| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-arginine catabolism | artP | med | Arginine transport ATP-binding protein ArtM (characterized) | 41% | 90% | 159.1 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| L-glutamate catabolism | gltL | med | GluA aka CGL1950, component of Glutamate porter (characterized) | 41% | 90% | 155.2 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| 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) | 39% | 89% | 164.9 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 38% | 60% | 161 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 38% | 60% | 161 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 38% | 60% | 161 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 38% | 60% | 161 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| 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) | 39% | 56% | 159.8 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| trehalose catabolism | thuK | 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) | 39% | 56% | 159.8 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| L-asparagine catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 37% | 91% | 154.5 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| L-aspartate catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 37% | 91% | 154.5 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 37% | 64% | 154.1 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 38% | 57% | 154.1 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 37% | 64% | 154.1 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 38% | 57% | 154.1 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 38% | 57% | 154.1 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| D-maltose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 38% | 57% | 154.1 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 38% | 57% | 154.1 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| sucrose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 38% | 57% | 154.1 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 38% | 57% | 154.1 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| trehalose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 38% | 57% | 154.1 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 38% | 57% | 154.1 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| L-histidine catabolism | PA5503 | lo | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 35% | 67% | 153.7 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| D-cellobiose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 64% | 152.5 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| D-glucose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 64% | 152.5 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| lactose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 64% | 152.5 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| D-maltose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 64% | 152.5 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| sucrose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 64% | 152.5 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| trehalose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 64% | 152.5 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| L-asparagine catabolism | bgtA | lo | ATPase (characterized, see rationale) | 38% | 84% | 149.8 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| L-aspartate catabolism | bgtA | lo | ATPase (characterized, see rationale) | 38% | 84% | 149.8 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 35% | 56% | 147.9 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 35% | 56% | 146.7 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| D-mannitol catabolism | mtlK | lo | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) | 37% | 64% | 146.7 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| putrescine catabolism | potA | lo | Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) | 37% | 56% | 146.7 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 37% | 54% | 146.7 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| D-maltose catabolism | thuK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 37% | 59% | 146 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| L-asparagine catabolism | aatP | lo | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 39% | 90% | 145.6 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| L-aspartate catabolism | aatP | lo | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 39% | 90% | 145.6 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| lactose catabolism | lacK | lo | LacK, component of Lactose porter (characterized) | 38% | 58% | 143.3 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 37% | 58% | 142.5 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 36% | 58% | 142.1 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| D-mannose catabolism | TM1750 | lo | TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) | 33% | 67% | 141 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 35% | 61% | 136 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 35% | 57% | 132.5 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| D-cellobiose catabolism | TM0027 | lo | TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) | 38% | 79% | 125.9 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| D-mannose catabolism | TM1749 | lo | TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) | 32% | 74% | 119.8 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| D-cellobiose catabolism | cbtD | lo | CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) | 34% | 64% | 119 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| 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) | 36% | 73% | 117.1 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| 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) | 36% | 73% | 117.1 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| glycerol catabolism | glpS | lo | GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) | 32% | 54% | 115.9 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
| D-cellobiose catabolism | cbtF | lo | CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) | 31% | 69% | 115.5 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 41% | 194.5 |
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