Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
D-alanine catabolism | Pf6N2E2_5405 | med | ABC transporter for D-Alanine, ATPase component (characterized) | 74% | 95% | 375.6 | 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) | 71% | 374.8 |
L-asparagine catabolism | aapP | med | 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) | 71% | 99% | 374.8 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
L-aspartate catabolism | aapP | med | 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) | 71% | 99% | 374.8 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
L-glutamate catabolism | aapP | med | 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) | 71% | 99% | 374.8 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
L-histidine catabolism | aapP | med | 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) | 71% | 99% | 374.8 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
L-leucine catabolism | aapP | med | 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) | 71% | 99% | 374.8 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
L-proline catabolism | aapP | med | 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) | 71% | 99% | 374.8 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
L-asparagine catabolism | bztD | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 70% | 93% | 352.4 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
L-aspartate catabolism | bztD | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 70% | 93% | 352.4 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
L-glutamate catabolism | gltL | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 70% | 93% | 352.4 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
L-lysine catabolism | hisP | med | Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) | 65% | 93% | 324.7 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
L-asparagine catabolism | aatP | med | ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) | 63% | 99% | 303.5 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
L-aspartate catabolism | aatP | med | ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) | 63% | 99% | 303.5 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
L-asparagine catabolism | bgtA | med | ATPase (characterized, see rationale) | 60% | 93% | 286.6 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
L-aspartate catabolism | bgtA | med | ATPase (characterized, see rationale) | 60% | 93% | 286.6 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
L-asparagine catabolism | peb1C | med | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 53% | 99% | 256.5 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
L-aspartate catabolism | peb1C | med | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 53% | 99% | 256.5 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
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) | 52% | 97% | 252.7 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
L-arginine catabolism | artP | med | Arginine transport ATP-binding protein ArtM (characterized) | 52% | 100% | 251.5 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
L-histidine catabolism | bgtA | med | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 52% | 96% | 245.4 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
D-glucosamine (chitosamine) catabolism | AO353_21725 | med | ABC transporter for D-Glucosamine, putative ATPase component (characterized) | 54% | 93% | 244.2 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
L-histidine catabolism | hisP | med | 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) | 49% | 97% | 228.4 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
L-citrulline catabolism | AO353_03040 | med | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 46% | 98% | 225.7 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
L-histidine catabolism | BPHYT_RS24015 | med | ABC transporter related (characterized, see rationale) | 45% | 97% | 220.7 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
L-citrulline catabolism | PS417_17605 | med | 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) | 45% | 94% | 218.8 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
L-histidine catabolism | PA5503 | lo | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 40% | 67% | 166 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
L-proline catabolism | proV | lo | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 38% | 56% | 156 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 34% | 62% | 155.2 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 37% | 69% | 152.9 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 35% | 66% | 151 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
D-mannitol catabolism | mtlK | lo | ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) | 37% | 63% | 150.6 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
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) | 38% | 57% | 150.2 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 35% | 67% | 149.8 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 37% | 70% | 148.3 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 37% | 70% | 148.3 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
D-maltose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 35% | 64% | 148.3 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
D-maltose catabolism | thuK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 35% | 64% | 148.3 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
sucrose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 35% | 64% | 148.3 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
trehalose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 35% | 64% | 148.3 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 38% | 63% | 147.1 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
D-cellobiose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 34% | 61% | 144.4 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 34% | 61% | 144.4 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
D-glucose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 34% | 61% | 144.4 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
lactose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 34% | 61% | 144.4 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
D-maltose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 34% | 61% | 144.4 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
sucrose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 34% | 61% | 144.4 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
trehalose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 34% | 61% | 144.4 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
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) | 37% | 81% | 143.3 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
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) | 37% | 81% | 143.3 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
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) | 35% | 63% | 140.2 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
trehalose catabolism | thuK | 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) | 35% | 63% | 140.2 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 37% | 65% | 133.7 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
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) | 36% | 74% | 128.3 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
L-tryptophan catabolism | ecfA2 | lo | Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) | 34% | 77% | 115.5 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
glycerol catabolism | glpS | lo | ABC transporter for Glycerol, ATPase component 1 (characterized) | 33% | 63% | 111.3 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
L-proline catabolism | HSERO_RS00900 | lo | ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) | 30% | 94% | 106.3 | ABC transporter for D-Alanine, ATPase component | 74% | 375.6 |
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