Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
L-fucose catabolism | HSERO_RS05250 | med | Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) | 49% | 94% | 462.2 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
D-ribose catabolism | rbsA | med | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized) | 49% | 98% | 458.8 | RbsA, 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) | 50% | 454.1 |
D-cellobiose catabolism | mglA | med | Monosaccharide-transporting ATPase, 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) | 46% | 99% | 451.1 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
D-glucose catabolism | mglA | med | Monosaccharide-transporting ATPase, 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) | 46% | 99% | 451.1 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
lactose catabolism | mglA | med | Monosaccharide-transporting ATPase, 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) | 46% | 99% | 451.1 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
D-maltose catabolism | mglA | med | Monosaccharide-transporting ATPase, 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) | 46% | 99% | 451.1 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
sucrose catabolism | mglA | med | Monosaccharide-transporting ATPase, 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) | 46% | 99% | 451.1 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
trehalose catabolism | mglA | med | Monosaccharide-transporting ATPase, 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) | 46% | 99% | 451.1 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
D-xylose catabolism | xylG | med | Monosaccharide-transporting ATPase, 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) | 46% | 99% | 451.1 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
myo-inositol catabolism | PS417_11890 | med | Inositol transport system ATP-binding protein (characterized) | 45% | 95% | 443.7 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
D-mannose catabolism | HSERO_RS03640 | med | Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) | 44% | 94% | 428.7 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
D-xylose catabolism | xylK_Tm | med | Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale) | 44% | 96% | 412.5 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
D-galactose catabolism | mglA | med | Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized) | 43% | 97% | 411 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
myo-inositol catabolism | iatA | med | Inositol transport ATP-binding protein IatA, 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) | 43% | 97% | 408.7 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
D-galactose catabolism | BPHYT_RS16930 | med | Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale) | 43% | 96% | 401 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
D-fructose catabolism | frcA | med | ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) | 43% | 93% | 381.7 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
sucrose catabolism | frcA | med | ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) | 43% | 93% | 381.7 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
L-arabinose catabolism | araG | med | L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized) | 42% | 97% | 380.9 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
L-arabinose catabolism | gguA | med | GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) | 40% | 97% | 360.5 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
D-galactose catabolism | gguA | med | GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) | 40% | 97% | 360.5 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
L-rhamnose catabolism | rhaT' | lo | RhaT, 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) | 39% | 96% | 374.4 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
L-arabinose catabolism | araVsh | lo | ABC transporter related (characterized, see rationale) | 38% | 99% | 353.6 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
D-galactose catabolism | ytfR | lo | galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized) | 39% | 97% | 350.5 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
xylitol catabolism | PS417_12065 | lo | D-ribose transporter ATP-binding protein; SubName: Full=Putative xylitol transport system ATP-binding protein; SubName: Full=Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 40% | 99% | 349.4 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
2'-deoxyinosine catabolism | nupA | lo | Purine/cytidine ABC transporter ATP-binding protein, component of General nucleoside uptake porter, NupABC/BmpA (transports all common nucleosides as well as 5-fluorocytidine, inosine, deoxyuridine and xanthosine) (Martinussen et al., 2010) (Most similar to 3.A.1.2.12). NupA is 506aas with two ABC (C) domains. NupB has 8 predicted TMSs, NupC has 9 or 10 predicted TMSs in a 4 + 1 (or 2) + 4 arrangement (characterized) | 39% | 98% | 345.5 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
2'-deoxyinosine catabolism | H281DRAFT_01113 | lo | deoxynucleoside transporter, ATPase component (characterized) | 38% | 95% | 341.3 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
D-fructose catabolism | fruK | lo | Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) | 38% | 97% | 335.1 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
sucrose catabolism | fruK | lo | Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) | 38% | 97% | 335.1 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
L-fucose catabolism | BPHYT_RS34245 | lo | ABC transporter related; Flags: Precursor (characterized, see rationale) | 35% | 93% | 283.9 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
L-rhamnose catabolism | BPHYT_RS34245 | lo | ABC transporter related; Flags: Precursor (characterized, see rationale) | 35% | 93% | 283.9 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
L-arabinose catabolism | xylGsa | lo | Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) | 36% | 95% | 170.2 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
myo-inositol catabolism | PGA1_c07320 | lo | Inositol transport system ATP-binding protein (characterized) | 37% | 93% | 167.5 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
D-mannose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 35% | 93% | 153.3 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
D-ribose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 35% | 93% | 153.3 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
L-isoleucine catabolism | livG | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 34% | 87% | 137.9 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
L-leucine catabolism | livG | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 34% | 87% | 137.9 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
L-phenylalanine catabolism | livG | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 34% | 87% | 137.9 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
L-proline catabolism | HSERO_RS00895 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 34% | 87% | 137.9 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
L-serine catabolism | Ac3H11_1693 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 34% | 87% | 137.9 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
L-tyrosine catabolism | Ac3H11_1693 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 34% | 87% | 137.9 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
D-lactate catabolism | PGA1_c12640 | lo | D-lactate transporter, ATP-binding component (characterized) | 31% | 88% | 122.1 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
L-isoleucine catabolism | livF | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 32% | 86% | 119.8 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
L-leucine catabolism | livF | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 32% | 86% | 119.8 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
L-phenylalanine catabolism | livF | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 32% | 86% | 119.8 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
L-proline catabolism | HSERO_RS00900 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 32% | 86% | 119.8 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
L-serine catabolism | Ac3H11_1692 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 32% | 86% | 119.8 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
L-tyrosine catabolism | Ac3H11_1692 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 32% | 86% | 119.8 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
L-alanine catabolism | braG | lo | NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 30% | 85% | 115.5 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
L-isoleucine catabolism | natE | lo | NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 30% | 85% | 115.5 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
L-leucine catabolism | natE | lo | NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 30% | 85% | 115.5 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
L-proline catabolism | natE | lo | NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 30% | 85% | 115.5 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
L-serine catabolism | braG | lo | NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 30% | 85% | 115.5 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
L-threonine catabolism | braG | lo | NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 30% | 85% | 115.5 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
L-valine catabolism | natE | lo | NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 30% | 85% | 115.5 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 49% | 458.8 |
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