| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| putrescine catabolism | potA | hi | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) | 54% | 97% | 386.3 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 45% | 267.3 |
| D-maltose catabolism | thuK | med | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 46% | 78% | 262.3 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| trehalose catabolism | thuK | med | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 46% | 78% | 262.3 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| L-arabinose catabolism | xacJ | med | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 45% | 80% | 252.3 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| D-maltose catabolism | malK_Aa | med | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 45% | 76% | 251.5 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| D-mannitol catabolism | mtlK | med | MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) | 41% | 88% | 248.8 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| D-sorbitol (glucitol) catabolism | mtlK | med | MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) | 41% | 88% | 248.8 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| L-arabinose catabolism | xacK | med | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 40% | 95% | 246.5 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| D-maltose catabolism | malK_Bb | med | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 48% | 71% | 245 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| D-maltose catabolism | malK | med | Maltose-transporting ATPase (EC 3.6.3.19) (characterized) | 42% | 80% | 244.2 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| 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) | 43% | 79% | 242.7 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| lactose catabolism | lacK | med | ABC transporter for Lactose, ATPase component (characterized) | 42% | 78% | 240.4 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| sucrose catabolism | thuK | med | ABC transporter (characterized, see rationale) | 42% | 80% | 238.8 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| xylitol catabolism | HSERO_RS17020 | med | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 42% | 77% | 237.3 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| D-maltose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 41% | 84% | 236.9 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| sucrose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 41% | 84% | 236.9 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| trehalose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 41% | 84% | 236.9 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| trehalose catabolism | treV | med | TreV, component of Trehalose porter (characterized) | 46% | 79% | 232.3 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 40% | 89% | 230.3 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 40% | 89% | 230.3 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | med | ABC transporter for D-Glucosamine, ATPase component (characterized) | 42% | 81% | 228.4 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| D-cellobiose catabolism | SMc04256 | med | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 42% | 81% | 225.7 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| D-maltose catabolism | musK | med | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 43% | 73% | 225.7 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| D-cellobiose catabolism | gtsD | med | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 44% | 75% | 223.4 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| D-galactose catabolism | PfGW456L13_1897 | med | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 44% | 75% | 223.4 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| D-glucose catabolism | gtsD | med | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 44% | 75% | 223.4 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| lactose catabolism | gtsD | med | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 44% | 75% | 223.4 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| D-maltose catabolism | gtsD | med | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 44% | 75% | 223.4 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| sucrose catabolism | gtsD | med | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 44% | 75% | 223.4 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| trehalose catabolism | gtsD | med | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 44% | 75% | 223.4 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| D-cellobiose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 42% | 77% | 221.9 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| D-glucose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 42% | 77% | 221.9 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| lactose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 42% | 77% | 221.9 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| D-maltose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 42% | 77% | 221.9 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| sucrose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 42% | 77% | 221.9 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| trehalose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 42% | 77% | 221.9 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| D-xylose catabolism | gtsD | med | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 41% | 80% | 221.9 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 40% | 94% | 265 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| 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) | 40% | 95% | 254.2 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| 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% | 95% | 241.9 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| 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% | 91% | 241.9 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 48% | 70% | 231.5 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| 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) | 45% | 68% | 228.8 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 95% | 204.9 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 95% | 204.9 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 95% | 204.9 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 95% | 204.9 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 95% | 204.9 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 95% | 204.9 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 95% | 204.9 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 95% | 204.9 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 38% | 78% | 196.1 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 38% | 78% | 196.1 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 38% | 78% | 196.1 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 38% | 78% | 196.1 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| L-proline catabolism | opuBA | lo | BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) | 39% | 80% | 189.1 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| glycerol catabolism | glpT | lo | GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) | 36% | 81% | 182.2 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| L-proline catabolism | proV | lo | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 37% | 65% | 171.4 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| glycerol catabolism | glpS | lo | GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) | 34% | 72% | 160.2 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| 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) | 38% | 85% | 158.3 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
| 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) | 38% | 85% | 158.3 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 54% | 386.3 |
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