| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-histidine catabolism | Ac3H11_2560 | med | ABC transporter for L-Histidine, ATPase component (characterized) | 42% | 78% | 158.7 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 37% | 57% | 157.5 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| trehalose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 37% | 57% | 157.5 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 36% | 54% | 151.8 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 38% | 55% | 149.8 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| lactose catabolism | lacK | lo | ABC transporter for Lactose, ATPase component (characterized) | 40% | 57% | 148.3 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 37% | 63% | 147.9 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 37% | 63% | 147.9 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| putrescine catabolism | potA | lo | PotG aka B0855, component of Putrescine porter (characterized) | 37% | 55% | 147.9 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| D-mannitol catabolism | mtlK | lo | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) | 39% | 63% | 146 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| D-cellobiose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 41% | 55% | 144.4 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| D-glucose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 41% | 55% | 144.4 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| lactose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 41% | 55% | 144.4 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| D-maltose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 41% | 55% | 144.4 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| sucrose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 41% | 55% | 144.4 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| trehalose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 41% | 55% | 144.4 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| L-proline catabolism | proV | lo | Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) | 39% | 54% | 142.5 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 40% | 55% | 142.1 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 40% | 55% | 142.1 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 40% | 55% | 142.1 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| D-maltose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 40% | 55% | 142.1 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 40% | 55% | 142.1 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| sucrose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 40% | 55% | 142.1 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 40% | 55% | 142.1 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| trehalose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 40% | 55% | 142.1 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 40% | 55% | 142.1 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| D-maltose catabolism | malK | lo | Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 37% | 56% | 141 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 39% | 59% | 139.8 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 34% | 69% | 139.4 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 38% | 53% | 139 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| D-glucosamine (chitosamine) catabolism | AO353_21725 | lo | ABC transporter for D-glucosamine, ATPase component (characterized) | 35% | 87% | 138.7 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| 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) | 35% | 54% | 138.7 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| sucrose catabolism | thuK | 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) | 35% | 54% | 138.7 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| 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) | 34% | 61% | 137.9 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| L-lysine catabolism | hisP | lo | Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) | 38% | 81% | 137.5 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 36% | 52% | 137.1 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 36% | 52% | 137.1 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 36% | 52% | 137.1 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 36% | 52% | 137.1 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| L-proline catabolism | opuBA | lo | BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport (characterized) | 38% | 53% | 135.6 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| trehalose catabolism | malK | lo | MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized) | 33% | 56% | 135.2 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| L-asparagine catabolism | aatP | lo | ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) | 33% | 95% | 134.4 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| L-aspartate catabolism | aatP | lo | ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) | 33% | 95% | 134.4 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 38% | 53% | 134.4 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| L-glutamate catabolism | gltL | lo | ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) | 33% | 95% | 134.4 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 36% | 59% | 134.4 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| L-asparagine catabolism | bgtA | lo | ATPase (characterized, see rationale) | 36% | 87% | 134 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| L-aspartate catabolism | bgtA | lo | ATPase (characterized, see rationale) | 36% | 87% | 134 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| L-asparagine catabolism | glnQ | lo | Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) | 35% | 85% | 132.9 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 58% | 131 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 58% | 131 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 58% | 131 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 58% | 131 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 58% | 131 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 58% | 131 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 58% | 131 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 58% | 131 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 37% | 53% | 128.3 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| 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) | 33% | 55% | 127.1 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 35% | 51% | 126.7 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| L-histidine catabolism | hutV | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 36% | 75% | 124 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| D-cellobiose catabolism | msiK | lo | MsiK protein, 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) | 36% | 51% | 123.6 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| L-proline catabolism | hutV | lo | HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) | 35% | 76% | 123.6 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| L-asparagine catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 32% | 87% | 123.2 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| L-aspartate catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 32% | 87% | 123.2 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| L-alanine catabolism | braF | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 31% | 88% | 115.5 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| L-isoleucine catabolism | livG | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 31% | 88% | 115.5 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| L-leucine catabolism | livG | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 31% | 88% | 115.5 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| L-serine catabolism | braF | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 31% | 88% | 115.5 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| L-threonine catabolism | braF | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 31% | 88% | 115.5 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| L-valine catabolism | livG | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 31% | 88% | 115.5 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| D-lactate catabolism | PGA1_c12640 | lo | D-lactate transporter, ATP-binding component (characterized) | 30% | 88% | 102.8 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| D-fructose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 31% | 80% | 98.2 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| D-mannose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 31% | 80% | 98.2 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| D-ribose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 31% | 80% | 98.2 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| sucrose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 31% | 80% | 98.2 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| D-alanine catabolism | AZOBR_RS08250 | lo | Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) | 31% | 86% | 92.8 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
| L-proline catabolism | AZOBR_RS08250 | lo | Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) | 31% | 86% | 92.8 | CynD, component of Bispecific cyanate/nitrite transporter | 44% | 174.9 |
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