| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 43% | 56% | 173.3 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 39% | 173.3 |
| trehalose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 43% | 56% | 173.3 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 39% | 173.3 |
| putrescine catabolism | potA | lo | PotG aka B0855, component of Putrescine porter (characterized) | 38% | 61% | 166.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 42% | 53% | 164.1 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 43% | 57% | 161.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| D-cellobiose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 38% | 64% | 161 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| D-glucose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 38% | 64% | 161 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| lactose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 38% | 64% | 161 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| D-maltose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 38% | 64% | 161 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| sucrose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 38% | 64% | 161 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| trehalose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 38% | 64% | 161 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| 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) | 40% | 55% | 157.9 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 74% | 157.1 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 74% | 157.1 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 74% | 157.1 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 74% | 157.1 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 74% | 157.1 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 74% | 157.1 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 74% | 157.1 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 74% | 157.1 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 35% | 76% | 156.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 41% | 62% | 156.4 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 36% | 75% | 156.4 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 40% | 58% | 155.6 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| D-maltose catabolism | malK | lo | Maltose-transporting ATPase (EC 3.6.3.19) (characterized) | 37% | 68% | 155.6 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| D-mannitol catabolism | mtlK | lo | ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) | 36% | 76% | 154.5 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| 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) | 38% | 58% | 154.5 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| D-cellobiose catabolism | msiK | lo | MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized) | 37% | 68% | 154.1 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| 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) | 38% | 58% | 153.7 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 37% | 69% | 152.9 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| lactose catabolism | lacK | lo | ABC transporter for Lactose, ATPase component (characterized) | 37% | 70% | 152.5 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| sucrose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 39% | 70% | 152.5 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 39% | 56% | 151.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 69% | 151.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 39% | 56% | 151.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 69% | 151.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 69% | 151.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| D-maltose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 69% | 151.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 69% | 151.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| sucrose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 69% | 151.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 69% | 151.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 39% | 56% | 151.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| trehalose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 69% | 151.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 69% | 151.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 39% | 56% | 151.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 39% | 56% | 150.2 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 36% | 78% | 150.2 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 36% | 69% | 149.4 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 36% | 69% | 149.4 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 39% | 60% | 148.3 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 39% | 58% | 147.5 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| 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) | 39% | 55% | 145.6 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| 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% | 63% | 144.8 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 39% | 59% | 144.4 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 38% | 61% | 142.5 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 38% | 56% | 138.7 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| D-glucosamine (chitosamine) catabolism | AO353_21725 | lo | ABC transporter for D-Glucosamine, putative ATPase component (characterized) | 38% | 85% | 138.3 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| 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) | 32% | 76% | 130.6 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| 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) | 32% | 76% | 130.6 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| L-histidine catabolism | Ac3H11_2560 | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 38% | 73% | 128.6 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| glycerol catabolism | glpS | lo | GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) | 34% | 61% | 124.4 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| D-mannose catabolism | TM1750 | lo | TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) | 33% | 68% | 118.2 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| L-isoleucine catabolism | livG | lo | High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) | 32% | 86% | 103.2 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| L-leucine catabolism | livG | lo | High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) | 32% | 86% | 103.2 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| L-phenylalanine catabolism | livG | lo | High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) | 32% | 86% | 103.2 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| L-valine catabolism | livG | lo | High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) | 32% | 86% | 103.2 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| L-alanine catabolism | braF | lo | NatA, 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) | 30% | 83% | 100.9 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| L-isoleucine catabolism | natA | lo | NatA, 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) | 30% | 83% | 100.9 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| L-leucine catabolism | natA | lo | NatA, 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) | 30% | 83% | 100.9 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| L-proline catabolism | natA | lo | NatA, 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) | 30% | 83% | 100.9 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| L-serine catabolism | braF | lo | NatA, 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) | 30% | 83% | 100.9 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| L-threonine catabolism | braF | lo | NatA, 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) | 30% | 83% | 100.9 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| L-valine catabolism | natA | lo | NatA, 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) | 30% | 83% | 100.9 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| L-isoleucine catabolism | livF | lo | High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale) | 32% | 88% | 100.5 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| L-phenylalanine catabolism | livF | lo | High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale) | 32% | 88% | 100.5 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
| L-proline catabolism | HSERO_RS00900 | lo | ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) | 32% | 86% | 90.1 | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 | 43% | 173.3 |
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