Potential Gaps in catabolism of small carbon sources in Lutibaculum baratangense AMV1
Found 96 low-confidence and 76 medium-confidence steps on the best paths for 62 pathways.
Pathway | Step | Best candidate | 2nd candidate |
4-hydroxybenzoate | pcaF: succinyl-CoA:acetyl-CoA C-succinyltransferase | N177_RS02410 | N177_RS12075 |
4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
alanine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | N177_RS20180 | N177_RS02905 |
alanine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | N177_RS20205 | N177_RS02910 |
alanine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | N177_RS20195 | N177_RS07365 |
alanine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | N177_RS20190 | N177_RS07360 |
arabinose | araE: L-arabinose:H+ symporter | | |
arabinose | xacB: L-arabinose 1-dehydrogenase | N177_RS09215 | N177_RS07140 |
arabinose | xacC: L-arabinono-1,4-lactonase | | |
arabinose | xacE: 2-dehydro-3-deoxy-L-arabinonate dehydratase | N177_RS16675 | |
arginine | braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) | N177_RS20205 | N177_RS14315 |
arginine | kauB: 4-guanidinobutyraldehyde dehydrogenase | N177_RS08305 | N177_RS12830 |
cellobiose | cbp: cellobiose phosphorylase | | |
cellobiose | cdt: cellobiose transporter cdt-1/cdt-2 | | |
cellobiose | glk: glucokinase | N177_RS17690 | |
citrate | tctB: citrate/Na+ symporter, small transmembrane component TctB | | |
citrate | tctC: citrate/Na+ symporter, substrate-binding component TctC | N177_RS03190 | |
citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | N177_RS07680 | N177_RS05245 |
citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | N177_RS02595 | N177_RS07665 |
citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | N177_RS07670 | N177_RS02600 |
citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | N177_RS02605 | N177_RS07675 |
citrulline | citrullinase: putative citrullinase | N177_RS04695 | |
citrulline | odc: L-ornithine decarboxylase | N177_RS01880 | |
citrulline | puuC: gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase | N177_RS08305 | N177_RS12830 |
D-alanine | AZOBR_RS08240: D-alanine ABC transporter, permease component 2 | N177_RS20200 | N177_RS02915 |
D-alanine | dadA: D-alanine dehydrogenase | N177_RS00430 | |
D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | N177_RS13370 | |
D-serine | cycA: D-serine:H+ symporter CycA | | |
D-serine | dsdA: D-serine ammonia-lyase | N177_RS12980 | N177_RS16030 |
deoxyinosine | adh: acetaldehyde dehydrogenase (not acylating) | N177_RS19425 | N177_RS12830 |
deoxyinosine | deoB: phosphopentomutase | N177_RS05055 | |
deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
deoxyinosine | deoD: deoxyinosine phosphorylase | N177_RS15650 | |
deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | N177_RS01090 | N177_RS16495 |
deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
deoxyribose | adh: acetaldehyde dehydrogenase (not acylating) | N177_RS19425 | N177_RS12830 |
deoxyribose | deoC: deoxyribose-5-phosphate aldolase | | |
deoxyribose | deoP: deoxyribose transporter | | |
ethanol | adh: acetaldehyde dehydrogenase (not acylating) | N177_RS19425 | N177_RS12830 |
fructose | Slc2a5: fructose:H+ symporter | | |
fucose | aldA: lactaldehyde dehydrogenase | N177_RS08305 | N177_RS14415 |
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 | dgoD: D-galactonate dehydratase | N177_RS12545 | N177_RS00815 |
galactose | galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) | | |
galactose | galdh: D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) | N177_RS09215 | N177_RS07140 |
galactose | galP: galactose:H+ symporter GalP | | |
galacturonate | eda: 2-keto-3-deoxygluconate 6-phosphate aldolase | N177_RS12535 | |
galacturonate | exuT: D-galacturonate transporter ExuT | | |
galacturonate | uxaA: D-altronate dehydratase | | |
galacturonate | uxaB: tagaturonate reductase | | |
galacturonate | uxaC: D-galacturonate isomerase | | |
