Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
trehalose catabolism | thuK | med | Trehalose import ATP-binding protein SugC; EC 7.5.2.- (characterized) | 52% | 84% | 321.6 | AlgS, component of Alginate (MW 27,000 Da) (and Alginate oligosaccharides) uptake porter. Sphingomonas species A1 is a 'pit-forming' bacterium that directly incorporates alginate into its cytoplasm through a pit-dependent transport system, termed a 'superchannel' (Murata et al., 2008). The pit is a novel organ acquired through the fluidity and reconstitution of cell surface molecules, and through cooperation with the transport machinery in the cells. It confers upon bacterial cells a more efficient way to secure and assimilate macromolecules | 49% | 318.5 |
D-cellobiose catabolism | msiK | med | 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) | 47% | 100% | 314.7 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
sucrose catabolism | thuK | med | ABC transporter (characterized, see rationale) | 52% | 91% | 312.4 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
D-maltose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 48% | 99% | 308.9 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
D-maltose catabolism | thuK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 48% | 99% | 308.9 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
sucrose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 48% | 99% | 308.9 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
trehalose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 48% | 99% | 308.9 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
D-mannitol catabolism | mtlK | med | ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) | 47% | 98% | 306.6 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
D-cellobiose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 50% | 92% | 305.8 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
D-glucose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 50% | 92% | 305.8 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
lactose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 50% | 92% | 305.8 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
D-maltose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 50% | 92% | 305.8 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
sucrose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 50% | 92% | 305.8 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
trehalose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 50% | 92% | 305.8 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
D-maltose catabolism | malK | med | Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 47% | 97% | 304.7 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
D-sorbitol (glucitol) catabolism | mtlK | med | ABC transporter for D-Sorbitol, ATPase component (characterized) | 50% | 99% | 303.1 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
xylitol catabolism | Dshi_0546 | med | ABC transporter for Xylitol, ATPase component (characterized) | 48% | 100% | 302.4 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
D-cellobiose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 49% | 97% | 298.5 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
D-glucose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 49% | 97% | 298.5 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
lactose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 49% | 97% | 298.5 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
D-maltose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 49% | 97% | 298.5 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
sucrose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 49% | 97% | 298.5 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
trehalose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 49% | 97% | 298.5 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
D-maltose catabolism | malK_Aa | med | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 44% | 96% | 298.1 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
L-arabinose catabolism | xacJ | med | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 47% | 96% | 297 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
N-acetyl-D-glucosamine catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 46% | 94% | 295.8 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
D-glucosamine (chitosamine) catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 46% | 94% | 295.8 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
D-mannose catabolism | TT_C0211 | med | 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) | 47% | 95% | 293.9 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
lactose catabolism | lacK | med | ABC transporter for Lactose, ATPase component (characterized) | 44% | 99% | 290.8 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
D-glucosamine (chitosamine) catabolism | SM_b21216 | med | ABC transporter for D-Glucosamine, ATPase component (characterized) | 45% | 99% | 290.4 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
D-maltose catabolism | musK | med | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 47% | 90% | 288.9 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
D-xylose catabolism | gtsD | med | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 44% | 95% | 288.5 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
D-galactose catabolism | PfGW456L13_1897 | med | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 44% | 95% | 286.6 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
xylitol catabolism | HSERO_RS17020 | med | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 46% | 90% | 286.2 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
L-arabinose catabolism | xacK | med | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 45% | 96% | 283.1 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
L-fucose catabolism | SM_b21106 | med | ABC transporter for L-Fucose, ATPase component (characterized) | 45% | 100% | 282.7 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
D-maltose catabolism | malK1 | med | 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) | 48% | 87% | 280.8 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
trehalose catabolism | malK | med | 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) | 43% | 99% | 278.5 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
D-maltose catabolism | malK_Bb | med | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 43% | 98% | 271.2 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
D-maltose catabolism | malK_Sm | med | 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) | 42% | 98% | 270 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
D-cellobiose catabolism | SMc04256 | med | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 44% | 99% | 259.6 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
trehalose catabolism | treV | med | TreV, component of Trehalose porter (characterized) | 43% | 85% | 232.6 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
putrescine catabolism | potA | med | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) | 42% | 78% | 208.8 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 87% | 217.2 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 87% | 217.2 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 87% | 217.2 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 87% | 217.2 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 87% | 217.2 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 87% | 217.2 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 87% | 217.2 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 87% | 217.2 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
glycerol catabolism | glpT | lo | GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) | 37% | 88% | 205.7 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
glycerol catabolism | glpS | lo | ABC transporter for Glycerol, ATPase component 1 (characterized) | 36% | 96% | 204.5 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 37% | 84% | 201.8 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 37% | 84% | 201.8 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 37% | 84% | 201.8 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 37% | 84% | 201.8 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
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) | 38% | 57% | 171 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
L-proline catabolism | proV | lo | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 37% | 58% | 160.6 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
L-arginine catabolism | artP | lo | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- (characterized) | 39% | 91% | 147.1 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
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) | 36% | 84% | 145.2 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
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) | 36% | 84% | 145.2 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
L-histidine catabolism | Ac3H11_2560 | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 35% | 84% | 141 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
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) | 32% | 74% | 134.8 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
L-tryptophan catabolism | ecfA2 | lo | Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) | 36% | 79% | 127.5 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
D-cellobiose catabolism | cbtF | lo | CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) | 34% | 74% | 126.3 | Trehalose import ATP-binding protein SugC; EC 7.5.2.- | 52% | 321.6 |
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