Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
L-glutamate catabolism | gltL | med | GluA aka CGL1950, component of Glutamate porter (characterized) | 62% | 93% | 283.9 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 277.7 |
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) | 57% | 95% | 280.4 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
L-asparagine catabolism | bztD | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 56% | 93% | 277.3 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
L-aspartate catabolism | bztD | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 56% | 93% | 277.3 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
L-histidine catabolism | aapP | med | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 54% | 94% | 271.2 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
L-arginine catabolism | artP | med | Arginine transport ATP-binding protein ArtM (characterized) | 56% | 100% | 270.8 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
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) | 57% | 88% | 270.4 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
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) | 57% | 88% | 270.4 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
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) | 57% | 88% | 270.4 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
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) | 57% | 88% | 270.4 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
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) | 57% | 88% | 270.4 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
L-asparagine catabolism | bgtA | med | ATPase (characterized, see rationale) | 56% | 93% | 269.6 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
L-aspartate catabolism | bgtA | med | ATPase (characterized, see rationale) | 56% | 93% | 269.6 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
D-alanine catabolism | Pf6N2E2_5405 | med | ABC transporter for D-Alanine, ATPase component (characterized) | 54% | 95% | 268.5 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
L-asparagine catabolism | aatP | med | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 58% | 94% | 267.3 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
L-aspartate catabolism | aatP | med | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 58% | 94% | 267.3 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
L-histidine catabolism | bgtA | med | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 54% | 96% | 253.8 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
L-lysine catabolism | hisP | med | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 54% | 96% | 253.8 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
D-glucosamine (chitosamine) catabolism | AO353_21725 | med | ABC transporter for D-glucosamine, ATPase component (characterized) | 49% | 95% | 245 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
L-histidine catabolism | BPHYT_RS24015 | med | ABC transporter related (characterized, see rationale) | 49% | 94% | 242.3 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
L-citrulline catabolism | AO353_03040 | med | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 50% | 98% | 238.4 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
L-histidine catabolism | hisP | med | Histidine transport ATP-binding protein HisP (characterized) | 50% | 99% | 235.3 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
L-asparagine catabolism | peb1C | med | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 51% | 93% | 229.9 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
L-aspartate catabolism | peb1C | med | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 51% | 93% | 229.9 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
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) | 47% | 89% | 216.5 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
L-tryptophan catabolism | ecfA1 | med | Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) | 41% | 76% | 135.2 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
L-histidine catabolism | PA5503 | lo | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 40% | 71% | 179.5 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
L-proline catabolism | proV | lo | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 42% | 58% | 178.3 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
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% | 58% | 177.6 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
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) | 39% | 63% | 164.5 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
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% | 63% | 164.5 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
putrescine catabolism | potA | lo | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) | 42% | 61% | 164.1 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
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) | 39% | 82% | 161 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
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) | 39% | 82% | 161 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 39% | 67% | 153.3 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 38% | 68% | 152.1 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 38% | 68% | 152.1 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 37% | 63% | 148.3 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 36% | 61% | 146.4 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 36% | 66% | 143.3 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 36% | 59% | 143.3 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 36% | 61% | 142.9 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
D-maltose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 34% | 65% | 142.5 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
sucrose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 34% | 65% | 142.5 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
trehalose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 34% | 65% | 142.5 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
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) | 34% | 64% | 141.7 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 68% | 141 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 68% | 141 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 68% | 141 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 68% | 141 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 68% | 141 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 68% | 141 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 68% | 141 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 68% | 141 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 60% | 139.8 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 60% | 139.8 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 60% | 139.8 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 60% | 139.8 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 60% | 139.8 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 60% | 139.8 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
D-mannitol catabolism | mtlK | lo | ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) | 37% | 62% | 139.4 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
D-cellobiose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 68% | 139 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
D-glucose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 68% | 139 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
lactose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 68% | 139 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
D-maltose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 68% | 139 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
sucrose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 68% | 139 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
trehalose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 68% | 139 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
lactose catabolism | lacK | lo | ABC transporter for Lactose, ATPase component (characterized) | 36% | 61% | 138.3 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 36% | 61% | 137.9 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
D-maltose catabolism | malK | lo | Maltose-transporting ATPase (EC 3.6.3.19) (characterized) | 36% | 60% | 137.1 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
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) | 36% | 61% | 136 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 33% | 58% | 133.3 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
L-tryptophan catabolism | ecfA2 | lo | Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) | 37% | 77% | 129 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
myo-inositol catabolism | PGA1_c07320 | lo | Inositol transport system ATP-binding protein (characterized) | 31% | 93% | 113.6 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
glycerol catabolism | glpT | lo | GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) | 31% | 67% | 108.6 | GluA aka CGL1950, component of Glutamate porter | 62% | 283.9 |
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