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) | 59% | 99% | 279.3 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
L-arginine catabolism | artP | med | Arginine transport ATP-binding protein ArtM (characterized) | 58% | 100% | 277.3 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
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% | 97% | 274.2 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
L-asparagine catabolism | bztD | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 59% | 86% | 268.9 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
L-aspartate catabolism | bztD | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 59% | 86% | 268.9 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
L-asparagine catabolism | bgtA | med | ATPase (characterized, see rationale) | 56% | 92% | 264.6 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
L-aspartate catabolism | bgtA | med | ATPase (characterized, see rationale) | 56% | 92% | 264.6 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
L-asparagine catabolism | aatP | med | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 54% | 100% | 264.2 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
L-aspartate catabolism | aatP | med | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 54% | 100% | 264.2 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
L-histidine catabolism | aapP | med | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 56% | 87% | 264.2 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 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) | 56% | 88% | 262.7 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 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) | 56% | 88% | 262.7 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 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) | 56% | 88% | 262.7 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 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) | 56% | 88% | 262.7 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 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) | 56% | 88% | 262.7 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
D-alanine catabolism | Pf6N2E2_5405 | med | ABC transporter for D-Alanine, ATPase component (characterized) | 55% | 89% | 260 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
L-lysine catabolism | hisP | med | Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) | 51% | 92% | 250.4 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
L-histidine catabolism | bgtA | med | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 51% | 96% | 246.9 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
L-histidine catabolism | BPHYT_RS24015 | med | ABC transporter related (characterized, see rationale) | 48% | 94% | 241.1 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
L-histidine catabolism | hisP | med | Histidine transport ATP-binding protein HisP (characterized) | 53% | 95% | 239.6 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
D-glucosamine (chitosamine) catabolism | AO353_21725 | med | ABC transporter for D-glucosamine, ATPase component (characterized) | 49% | 94% | 238.4 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
L-citrulline catabolism | AO353_03040 | med | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 49% | 98% | 238 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
L-asparagine catabolism | peb1C | med | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 48% | 99% | 229.6 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
L-aspartate catabolism | peb1C | med | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 48% | 99% | 229.6 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 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% | 90% | 214.2 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 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) | 40% | 76% | 133.7 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
L-histidine catabolism | PA5503 | lo | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 39% | 73% | 180.6 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
L-proline catabolism | proV | lo | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 41% | 60% | 175.6 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 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% | 171.8 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 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% | 64% | 162.2 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 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% | 64% | 162.2 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 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% | 158.3 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 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% | 158.3 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
putrescine catabolism | potA | lo | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) | 40% | 61% | 153.7 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 38% | 68% | 148.3 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 38% | 68% | 148.3 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 36% | 69% | 147.1 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 38% | 63% | 146 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 37% | 59% | 143.3 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 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% | 142.1 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 36% | 67% | 139.8 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
D-maltose catabolism | malK_Sm | lo | MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) | 34% | 64% | 139.4 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
D-maltose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 36% | 67% | 138.7 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 36% | 60% | 138.3 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 36% | 60% | 138.3 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 36% | 60% | 138.3 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
D-maltose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 36% | 60% | 138.3 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 36% | 60% | 138.3 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
sucrose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 36% | 60% | 138.3 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 36% | 60% | 138.3 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
trehalose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 36% | 60% | 138.3 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 36% | 60% | 138.3 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
D-cellobiose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 35% | 60% | 137.5 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
D-glucose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 35% | 60% | 137.5 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
lactose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 35% | 60% | 137.5 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
D-maltose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 35% | 60% | 137.5 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
sucrose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 35% | 60% | 137.5 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
trehalose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 35% | 60% | 137.5 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
D-maltose catabolism | malK | lo | Maltose-transporting ATPase (EC 3.6.3.19) (characterized) | 35% | 60% | 137.1 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 36% | 60% | 137.1 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
lactose catabolism | lacK | lo | ABC transporter for Lactose, ATPase component (characterized) | 37% | 61% | 135.6 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 35% | 64% | 134.4 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 35% | 60% | 134 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
D-cellobiose catabolism | TM0027 | lo | TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) | 34% | 95% | 132.9 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 34% | 55% | 132.5 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 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) | 38% | 77% | 129.8 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
glycerol catabolism | glpS | lo | ABC transporter for Glycerol, ATPase component 1 (characterized) | 33% | 60% | 111.7 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
myo-inositol catabolism | PGA1_c07320 | lo | Inositol transport system ATP-binding protein (characterized) | 31% | 87% | 111.7 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 58% | 283.9 |
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