| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-asparagine catabolism | aatP | med | ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) | 44% | 88% | 152.9 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| L-aspartate catabolism | aatP | med | ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) | 44% | 88% | 152.9 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| L-glutamate catabolism | gltL | med | ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) | 44% | 88% | 152.9 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| 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% | 96% | 149.1 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| L-arginine catabolism | artP | lo | Arginine transport ATP-binding protein ArtM (characterized) | 36% | 98% | 148.3 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| L-histidine catabolism | bgtA | lo | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 35% | 96% | 141.7 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| 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% | 99% | 141.7 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| L-lysine catabolism | hisP | lo | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 35% | 96% | 141.7 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| 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) | 35% | 74% | 141.7 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| L-asparagine catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 32% | 93% | 139.4 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| L-aspartate catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 32% | 93% | 139.4 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 34% | 61% | 139.4 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| putrescine catabolism | potA | lo | PotG aka B0855, component of Putrescine porter (characterized) | 36% | 62% | 139 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| 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) | 33% | 95% | 137.5 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| 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) | 33% | 95% | 137.5 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| 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) | 33% | 95% | 137.5 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| L-histidine 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) | 33% | 95% | 137.5 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| 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) | 33% | 95% | 137.5 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| 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) | 33% | 95% | 137.5 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 34% | 63% | 136.7 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| D-alanine catabolism | Pf6N2E2_5405 | lo | ABC transporter for D-Alanine, ATPase component (characterized) | 32% | 93% | 132.1 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| D-maltose catabolism | malK | lo | Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 32% | 63% | 127.9 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 33% | 58% | 125.6 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| D-cellobiose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 34% | 61% | 124 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| D-glucose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 34% | 61% | 124 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| lactose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 34% | 61% | 124 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| D-maltose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 34% | 62% | 124 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| D-maltose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 34% | 61% | 124 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| D-maltose catabolism | thuK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 34% | 62% | 124 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| sucrose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 34% | 62% | 124 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| sucrose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 34% | 61% | 124 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| trehalose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 34% | 62% | 124 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| trehalose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 34% | 61% | 124 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 34% | 60% | 123.6 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| 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) | 31% | 62% | 122.5 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| trehalose 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) | 31% | 62% | 122.5 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 33% | 67% | 122.1 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| L-tryptophan catabolism | ecfA2 | lo | Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) | 35% | 77% | 122.1 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 34% | 69% | 120.9 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| citrate catabolism | fecE | lo | iron(III) dicitrate transport ATP-binding protein FecE (characterized) | 34% | 88% | 116.7 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| trehalose catabolism | malK | lo | 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) | 31% | 61% | 116.7 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 32% | 62% | 115.9 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 32% | 62% | 115.9 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 32% | 62% | 115.9 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 32% | 62% | 115.9 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 32% | 62% | 115.9 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 32% | 62% | 115.9 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 30% | 64% | 115.2 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 71% | 372.1 |
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