| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-cellobiose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 51% | 77% | 266.2 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| D-glucose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 51% | 77% | 266.2 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| lactose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 51% | 77% | 266.2 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| D-maltose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 51% | 77% | 266.2 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| sucrose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 51% | 77% | 266.2 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| trehalose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 51% | 77% | 266.2 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| D-maltose catabolism | thuK | med | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 46% | 80% | 255.4 | MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) | 46% | 252.3 |
| trehalose catabolism | thuK | med | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 46% | 80% | 255.4 | MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) | 46% | 252.3 |
| L-arabinose catabolism | xacK | med | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 48% | 71% | 253.4 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | med | ABC transporter for D-Glucosamine, ATPase component (characterized) | 42% | 99% | 250.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| sucrose catabolism | thuK | med | ABC transporter (characterized, see rationale) | 42% | 81% | 238.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| L-fucose catabolism | SM_b21106 | med | ABC transporter for L-Fucose, ATPase component (characterized) | 42% | 78% | 238.4 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 48% | 72% | 235.7 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 48% | 72% | 235.7 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| D-maltose catabolism | malK_Bb | med | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 43% | 81% | 234.2 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| xylitol catabolism | Dshi_0546 | med | ABC transporter for Xylitol, ATPase component (characterized) | 43% | 79% | 233 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| D-sorbitol (glucitol) catabolism | mtlK | med | ABC transporter for D-Sorbitol, ATPase component (characterized) | 42% | 82% | 231.9 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| lactose catabolism | lacK | med | ABC transporter for Lactose, ATPase component (characterized) | 41% | 83% | 231.1 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| putrescine catabolism | potA | med | PotG aka B0855, component of Putrescine porter (characterized) | 43% | 74% | 229.2 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| D-maltose catabolism | malK1 | med | 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) | 44% | 80% | 228 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| 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% | 80% | 227.3 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| L-histidine catabolism | hutV | med | HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) | 42% | 85% | 172.6 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| L-proline catabolism | hutV | med | HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) | 42% | 85% | 172.6 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| L-histidine catabolism | aapP | med | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 40% | 90% | 159.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| L-asparagine catabolism | bgtA | med | ATPase (characterized, see rationale) | 41% | 88% | 156 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| L-aspartate catabolism | bgtA | med | ATPase (characterized, see rationale) | 41% | 88% | 156 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 78% | 185.7 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 78% | 185.7 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 78% | 185.7 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 78% | 185.7 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 78% | 185.7 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 78% | 185.7 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 78% | 185.7 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 78% | 185.7 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| L-lysine catabolism | hisP | lo | Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) | 39% | 92% | 164.9 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| L-asparagine catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 37% | 92% | 157.9 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| L-aspartate catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 37% | 92% | 157.9 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| L-glutamate catabolism | gltL | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 37% | 92% | 157.9 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| L-arginine catabolism | artP | lo | Arginine transport ATP-binding protein ArtM (characterized) | 37% | 98% | 156.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| 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) | 39% | 90% | 156.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| 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) | 39% | 90% | 156.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| 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) | 39% | 90% | 156.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| 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) | 39% | 90% | 156.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| 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) | 39% | 90% | 156.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| D-alanine catabolism | Pf6N2E2_5405 | lo | ABC transporter for D-Alanine, ATPase component (characterized) | 40% | 89% | 156 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| D-glucosamine (chitosamine) catabolism | AO353_21725 | lo | ABC transporter for D-Glucosamine, putative ATPase component (characterized) | 37% | 93% | 153.3 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| L-asparagine catabolism | aatP | lo | ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) | 39% | 91% | 149.4 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| L-aspartate catabolism | aatP | lo | ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) | 39% | 91% | 149.4 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| L-histidine catabolism | BPHYT_RS24015 | lo | ABC transporter related (characterized, see rationale) | 40% | 95% | 149.4 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| 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) | 35% | 99% | 149.1 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| L-asparagine catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 36% | 98% | 147.1 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| L-aspartate catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 36% | 98% | 147.1 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| 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) | 37% | 94% | 146.7 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| 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) | 36% | 92% | 144.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| L-histidine catabolism | bgtA | lo | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 37% | 96% | 144.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
| L-citrulline catabolism | AO353_03040 | lo | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 35% | 98% | 140.2 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 46% | 255.4 |
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