| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-histidine catabolism | aapP | med | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 41% | 84% | 146.7 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| L-arginine catabolism | artP | med | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- (characterized) | 41% | 88% | 145.6 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| L-asparagine catabolism | aapP | med | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 41% | 85% | 145.2 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| L-aspartate catabolism | aapP | med | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 41% | 85% | 145.2 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| L-glutamate catabolism | aapP | med | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 41% | 85% | 145.2 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| L-leucine catabolism | aapP | med | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 41% | 85% | 145.2 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| L-proline catabolism | aapP | med | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 41% | 85% | 145.2 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| L-glutamate catabolism | gltL | med | Amino acid ABC transporter ATP binding protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida (characterized) | 41% | 81% | 139 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 46% | 55% | 177.2 | MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) | 40% | 176.8 |
| trehalose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 46% | 55% | 177.2 | MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) | 40% | 176.8 |
| putrescine catabolism | potA | lo | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) | 45% | 52% | 168.3 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 41% | 68% | 165.6 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 41% | 68% | 165.6 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 41% | 68% | 165.6 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 41% | 68% | 165.6 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 41% | 68% | 165.6 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 41% | 68% | 165.6 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 41% | 68% | 165.6 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 41% | 68% | 165.6 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 43% | 53% | 162.5 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| D-maltose catabolism | malK | lo | ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) | 39% | 66% | 158.7 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 43% | 53% | 155.2 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 43% | 52% | 151.4 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| D-cellobiose catabolism | gtsD | lo | Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 41% | 53% | 149.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| D-glucose catabolism | gtsD | lo | Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 41% | 53% | 149.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| lactose catabolism | gtsD | lo | Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 41% | 53% | 149.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| D-maltose catabolism | gtsD | lo | Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 41% | 53% | 149.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| D-mannose catabolism | TT_C0211 | lo | Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 41% | 53% | 149.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| sucrose catabolism | gtsD | lo | Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 41% | 53% | 149.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| trehalose catabolism | gtsD | lo | Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 41% | 53% | 149.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 43% | 52% | 148.7 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 40% | 59% | 148.3 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 35% | 68% | 147.5 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 35% | 68% | 147.5 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 35% | 68% | 147.5 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 35% | 68% | 147.5 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 40% | 53% | 145.2 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| D-maltose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 34% | 80% | 144.4 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| sucrose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 34% | 80% | 144.4 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| trehalose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 34% | 80% | 144.4 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 39% | 62% | 144.1 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 39% | 62% | 144.1 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| D-cellobiose catabolism | msiK | lo | MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized) | 40% | 53% | 143.7 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| D-maltose catabolism | malK1 | lo | MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized) | 40% | 53% | 143.7 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 39% | 55% | 143.7 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| D-mannitol catabolism | mtlK | lo | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) | 39% | 62% | 142.5 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 40% | 58% | 140.2 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| lactose catabolism | lacK | lo | LacK, component of Lactose porter (characterized) | 38% | 55% | 139.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 36% | 72% | 137.9 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| D-alanine catabolism | Pf6N2E2_5405 | lo | ABC transporter for D-Alanine, ATPase component (characterized) | 39% | 86% | 137.1 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 40% | 53% | 134.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 40% | 53% | 134.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 40% | 53% | 134.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 40% | 53% | 134.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 40% | 53% | 134.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 40% | 53% | 134.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| D-glucosamine (chitosamine) catabolism | AO353_21725 | lo | ABC transporter for D-glucosamine, ATPase component (characterized) | 37% | 86% | 131.3 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| L-histidine catabolism | hutV | lo | HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) | 40% | 74% | 131 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| L-proline catabolism | hutV | lo | HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) | 40% | 74% | 131 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| D-cellobiose catabolism | TM0027 | lo | TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) | 31% | 79% | 107.1 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
| glycerol catabolism | glpS | lo | GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) | 33% | 55% | 105.5 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 177.2 |
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