GapMind for catabolism of small carbon sources

 

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:

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:

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:

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