| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-alanine catabolism | Pf6N2E2_5405 | med | ABC transporter for D-Alanine, ATPase component (characterized) | 75% | 98% | 391 | uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ | 75% | 387.5 |
| L-histidine catabolism | aapP | med | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 72% | 98% | 382.9 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| 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) | 72% | 96% | 377.9 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| 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) | 72% | 96% | 377.9 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| 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) | 72% | 96% | 377.9 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| 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) | 72% | 96% | 377.9 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| 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) | 72% | 96% | 377.9 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| L-asparagine catabolism | bztD | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 71% | 93% | 365.5 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| L-aspartate catabolism | bztD | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 71% | 93% | 365.5 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| L-glutamate catabolism | gltL | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 71% | 93% | 365.5 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| L-lysine catabolism | hisP | med | Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) | 64% | 100% | 322.4 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| L-asparagine catabolism | bgtA | med | ATPase (characterized, see rationale) | 64% | 100% | 316.2 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| L-aspartate catabolism | bgtA | med | ATPase (characterized, see rationale) | 64% | 100% | 316.2 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| L-asparagine catabolism | aatP | med | ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) | 61% | 100% | 290.8 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| L-aspartate catabolism | aatP | med | ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) | 61% | 100% | 290.8 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| L-asparagine catabolism | peb1C | med | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 58% | 100% | 278.9 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| L-aspartate catabolism | peb1C | med | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 58% | 100% | 278.9 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| D-glucosamine (chitosamine) catabolism | AO353_21725 | med | ABC transporter for D-Glucosamine, putative ATPase component (characterized) | 52% | 98% | 261.9 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| L-arginine catabolism | artP | med | Arginine transport ATP-binding protein ArtM (characterized) | 53% | 100% | 256.5 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| L-histidine catabolism | bgtA | med | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 54% | 99% | 252.7 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| 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) | 53% | 97% | 248.4 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| 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% | 100% | 230.3 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| L-histidine catabolism | BPHYT_RS24015 | med | ABC transporter related (characterized, see rationale) | 48% | 96% | 226.1 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| 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) | 47% | 96% | 221.5 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| L-citrulline catabolism | AO353_03040 | med | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 46% | 99% | 221.1 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| L-histidine catabolism | PA5503 | med | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 41% | 72% | 173.7 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| putrescine catabolism | potA | lo | PotG aka B0855, component of Putrescine porter (characterized) | 38% | 66% | 171 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| L-proline catabolism | proV | lo | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 38% | 61% | 162.2 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 39% | 69% | 158.3 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| D-cellobiose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 39% | 61% | 155.2 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| D-glucose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 39% | 61% | 155.2 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| lactose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 39% | 61% | 155.2 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| D-maltose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 39% | 61% | 155.2 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| sucrose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 39% | 61% | 155.2 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| trehalose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 39% | 61% | 155.2 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 39% | 61% | 155.2 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 37% | 66% | 152.9 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 37% | 66% | 152.9 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 35% | 61% | 152.1 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 38% | 61% | 151.8 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| lactose catabolism | lacK | lo | ABC transporter for Lactose, ATPase component (characterized) | 39% | 65% | 151.4 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| D-mannitol catabolism | mtlK | lo | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) | 37% | 70% | 148.3 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 36% | 67% | 146 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| D-maltose catabolism | malK | lo | Maltose-transporting ATPase (EC 3.6.3.19) (characterized) | 37% | 63% | 140.2 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| 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% | 63% | 140.2 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 36% | 65% | 139.8 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 35% | 61% | 139.4 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| 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) | 34% | 80% | 133.3 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| 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) | 34% | 62% | 130.2 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 36% | 65% | 128.6 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| D-cellobiose catabolism | cbtF | lo | CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) | 32% | 78% | 127.9 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| L-arabinose catabolism | xylGsa | lo | Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) | 31% | 96% | 122.9 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| 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) | 32% | 65% | 118.6 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| L-arginine catabolism | braG | lo | ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) | 30% | 93% | 115.2 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| L-glutamate catabolism | braG | lo | ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) | 30% | 93% | 115.2 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| L-histidine catabolism | braG | lo | ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) | 30% | 93% | 115.2 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| L-isoleucine catabolism | livF | lo | ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) | 30% | 93% | 115.2 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| L-leucine catabolism | livF | lo | ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) | 30% | 93% | 115.2 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| L-valine catabolism | livF | lo | ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) | 30% | 93% | 115.2 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| 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) | 30% | 94% | 112.8 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| 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) | 30% | 94% | 112.8 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
| 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) | 30% | 94% | 112.8 | ABC transporter for D-Alanine, ATPase component | 75% | 391.0 |
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