| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-lysine catabolism | hisP | med | ABC transporter for L-Lysine, ATPase component (characterized) | 56% | 95% | 282.3 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| L-arginine catabolism | artP | 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) | 58% | 95% | 281.6 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| 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) | 58% | 95% | 281.6 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| L-histidine catabolism | BPHYT_RS24015 | med | ABC transporter related (characterized, see rationale) | 57% | 94% | 280.8 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| 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) | 57% | 96% | 273.9 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| 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) | 57% | 96% | 273.9 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| L-citrulline catabolism | AO353_03040 | med | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 53% | 98% | 268.1 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| D-glucosamine (chitosamine) catabolism | AO353_21725 | med | ABC transporter for D-Glucosamine, putative ATPase component (characterized) | 55% | 93% | 263.5 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| L-asparagine catabolism | bgtA | med | ATPase (characterized, see rationale) | 52% | 92% | 263.1 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| L-aspartate catabolism | bgtA | med | ATPase (characterized, see rationale) | 52% | 92% | 263.1 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| L-histidine catabolism | bgtA | med | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 54% | 97% | 255.4 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| L-asparagine catabolism | aatP | med | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 53% | 100% | 254.2 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| L-aspartate catabolism | aatP | med | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 53% | 100% | 254.2 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| L-histidine catabolism | aapP | med | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 51% | 91% | 249.6 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| 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) | 51% | 92% | 247.7 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| 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) | 51% | 92% | 247.7 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| 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) | 53% | 90% | 247.7 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| 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) | 51% | 92% | 247.7 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| 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) | 51% | 92% | 247.7 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| 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) | 51% | 92% | 247.7 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| D-alanine catabolism | Pf6N2E2_5405 | med | ABC transporter for D-Alanine, ATPase component (characterized) | 51% | 95% | 246.9 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| L-asparagine catabolism | bztD | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 51% | 90% | 245 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| L-aspartate catabolism | bztD | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 51% | 90% | 245 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| L-asparagine catabolism | peb1C | med | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 50% | 100% | 234.6 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| L-aspartate catabolism | peb1C | med | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 50% | 100% | 234.6 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| L-histidine catabolism | PA5503 | lo | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 39% | 76% | 177.9 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| D-maltose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 39% | 72% | 163.7 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| sucrose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 39% | 72% | 163.7 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| trehalose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 39% | 72% | 163.7 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| 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) | 39% | 59% | 161.4 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 41% | 64% | 161 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| L-proline catabolism | proV | lo | Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) | 38% | 61% | 160.2 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 35% | 72% | 156.4 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 38% | 71% | 155.2 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 38% | 71% | 155.2 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 37% | 65% | 152.9 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 37% | 65% | 152.9 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 37% | 65% | 152.9 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 37% | 65% | 152.9 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 37% | 65% | 152.9 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 37% | 65% | 152.9 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 38% | 69% | 152.9 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 37% | 65% | 152.9 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 37% | 65% | 152.9 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| lactose catabolism | lacK | lo | ABC transporter for Lactose, ATPase component (characterized) | 38% | 66% | 149.8 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 62% | 148.7 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 62% | 148.7 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 62% | 148.7 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| D-maltose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 37% | 65% | 148.7 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 62% | 148.7 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| sucrose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 37% | 65% | 148.7 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 62% | 148.7 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| trehalose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 37% | 65% | 148.7 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 62% | 148.7 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 37% | 68% | 148.7 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| D-mannitol catabolism | mtlK | lo | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) | 38% | 63% | 147.9 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| 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) | 37% | 64% | 145.6 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| 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) | 35% | 74% | 144.8 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| D-cellobiose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 66% | 142.5 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| D-glucose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 66% | 142.5 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| lactose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 66% | 142.5 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| D-maltose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 66% | 142.5 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| sucrose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 66% | 142.5 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| trehalose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 66% | 142.5 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 34% | 61% | 140.6 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| 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% | 140.6 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| 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% | 140.6 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| 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% | 140.2 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
| D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 32% | 65% | 125.6 | NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter | 60% | 293.9 |
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