Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
L-proline catabolism | opuBA | med | 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) | 51% | 75% | 249.2 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
L-histidine catabolism | hutV | med | ABC transporter for L-Histidine, ATPase component (characterized) | 42% | 82% | 181 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
L-proline catabolism | hutV | med | HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) | 41% | 82% | 176.8 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
L-proline catabolism | proV | lo | Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) | 36% | 94% | 230.3 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
putrescine catabolism | potA | lo | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) | 35% | 81% | 184.9 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
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) | 35% | 83% | 180.6 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
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) | 35% | 83% | 180.6 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
D-mannitol catabolism | mtlK | lo | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) | 38% | 79% | 174.1 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 36% | 68% | 173.3 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 37% | 69% | 171 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 37% | 69% | 171 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 39% | 64% | 169.9 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
D-maltose catabolism | malK | lo | Maltose-transporting ATPase (EC 3.6.3.19) (characterized) | 37% | 64% | 169.1 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 36% | 78% | 169.1 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 38% | 64% | 169.1 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 37% | 75% | 168.3 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
lactose catabolism | lacK | lo | ABC transporter for Lactose, ATPase component (characterized) | 38% | 67% | 167.9 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
D-maltose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 38% | 68% | 167.5 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
D-maltose catabolism | thuK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 38% | 68% | 167.5 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
sucrose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 38% | 68% | 167.5 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
trehalose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 38% | 68% | 167.5 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
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) | 37% | 64% | 166.4 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
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) | 37% | 64% | 166.4 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
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) | 37% | 64% | 166.4 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
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) | 37% | 64% | 166.4 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
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) | 37% | 64% | 166.4 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
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) | 37% | 64% | 166.4 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
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) | 37% | 64% | 166.4 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 41% | 62% | 166 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
L-glutamate catabolism | gltL | lo | GluA aka CGL1950, component of Glutamate porter (characterized) | 40% | 98% | 166 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
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) | 36% | 62% | 165.2 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 40% | 54% | 164.1 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 34% | 73% | 161.4 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 37% | 62% | 158.3 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
L-asparagine catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 36% | 98% | 157.1 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
L-aspartate catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 36% | 98% | 157.1 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 39% | 61% | 156.8 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 36% | 61% | 156.8 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
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) | 32% | 69% | 156 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 36% | 73% | 156 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
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) | 35% | 66% | 155.6 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 36% | 62% | 154.1 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 36% | 62% | 154.1 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 36% | 62% | 154.1 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 36% | 62% | 154.1 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 36% | 62% | 154.1 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 36% | 62% | 154.1 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
L-asparagine catabolism | aatP | lo | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 37% | 99% | 152.9 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
L-aspartate catabolism | aatP | lo | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 37% | 99% | 152.9 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 35% | 62% | 150.2 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
L-lysine catabolism | hisP | lo | Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) | 35% | 92% | 149.1 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
L-histidine catabolism | aapP | lo | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 35% | 92% | 146 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
glycerol catabolism | glpT | lo | GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) | 35% | 68% | 139 | Choline transport ATP-binding protein OpuBA | 45% | 307.0 |
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