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:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
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:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
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:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
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