Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
L-glutamate catabolism | gltL | med | GluA aka CGL1950, component of Glutamate porter (characterized) | 45% | 84% | 155.2 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
L-asparagine catabolism | bgtA | med | ATPase (characterized, see rationale) | 40% | 80% | 141.4 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
L-aspartate catabolism | bgtA | med | ATPase (characterized, see rationale) | 40% | 80% | 141.4 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
L-arginine catabolism | artP | med | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- (characterized) | 43% | 85% | 136.7 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
L-histidine catabolism | PA5503 | lo | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 43% | 63% | 162.2 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
L-asparagine catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 38% | 83% | 139.8 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
L-aspartate catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 38% | 83% | 139.8 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
L-histidine catabolism | aapP | lo | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 38% | 88% | 139.4 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 35% | 58% | 137.5 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
L-asparagine catabolism | aapP | lo | 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) | 37% | 87% | 137.5 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
L-aspartate catabolism | aapP | lo | 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) | 37% | 87% | 137.5 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 35% | 58% | 137.5 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
L-glutamate catabolism | aapP | lo | 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) | 37% | 87% | 137.5 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
L-leucine catabolism | aapP | lo | 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) | 37% | 87% | 137.5 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
L-proline catabolism | aapP | lo | 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) | 37% | 87% | 137.5 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 35% | 58% | 137.5 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 35% | 58% | 137.5 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
L-asparagine catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 37% | 87% | 135.2 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
L-aspartate catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 37% | 87% | 135.2 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 65% | 133.3 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 65% | 133.3 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 65% | 133.3 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
L-histidine catabolism | Ac3H11_2560 | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 40% | 83% | 133.3 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 65% | 133.3 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 65% | 133.3 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 65% | 133.3 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 65% | 133.3 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 65% | 133.3 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
D-alanine catabolism | Pf6N2E2_5405 | lo | ABC transporter for D-Alanine, ATPase component (characterized) | 39% | 85% | 131.7 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
L-asparagine catabolism | aatP | lo | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 39% | 84% | 129.4 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
L-aspartate catabolism | aatP | lo | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 39% | 84% | 129.4 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
D-cellobiose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 57% | 125.9 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
D-glucose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 57% | 125.9 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
lactose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 57% | 125.9 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
D-maltose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 57% | 125.9 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
sucrose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 57% | 125.9 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
trehalose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 57% | 125.9 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
trehalose catabolism | thuK | lo | Trehalose import ATP-binding protein SugC; EC 7.5.2.- (characterized) | 35% | 56% | 123.6 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 37% | 55% | 123.2 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 35% | 59% | 121.7 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 35% | 54% | 121.7 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 32% | 65% | 120.9 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 32% | 65% | 120.9 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 34% | 54% | 114.4 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
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) | 33% | 57% | 113.2 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 35% | 56% | 111.3 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
D-maltose catabolism | thuK | 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) | 32% | 56% | 107.5 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
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) | 32% | 56% | 107.5 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
sucrose catabolism | thuK | 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) | 32% | 56% | 107.5 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 33% | 55% | 106.7 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
D-cellobiose catabolism | cbtF | lo | CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) | 31% | 65% | 104 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
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) | 30% | 85% | 102.8 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
myo-inositol catabolism | PGA1_c07320 | lo | Inositol transport system ATP-binding protein (characterized) | 31% | 73% | 80.1 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 44% | 182.2 |
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