Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
L-arabinose catabolism | aldA | med | lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) | 44% | 99% | 416.8 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
L-fucose catabolism | aldA | med | lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) | 44% | 99% | 416.8 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
L-rhamnose catabolism | aldA | med | lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) | 44% | 99% | 416.8 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
L-threonine catabolism | aldA | med | lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) | 44% | 99% | 416.8 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
D-xylose catabolism | aldA | med | lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) | 44% | 99% | 416.8 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
L-arginine catabolism | gabD | lo | succinate-semialdehyde dehydrogenase (NAD+) (EC 1.2.1.24) (characterized) | 40% | 98% | 362.1 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
L-citrulline catabolism | gabD | lo | succinate-semialdehyde dehydrogenase (NAD+) (EC 1.2.1.24) (characterized) | 40% | 98% | 362.1 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
putrescine catabolism | gabD | lo | succinate-semialdehyde dehydrogenase (NAD+) (EC 1.2.1.24) (characterized) | 40% | 98% | 362.1 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
L-arginine catabolism | davD | lo | glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) | 39% | 99% | 357.1 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
L-citrulline catabolism | davD | lo | glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) | 39% | 99% | 357.1 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
L-lysine catabolism | davD | lo | glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) | 39% | 99% | 357.1 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
L-proline catabolism | davD | lo | glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) | 39% | 99% | 357.1 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
4-hydroxybenzoate catabolism | adh | lo | aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) | 39% | 90% | 349.4 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
2'-deoxyinosine catabolism | adh | lo | aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) | 39% | 90% | 349.4 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
2-deoxy-D-ribose catabolism | adh | lo | aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) | 39% | 90% | 349.4 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
ethanol catabolism | adh | lo | aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) | 39% | 90% | 349.4 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
L-threonine catabolism | adh | lo | aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) | 39% | 90% | 349.4 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
thymidine catabolism | adh | lo | aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) | 39% | 90% | 349.4 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
L-tryptophan catabolism | adh | lo | aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) | 39% | 90% | 349.4 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
L-phenylalanine catabolism | pad-dh | lo | aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) | 37% | 92% | 320.9 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
L-arabinose catabolism | xacF | lo | Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized) | 37% | 99% | 317.8 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
D-galacturonate catabolism | dopDH | lo | Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized) | 37% | 99% | 317.8 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
D-glucuronate catabolism | dopDH | lo | Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized) | 37% | 99% | 317.8 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
D-xylose catabolism | dopDH | lo | Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized) | 37% | 99% | 317.8 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
L-arginine catabolism | patD | lo | aminobutyraldehyde dehydrogenase (EC 1.2.1.19); betaine-aldehyde dehydrogenase (EC 1.2.1.8) (characterized) | 37% | 97% | 309.3 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
L-citrulline catabolism | patD | lo | aminobutyraldehyde dehydrogenase (EC 1.2.1.19); betaine-aldehyde dehydrogenase (EC 1.2.1.8) (characterized) | 37% | 97% | 309.3 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
putrescine catabolism | patD | lo | aminobutyraldehyde dehydrogenase (EC 1.2.1.19); betaine-aldehyde dehydrogenase (EC 1.2.1.8) (characterized) | 37% | 97% | 309.3 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
4-hydroxybenzoate catabolism | praB | lo | 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) | 34% | 96% | 296.2 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
L-tryptophan catabolism | praB | lo | 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) | 34% | 96% | 296.2 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
L-arginine catabolism | kauB | lo | gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) | 36% | 98% | 288.5 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
L-arginine catabolism | puuC | lo | gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) | 36% | 98% | 288.5 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
L-citrulline catabolism | puuC | lo | gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) | 36% | 98% | 288.5 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
putrescine catabolism | puuC | lo | gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) | 36% | 98% | 288.5 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
L-lysine catabolism | patD | lo | aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) | 36% | 98% | 277.3 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
L-tryptophan catabolism | nbaE | lo | 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) | 32% | 100% | 268.5 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
L-arginine catabolism | putA | lo | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) | 32% | 91% | 253.4 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
L-arginine catabolism | rocA | lo | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) | 32% | 91% | 253.4 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
L-citrulline catabolism | putA | lo | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) | 32% | 91% | 253.4 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
L-citrulline catabolism | rocA | lo | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) | 32% | 91% | 253.4 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
L-proline catabolism | putA | lo | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) | 32% | 91% | 253.4 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
L-isoleucine catabolism | iolA | lo | methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) | 31% | 98% | 240.7 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
myo-inositol catabolism | mmsA | lo | methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) | 31% | 98% | 240.7 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
propionate catabolism | iolA | lo | methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) | 31% | 98% | 240.7 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
L-threonine catabolism | iolA | lo | methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) | 31% | 98% | 240.7 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
L-valine catabolism | iolA | lo | methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) | 31% | 98% | 240.7 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
L-valine catabolism | mmsA | lo | methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) | 31% | 98% | 240.7 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
L-lysine catabolism | amaB | lo | Alpha-aminoadipic semialdehyde dehydrogenase; Alpha-AASA dehydrogenase; Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Betaine aldehyde dehydrogenase; Delta1-piperideine-6-carboxylate dehydrogenase; P6c dehydrogenase; EC 1.2.1.31; EC 1.2.1.3; EC 1.2.1.8 (characterized) | 31% | 89% | 240 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
L-arginine catabolism | astD | lo | N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) | 30% | 94% | 183 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
L-citrulline catabolism | astD | lo | N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) | 30% | 94% | 183 | 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 | 74% | 726.9 |
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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.
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).
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know