| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-cellobiose catabolism | cebG | lo | CBP protein aka CebG, 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) | 38% | 93% | 186.8 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| lactose catabolism | lacG | lo | ABC transporter for Lactose, permease component 2 (characterized) | 36% | 94% | 174.9 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| D-maltose catabolism | malG_Bb | lo | ABC-type Maltose/ Maltodextrin permease (characterized, see rationale) | 33% | 95% | 163.3 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| D-maltose catabolism | thuG | lo | Maltose transport system permease protein malG aka TT_C1629, 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% | 99% | 159.8 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| sucrose catabolism | thuG | lo | Maltose transport system permease protein malG aka TT_C1629, 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% | 99% | 159.8 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| trehalose catabolism | thuG | lo | Maltose transport system permease protein malG aka TT_C1629, 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% | 99% | 159.8 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| D-cellobiose catabolism | msdC2 | lo | Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) | 35% | 91% | 159.5 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| N-acetyl-D-glucosamine catabolism | ngcG | lo | NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized) | 33% | 88% | 156.4 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| D-glucosamine (chitosamine) catabolism | ngcG | lo | NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized) | 33% | 88% | 156.4 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| D-maltose catabolism | aglG | lo | ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized) | 38% | 62% | 155.2 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| sucrose catabolism | aglG | lo | ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized) | 38% | 62% | 155.2 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| trehalose catabolism | aglG | lo | ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized) | 38% | 62% | 155.2 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| L-fucose catabolism | SM_b21105 | lo | ABC transporter for L-Fucose, permease component 2 (characterized) | 34% | 96% | 151.8 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| D-cellobiose catabolism | gtsC | lo | Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) | 38% | 98% | 149.4 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| D-glucose catabolism | gtsC | lo | Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) | 38% | 98% | 149.4 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| lactose catabolism | gtsC | lo | Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) | 38% | 98% | 149.4 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| D-maltose catabolism | gtsC | lo | Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) | 38% | 98% | 149.4 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| D-mannose catabolism | TT_C0326 | lo | Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) | 38% | 98% | 149.4 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| sucrose catabolism | gtsC | lo | Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) | 38% | 98% | 149.4 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| trehalose catabolism | gtsC | lo | Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) | 38% | 98% | 149.4 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| D-maltose catabolism | malG_Sm | lo | MalG, 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) | 33% | 98% | 147.5 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| trehalose catabolism | malG | lo | MalG, 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) | 33% | 98% | 147.5 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| D-cellobiose catabolism | msdB2 | lo | Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) | 33% | 95% | 145.2 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| xylitol catabolism | Dshi_0549 | lo | ABC transporter for Xylitol, permease component 2 (characterized) | 34% | 96% | 136.7 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| N-acetyl-D-glucosamine catabolism | SMc02871 | lo | N-Acetyl-D-glucosamine ABC transport system, permease component 2 (characterized) | 31% | 95% | 134 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| D-glucosamine (chitosamine) catabolism | SMc02871 | lo | N-Acetyl-D-glucosamine ABC transport system, permease component 2 (characterized) | 31% | 95% | 134 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| D-cellobiose catabolism | aglG' | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 33% | 61% | 132.5 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| D-glucose catabolism | aglG' | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 33% | 61% | 132.5 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| lactose catabolism | aglG' | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 33% | 61% | 132.5 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| D-maltose catabolism | aglG' | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 33% | 61% | 132.5 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| sucrose catabolism | aglG' | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 33% | 61% | 132.5 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| trehalose catabolism | aglG' | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 33% | 61% | 132.5 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| D-glucosamine (chitosamine) catabolism | SM_b21219 | lo | ABC transporter for D-Glucosamine, permease component 1 (characterized) | 33% | 99% | 127.1 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| D-galactose catabolism | PfGW456L13_1896 | lo | ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized) | 32% | 95% | 124 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| D-xylose catabolism | gtsC | lo | ABC transporter for D-Glucose-6-Phosphate, permease component 1 (characterized) | 30% | 96% | 124 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| D-cellobiose catabolism | glcU | lo | GlcU, component of Glucose, mannose, galactose porter (characterized) | 30% | 98% | 115.2 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| D-galactose catabolism | glcU | lo | GlcU, component of Glucose, mannose, galactose porter (characterized) | 30% | 98% | 115.2 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| D-glucose catabolism | glcU | lo | GlcU, component of Glucose, mannose, galactose porter (characterized) | 30% | 98% | 115.2 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| lactose catabolism | glcU | lo | GlcU, component of Glucose, mannose, galactose porter (characterized) | 30% | 98% | 115.2 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| D-maltose catabolism | glcU | lo | GlcU, component of Glucose, mannose, galactose porter (characterized) | 30% | 98% | 115.2 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| D-mannose catabolism | glcU | lo | GlcU, component of Glucose, mannose, galactose porter (characterized) | 30% | 98% | 115.2 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| sucrose catabolism | glcU | lo | GlcU, component of Glucose, mannose, galactose porter (characterized) | 30% | 98% | 115.2 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| trehalose catabolism | glcU | lo | GlcU, component of Glucose, mannose, galactose porter (characterized) | 30% | 98% | 115.2 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| D-cellobiose catabolism | gtsB | lo | Glucose transport system permease protein aka TT_C0327, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) | 31% | 50% | 60.1 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| D-glucose catabolism | gtsB | lo | Glucose transport system permease protein aka TT_C0327, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) | 31% | 50% | 60.1 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| lactose catabolism | gtsB | lo | Glucose transport system permease protein aka TT_C0327, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) | 31% | 50% | 60.1 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| D-maltose catabolism | gtsB | lo | Glucose transport system permease protein aka TT_C0327, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) | 31% | 50% | 60.1 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| D-mannose catabolism | TT_C0327 | lo | Glucose transport system permease protein aka TT_C0327, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) | 31% | 50% | 60.1 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| sucrose catabolism | gtsB | lo | Glucose transport system permease protein aka TT_C0327, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) | 31% | 50% | 60.1 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
| trehalose catabolism | gtsB | lo | Glucose transport system permease protein aka TT_C0327, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) | 31% | 50% | 60.1 | Alpha-1,4-digalacturonate porter (Nanavati et al., 2006). Regulated by pectin utilization regulon UxaR | 37% | 188.3 |
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