gluconate | gnd: 6-phosphogluconate dehydrogenase, decarboxylating | | |
gluconate | gntK: D-gluconate kinase | | |
gluconate | gntT: gluconate:H+ symporter GntT | | |
glucosamine | AO353_21710: glucosaminate ABC transporter, substrate-binding component | N177_RS02605 | |
glucosamine | AO353_21715: glucosaminate ABC transporter, permease component 1 | N177_RS05255 | N177_RS11635 |
glucosamine | AO353_21720: glucosaminate ABC transporter, permease component 2 | N177_RS05250 | N177_RS11630 |
glucosamine | AO353_21725: glucosaminate ABC transporter, ATPase component | N177_RS11640 | N177_RS07680 |
glucosamine | gdh: quinoprotein glucose dehydrogenase | N177_RS19245 | N177_RS06445 |
glucosamine | glucosaminate-lyase: glucosaminate ammonia-lyase | N177_RS03415 | |
glucosamine | kdgA: 2-keto-3-deoxygluconate-6-phosphate aldolase EC:4.1.2.14 | N177_RS12535 | |
glucose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
glucuronate | eda: 2-keto-3-deoxygluconate 6-phosphate aldolase | N177_RS12535 | |
glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
glucuronate | uxaC: D-glucuronate isomerase | | |
histidine | hutG': N-formylglutamate amidohydrolase | | |
isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | N177_RS14805 | N177_RS14635 |
isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | N177_RS13470 | N177_RS01090 |
isoleucine | livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) | N177_RS20205 | N177_RS14315 |
L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | N177_RS13370 | |
L-lactate | lutC: L-lactate dehydrogenase, LutC subunit | N177_RS08090 | |
lactose | dgoD: D-galactonate dehydratase | N177_RS12545 | N177_RS00815 |
lactose | galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) | | |
lactose | galdh: D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) | N177_RS09215 | N177_RS07140 |
lactose | glk: glucokinase | N177_RS17690 | |
lactose | lacP: lactose permease LacP | | |
lactose | lacZ: lactase (homomeric) | | |
leucine | liuC: 3-methylglutaconyl-CoA hydratase | N177_RS05770 | N177_RS14645 |
leucine | liuE: hydroxymethylglutaryl-CoA lyase | N177_RS14845 | |
lysine | cadA: lysine decarboxylase | N177_RS19565 | N177_RS01880 |
lysine | davD: glutarate semialdehyde dehydrogenase | N177_RS19425 | N177_RS00820 |
lysine | davT: 5-aminovalerate aminotransferase | N177_RS00515 | N177_RS19680 |
lysine | fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase | N177_RS04545 | N177_RS13530 |
lysine | hisP: L-lysine ABC transporter, ATPase component HisP | N177_RS07680 | N177_RS16485 |
lysine | patA: cadaverine aminotransferase | N177_RS00515 | N177_RS19680 |
lysine | patD: 5-aminopentanal dehydrogenase | N177_RS08305 | N177_RS12830 |
maltose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
maltose | susB: alpha-glucosidase (maltase) | N177_RS19985 | N177_RS17980 |
mannitol | mt2d: mannitol 2-dehydrogenase | N177_RS02290 | N177_RS18515 |
mannitol | PLT5: polyol transporter PLT5 | | |
mannose | manA: mannose-6-phosphate isomerase | N177_RS15085 | N177_RS18150 |
mannose | STP6: mannose:H+ symporter | | |
myoinositol | eda: 2-keto-3-deoxygluconate 6-phosphate aldolase | N177_RS12535 | |
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 | uxaE: D-tagaturonate epimerase | | |
NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | N177_RS03970 | |
NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
phenylacetate | paaA: phenylacetyl-CoA 1,2-epoxidase, subunit A | | |
phenylacetate | paaB: phenylacetyl-CoA 1,2-epoxidase, subunit B | | |
phenylacetate | paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C | | |
phenylacetate | paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E | | |
phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | N177_RS05770 | N177_RS14645 |
phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | N177_RS02695 | N177_RS14850 |
phenylacetate | paaH: 3-hydroxyadipyl-CoA dehydrogenase | N177_RS04545 | N177_RS13530 |
phenylacetate | paaK: phenylacetate-CoA ligase | N177_RS05440 | N177_RS08505 |
