Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 47% | 63% | 180.3 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 42% | 63% | 178.3 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
trehalose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 42% | 63% | 178.3 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 41% | 60% | 177.9 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
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) | 42% | 64% | 177.6 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
D-cellobiose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 41% | 61% | 174.1 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
D-glucose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 41% | 61% | 174.1 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
lactose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 41% | 61% | 174.1 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
D-maltose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 41% | 61% | 174.1 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
sucrose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 41% | 61% | 174.1 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
trehalose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 41% | 61% | 174.1 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 41% | 61% | 174.1 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
D-maltose catabolism | malK | lo | ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) | 41% | 61% | 173.7 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 41% | 58% | 172.9 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
putrescine catabolism | potA | lo | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) | 39% | 60% | 172.9 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 40% | 61% | 171.4 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
D-mannitol catabolism | mtlK | lo | MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) | 40% | 62% | 169.5 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
D-sorbitol (glucitol) catabolism | mtlK | lo | MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) | 40% | 62% | 169.5 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 39% | 72% | 168.7 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 39% | 72% | 168.7 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
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) | 42% | 60% | 168.7 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
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) | 42% | 60% | 168.7 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 40% | 66% | 165.6 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 41% | 64% | 164.9 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 41% | 59% | 164.1 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
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) | 40% | 60% | 163.7 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
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) | 39% | 55% | 162.9 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 38% | 66% | 158.3 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 38% | 62% | 157.5 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 37% | 57% | 157.1 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 42% | 59% | 156.4 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 37% | 60% | 155.6 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
lactose catabolism | lacK | lo | ABC transporter for Lactose, ATPase component (characterized) | 37% | 64% | 155.2 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 40% | 62% | 151.8 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 40% | 62% | 151.8 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 40% | 62% | 151.8 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
D-maltose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 40% | 62% | 151.8 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 40% | 62% | 151.8 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
sucrose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 40% | 62% | 151.8 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 40% | 62% | 151.8 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
trehalose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 40% | 62% | 151.8 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 40% | 62% | 151.8 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
glycerol catabolism | glpT | lo | GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) | 36% | 64% | 149.8 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
glycerol catabolism | glpS | lo | GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) | 37% | 65% | 140.6 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
L-histidine catabolism | Ac3H11_2560 | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 36% | 71% | 115.2 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 66% | 319.7 |
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