| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-asparagine catabolism | peb1C | hi | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 67% | 99% | 320.9 | ABC transporter for D-Alanine, ATPase component | 61% | 298.5 |
| L-aspartate catabolism | peb1C | hi | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 67% | 99% | 320.9 | ABC transporter for D-Alanine, ATPase component | 61% | 298.5 |
| L-glutamate catabolism | gltL | hi | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 67% | 99% | 320.9 | ABC transporter for D-Alanine, ATPase component | 61% | 298.5 |
| D-alanine catabolism | Pf6N2E2_5405 | med | ABC transporter for D-Alanine, ATPase component (characterized) | 61% | 95% | 298.5 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| L-histidine catabolism | aapP | med | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 60% | 93% | 293.9 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| L-asparagine catabolism | aapP | med | 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) | 59% | 93% | 292 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| L-aspartate catabolism | aapP | med | 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) | 59% | 93% | 292 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| L-glutamate catabolism | aapP | med | 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) | 59% | 93% | 292 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| L-leucine catabolism | aapP | med | 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) | 59% | 93% | 292 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| L-proline catabolism | aapP | med | 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) | 59% | 93% | 292 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| L-asparagine catabolism | bztD | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 59% | 91% | 288.1 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| L-aspartate catabolism | bztD | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 59% | 91% | 288.1 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| L-asparagine catabolism | aatP | med | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 57% | 100% | 270.4 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| L-aspartate catabolism | aatP | med | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 57% | 100% | 270.4 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| L-lysine catabolism | hisP | med | Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) | 56% | 93% | 270.4 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| L-asparagine catabolism | glnQ | med | 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) | 55% | 98% | 264.2 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| L-arginine catabolism | artP | med | Arginine transport ATP-binding protein ArtM (characterized) | 53% | 100% | 254.2 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| L-asparagine catabolism | bgtA | med | ATPase (characterized, see rationale) | 54% | 92% | 245 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| L-aspartate catabolism | bgtA | med | ATPase (characterized, see rationale) | 54% | 92% | 245 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| L-histidine catabolism | hisP | med | 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) | 48% | 96% | 238 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| L-histidine catabolism | BPHYT_RS24015 | med | ABC transporter related (characterized, see rationale) | 48% | 94% | 228.8 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| D-glucosamine (chitosamine) catabolism | AO353_21725 | med | ABC transporter for D-Glucosamine, putative ATPase component (characterized) | 48% | 94% | 226.9 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| L-histidine catabolism | bgtA | med | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 50% | 97% | 224.2 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| L-citrulline catabolism | PS417_17605 | med | 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) | 48% | 91% | 221.9 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| L-proline catabolism | proV | lo | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 42% | 56% | 171 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| 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) | 42% | 55% | 168.7 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 39% | 63% | 166.4 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 39% | 63% | 166.4 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 39% | 63% | 166.4 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| D-maltose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 39% | 63% | 166.4 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 39% | 63% | 166.4 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| sucrose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 39% | 63% | 166.4 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 39% | 63% | 166.4 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| trehalose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 39% | 63% | 166.4 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 39% | 63% | 166.4 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 39% | 70% | 159.8 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 39% | 70% | 159.8 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| D-maltose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 38% | 69% | 157.1 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| sucrose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 38% | 69% | 157.1 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| trehalose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 38% | 69% | 157.1 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 38% | 67% | 152.1 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| lactose catabolism | lacK | lo | LacK, component of Lactose porter (characterized) | 37% | 65% | 151.4 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| 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) | 35% | 64% | 148.3 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 68% | 143.3 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 68% | 143.3 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 68% | 143.3 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 68% | 143.3 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 68% | 143.3 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 68% | 143.3 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 68% | 143.3 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 68% | 143.3 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| L-isoleucine catabolism | livG | lo | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 32% | 95% | 137.5 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| L-leucine catabolism | livG | lo | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 32% | 95% | 137.5 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| L-valine catabolism | livG | lo | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 32% | 95% | 137.5 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 37% | 62% | 127.1 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
| glycerol catabolism | glpS | lo | ABC transporter for Glycerol, ATPase component 1 (characterized) | 33% | 62% | 117.5 | PEB1C, component of Uptake system for glutamate and aspartate | 67% | 320.9 |
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