phenylacetate | paaT: phenylacetate transporter Paa | | |
phenylacetate | paaZ1: oxepin-CoA hydrolase | N177_RS05770 | N177_RS16245 |
phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
phenylalanine | fahA: fumarylacetoacetate hydrolase | N177_RS19785 | |
phenylalanine | hmgA: homogentisate dioxygenase | | |
phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
phenylalanine | livH: L-phenylalanine ABC transporter, permease component 1 (LivH) | N177_RS20205 | N177_RS03605 |
phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | N177_RS20180 | N177_RS02905 |
phenylalanine | maiA: maleylacetoacetate isomerase | N177_RS18640 | |
phenylalanine | PAH: phenylalanine 4-monooxygenase | | |
phenylalanine | QDPR: 6,7-dihydropteridine reductase | | |
propionate | putP: propionate transporter; proline:Na+ symporter | | |
putrescine | puuC: gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase | N177_RS08305 | N177_RS12830 |
pyruvate | dctQ: pyruvate TRAP transporter, small permease component | N177_RS10320 | N177_RS13425 |
rhamnose | LRA1: L-rhamnofuranose dehydrogenase | N177_RS12725 | N177_RS18240 |
rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
rhamnose | LRA3: L-rhamnonate dehydratase | | |
rhamnose | LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase | N177_RS01090 | N177_RS12080 |
rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
ribose | rbsU: probable D-ribose transporter RbsU | | |
serine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | N177_RS20180 | N177_RS02905 |
serine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | N177_RS20205 | N177_RS02910 |
serine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | N177_RS20195 | N177_RS07365 |
serine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | N177_RS20190 | N177_RS07360 |
sorbitol | sdh: sorbitol dehydrogenase | N177_RS13470 | N177_RS18240 |
sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
sucrose | SUS: sucrose synthase | | |
sucrose | sut: sucrose:proton symporter SUT/SUC | | |
threonine | adh: acetaldehyde dehydrogenase (not acylating) | N177_RS19425 | N177_RS12830 |
threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | N177_RS20180 | N177_RS02905 |
threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | N177_RS20205 | N177_RS02910 |
threonine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | N177_RS20195 | N177_RS07365 |
threonine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | N177_RS20190 | N177_RS07360 |
threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | N177_RS05320 | N177_RS05325 |
threonine | ltaE: L-threonine aldolase | N177_RS13060 | N177_RS16095 |
thymidine | adh: acetaldehyde dehydrogenase (not acylating) | N177_RS19425 | N177_RS12830 |
thymidine | deoA: thymidine phosphorylase DeoA | | |
thymidine | deoB: phosphopentomutase | N177_RS05055 | |
thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
thymidine | nupG: thymidine permease NupG/XapB | | |
trehalose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
trehalose | treF: trehalase | N177_RS19985 | N177_RS11155 |
tryptophan | aroP: tryptophan:H+ symporter AroP | | |
tryptophan | tnaA: tryptophanase | | |
tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
tyrosine | fahA: fumarylacetoacetate hydrolase | N177_RS19785 | |
tyrosine | hmgA: homogentisate dioxygenase | | |
tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
tyrosine | maiA: maleylacetoacetate isomerase | N177_RS18640 | |
valine | acdH: isobutyryl-CoA dehydrogenase | N177_RS14805 | N177_RS14635 |
valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | N177_RS20205 | N177_RS14315 |
valine | mmsA: methylmalonate-semialdehyde dehydrogenase | N177_RS13385 | N177_RS02270 |
valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | N177_RS02590 | N177_RS21040 |
xylitol | PLT5: xylitol:H+ symporter PLT5 | | |
xylitol | xdhA: xylitol dehydrogenase | N177_RS02320 | N177_RS00865 |
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