Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
L-histidine catabolism | PA5503 | lo | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 40% | 65% | 157.1 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 37% | 58% | 134 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 37% | 58% | 134 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 37% | 58% | 134 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 37% | 58% | 134 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 61% | 130.6 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 61% | 130.6 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 61% | 130.6 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 61% | 130.6 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 61% | 130.6 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 61% | 130.6 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 61% | 130.6 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 61% | 130.6 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 34% | 54% | 127.9 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
trehalose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 34% | 54% | 127.9 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 33% | 57% | 124.4 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 35% | 62% | 122.5 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 33% | 55% | 121.3 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
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) | 33% | 58% | 121.3 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
D-mannitol catabolism | mtlK | lo | ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) | 32% | 57% | 118.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 33% | 61% | 117.5 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 33% | 55% | 117.1 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 33% | 58% | 117.1 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 32% | 55% | 117.1 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
lactose catabolism | lacK | lo | ABC transporter for Lactose, ATPase component (characterized) | 34% | 59% | 114.4 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
D-maltose catabolism | malK | lo | Maltose-transporting ATPase (EC 3.6.3.19) (characterized) | 32% | 57% | 114.4 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
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) | 32% | 56% | 113.6 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
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) | 32% | 56% | 113.6 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
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) | 32% | 56% | 113.6 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
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) | 32% | 56% | 113.6 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
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) | 32% | 56% | 113.6 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
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) | 32% | 56% | 113.6 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
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) | 32% | 56% | 113.6 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 34% | 60% | 109 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 34% | 60% | 109 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
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) | 31% | 55% | 104.4 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
trehalose catabolism | malK | 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) | 31% | 55% | 104.4 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
D-alanine catabolism | AZOBR_RS08250 | lo | Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) | 34% | 85% | 103.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
L-proline catabolism | AZOBR_RS08250 | lo | Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) | 34% | 85% | 103.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
citrate catabolism | fecE | lo | iron(III) dicitrate transport ATP-binding protein FecE (characterized) | 31% | 84% | 102.4 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
L-leucine catabolism | livF | lo | high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) | 31% | 87% | 98.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
L-phenylalanine catabolism | livF | lo | high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) | 31% | 87% | 98.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
L-valine catabolism | livF | lo | high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) | 31% | 87% | 98.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
glycerol catabolism | glpS | lo | GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) | 31% | 53% | 92.8 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 50% | 215.3 |
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