Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
D-maltose catabolism | malK | lo | Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 35% | 86% | 167.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
D-mannitol catabolism | mtlK | lo | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) | 33% | 97% | 167.5 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 31% | 98% | 165.6 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
trehalose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 31% | 98% | 165.6 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
D-maltose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 34% | 90% | 162.5 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
sucrose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 34% | 90% | 162.5 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
trehalose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 34% | 90% | 162.5 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 32% | 95% | 162.2 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 32% | 95% | 162.2 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 32% | 95% | 162.2 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 32% | 95% | 162.2 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 32% | 95% | 162.2 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 34% | 86% | 162.2 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 32% | 95% | 162.2 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 32% | 93% | 160.2 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 32% | 94% | 159.1 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 32% | 94% | 159.1 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 31% | 94% | 157.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 31% | 97% | 157.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 32% | 85% | 155.6 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
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) | 31% | 92% | 154.5 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 38% | 70% | 153.7 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
putrescine catabolism | potA | lo | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) | 32% | 84% | 153.3 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
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) | 37% | 88% | 152.5 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
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) | 37% | 88% | 152.5 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
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) | 30% | 90% | 151.8 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
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) | 30% | 90% | 151.8 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
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) | 30% | 90% | 151.8 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
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) | 30% | 90% | 151.8 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
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) | 30% | 90% | 151.8 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
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) | 30% | 90% | 151.8 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
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) | 30% | 90% | 151.8 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
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) | 34% | 79% | 150.6 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 36% | 75% | 146.7 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 33% | 75% | 145.6 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 31% | 84% | 145.6 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
lactose catabolism | lacK | lo | LacK, component of Lactose porter (characterized) | 36% | 66% | 144.8 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
L-proline catabolism | proV | lo | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 36% | 58% | 144.4 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
L-arginine catabolism | artP | lo | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- (characterized) | 35% | 99% | 132.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
L-tryptophan catabolism | ecfA1 | lo | Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) | 35% | 88% | 132.1 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
L-lysine catabolism | hisP | lo | ABC transporter for L-Lysine, ATPase component (characterized) | 32% | 98% | 130.6 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
L-asparagine catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 33% | 98% | 125.2 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
L-aspartate catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 33% | 98% | 125.2 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
L-glutamate catabolism | gltL | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 33% | 98% | 125.2 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
citrate catabolism | fecE | lo | iron(III) dicitrate transport ATP-binding protein FecE (characterized) | 34% | 91% | 111.7 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
L-isoleucine catabolism | livF | lo | High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale) | 33% | 94% | 106.3 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
L-phenylalanine catabolism | livF | lo | High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale) | 33% | 94% | 106.3 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
glycerol catabolism | glpS | lo | ABC transporter for Glycerol, ATPase component 1 (characterized) | 31% | 68% | 103.6 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
L-leucine catabolism | livF | lo | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 30% | 94% | 103.2 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
L-valine catabolism | livF | lo | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 30% | 94% | 103.2 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
L-alanine catabolism | braG | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 35% | 92% | 101.3 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
L-histidine catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 35% | 92% | 101.3 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
L-leucine catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 35% | 92% | 101.3 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
L-proline catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 35% | 92% | 101.3 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
L-serine catabolism | braG | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 35% | 92% | 101.3 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
L-threonine catabolism | braG | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 35% | 92% | 101.3 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
L-isoleucine catabolism | natE | lo | NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 31% | 96% | 99.4 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
L-valine catabolism | natE | lo | NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 31% | 96% | 99.4 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 201.8 |
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