GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Marinobacter adhaerens HP15

Found 98 low-confidence and 42 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 pobA: 4-hydroxybenzoate 3-monooxygenase
4-hydroxybenzoate praA: protocatechuate 2,3-dioxygenase
acetate actP: cation/acetate symporter ActP
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter
asparagine ans: asparaginase HP15_1914
cellobiose bgl: cellobiase
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component HP15_3030 HP15_2920
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 HP15_3032 HP15_2919
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component HP15_3031
citrulline gabT: gamma-aminobutyrate transaminase HP15_3708 HP15_2925
citrulline odc: L-ornithine decarboxylase HP15_3785
citrulline puuD: gamma-glutamyl-gamma-aminobutyrate hydrolase HP15_2338
D-alanine Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component HP15_2196
D-lactate lctP: D-lactate:H+ symporter LctP or LidP
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase HP15_3213
deoxyinosine deoB: phosphopentomutase HP15_3072
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine deoD: deoxyinosine phosphorylase HP15_2259
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase HP15_825 HP15_1707
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 HP15_943 HP15_3144
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 HP15_2048 HP15_p187g66
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 gntK: D-gluconate kinase
gluconate gntT: gluconate:H+ symporter GntT
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) HP15_3676 HP15_p187g69
glucosamine SLC2A2: glucosamine transporter SLC2A2
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate dopDH: 2,5-dioxopentanonate dehydrogenase HP15_2020 HP15_3626
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate kdgD: 5-dehydro-4-deoxyglucarate dehydratase HP15_2027
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 HP15_1251
L-lactate Shew_2732: L-lactate:Na+ symporter, small component HP15_1252
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 HP15_3031 HP15_2918
lysine davA: 5-aminovaleramidase HP15_2074 HP15_3653
lysine davB: L-lysine 2-monooxygenase
lysine gcdG: succinyl-CoA:glutarate CoA-transferase HP15_1416 HP15_2609
lysine hisM: L-lysine ABC transporter, permease component 1 (HisM) HP15_3033 HP15_3032
lysine hisP: L-lysine ABC transporter, ATPase component HisP HP15_2193 HP15_3030
lysine hisQ: L-lysine ABC transporter, permease component 2 (HisQ) HP15_3032 HP15_2919
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 HP15_444 HP15_3072
mannose manP: mannose PTS system, EII-CBA components HP15_3725
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 HP15_2910
myoinositol iolT: myo-inositol:H+ symporter
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) HP15_3676 HP15_p187g69
NAG nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components
phenylacetate paaF: 2,3-dehydroadipyl-CoA hydratase HP15_12 HP15_908
phenylacetate paaT: phenylacetate transporter Paa
phenylalanine paaF: 2,3-dehydroadipyl-CoA hydratase HP15_12 HP15_908
propionate putP: propionate transporter; proline:Na+ symporter HP15_2205
putrescine gabT: gamma-aminobutyrate transaminase HP15_3708 HP15_2925
putrescine puuD: gamma-glutamyl-gamma-aminobutyrate hydrolase HP15_2338
rhamnose aldA: lactaldehyde dehydrogenase HP15_943 HP15_3144
rhamnose LRA1: L-rhamnofuranose dehydrogenase HP15_42 HP15_2784
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase
rhamnose LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsK: ribokinase
ribose rbsU: probable D-ribose transporter RbsU
serine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) HP15_3056 HP15_2706
serine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) HP15_3058 HP15_2704
serine sdaB: L-serine ammonia-lyase HP15_3213
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase HP15_2361 HP15_2784
sucrose ams: sucrose hydrolase (invertase)
threonine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) HP15_3056 HP15_2706
threonine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) HP15_3058 HP15_2704
threonine tdcE: 2-ketobutyrate formate-lyase
thymidine deoA: thymidine phosphorylase DeoA HP15_2594
thymidine deoB: phosphopentomutase HP15_3072
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
trehalose treF: trehalase
tryptophan antA: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA HP15_1106 HP15_39
tryptophan antB: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB
tryptophan antC: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC HP15_1107 HP15_4029
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan kyn: kynureninase
tryptophan kynA: tryptophan 2,3-dioxygenase
tryptophan kynB: kynurenine formamidase
tyrosine Ac3H11_1692: L-tyrosine ABC transporter, ATPase component 2 HP15_2703 HP15_3059
tyrosine Ac3H11_1694: L-tyrosine ABC transporter, permease component 2 HP15_3057 HP15_2705
tyrosine Ac3H11_1695: L-tyrosine ABC transporter, permease component 1 HP15_3056 HP15_2706
tyrosine Ac3H11_2396: L-tyrosine ABC transporter, substrate-binding component component HP15_3055
tyrosine fahA: fumarylacetoacetate hydrolase
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase HP15_907 HP15_2
valine bch: 3-hydroxyisobutyryl-CoA hydrolase HP15_3410 HP15_909
xylitol fruI: xylitol PTS, enzyme IIABC (FruI) HP15_3725
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase
xylose gtsA: xylose ABC transporter, periplasmic substrate-binding component GtsA HP15_2958
xylose gtsB: xylose ABC transporter, permease component 1 GtsB HP15_2957
xylose gtsC: xylose ABC transporter, permease component 2 GtsC HP15_2956
xylose gtsD: xylose ABC transporter, ATPase component GtsD HP15_2955 HP15_939
xylose xylA: xylose isomerase
xylose xylB: xylulokinase

Confidence: high confidence medium confidence low confidence

This GapMind analysis is from Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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