GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Bradyrhizobium sp. BTAi1

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

Pathway Step Best candidate 2nd candidate
4-hydroxybenzoate ligU: 4-oxalomesaconate tautomerase
alanine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) BBTA_RS24925
alanine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) BBTA_RS24905 BBTA_RS28020
alanine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) BBTA_RS24915 BBTA_RS33150
arginine braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) BBTA_RS24905 BBTA_RS28020
arginine odc: L-ornithine decarboxylase BBTA_RS14635 BBTA_RS06365
arginine patD: gamma-aminobutyraldehyde dehydrogenase BBTA_RS18005 BBTA_RS22610
asparagine aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) BBTA_RS37100 BBTA_RS18360
asparagine aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) BBTA_RS18355 BBTA_RS37095
asparagine ans: asparaginase BBTA_RS16710
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component BBTA_RS09765 BBTA_RS18365
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 BBTA_RS09760 BBTA_RS18360
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 BBTA_RS09760 BBTA_RS18360
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component BBTA_RS03690
citrulline arcC: carbamate kinase
citrulline odc: L-ornithine decarboxylase BBTA_RS14635 BBTA_RS06365
citrulline patD: gamma-aminobutyraldehyde dehydrogenase BBTA_RS18005 BBTA_RS22610
D-alanine dadA: D-alanine dehydrogenase
D-alanine Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component BBTA_RS18350 BBTA_RS03295
D-alanine Pf6N2E2_5404: ABC transporter for D-Alanine, permease component 1 BBTA_RS37100 BBTA_RS18360
D-alanine Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component BBTA_RS37105 BBTA_RS18365
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase BBTA_RS25980 BBTA_RS18660
deoxyinosine deoB: phosphopentomutase
deoxyinosine deoD: deoxyinosine phosphorylase BBTA_RS03010
deoxyinosine nupC: deoxyinosine:H+ symporter NupC BBTA_RS24690
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase BBTA_RS07425 BBTA_RS15285
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter BBTA_RS26000 BBTA_RS14575
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme BBTA_RS03140
deoxyribose deoP: deoxyribose transporter
fucose fucD: L-fuconate dehydratase BBTA_RS13750 BBTA_RS30415
fucose fucP: L-fucose:H+ symporter FucP
galactose dgoD: D-galactonate dehydratase BBTA_RS09935 BBTA_RS02575
gluconate gntT: gluconate:H+ symporter GntT
glucosamine AO353_21710: glucosaminate ABC transporter, substrate-binding component
glucosamine AO353_21715: glucosaminate ABC transporter, permease component 1 BBTA_RS05925 BBTA_RS18360
glucosamine AO353_21720: glucosaminate ABC transporter, permease component 2 BBTA_RS18360 BBTA_RS18355
glucosamine AO353_21725: glucosaminate ABC transporter, ATPase component BBTA_RS09765 BBTA_RS18365
glucosamine glucosaminate-lyase: glucosaminate ammonia-lyase BBTA_RS31855
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate dctQ: D-glucuronate TRAP transporter, small permease component BBTA_RS26850
glucuronate uxuL: D-glucaro-1,5-lactonase UxuL or UxuF BBTA_RS29500
glutamate braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) BBTA_RS24905 BBTA_RS28020
histidine braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) BBTA_RS24905 BBTA_RS28020
histidine hutG': N-formylglutamate amidohydrolase BBTA_RS06560
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase BBTA_RS16750 BBTA_RS31195
isoleucine livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) BBTA_RS24905 BBTA_RS28020
lactose dgoD: D-galactonate dehydratase BBTA_RS09935 BBTA_RS02575
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric) BBTA_RS30350 BBTA_RS19130
leucine liuC: 3-methylglutaconyl-CoA hydratase BBTA_RS18965 BBTA_RS13630
leucine livH: L-leucine ABC transporter, permease component 1 (LivH/BraD) BBTA_RS24905 BBTA_RS28020
