| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-cellobiose catabolism | mglC | hi | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) | 49% | 97% | 283.1 | Ribose import permease protein RbsC | 47% | 268.1 |
| D-glucose catabolism | mglC | hi | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) | 49% | 97% | 283.1 | Ribose import permease protein RbsC | 47% | 268.1 |
| lactose catabolism | mglC | hi | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) | 49% | 97% | 283.1 | Ribose import permease protein RbsC | 47% | 268.1 |
| D-maltose catabolism | mglC | hi | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) | 49% | 97% | 283.1 | Ribose import permease protein RbsC | 47% | 268.1 |
| sucrose catabolism | mglC | hi | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) | 49% | 97% | 283.1 | Ribose import permease protein RbsC | 47% | 268.1 |
| trehalose catabolism | mglC | hi | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) | 49% | 97% | 283.1 | Ribose import permease protein RbsC | 47% | 268.1 |
| D-xylose catabolism | xylH | hi | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) | 49% | 97% | 283.1 | Ribose import permease protein RbsC | 47% | 268.1 |
| D-ribose catabolism | rbsC | med | Ribose import permease protein RbsC (characterized) | 47% | 98% | 268.1 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 49% | 283.1 |
| D-xylose catabolism | xylF_Tm | med | ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized) | 45% | 97% | 253.4 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 49% | 283.1 |
| L-fucose catabolism | HSERO_RS05255 | med | ABC-type sugar transport system, permease component protein (characterized, see rationale) | 44% | 94% | 249.2 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 49% | 283.1 |
| xylitol catabolism | PS417_12060 | med | ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale) | 44% | 94% | 247.7 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 49% | 283.1 |
| D-ribose catabolism | rbsB | med | D-ribose-binding periplasmic protein; EC 3.6.3.17 (characterized) | 43% | 98% | 235.3 | RbsB, component of The probable autoinducer-2 (AI-2;, a furanosyl borate diester: 3aS,6S,6aR)-2,2,6,6a-tetrahydroxy-3a-methyltetrahydrofuro[3,2-d][1,3,2]dioxaborolan-2-uide) uptake porter (Shao et al., 2007) (50-70% identical to RbsABC of E. coli; TC# 3.A.1.2.1) | 44% | 238.4 |
| D-fructose catabolism | frcC | med | Ribose ABC transport system, permease protein RbsC (characterized, see rationale) | 45% | 99% | 235 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 49% | 283.1 |
| sucrose catabolism | frcC | med | Ribose ABC transport system, permease protein RbsC (characterized, see rationale) | 45% | 99% | 235 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 49% | 283.1 |
| D-mannose catabolism | HSERO_RS03645 | med | ABC-type sugar transport system, permease component protein (characterized, see rationale) | 45% | 90% | 229.9 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 49% | 283.1 |
| myo-inositol catabolism | iatP | med | Inositol ABC transport system, permease protein IatP, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized) | 42% | 92% | 227.3 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 49% | 283.1 |
| myo-inositol catabolism | PS417_11895 | lo | m-Inositol ABC transporter, permease component (iatP) (characterized) | 40% | 94% | 221.1 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 49% | 283.1 |
| L-arabinose catabolism | araH | lo | L-arabinose ABC transporter, permease protein AraH (characterized) | 38% | 94% | 206.5 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 49% | 283.1 |
| D-galactose catabolism | BPHYT_RS16925 | lo | Arabinose ABC transporter permease (characterized, see rationale) | 36% | 95% | 199.9 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 49% | 283.1 |
| D-galactose catabolism | mglC | lo | MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) | 36% | 95% | 187.6 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 49% | 283.1 |
| L-rhamnose catabolism | rhaP | lo | RhaP, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized) | 36% | 94% | 177.2 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 49% | 283.1 |
| D-mannose catabolism | frcC | lo | Fructose import permease protein FrcC (characterized) | 35% | 89% | 176.8 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 49% | 283.1 |
