| 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) | 41% | 86% | 177.9 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 40% | 67% | 161.4 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 40% | 67% | 161.4 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| D-maltose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 38% | 63% | 146.7 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| D-maltose catabolism | thuK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 38% | 63% | 146.7 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| sucrose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 38% | 63% | 146.7 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| trehalose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 38% | 63% | 146.7 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| D-maltose catabolism | malK | lo | ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) | 39% | 61% | 146 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| L-histidine catabolism | hutV | lo | HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) | 36% | 97% | 145.2 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| 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) | 36% | 97% | 145.2 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| sucrose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 38% | 67% | 144.4 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| trehalose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 38% | 67% | 144.4 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| D-cellobiose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 37% | 55% | 144.1 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| D-glucose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 37% | 55% | 144.1 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| lactose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 37% | 55% | 144.1 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| D-maltose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 37% | 55% | 144.1 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| sucrose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 37% | 55% | 144.1 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| trehalose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 37% | 55% | 144.1 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 37% | 55% | 144.1 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| L-proline catabolism | proV | lo | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 34% | 62% | 143.7 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| putrescine catabolism | potA | lo | Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) | 37% | 54% | 142.9 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 35% | 65% | 142.1 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 38% | 61% | 140.2 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 38% | 61% | 140.2 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 38% | 61% | 140.2 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 38% | 61% | 140.2 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| 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% | 60% | 140.2 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 38% | 61% | 140.2 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 38% | 61% | 140.2 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 38% | 55% | 139 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| D-mannitol catabolism | mtlK | lo | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) | 35% | 65% | 138.7 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| lactose catabolism | lacK | lo | LacK, component of Lactose porter (characterized) | 36% | 58% | 138.3 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 34% | 58% | 137.5 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| 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) | 36% | 57% | 136.7 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| 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) | 36% | 57% | 136.7 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 35% | 62% | 136.3 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 36% | 58% | 135.2 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| 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) | 32% | 71% | 135.2 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 35% | 55% | 134.8 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 34% | 65% | 134.8 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 32% | 58% | 129.8 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 36% | 56% | 129.8 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 33% | 58% | 126.7 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| 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) | 33% | 56% | 126.7 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| 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) | 34% | 56% | 123.2 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| L-arabinose catabolism | xylGsa | lo | Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) | 31% | 91% | 116.7 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| glycerol catabolism | glpS | lo | GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) | 31% | 62% | 110.2 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| D-cellobiose catabolism | cbtF | lo | CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) | 32% | 60% | 106.7 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| L-alanine catabolism | braG | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 32% | 89% | 102.8 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| L-histidine catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 32% | 89% | 102.8 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| L-leucine catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 32% | 89% | 102.8 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| L-proline catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 32% | 89% | 102.8 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| L-serine catabolism | braG | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 32% | 89% | 102.8 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| L-threonine catabolism | braG | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 32% | 89% | 102.8 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
| D-mannose catabolism | TM1749 | lo | TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) | 32% | 71% | 92.8 | ABC transporter for nitrate, ATPase component | 57% | 302.4 |
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