| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-asparagine catabolism | bgtA | med | ATPase (characterized, see rationale) | 41% | 84% | 145.6 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| L-aspartate catabolism | bgtA | med | ATPase (characterized, see rationale) | 41% | 84% | 145.6 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| L-glutamate catabolism | gltL | med | GluA aka CGL1950, component of Glutamate porter (characterized) | 40% | 83% | 137.9 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| L-histidine catabolism | PA5503 | lo | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 40% | 64% | 149.8 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| L-histidine catabolism | BPHYT_RS24015 | lo | ABC transporter related (characterized, see rationale) | 39% | 86% | 139 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| 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) | 38% | 88% | 138.7 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| L-asparagine catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 38% | 84% | 133.3 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| L-aspartate catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 38% | 84% | 133.3 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| L-proline catabolism | opuBA | lo | BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) | 37% | 66% | 129.8 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| L-asparagine catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 35% | 84% | 129.4 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| L-aspartate catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 35% | 84% | 129.4 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 61% | 128.6 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 61% | 128.6 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 61% | 128.6 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 61% | 128.6 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 61% | 128.6 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 61% | 128.6 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 61% | 128.6 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 61% | 128.6 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| D-alanine catabolism | Pf6N2E2_5405 | lo | ABC transporter for D-Alanine, ATPase component (characterized) | 37% | 83% | 128.3 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| L-asparagine catabolism | aatP | lo | ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) | 39% | 83% | 127.1 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| L-aspartate catabolism | aatP | lo | ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) | 39% | 83% | 127.1 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| L-histidine catabolism | aapP | lo | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 38% | 81% | 126.7 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| L-histidine catabolism | Ac3H11_2560 | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 39% | 81% | 126.3 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| L-asparagine catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 37% | 79% | 125.9 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| L-aspartate catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 37% | 79% | 125.9 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| L-glutamate catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 37% | 79% | 125.9 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| L-leucine catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 37% | 79% | 125.9 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| L-proline catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 37% | 79% | 125.9 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 35% | 60% | 125.6 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 35% | 60% | 125.6 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 35% | 60% | 125.6 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 35% | 60% | 125.6 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| D-cellobiose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 34% | 56% | 123.6 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| D-glucose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 34% | 56% | 123.6 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| lactose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 34% | 56% | 123.6 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| D-maltose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 34% | 56% | 123.6 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| sucrose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 34% | 56% | 123.6 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| trehalose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 34% | 56% | 123.6 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 34% | 56% | 123.6 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 36% | 60% | 119 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| 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) | 35% | 57% | 118.6 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 34% | 54% | 117.9 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 34% | 61% | 115.9 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 35% | 53% | 113.6 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 34% | 56% | 112.8 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 33% | 55% | 110.5 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 34% | 55% | 105.5 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| 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) | 31% | 58% | 102.1 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| trehalose catabolism | malK | 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) | 31% | 58% | 102.1 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
| myo-inositol catabolism | PGA1_c07320 | lo | Inositol transport system ATP-binding protein (characterized) | 31% | 85% | 81.3 | Uncharacterized ABC transporter ATP-binding protein Rv0986 | 44% | 177.6 |
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