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) | 42% | 100% | 254.2 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
L-arginine catabolism | artP | med | Arginine transport ATP-binding protein ArtM (characterized) | 42% | 99% | 192.2 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
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) | 40% | 97% | 187.6 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
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) | 40% | 97% | 187.6 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
L-asparagine catabolism | aatP | med | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 42% | 90% | 171.4 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
L-aspartate catabolism | aatP | med | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 42% | 90% | 171.4 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
L-histidine catabolism | bgtA | med | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 44% | 85% | 170.6 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
L-lysine catabolism | hisP | med | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 44% | 85% | 170.6 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
L-asparagine catabolism | bgtA | med | ATPase (characterized, see rationale) | 40% | 83% | 164.1 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
L-aspartate catabolism | bgtA | med | ATPase (characterized, see rationale) | 40% | 83% | 164.1 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
L-proline catabolism | proV | lo | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 42% | 59% | 182.2 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
L-asparagine catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 40% | 98% | 178.3 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
L-aspartate catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 40% | 98% | 178.3 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
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) | 34% | 71% | 174.5 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
L-asparagine catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 37% | 90% | 168.3 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
L-aspartate catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 37% | 90% | 168.3 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
L-histidine catabolism | aapP | lo | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 38% | 96% | 167.9 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
L-histidine catabolism | hisP | lo | Histidine transport ATP-binding protein HisP (characterized) | 39% | 91% | 166 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
L-histidine catabolism | hutV | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 39% | 89% | 166 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
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) | 39% | 86% | 164.5 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
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) | 39% | 86% | 164.5 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
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) | 39% | 86% | 164.5 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
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) | 39% | 86% | 164.5 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
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) | 39% | 86% | 164.5 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
D-glucosamine (chitosamine) catabolism | AO353_21725 | lo | ABC transporter for D-glucosamine, ATPase component (characterized) | 36% | 99% | 163.3 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
L-citrulline catabolism | AO353_03040 | lo | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 36% | 92% | 161.8 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
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) | 37% | 84% | 160.6 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
D-alanine catabolism | Pf6N2E2_5405 | lo | ABC transporter for D-Alanine, ATPase component (characterized) | 37% | 93% | 159.8 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
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% | 158.7 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 33% | 69% | 154.8 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 33% | 69% | 154.8 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 33% | 69% | 154.8 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 33% | 69% | 154.8 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
L-histidine catabolism | BPHYT_RS24015 | lo | ABC transporter related (characterized, see rationale) | 36% | 90% | 154.1 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
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% | 89% | 151 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
putrescine catabolism | potA | lo | PotG aka B0855, component of Putrescine porter (characterized) | 30% | 72% | 150.2 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
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% | 78% | 148.3 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
D-cellobiose catabolism | cbtF | lo | CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) | 35% | 84% | 145.2 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
D-cellobiose catabolism | cbtD | lo | CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) | 34% | 77% | 141.4 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
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) | 33% | 85% | 136.7 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
L-tryptophan catabolism | ecfA1 | lo | Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) | 34% | 91% | 132.1 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
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) | 30% | 88% | 109 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
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) | 30% | 88% | 109 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
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) | 30% | 88% | 109 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
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) | 30% | 88% | 109 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
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) | 30% | 88% | 109 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
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) | 30% | 88% | 109 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
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) | 30% | 88% | 109 | AtmD (MetN), component of The methionine porter, AtmBDE | 56% | 379.4 |
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