| 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) | 42% | 99% | 266.2 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| D-sorbitol (glucitol) catabolism | mtlK | med | ABC transporter for D-Sorbitol, ATPase component (characterized) | 41% | 86% | 245.7 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| xylitol catabolism | HSERO_RS17020 | med | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 41% | 89% | 243.4 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 41% | 90% | 235.3 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 41% | 90% | 235.3 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| D-mannitol catabolism | mtlK | med | ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) | 41% | 89% | 235 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| L-arabinose catabolism | xacK | med | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 40% | 93% | 234.6 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| D-maltose catabolism | malK_Bb | med | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 42% | 89% | 228.8 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| D-maltose catabolism | malK | med | Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 41% | 89% | 226.9 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| D-maltose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 43% | 80% | 226.1 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| D-maltose catabolism | thuK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 43% | 80% | 226.1 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| sucrose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 43% | 80% | 226.1 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| trehalose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 43% | 80% | 226.1 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| trehalose catabolism | treV | med | TreV, component of Trehalose porter (characterized) | 46% | 72% | 213.4 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 39% | 91% | 249.2 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| lactose catabolism | lacK | lo | ABC transporter for Lactose, ATPase component (characterized) | 38% | 99% | 239.2 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 37% | 99% | 234.6 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| D-cellobiose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 40% | 94% | 233.4 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| D-glucose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 40% | 94% | 233.4 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| lactose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 40% | 94% | 233.4 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| D-maltose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 40% | 94% | 233.4 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| sucrose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 40% | 94% | 233.4 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| trehalose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 40% | 94% | 233.4 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 39% | 96% | 233.4 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| trehalose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 37% | 99% | 231.5 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| 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) | 38% | 92% | 230.7 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 39% | 99% | 227.3 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 40% | 92% | 224.9 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| 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) | 36% | 92% | 223.4 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 35% | 93% | 217.2 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 39% | 93% | 216.5 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 39% | 93% | 216.5 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 39% | 93% | 216.5 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 39% | 93% | 216.5 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 39% | 93% | 216.5 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 39% | 93% | 216.5 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 39% | 88% | 216.1 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| 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) | 35% | 96% | 213 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 39% | 87% | 210.7 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| 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) | 38% | 89% | 209.5 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 37% | 86% | 207.6 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| 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) | 42% | 65% | 195.7 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 37% | 86% | 194.9 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| glycerol catabolism | glpT | lo | GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) | 34% | 96% | 190.3 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 33% | 95% | 184.1 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 33% | 95% | 184.1 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 33% | 95% | 184.1 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 33% | 95% | 184.1 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 33% | 95% | 184.1 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 33% | 95% | 184.1 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 33% | 95% | 184.1 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 33% | 95% | 184.1 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| L-proline catabolism | proV | lo | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 34% | 70% | 172.9 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| 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) | 32% | 82% | 166 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 34% | 67% | 164.5 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 34% | 67% | 164.5 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 34% | 67% | 164.5 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 34% | 67% | 164.5 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| L-histidine catabolism | hutV | lo | HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) | 40% | 83% | 163.7 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| 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) | 40% | 83% | 163.7 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| glycerol catabolism | glpS | lo | ABC transporter for Glycerol, ATPase component 1 (characterized) | 35% | 98% | 162.2 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| D-glucosamine (chitosamine) catabolism | AO353_21725 | lo | ABC transporter for D-Glucosamine, putative ATPase component (characterized) | 37% | 95% | 154.8 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| L-asparagine catabolism | aatP | lo | ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) | 38% | 94% | 153.7 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| L-aspartate catabolism | aatP | lo | ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) | 38% | 94% | 153.7 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| L-glutamate catabolism | gltL | lo | ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) | 38% | 94% | 153.7 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| D-alanine catabolism | Pf6N2E2_5405 | lo | ABC transporter for D-Alanine, ATPase component (characterized) | 37% | 89% | 153.3 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| L-histidine catabolism | aapP | lo | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 37% | 90% | 153.3 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| L-histidine catabolism | Ac3H11_2560 | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 39% | 81% | 149.4 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| L-lysine catabolism | hisP | lo | Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) | 37% | 91% | 149.4 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| L-tryptophan catabolism | ecfA1 | lo | Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) | 37% | 81% | 129 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| L-alanine catabolism | braG | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 31% | 99% | 120.2 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| L-isoleucine catabolism | livF | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 31% | 99% | 120.2 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| L-leucine catabolism | livF | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 31% | 99% | 120.2 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| L-serine catabolism | braG | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 31% | 99% | 120.2 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| L-threonine catabolism | braG | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 31% | 99% | 120.2 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| L-valine catabolism | livF | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 31% | 99% | 120.2 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
| L-phenylalanine catabolism | livF | lo | High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale) | 30% | 99% | 114.8 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 47% | 292.4 |
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