Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
L-citrulline catabolism | PS417_17605 | lo | ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) | 36% | 84% | 150.2 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
L-asparagine catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 37% | 89% | 149.4 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
L-aspartate catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 37% | 89% | 149.4 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
L-glutamate catabolism | gltL | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 37% | 89% | 149.4 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 35% | 66% | 149.1 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 35% | 66% | 149.1 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 35% | 66% | 149.1 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 35% | 66% | 149.1 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
D-cellobiose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 35% | 60% | 148.3 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
D-glucose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 35% | 60% | 148.3 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
lactose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 35% | 60% | 148.3 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
D-maltose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 35% | 60% | 148.3 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
sucrose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 35% | 60% | 148.3 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
trehalose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 35% | 60% | 148.3 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 36% | 55% | 147.9 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
L-histidine catabolism | BPHYT_RS24015 | lo | ABC transporter related (characterized, see rationale) | 35% | 94% | 147.5 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
L-asparagine catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 35% | 91% | 143.7 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
L-aspartate catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 35% | 91% | 143.7 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
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) | 36% | 85% | 142.9 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
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) | 36% | 85% | 142.9 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 34% | 55% | 142.9 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
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) | 36% | 85% | 142.9 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
L-histidine 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) | 36% | 85% | 142.9 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
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) | 36% | 85% | 142.9 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
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) | 36% | 85% | 142.9 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
L-asparagine catabolism | aatP | lo | PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized) | 36% | 88% | 140.6 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
L-aspartate catabolism | aatP | lo | PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized) | 36% | 88% | 140.6 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
L-citrulline catabolism | AO353_03040 | lo | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 34% | 91% | 137.9 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 35% | 60% | 136.7 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
L-histidine catabolism | Ac3H11_2560 | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 34% | 85% | 132.5 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 37% | 54% | 131.7 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
D-maltose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 35% | 58% | 127.9 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
D-maltose catabolism | thuK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 35% | 58% | 127.9 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
sucrose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 35% | 58% | 127.9 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
trehalose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 35% | 58% | 127.9 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
lactose catabolism | lacK | lo | LacK, component of Lactose porter (characterized) | 33% | 58% | 126.3 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 33% | 54% | 126.3 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
D-cellobiose catabolism | TM0027 | lo | TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) | 35% | 89% | 124.8 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
D-cellobiose catabolism | cbtD | lo | CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) | 36% | 65% | 119.8 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
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) | 33% | 73% | 112.8 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
glycerol catabolism | glpS | lo | GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) | 32% | 53% | 104.8 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
D-cellobiose catabolism | TM0028 | lo | TM0028, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) | 33% | 73% | 99.8 | Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB | 52% | 281.6 |
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