| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-histidine catabolism | hutV | med | ABC transporter for L-Histidine, ATPase component (characterized) | 41% | 81% | 154.5 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| L-histidine catabolism | PA5503 | lo | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 38% | 72% | 156.8 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| putrescine catabolism | potA | lo | PotG aka B0855, component of Putrescine porter (characterized) | 37% | 66% | 156.8 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| L-lysine catabolism | hisP | lo | ABC transporter for L-Lysine, ATPase component (characterized) | 34% | 100% | 155.6 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| L-proline catabolism | proV | lo | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 37% | 66% | 155.6 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| 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) | 34% | 99% | 155.2 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| 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) | 34% | 99% | 155.2 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| 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) | 37% | 91% | 149.1 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| 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) | 34% | 96% | 147.1 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| L-glutamate catabolism | gltL | 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) | 34% | 96% | 147.1 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| L-citrulline catabolism | PS417_17605 | lo | ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) | 34% | 91% | 142.9 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| L-histidine catabolism | BPHYT_RS24015 | lo | ABC transporter related (characterized, see rationale) | 33% | 97% | 142.9 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| L-citrulline catabolism | AO353_03040 | lo | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 34% | 99% | 139 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 34% | 61% | 138.7 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 32% | 71% | 137.5 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 32% | 71% | 137.5 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 32% | 71% | 137.5 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 32% | 71% | 137.5 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 32% | 71% | 137.5 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 32% | 71% | 137.5 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 32% | 71% | 137.5 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 32% | 71% | 137.5 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 34% | 71% | 135.6 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 34% | 71% | 135.6 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 33% | 61% | 133.7 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 34% | 66% | 133.7 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| L-proline catabolism | opuBA | lo | BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport (characterized) | 36% | 54% | 133.3 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 32% | 66% | 132.5 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 30% | 65% | 130.6 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| trehalose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 30% | 65% | 130.6 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 31% | 64% | 129 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| 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) | 31% | 62% | 127.9 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| 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) | 31% | 62% | 127.9 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| 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) | 31% | 62% | 127.9 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| 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) | 31% | 62% | 127.9 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| 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% | 127.9 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| 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) | 31% | 62% | 127.9 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| 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) | 31% | 62% | 127.9 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| 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) | 33% | 58% | 127.5 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 33% | 60% | 124.4 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| L-tryptophan catabolism | ecfA2 | lo | Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) | 32% | 78% | 122.9 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 32% | 65% | 122.5 | Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) | 46% | 236.9 |
This GapMind analysis is from Apr 09 2024. 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