| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 86% | 169.1 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 86% | 169.1 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 86% | 169.1 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 86% | 169.1 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 86% | 169.1 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 86% | 169.1 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 86% | 169.1 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 86% | 169.1 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 37% | 70% | 157.1 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 37% | 70% | 157.1 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 37% | 70% | 157.1 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 37% | 70% | 157.1 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 35% | 61% | 156.8 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| trehalose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 35% | 61% | 156.8 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 38% | 59% | 154.1 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| putrescine catabolism | potA | lo | Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) | 31% | 63% | 153.7 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 35% | 71% | 150.2 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 33% | 62% | 149.8 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| 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) | 33% | 63% | 149.1 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| D-maltose catabolism | malK | lo | ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) | 34% | 63% | 148.7 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 36% | 65% | 148.3 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| D-mannitol catabolism | mtlK | lo | ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) | 34% | 64% | 147.9 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) | 34% | 64% | 147.9 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 31% | 90% | 146.4 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 32% | 62% | 144.1 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 31% | 77% | 144.1 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 31% | 80% | 142.1 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 31% | 80% | 142.1 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 31% | 62% | 141.4 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 34% | 58% | 140.6 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| 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) | 34% | 58% | 140.2 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| 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) | 34% | 58% | 140.2 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| 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) | 34% | 58% | 140.2 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| 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) | 34% | 58% | 140.2 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| 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) | 34% | 58% | 140.2 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| 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) | 34% | 58% | 140.2 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| 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) | 34% | 58% | 140.2 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| D-maltose catabolism | malK_Sm | lo | MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) | 31% | 73% | 138.7 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| trehalose catabolism | malK | lo | MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) | 31% | 73% | 138.7 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 31% | 79% | 138.7 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 31% | 61% | 138.3 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| lactose catabolism | lacK | lo | ABC transporter for Lactose, ATPase component (characterized) | 32% | 65% | 138.3 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 32% | 63% | 138.3 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| D-maltose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 32% | 66% | 137.9 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| sucrose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 32% | 66% | 137.9 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| trehalose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 32% | 66% | 137.9 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 31% | 61% | 137.1 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 30% | 64% | 134.4 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| 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% | 96% | 130.6 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| 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) | 31% | 68% | 128.3 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 33% | 61% | 124 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 33% | 61% | 124 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 33% | 61% | 124 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 33% | 61% | 124 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 33% | 61% | 124 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 33% | 61% | 124 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
| L-histidine catabolism | hutV | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 30% | 87% | 121.7 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 31% | 171.4 |
This GapMind analysis is from Sep 17 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