| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-histidine catabolism | PA5503 | med | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 48% | 100% | 295.8 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| L-arginine catabolism | artP | med | Arginine transport ATP-binding protein ArtM (characterized) | 44% | 96% | 184.5 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| L-asparagine catabolism | glnQ | med | 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) | 41% | 98% | 184.1 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| L-glutamate catabolism | gltL | med | 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) | 41% | 98% | 184.1 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| L-histidine catabolism | hutV | med | ABC transporter for L-Histidine, ATPase component (characterized) | 43% | 89% | 180.3 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| L-proline catabolism | hutV | med | HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) | 42% | 83% | 161.4 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| L-asparagine catabolism | aatP | med | ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) | 41% | 89% | 156 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| L-aspartate catabolism | aatP | med | ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) | 41% | 89% | 156 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| L-proline catabolism | proV | lo | Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) | 35% | 91% | 181.4 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| 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) | 37% | 65% | 175.3 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| L-asparagine catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 38% | 100% | 167.9 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| L-aspartate catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 38% | 100% | 167.9 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| L-histidine catabolism | aapP | lo | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 40% | 93% | 167.2 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| L-lysine catabolism | hisP | lo | ABC transporter for L-Lysine, ATPase component (characterized) | 38% | 100% | 165.6 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| D-alanine catabolism | Pf6N2E2_5405 | lo | ABC transporter for D-Alanine, ATPase component (characterized) | 37% | 95% | 165.2 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| L-histidine catabolism | hisP | lo | Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) | 37% | 96% | 165.2 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| L-asparagine catabolism | bgtA | lo | ATPase (characterized, see rationale) | 37% | 92% | 163.3 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| L-aspartate catabolism | bgtA | lo | ATPase (characterized, see rationale) | 37% | 92% | 163.3 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| L-histidine catabolism | BPHYT_RS24015 | lo | ABC transporter related (characterized, see rationale) | 38% | 89% | 162.5 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| L-asparagine catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 37% | 91% | 162.2 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| L-aspartate catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 37% | 91% | 162.2 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| L-citrulline catabolism | AO353_03040 | lo | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 36% | 100% | 161.4 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| D-mannose catabolism | TM1750 | lo | TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) | 36% | 76% | 161.4 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| L-histidine catabolism | bgtA | lo | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 40% | 90% | 160.2 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| 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% | 93% | 159.8 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| 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% | 93% | 159.8 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| 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% | 93% | 159.8 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| 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% | 93% | 159.8 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| 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% | 93% | 159.8 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| 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) | 39% | 91% | 157.1 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 31% | 93% | 153.3 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| putrescine catabolism | potA | lo | Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) | 36% | 58% | 147.9 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 34% | 70% | 147.5 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| D-cellobiose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 33% | 71% | 145.2 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| D-glucose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 33% | 71% | 145.2 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| lactose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 33% | 71% | 145.2 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| D-maltose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 33% | 71% | 145.2 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| sucrose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 33% | 71% | 145.2 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| trehalose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 33% | 71% | 145.2 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 34% | 64% | 144.8 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| trehalose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 34% | 64% | 144.8 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| sucrose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 38% | 64% | 143.3 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| L-tryptophan catabolism | ecfA1 | lo | Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) | 38% | 90% | 142.5 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| L-tryptophan catabolism | ecfA2 | lo | Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) | 37% | 81% | 140.2 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| 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) | 34% | 83% | 137.5 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 33% | 64% | 136.7 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 32% | 76% | 136.7 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| glycerol catabolism | glpS | lo | ABC transporter for Glycerol, ATPase component 1 (characterized) | 31% | 84% | 126.3 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| D-lactate catabolism | PGA1_c12640 | lo | D-lactate transporter, ATP-binding component (characterized) | 30% | 90% | 114.8 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| L-alanine catabolism | braF | lo | NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 31% | 88% | 112.1 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| L-isoleucine catabolism | natA | lo | NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 31% | 88% | 112.1 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| L-leucine catabolism | natA | lo | NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 31% | 88% | 112.1 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| L-proline catabolism | natA | lo | NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 31% | 88% | 112.1 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| L-serine catabolism | braF | lo | NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 31% | 88% | 112.1 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| L-threonine catabolism | braF | lo | NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 31% | 88% | 112.1 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| L-valine catabolism | natA | lo | NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 31% | 88% | 112.1 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
| citrate catabolism | fecE | lo | iron(III) dicitrate transport ATP-binding protein FecE (characterized) | 32% | 83% | 98.2 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 48% | 314.3 |
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