| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| myo-inositol catabolism | PS417_11890 | hi | m-Inositol ABC transporter, ATPase component (itaA) (characterized) | 46% | 94% | 426 | 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 | 43% | 404.8 |
| L-fucose catabolism | HSERO_RS05250 | med | Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) | 46% | 95% | 433.3 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| 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) | 43% | 99% | 404.8 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| 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) | 43% | 99% | 404.8 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| 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) | 43% | 99% | 404.8 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| 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) | 43% | 99% | 404.8 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| 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) | 43% | 99% | 404.8 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| 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) | 43% | 99% | 404.8 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| 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) | 43% | 99% | 404.8 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| D-ribose catabolism | rbsA | med | Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized) | 44% | 96% | 402.9 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| D-fructose catabolism | frcA | med | ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) | 47% | 89% | 391.3 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| sucrose catabolism | frcA | med | ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) | 47% | 89% | 391.3 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| D-mannose catabolism | HSERO_RS03640 | med | Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) | 43% | 95% | 389.8 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| D-xylose catabolism | xylK_Tm | med | Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale) | 42% | 95% | 382.9 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| D-galactose catabolism | BPHYT_RS16930 | med | Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale) | 43% | 95% | 381.7 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| L-arabinose catabolism | araG | med | L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized) | 40% | 97% | 379.8 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| D-galactose catabolism | mglA | med | Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) | 40% | 97% | 379.8 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| 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) | 42% | 96% | 376.3 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| 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% | 369.4 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| 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) | 39% | 100% | 357.8 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| D-galactose catabolism | ytfR | lo | galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized) | 39% | 98% | 352.1 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| L-arabinose catabolism | araVsh | lo | ABC transporter related (characterized, see rationale) | 39% | 98% | 348.2 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| L-arabinose catabolism | gguA | lo | GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) | 39% | 99% | 346.7 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| D-galactose catabolism | gguA | lo | GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) | 39% | 99% | 346.7 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| D-fructose catabolism | fruK | lo | Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) | 37% | 97% | 341.3 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| sucrose catabolism | fruK | lo | Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) | 37% | 97% | 341.3 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| 2'-deoxyinosine catabolism | H281DRAFT_01113 | lo | deoxynucleoside transporter, ATPase component (characterized) | 35% | 97% | 313.5 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| 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) | 34% | 97% | 297.4 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| L-fucose catabolism | BPHYT_RS34245 | lo | ABC transporter related; Flags: Precursor (characterized, see rationale) | 34% | 93% | 290 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| L-rhamnose catabolism | BPHYT_RS34245 | lo | ABC transporter related; Flags: Precursor (characterized, see rationale) | 34% | 93% | 290 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| myo-inositol catabolism | PGA1_c07320 | lo | Inositol transport system ATP-binding protein (characterized) | 34% | 94% | 159.1 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| D-mannose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 34% | 95% | 144.1 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| D-ribose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 34% | 95% | 144.1 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| L-arabinose catabolism | xylGsa | lo | Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) | 33% | 94% | 142.5 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| L-isoleucine catabolism | livG | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 96% | 119.4 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| L-leucine catabolism | livG | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 96% | 119.4 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| L-phenylalanine catabolism | livG | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 96% | 119.4 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| L-proline catabolism | HSERO_RS00895 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 96% | 119.4 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| L-serine catabolism | Ac3H11_1693 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 96% | 119.4 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| L-tyrosine catabolism | Ac3H11_1693 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 96% | 119.4 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| L-alanine catabolism | braG | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 31% | 90% | 102.1 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| L-histidine catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 31% | 90% | 102.1 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| L-leucine catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 31% | 90% | 102.1 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| L-proline catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 31% | 90% | 102.1 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| L-serine catabolism | braG | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 31% | 90% | 102.1 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
| L-threonine catabolism | braG | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 31% | 90% | 102.1 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 426.0 |
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