GapMind for catabolism of small carbon sources


Potential Gaps in catabolism of small carbon sources in Phaeobacter inhibens BS107

Found 53 low-confidence and 46 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
4-hydroxybenzoate pcaB: 3-carboxymuconate cycloisomerase PGA1_c04560
4-hydroxybenzoate pcaF: succinyl-CoA:acetyl-CoA C-succinyltransferase PGA1_c04090 PGA1_c34350
4-hydroxybenzoate pcaI: 3-oxoadipate CoA-transferase subunit A (PcaI) PGA1_c06210
4-hydroxybenzoate pcaJ: 3-oxoadipate CoA-transferase subunit B (PcaJ) PGA1_c06200
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK
acetate ybhL: acetate uptake transporter YbhL PGA1_c21920
arabinose araE: L-arabinose:H+ symporter
arabinose xacB: L-arabinose 1-dehydrogenase PGA1_c07370 PGA1_c13170
arabinose xacE: 2-dehydro-3-deoxy-L-arabinonate dehydratase
arginine artM: L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) PGA1_c11550 PGA1_262p02380
arginine artQ: L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) PGA1_262p02370 PGA1_c11560
citrulline PS417_17590: ABC transporter for L-Citrulline, periplasmic substrate-binding component PGA1_262p02360
citrulline PS417_17595: ABC transporter for L-Citrulline, permease component 1 PGA1_262p02370 PGA1_c26600
citrulline PS417_17600: ABC transporter for L-Citrulline, permease component 2 PGA1_c11550 PGA1_262p02380
citrulline PS417_17605: ABC transporter for L-Citrulline, ATPase component PGA1_262p02350 PGA1_c11580
D-alanine dadA: D-alanine dehydrogenase
D-alanine Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component PGA1_c01980
D-alanine Pf6N2E2_5403: ABC transporter for D-Alanine, permease component 2 PGA1_c01990
D-alanine Pf6N2E2_5404: ABC transporter for D-Alanine, permease component 1 PGA1_c02000 PGA1_65p00120
D-alanine Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component PGA1_c02010 PGA1_262p02350
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase PGA1_c33720 PGA1_c04590
deoxyinosine bmpA: deoxyinosine ABC transporter, substrate-binding component PGA1_c03970
deoxyinosine nupB: deoxyinosine ABC transporter, permease component 1 PGA1_c03950 PGA1_c26920
deoxyinosine nupC': deoxyinosine ABC transporter, permease component 2 PGA1_c28160 PGA1_c03940
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate garK: glycerate 2-kinase PGA1_c31360
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme PGA1_c08400
deoxyribose deoK: deoxyribokinase PGA1_c34980
deoxyribose deoP: deoxyribose transporter
fucose aldA: lactaldehyde dehydrogenase PGA1_c21070 PGA1_c32800
fucose fucA: L-fuculose-phosphate aldolase FucA PGA1_c16250
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 PGA1_c07380 PGA1_c04540
galactose dgoK: 2-dehydro-3-deoxygalactonokinase PGA1_c07360
galactose galP: galactose:H+ symporter GalP
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 nagX: transmembrane glucosamine N-acetyltransferase NagX
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate garK: glycerate 2-kinase PGA1_c31360
glucuronate garL: 5-dehydro-4-deoxy-D-glucarate aldolase PGA1_c31400 PGA1_c19370
glucuronate garR: tartronate semialdehyde reductase PGA1_c14880 PGA1_c17360
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase PGA1_c04540
glucuronate udh: D-glucuronate dehydrogenase
histidine hutX: L-histidine ABC transporter, substrate-binding component HutX PGA1_c25570 PGA1_c22800
isoleucine Bap2: L-isoleucine permease Bap2
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
lactose dgoD: D-galactonate dehydratase PGA1_c07380 PGA1_c04540
lactose dgoK: 2-dehydro-3-deoxygalactonokinase PGA1_c07360
lactose lacP: lactose permease LacP
leucine leuT: L-leucine:Na+ symporter LeuT
lysine davA: 5-aminovaleramidase PGA1_c26450 PGA1_c34700
lysine davB: L-lysine 2-monooxygenase
lysine davT: 5-aminovalerate aminotransferase PGA1_c24230 PGA1_c28750
lysine hisM: L-lysine ABC transporter, permease component 1 (HisM) PGA1_c11550 PGA1_262p02380
lysine hisP: L-lysine ABC transporter, ATPase component HisP PGA1_c02010 PGA1_262p02350
lysine hisQ: L-lysine ABC transporter, permease component 2 (HisQ) PGA1_262p02370 PGA1_c26600
mannitol mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE PGA1_c13210
mannitol mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) PGA1_c13200 PGA1_c16700
mannitol mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) PGA1_c13190
mannitol mtlK: polyol ABC transporter, ATP component MtlK/SmoG PGA1_c13180 PGA1_c16680
phenylacetate paaF: 2,3-dehydroadipyl-CoA hydratase PGA1_c36500 PGA1_262p01980
phenylacetate paaT: phenylacetate transporter Paa
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine paaF: 2,3-dehydroadipyl-CoA hydratase PGA1_c36500 PGA1_262p01980
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabT: gamma-aminobutyrate transaminase PGA1_c34400 PGA1_c09350
putrescine puuC: gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PGA1_c32250 PGA1_c21670
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose aldA: lactaldehyde dehydrogenase PGA1_c21070 PGA1_c32800
rhamnose LRA1: L-rhamnofuranose dehydrogenase PGA1_c27390 PGA1_c13170
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase
rhamnose LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase PGA1_c31400 PGA1_c19370
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsK: ribokinase PGA1_c34980
serine snatA: L-serine transporter PGA1_c19770
threonine snatA: L-threonine transporter snatA PGA1_c19770
thymidine nupG: thymidine permease NupG/XapB
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
valine acdH: isobutyryl-CoA dehydrogenase PGA1_c10280 PGA1_c17340
valine Bap2: L-valine permease Bap2
valine mmsA: methylmalonate-semialdehyde dehydrogenase PGA1_c17300 PGA1_c21670
xylitol PLT5: xylitol:H+ symporter PLT5
xylitol xdhA: xylitol dehydrogenase PGA1_c34320 PGA1_c13170
xylose xylF: ABC transporter for xylose, substrate binding component xylF PGA1_262p00430
xylose xylH: ABC transporter for xylose, permease component xylH PGA1_262p00440 PGA1_c28050

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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