| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| putrescine catabolism | potA | med | PotG aka B0855, component of Putrescine porter (characterized) | 44% | 95% | 275 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| D-maltose catabolism | thuK | med | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 44% | 94% | 272.7 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| trehalose catabolism | thuK | med | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 44% | 94% | 272.7 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| D-maltose catabolism | malK1 | med | 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) | 47% | 88% | 265.4 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| D-cellobiose catabolism | gtsD | med | 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) | 42% | 92% | 263.8 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| D-glucose catabolism | gtsD | med | 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) | 42% | 92% | 263.8 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| lactose catabolism | gtsD | med | 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) | 42% | 92% | 263.8 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| D-maltose catabolism | gtsD | med | 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) | 42% | 92% | 263.8 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| D-mannose catabolism | TT_C0211 | med | 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) | 42% | 92% | 263.8 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| sucrose catabolism | gtsD | med | 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) | 42% | 92% | 263.8 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| sucrose catabolism | thuK | med | 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) | 42% | 92% | 263.8 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| trehalose catabolism | gtsD | med | 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) | 42% | 92% | 263.8 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| D-maltose catabolism | malK_Aa | med | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 48% | 77% | 262.7 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| D-maltose catabolism | malK_Sm | med | 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) | 40% | 95% | 254.2 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| trehalose catabolism | malK | med | 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) | 40% | 95% | 254.2 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| D-maltose catabolism | malK | med | ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) | 41% | 95% | 253.8 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| D-maltose catabolism | musK | med | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 45% | 78% | 252.3 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| lactose catabolism | lacK | med | LacK, component of Lactose porter (characterized) | 42% | 87% | 247.7 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| D-sorbitol (glucitol) catabolism | mtlK | med | ABC transporter for D-Sorbitol, ATPase component (characterized) | 42% | 87% | 247.7 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| D-maltose catabolism | malK_Bb | med | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 43% | 87% | 243.4 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| L-arabinose catabolism | xacK | med | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 44% | 83% | 237.7 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| xylitol catabolism | Dshi_0546 | med | ABC transporter for Xylitol, ATPase component (characterized) | 41% | 88% | 234.2 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| xylitol catabolism | HSERO_RS17020 | med | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 43% | 77% | 230.7 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| D-cellobiose catabolism | msiK | med | 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) | 43% | 80% | 229.9 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| L-proline catabolism | opuBA | med | BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) | 41% | 77% | 199.9 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| L-histidine catabolism | hutV | med | HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) | 42% | 82% | 181 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| L-proline catabolism | hutV | med | HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) | 42% | 82% | 181 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 39% | 94% | 241.1 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| D-maltose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 39% | 93% | 235.3 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| sucrose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 39% | 93% | 235.3 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| trehalose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 39% | 93% | 235.3 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 40% | 85% | 224.9 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 40% | 85% | 224.9 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 40% | 85% | 224.9 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 40% | 85% | 224.9 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 40% | 85% | 224.9 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 40% | 85% | 224.9 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 37% | 77% | 200.3 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 37% | 77% | 200.3 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 37% | 77% | 200.3 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
| D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 37% | 77% | 200.3 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 46% | 283.9 |
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