| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-glutamate catabolism | gltL | lo | GluA aka CGL1950, component of Glutamate porter (characterized) | 38% | 91% | 150.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 61% | 147.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 61% | 147.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 61% | 147.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 61% | 147.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 61% | 147.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 61% | 147.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 61% | 147.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 61% | 147.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| L-histidine catabolism | BPHYT_RS24015 | lo | ABC transporter related (characterized, see rationale) | 37% | 88% | 143.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| L-arginine catabolism | artP | lo | Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) | 37% | 87% | 142.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| L-histidine catabolism | hisP | lo | Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) | 37% | 87% | 142.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| L-lysine catabolism | hisP | lo | Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) | 37% | 87% | 142.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 35% | 65% | 140.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| 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) | 38% | 57% | 139.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| trehalose catabolism | thuK | 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) | 38% | 57% | 139.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 39% | 58% | 136.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| D-mannitol catabolism | mtlK | lo | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) | 37% | 63% | 136 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| D-cellobiose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 35% | 56% | 135.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| D-glucose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 35% | 56% | 135.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| lactose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 35% | 56% | 135.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| D-maltose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 35% | 56% | 135.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| sucrose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 35% | 56% | 135.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| trehalose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 35% | 56% | 135.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 35% | 56% | 135.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| 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) | 37% | 55% | 134.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| 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) | 37% | 55% | 134.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| 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) | 37% | 55% | 134.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 38% | 59% | 129.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 38% | 59% | 129.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| D-maltose catabolism | malK | lo | Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 33% | 59% | 129.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 36% | 50% | 125.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| glycerol catabolism | glpT | lo | GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) | 36% | 55% | 115.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| D-mannose catabolism | TM1749 | lo | TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) | 32% | 71% | 112.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| L-arabinose catabolism | xylGsa | lo | Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) | 32% | 78% | 98.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| L-isoleucine catabolism | livG | lo | High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) | 31% | 77% | 89 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| L-leucine catabolism | livG | lo | High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) | 31% | 77% | 89 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| L-phenylalanine catabolism | livG | lo | High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) | 31% | 77% | 89 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| L-valine catabolism | livG | lo | High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) | 31% | 77% | 89 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| L-isoleucine catabolism | livF | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 30% | 80% | 80.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| L-leucine catabolism | livF | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 30% | 80% | 80.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| L-phenylalanine catabolism | livF | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 30% | 80% | 80.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| L-proline catabolism | HSERO_RS00900 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 30% | 80% | 80.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| L-serine catabolism | Ac3H11_1692 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 30% | 80% | 80.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
| L-tyrosine catabolism | Ac3H11_1692 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 30% | 80% | 80.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 47% | 218.4 |
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