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) | 54% | 100% | 274.2 | 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 | 53% | 268.9 |
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) | 53% | 97% | 268.9 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
L-glutamate catabolism | gltL | 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% | 268.9 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
L-histidine catabolism | bgtA | med | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 56% | 97% | 266.9 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
L-lysine catabolism | hisP | med | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 56% | 97% | 266.9 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
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) | 54% | 97% | 257.3 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
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) | 52% | 93% | 255.4 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
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) | 52% | 93% | 255.4 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
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) | 52% | 93% | 255.4 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
L-histidine 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) | 52% | 93% | 255.4 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
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) | 52% | 93% | 255.4 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
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) | 52% | 93% | 255.4 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
L-asparagine catabolism | bztD | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 52% | 90% | 254.6 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
L-aspartate catabolism | bztD | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 52% | 90% | 254.6 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
L-asparagine catabolism | aatP | med | ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) | 53% | 99% | 252.3 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
L-aspartate catabolism | aatP | med | ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) | 53% | 99% | 252.3 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
L-citrulline catabolism | AO353_03040 | med | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 50% | 97% | 250 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
D-alanine catabolism | Pf6N2E2_5405 | med | ABC transporter for D-Alanine, ATPase component (characterized) | 52% | 94% | 249.6 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
L-histidine catabolism | BPHYT_RS24015 | med | ABC transporter related (characterized, see rationale) | 51% | 94% | 243.8 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
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) | 51% | 91% | 240.7 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
D-glucosamine (chitosamine) catabolism | AO353_21725 | med | ABC transporter for D-Glucosamine, putative ATPase component (characterized) | 49% | 95% | 235.7 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
L-asparagine catabolism | bgtA | med | ATPase (characterized, see rationale) | 52% | 92% | 235 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
L-aspartate catabolism | bgtA | med | ATPase (characterized, see rationale) | 52% | 92% | 235 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
L-asparagine catabolism | peb1C | med | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 49% | 99% | 231.9 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
L-aspartate catabolism | peb1C | med | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 49% | 99% | 231.9 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
L-histidine catabolism | PA5503 | med | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 43% | 72% | 187.2 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
L-tryptophan catabolism | ecfA2 | med | Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) | 40% | 80% | 155.2 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
L-proline catabolism | proV | lo | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 41% | 59% | 183.3 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
putrescine catabolism | potA | lo | PotG aka B0855, component of Putrescine porter (characterized) | 37% | 66% | 171.8 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 35% | 64% | 161.4 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
trehalose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 35% | 64% | 161.4 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 35% | 66% | 160.2 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
L-histidine catabolism | hutV | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 39% | 84% | 159.8 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
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) | 38% | 85% | 159.1 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 38% | 67% | 158.7 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 37% | 64% | 156.4 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
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) | 33% | 80% | 156.4 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
D-maltose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 35% | 63% | 151 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
sucrose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 35% | 63% | 151 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
trehalose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 35% | 63% | 151 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
D-maltose catabolism | malK | lo | Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 35% | 63% | 150.6 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 34% | 62% | 150.6 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 35% | 70% | 149.8 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 30% | 78% | 149.8 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 30% | 78% | 149.8 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 35% | 70% | 149.8 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 30% | 78% | 149.8 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 30% | 78% | 149.8 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 30% | 78% | 149.8 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 30% | 78% | 149.8 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 30% | 78% | 149.8 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 30% | 78% | 149.8 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 35% | 62% | 149.1 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 35% | 62% | 149.1 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 35% | 62% | 149.1 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 35% | 62% | 149.1 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 35% | 62% | 149.1 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 35% | 62% | 149.1 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
lactose catabolism | lacK | lo | LacK, component of Lactose porter (characterized) | 34% | 65% | 148.3 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 34% | 61% | 147.1 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
D-mannitol catabolism | mtlK | lo | ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) | 33% | 63% | 147.1 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 33% | 81% | 146.4 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
D-cellobiose catabolism | gtsD | 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% | 63% | 141.4 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
D-glucose catabolism | gtsD | 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% | 63% | 141.4 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
lactose catabolism | gtsD | 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% | 63% | 141.4 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
D-maltose catabolism | gtsD | 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% | 63% | 141.4 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
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% | 63% | 141.4 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
sucrose catabolism | gtsD | 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% | 63% | 141.4 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
trehalose catabolism | gtsD | 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% | 63% | 141.4 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
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% | 98% | 139.4 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
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% | 98% | 139.4 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
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% | 98% | 139.4 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 34% | 62% | 136.7 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 34% | 57% | 135.2 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 36% | 66% | 129.8 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
L-proline catabolism | HSERO_RS00900 | lo | ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) | 32% | 95% | 121.3 | Arginine transport ATP-binding protein ArtM | 54% | 274.2 |
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