| D-ribose catabolism | frcC | lo | Fructose import permease protein FrcC (characterized) | 35% | 89% | 176.8 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 49% | 283.1 |
| D-fructose catabolism | fruG | lo | Fructose import permease protein FruG (characterized) | 35% | 91% | 176.4 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 49% | 283.1 |
| sucrose catabolism | fruG | lo | Fructose import permease protein FruG (characterized) | 35% | 91% | 176.4 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 49% | 283.1 |
| D-fructose catabolism | fruF | lo | Fructose import permease protein FruF (characterized) | 35% | 97% | 175.3 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 49% | 283.1 |
| sucrose catabolism | fruF | lo | Fructose import permease protein FruF (characterized) | 35% | 97% | 175.3 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 49% | 283.1 |
| L-arabinose catabolism | araWsh | lo | Inner-membrane translocator (characterized, see rationale) | 31% | 89% | 168.3 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 49% | 283.1 |
| L-fucose catabolism | BPHYT_RS34240 | lo | Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) | 35% | 91% | 168.3 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 49% | 283.1 |
| L-rhamnose catabolism | BPHYT_RS34240 | lo | Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) | 35% | 91% | 168.3 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 49% | 283.1 |
| L-arabinose catabolism | araZsh | lo | Inner-membrane translocator (characterized, see rationale) | 38% | 94% | 167.2 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 49% | 283.1 |
| L-rhamnose catabolism | rhaQ | lo | RhaQ (characterized, see rationale) | 32% | 92% | 165.6 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 49% | 283.1 |
| D-galactose catabolism | ytfT | lo | Galactofuranose transporter permease protein YtfT (characterized) | 37% | 89% | 164.1 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 49% | 283.1 |
| D-galactose catabolism | yjtF | lo | Inner membrane ABC transporter permease protein YjfF (characterized) | 38% | 85% | 161.4 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 49% | 283.1 |
| myo-inositol catabolism | PS417_11885 | lo | Inositol transport system sugar-binding protein (characterized) | 34% | 92% | 158.3 | RbsB, component of The probable autoinducer-2 (AI-2;, a furanosyl borate diester: 3aS,6S,6aR)-2,2,6,6a-tetrahydroxy-3a-methyltetrahydrofuro[3,2-d][1,3,2]dioxaborolan-2-uide) uptake porter (Shao et al., 2007) (50-70% identical to RbsABC of E. coli; TC# 3.A.1.2.1) | 44% | 238.4 |
| myo-inositol catabolism | ibpA | lo | Inositol ABC transporter, periplasmic inositol-binding protein IbpA, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized) | 34% | 95% | 157.1 | RbsB, component of The probable autoinducer-2 (AI-2;, a furanosyl borate diester: 3aS,6S,6aR)-2,2,6,6a-tetrahydroxy-3a-methyltetrahydrofuro[3,2-d][1,3,2]dioxaborolan-2-uide) uptake porter (Shao et al., 2007) (50-70% identical to RbsABC of E. coli; TC# 3.A.1.2.1) | 44% | 238.4 |
| 2'-deoxyinosine catabolism | H281DRAFT_01112 | lo | deoxynucleoside transporter, permease component 2 (characterized) | 33% | 89% | 156.4 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 49% | 283.1 |
| myo-inositol catabolism | PGA1_c07310 | lo | Inositol transport system permease protein (characterized) | 30% | 95% | 150.2 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 49% | 283.1 |
| 2'-deoxyinosine catabolism | H281DRAFT_01115 | lo | deoxynucleoside transporter, permease component 1 (characterized) | 32% | 99% | 146.4 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 49% | 283.1 |
| L-arabinose catabolism | gguB | lo | GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) | 33% | 80% | 132.1 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 49% | 283.1 |
| D-galactose catabolism | gguB | lo | GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) | 33% | 80% | 132.1 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 49% | 283.1 |
| L-arabinose catabolism | araUsh | lo | Periplasmic binding protein/LacI transcriptional regulator (characterized, see rationale) | 32% | 96% | 125.9 | RbsB, component of The probable autoinducer-2 (AI-2;, a furanosyl borate diester: 3aS,6S,6aR)-2,2,6,6a-tetrahydroxy-3a-methyltetrahydrofuro[3,2-d][1,3,2]dioxaborolan-2-uide) uptake porter (Shao et al., 2007) (50-70% identical to RbsABC of E. coli; TC# 3.A.1.2.1) | 44% | 238.4 |
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