lysine argT: L-lysine ABC transporter, substrate-binding component ArgT BBTA_RS03690 BBTA_RS09770
lysine hisM: L-lysine ABC transporter, permease component 1 (HisM) BBTA_RS30490 BBTA_RS41730
lysine hisP: L-lysine ABC transporter, ATPase component HisP BBTA_RS37105 BBTA_RS18365
lysine hisQ: L-lysine ABC transporter, permease component 2 (HisQ) BBTA_RS30490 BBTA_RS09760
maltose susB: alpha-glucosidase (maltase) BBTA_RS29620
mannitol mt2d: mannitol 2-dehydrogenase BBTA_RS09865 BBTA_RS04335
mannitol mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) BBTA_RS04325 BBTA_RS15095
mannitol mtlK: polyol ABC transporter, ATP component MtlK/SmoG BBTA_RS04330 BBTA_RS19305
mannose man-isomerase: D-mannose isomerase
myoinositol iolB: 5-deoxy-D-glucuronate isomerase
myoinositol iolC: 5-dehydro-2-deoxy-D-gluconate kinase
myoinositol iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase BBTA_RS02195 BBTA_RS02170
myoinositol PS417_11885: myo-inositol ABC transporter, substrate-binding component BBTA_RS31440 BBTA_RS09910
myoinositol PS417_11895: myo-inositol ABC transporter, permease component BBTA_RS31435 BBTA_RS11385
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) BBTA_RS19515
NAG nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase BBTA_RS13205 BBTA_RS35265
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine livH: L-phenylalanine ABC transporter, permease component 1 (LivH) BBTA_RS24905 BBTA_RS28020
phenylalanine livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK BBTA_RS24925
phenylalanine paaZ1: oxepin-CoA hydrolase BBTA_RS13205 BBTA_RS35265
phenylalanine paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine pad-dh: phenylacetaldehyde dehydrogenase BBTA_RS18025 BBTA_RS18005
proline aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) BBTA_RS37100 BBTA_RS18360
proline aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) BBTA_RS18355 BBTA_RS37095
propionate lctP: propionate permease BBTA_RS07735
putrescine patD: gamma-aminobutyraldehyde dehydrogenase BBTA_RS18005 BBTA_RS22610
rhamnose LRA1: L-rhamnofuranose dehydrogenase BBTA_RS21880 BBTA_RS15285
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase BBTA_RS13750 BBTA_RS30415
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsA: D-ribose ABC transporter, ATPase component RbsA BBTA_RS31430 BBTA_RS28795
ribose rbsB: D-ribose ABC transporter, substrate-binding component RbsB BBTA_RS31440
serine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) BBTA_RS24925
serine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) BBTA_RS24905 BBTA_RS28020
serine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) BBTA_RS24915 BBTA_RS33150
sorbitol sdh: sorbitol dehydrogenase BBTA_RS35470 BBTA_RS04165
sucrose ams: sucrose hydrolase (invertase) BBTA_RS29620
threonine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) BBTA_RS24925
threonine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) BBTA_RS24905 BBTA_RS28020
threonine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) BBTA_RS24915 BBTA_RS33150
thymidine deoB: phosphopentomutase
thymidine nupC: thymidine permease NupC BBTA_RS24690
trehalose treF: trehalase BBTA_RS29610 BBTA_RS29620
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
valine acdH: isobutyryl-CoA dehydrogenase BBTA_RS16750 BBTA_RS31195
valine bch: 3-hydroxyisobutyryl-CoA hydrolase BBTA_RS16755 BBTA_RS14030
valine livH: L-valine ABC transporter, permease component 1 (LivH/BraD) BBTA_RS24905 BBTA_RS28020
valine mmsA: methylmalonate-semialdehyde dehydrogenase BBTA_RS16745 BBTA_RS18005
valine mmsB: 3-hydroxyisobutyrate dehydrogenase BBTA_RS16180 BBTA_RS13510
xylitol PLT5: xylitol:H+ symporter PLT5
xylitol xdhA: xylitol dehydrogenase BBTA_RS09895 BBTA_RS19760

Confidence: high confidence medium confidence low confidence

This GapMind analysis is from Apr 09 2024. 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