GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Dinoroseobacter shibae DFL-12

Found 56 low-confidence and 54 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
4-hydroxybenzoate pcaI: 3-oxoadipate CoA-transferase subunit A (PcaI) Dshi_1136
4-hydroxybenzoate pcaJ: 3-oxoadipate CoA-transferase subunit B (PcaJ) Dshi_1134
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK
arabinose araE: L-arabinose:H+ symporter
arabinose xacB: L-arabinose 1-dehydrogenase Dshi_1243 Dshi_1358
arabinose xacC: L-arabinono-1,4-lactonase Dshi_1240
arginine artJ: L-arginine ABC transporter, periplasmic substrate-binding component ArtJ/HisJ/ArtI/AotJ/ArgT Dshi_2222
arginine artM: L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) Dshi_2224 Dshi_0320
arginine artP: L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA Dshi_2221 Dshi_0321
arginine artQ: L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) Dshi_2223 Dshi_2224
asparagine ans: asparaginase
citrulline PS417_17590: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline PS417_17595: ABC transporter for L-Citrulline, permease component 1 Dshi_2223 Dshi_2224
citrulline PS417_17600: ABC transporter for L-Citrulline, permease component 2 Dshi_2224
citrulline PS417_17605: ABC transporter for L-Citrulline, ATPase component Dshi_2221 Dshi_0321
D-alanine Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component Dshi_0318
D-alanine Pf6N2E2_5403: ABC transporter for D-Alanine, permease component 2 Dshi_0319
D-alanine Pf6N2E2_5404: ABC transporter for D-Alanine, permease component 1 Dshi_0320
D-alanine Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component Dshi_0321 Dshi_2221
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase Dshi_0888 Dshi_1439
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase Dshi_2891 Dshi_0620
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme Dshi_3475
deoxyribose deoP: deoxyribose transporter
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 Dshi_2430
galactose dgoD: D-galactonate dehydratase Dshi_1244 Dshi_0129
galactose galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) Dshi_1240
galactose SGLT1: sodium/galactose cotransporter Dshi_3906 Dshi_3904
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate kdgK: 2-keto-3-deoxygluconate kinase Dshi_1268 Dshi_2797
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) Dshi_1293
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase Dshi_0604
glucuronate kdgD: 5-dehydro-4-deoxyglucarate dehydratase Dshi_0149
glucuronate udh: D-glucuronate dehydrogenase
glutamate gdhA: glutamate dehydrogenase, NAD-dependent Dshi_3841
histidine aapJ: L-histidine ABC transporter, substrate-binding component AapJ Dshi_0318
histidine aapM: L-histidine ABC transporter, permease component 2 (AapM) Dshi_0320
histidine aapP: L-histidine ABC transporter, ATPase component AapP Dshi_0321 Dshi_2221
histidine aapQ: L-histidine ABC transporter, permease component 1 (AapQ) Dshi_0319
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
isoleucine Bap2: L-isoleucine permease Bap2
L-lactate Shew_2731: L-lactate:Na+ symporter, large component Dshi_3556
L-lactate Shew_2732: L-lactate:Na+ symporter, small component Dshi_3555
lactose dgoD: D-galactonate dehydratase Dshi_1244 Dshi_0129
lactose galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) Dshi_1240
lactose lacP: lactose permease LacP
leucine aapJ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ Dshi_0318
leucine aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) Dshi_0320
leucine aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP Dshi_0321 Dshi_2221
leucine aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) Dshi_0319
lysine argT: L-lysine ABC transporter, substrate-binding component ArgT Dshi_2222
lysine davA: 5-aminovaleramidase Dshi_3506
lysine davB: L-lysine 2-monooxygenase
lysine davD: glutarate semialdehyde dehydrogenase Dshi_2887 Dshi_0577
lysine davT: 5-aminovalerate aminotransferase Dshi_1446 Dshi_0798
lysine hisM: L-lysine ABC transporter, permease component 1 (HisM) Dshi_2224 Dshi_0320
lysine hisP: L-lysine ABC transporter, ATPase component HisP Dshi_0321 Dshi_2221
lysine hisQ: L-lysine ABC transporter, permease component 2 (HisQ) Dshi_2223 Dshi_2224
mannitol mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE Dshi_0974
mannitol mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) Dshi_0973 Dshi_3143
mannitol mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) Dshi_0972 Dshi_0549
mannitol mtlK: polyol ABC transporter, ATP component MtlK/SmoG Dshi_0971 Dshi_1357
mannose man-isomerase: D-mannose isomerase
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) Dshi_1293
NAG nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components
phenylacetate paaF: 2,3-dehydroadipyl-CoA hydratase Dshi_3370 Dshi_1048
phenylacetate paaT: phenylacetate transporter Paa
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine iorAB: phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB Dshi_1762
phenylalanine paaF: 2,3-dehydroadipyl-CoA hydratase Dshi_3370 Dshi_1048
proline aapJ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ Dshi_0318
proline aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) Dshi_0320
proline aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP Dshi_0321 Dshi_2221
proline aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) Dshi_0319
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabT: gamma-aminobutyrate transaminase Dshi_1366 Dshi_2042
putrescine potB: putrescine ABC transporter, permease component 1 (PotB/PotH) Dshi_1599 Dshi_1053
putrescine potC: putrescine ABC transporter, permease component 2 (PotC/PotI) Dshi_1598 Dshi_0549
putrescine potD: putrescine ABC transporter, substrate-binding component (PotD/PotF)
putrescine puuC: gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase Dshi_1430 Dshi_3017
putrescine puuD: gamma-glutamyl-gamma-aminobutyrate hydrolase Dshi_1229 Dshi_3925
serine snatA: L-serine transporter Dshi_1348
sorbitol sdh: sorbitol dehydrogenase Dshi_0551 Dshi_0554
threonine snatA: L-threonine transporter snatA Dshi_1348
thymidine nupG: thymidine permease NupG/XapB
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase Dshi_3308
valine acdH: isobutyryl-CoA dehydrogenase Dshi_1750 Dshi_1297
valine Bap2: L-valine permease Bap2
valine mmsA: methylmalonate-semialdehyde dehydrogenase Dshi_1747 Dshi_0577
xylose xylT: D-xylose transporter

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