| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| putrescine catabolism | potA | med | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) | 42% | 91% | 275.4 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| sucrose catabolism | thuK | med | ABC transporter (characterized, see rationale) | 41% | 85% | 261.2 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| trehalose catabolism | malK | med | MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized) | 41% | 95% | 259.6 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| lactose catabolism | lacK | med | ABC transporter for Lactose, ATPase component (characterized) | 41% | 97% | 255 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| D-maltose catabolism | thuK | med | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 44% | 91% | 253.4 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| trehalose catabolism | thuK | med | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 44% | 91% | 253.4 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| D-maltose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 41% | 96% | 252.3 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| 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) | 44% | 80% | 252.3 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| sucrose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 41% | 96% | 252.3 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| trehalose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 41% | 96% | 252.3 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| D-sorbitol (glucitol) catabolism | mtlK | med | ABC transporter for D-Sorbitol, ATPase component (characterized) | 42% | 83% | 251.5 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| D-maltose catabolism | malK | med | Maltose-transporting ATPase (EC 3.6.3.19) (characterized) | 44% | 77% | 245 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| 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) | 40% | 93% | 244.6 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| 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) | 40% | 93% | 244.6 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| 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) | 40% | 93% | 244.6 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| 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) | 40% | 93% | 244.6 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| 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) | 40% | 93% | 244.6 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| 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) | 40% | 93% | 244.6 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| 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) | 40% | 93% | 244.6 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| D-mannitol catabolism | mtlK | med | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) | 41% | 80% | 244.2 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| D-maltose catabolism | malK_Aa | med | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 46% | 75% | 243.4 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 44% | 81% | 243 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 44% | 81% | 243 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| L-fucose catabolism | SM_b21106 | med | ABC transporter for L-Fucose, ATPase component (characterized) | 40% | 94% | 242.7 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| D-maltose catabolism | musK | med | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 45% | 73% | 242.3 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| L-arabinose catabolism | xacJ | med | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 41% | 92% | 238.8 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| D-maltose catabolism | malK_Bb | med | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 42% | 86% | 238.4 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| D-cellobiose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 40% | 85% | 221.9 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| D-glucose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 40% | 85% | 221.9 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| lactose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 40% | 85% | 221.9 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| D-maltose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 40% | 85% | 221.9 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| sucrose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 40% | 85% | 221.9 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| trehalose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 40% | 85% | 221.9 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| D-cellobiose catabolism | SMc04256 | med | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 40% | 94% | 221.5 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| trehalose catabolism | treV | med | TreV, component of Trehalose porter (characterized) | 42% | 84% | 220.3 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| 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) | 52% | 63% | 245.4 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 39% | 92% | 238 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 39% | 92% | 237.7 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 47% | 70% | 230.3 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 37% | 92% | 229.2 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 40% | 80% | 226.9 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| L-proline catabolism | opuBA | lo | 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) | 38% | 89% | 184.9 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| L-proline catabolism | proV | lo | Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) | 35% | 74% | 177.2 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| glycerol catabolism | glpT | lo | ABC transporter for Glycerol, ATPase component 2 (characterized) | 34% | 95% | 174.1 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| L-histidine catabolism | hutV | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 39% | 89% | 169.1 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| 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) | 38% | 81% | 160.6 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| L-histidine catabolism | Ac3H11_2560 | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 40% | 91% | 159.8 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| L-arginine catabolism | artP | lo | Arginine transport ATP-binding protein ArtM (characterized) | 36% | 98% | 157.5 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| L-asparagine catabolism | glnQ | lo | Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) | 36% | 97% | 157.1 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| glycerol catabolism | glpS | lo | GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) | 37% | 67% | 155.6 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| D-alanine catabolism | Pf6N2E2_5405 | lo | ABC transporter for D-Alanine, ATPase component (characterized) | 36% | 89% | 151 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| L-asparagine catabolism | bgtA | lo | ATPase (characterized, see rationale) | 37% | 86% | 146.7 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
| L-aspartate catabolism | bgtA | lo | ATPase (characterized, see rationale) | 37% | 86% | 146.7 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 283.1 |
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