 5-aminovaleramidase | HALTITAN_RS00275 | HALTITAN_RS04660 |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | lysP: L-lysine:H+ symporter LysP | HALTITAN_RS15020 | |
| mannitol | mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE | HALTITAN_RS12030 | |
| mannitol | mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) | HALTITAN_RS12035 | |
| mannitol | mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) | HALTITAN_RS12040 | HALTITAN_RS10515 |
| mannose | HSERO_RS03635: mannose ABC transporter, substrate-binding component | HALTITAN_RS17130 | |
| mannose | HSERO_RS03640: mannose ABC transporter, ATPase component | HALTITAN_RS17125 | HALTITAN_RS14140 |
| mannose | HSERO_RS03645: mannose ABC transporter, permease component | HALTITAN_RS24150 | HALTITAN_RS17120 |
| myoinositol | PGA1_c07300: myo-inositol ABC transport, substrate-binding component | HALTITAN_RS01160 | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | HALTITAN_RS04115 | HALTITAN_RS21030 |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | HALTITAN_RS11900 | HALTITAN_RS01660 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | HALTITAN_RS15020 | |
| phenylalanine | paaF: 2,3-dehydroadipyl-CoA hydratase | HALTITAN_RS11900 | HALTITAN_RS01660 |
| putrescine | gabT: gamma-aminobutyrate transaminase | HALTITAN_RS00665 | HALTITAN_RS00620 |
| rhamnose | aldA: lactaldehyde dehydrogenase | HALTITAN_RS23055 | HALTITAN_RS00660 |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | HALTITAN_RS20020 | HALTITAN_RS08065 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | HALTITAN_RS14050 | HALTITAN_RS10935 |
| rhamnose | LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase | HALTITAN_RS13945 | HALTITAN_RS24165 |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsB: D-ribose ABC transporter, substrate-binding component RbsB | HALTITAN_RS24155 | HALTITAN_RS17130 |
| ribose | rbsK: ribokinase | HALTITAN_RS24160 | HALTITAN_RS10365 |
| sucrose | ams: sucrose hydrolase (invertase) | HALTITAN_RS10520 | HALTITAN_RS10490 |
| trehalose | treF: trehalase | HALTITAN_RS10520 | HALTITAN_RS10490 |
| tryptophan | antA: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA | HALTITAN_RS03380 | HALTITAN_RS03430 |
| tryptophan | antB: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB | HALTITAN_RS03375 | HALTITAN_RS03425 |
| tryptophan | antC: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC | HALTITAN_RS03420 | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | HALTITAN_RS15020 | |
| tryptophan | kynB: kynurenine formamidase | HALTITAN_RS05400 | HALTITAN_RS22520 |
| tryptophan | pcaD: 3-oxoadipate enol-lactone hydrolase | HALTITAN_RS03665 | HALTITAN_RS16980 |
| tryptophan | pcaF: succinyl-CoA:acetyl-CoA C-succinyltransferase | HALTITAN_RS03670 | HALTITAN_RS16805 |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | HALTITAN_RS15020 | |
| valine | acdH: isobutyryl-CoA dehydrogenase | HALTITAN_RS05190 | HALTITAN_RS16815 |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | HALTITAN_RS05195 | HALTITAN_RS11900 |
| valine | natB: L-valine ABC transporter, substrate-binding component NatB | HALTITAN_RS19895 | |
| valine | natC: L-valine ABC transporter, permease component 1 (NatC) | | |
| valine | natD: L-valine ABC transporter, permease component 2 (NatD) | HALTITAN_RS19880 | HALTITAN_RS02320 |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | | |
| xylose | gyaR: glyoxylate reductase | HALTITAN_RS15885 | HALTITAN_RS06650 |
| xylose | xdh: D-xylose dehydrogenase | HALTITAN_RS14165 | HALTITAN_RS17730 |
| xylose | xylC: xylonolactonase | HALTITAN_RS10390 | |
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