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 (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