Potential Gaps in catabolism of small carbon sources in Marinobacter psychrophilus 20041
Found 105 low-confidence and 31 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | | |
| 4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | ABA45_RS03455 | |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| 4-hydroxybenzoate | pobA: 4-hydroxybenzoate 3-monooxygenase | | |
| 4-hydroxybenzoate | praA: protocatechuate 2,3-dioxygenase | | |
| 4-hydroxybenzoate | xylF: 2-hydroxymuconate semialdehyde hydrolase | | |
| acetate | actP: cation/acetate symporter ActP | ABA45_RS06595 | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| cellobiose | cbp: cellobiose phosphorylase | | |
| cellobiose | cdt: cellobiose transporter cdt-1/cdt-2 | | |
| cellobiose | glk: glucokinase | ABA45_RS10740 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | ABA45_RS15525 | ABA45_RS14720 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | ABA45_RS15535 | ABA45_RS10560 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | ABA45_RS15530 | ABA45_RS11950 |
| citrulline | rocD: ornithine aminotransferase | ABA45_RS00035 | ABA45_RS01835 |
| D-alanine | Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component | ABA45_RS09160 | |
| D-alanine | Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component | ABA45_RS09175 | ABA45_RS14720 |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | ABA45_RS01635 | ABA45_RS16355 |
| deoxyinosine | deoB: phosphopentomutase | ABA45_RS15825 | |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyinosine | deoD: deoxyinosine phosphorylase | ABA45_RS05460 | |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | ABA45_RS12365 | ABA45_RS14380 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyribose | deoK: deoxyribokinase | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fructose | Slc2a5: fructose:H+ symporter | | |
| fucose | aldA: lactaldehyde dehydrogenase | ABA45_RS06205 | ABA45_RS14435 |
| 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 | ABA45_RS10925 | ABA45_RS11725 |
| galactose | galK: galactokinase (-1-phosphate forming) | | |
| galactose | galP: galactose:H+ symporter GalP | | |
| 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 | gntK: D-gluconate kinase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | ABA45_RS18045 | |
| glucose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
| glucuronate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | ABA45_RS10815 | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| glutamate | gltP: L-glutamate:cation symporter GltP/GltT | ABA45_RS13495 | ABA45_RS14535 |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| lactose | galE: UDP-glucose 4-epimerase | ABA45_RS10925 | ABA45_RS11725 |
| lactose | galK: galactokinase (-1-phosphate forming) | | |
| lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| lactose | glk: glucokinase | ABA45_RS10740 | |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | | |
| lysine | argT: L-lysine ABC transporter, substrate-binding component ArgT | ABA45_RS15530 | ABA45_RS07440 |
| lysine | davA: 5-aminovaleramidase | ABA45_RS09545 | |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | hisM: L-lysine ABC transporter, permease component 1 (HisM) | ABA45_RS15540 | ABA45_RS10555 |
| lysine | hisP: L-lysine ABC transporter, ATPase component HisP | ABA45_RS09175 | ABA45_RS15525 |
| lysine | hisQ: L-lysine ABC transporter, permease component 2 (HisQ) | ABA45_RS15535 | ABA45_RS14715 |
| maltose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
| maltose | susB: alpha-glucosidase (maltase) | | |
| mannitol | manA: mannose-6-phosphate isomerase | ABA45_RS03490 | ABA45_RS10310 |
| mannitol | mt1d: mannitol 1-dehydrogenase | ABA45_RS04285 | |
| mannitol | PLT5: polyol transporter PLT5 | | |
| mannose | manA: mannose-6-phosphate isomerase | ABA45_RS03490 | ABA45_RS10310 |
| mannose | STP6: mannose:H+ symporter | | |
| 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 | ABA45_RS14670 | |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | ABA45_RS18045 | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylalanine | ARO10: phenylpyruvate decarboxylase | | |
| phenylalanine | pad-dh: phenylacetaldehyde dehydrogenase | ABA45_RS08400 | ABA45_RS06205 |
| putrescine | gabT: gamma-aminobutyrate transaminase | ABA45_RS00035 | ABA45_RS01835 |
| putrescine | puuC: gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase | ABA45_RS06205 | ABA45_RS14435 |
| putrescine | puuD: gamma-glutamyl-gamma-aminobutyrate hydrolase | ABA45_RS05095 | |
| rhamnose | aldA: lactaldehyde dehydrogenase | ABA45_RS06205 | ABA45_RS14435 |
| 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 | rbsK: ribokinase | | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| sorbitol | sdh: sorbitol dehydrogenase | ABA45_RS13685 | ABA45_RS14380 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
| sucrose | scrP: sucrose phosphorylase | ABA45_RS17615 | |
| sucrose | sut: sucrose:proton symporter SUT/SUC | | |
| threonine | tdcE: 2-ketobutyrate formate-lyase | | |
| thymidine | deoA: thymidine phosphorylase DeoA | ABA45_RS13310 | |
| thymidine | deoB: phosphopentomutase | ABA45_RS15825 | |
| thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | glk: glucokinase | ABA45_RS10740 | |
| trehalose | PsTP: trehalose phosphorylase | | |
| trehalose | TRET1: facilitated trehalose transporter Tret1 | | |
| tryptophan | antA: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA | ABA45_RS01240 | |
| tryptophan | antB: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB | ABA45_RS01245 | |
| tryptophan | antC: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC | ABA45_RS01250 | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | kyn: kynureninase | | |
| tryptophan | kynA: tryptophan 2,3-dioxygenase | | |
| tryptophan | kynB: kynurenine formamidase | | |
| tryptophan | pcaD: 3-oxoadipate enol-lactone hydrolase | ABA45_RS01195 | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | fahA: fumarylacetoacetate hydrolase | | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | ABA45_RS12255 | ABA45_RS12140 |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | ABA45_RS13685 | |
| xylose | xylA: xylose isomerase | | |
| xylose | xylB: xylulokinase | | |
| 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