Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
L-arginine catabolism | artP | med | Arginine transport ATP-binding protein ArtM (characterized) | 42% | 90% | 170.2 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
L-asparagine catabolism | peb1C | med | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 43% | 90% | 161 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
L-aspartate catabolism | peb1C | med | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 43% | 90% | 161 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
L-glutamate catabolism | gltL | med | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 43% | 90% | 161 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
L-asparagine catabolism | aatP | med | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 41% | 90% | 159.8 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
L-aspartate catabolism | aatP | med | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 41% | 90% | 159.8 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
L-histidine catabolism | hisP | med | Histidine transport ATP-binding protein HisP (characterized) | 40% | 88% | 154.5 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
L-lysine catabolism | hisP | med | Histidine transport ATP-binding protein HisP (characterized) | 40% | 88% | 154.5 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
L-tryptophan catabolism | ecfA2 | med | Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) | 41% | 73% | 139.8 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
L-asparagine catabolism | glnQ | lo | 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) | 38% | 87% | 151.8 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
L-asparagine catabolism | bgtA | lo | ATPase (characterized, see rationale) | 40% | 84% | 150.2 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
L-aspartate catabolism | bgtA | lo | ATPase (characterized, see rationale) | 40% | 84% | 150.2 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
L-citrulline catabolism | AO353_03040 | lo | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 37% | 90% | 149.1 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
L-asparagine catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 39% | 82% | 148.7 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
L-aspartate catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 39% | 82% | 148.7 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
L-histidine catabolism | BPHYT_RS24015 | lo | ABC transporter related (characterized, see rationale) | 37% | 85% | 148.3 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
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) | 37% | 84% | 144.4 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
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) | 37% | 84% | 144.4 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
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) | 37% | 84% | 144.4 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
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) | 37% | 84% | 144.4 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
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) | 37% | 84% | 144.4 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
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) | 37% | 84% | 144.4 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
D-alanine catabolism | Pf6N2E2_5405 | lo | ABC transporter for D-Alanine, ATPase component (characterized) | 37% | 85% | 141.4 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
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) | 33% | 82% | 137.5 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
D-glucosamine (chitosamine) catabolism | AO353_21725 | lo | ABC transporter for D-glucosamine, ATPase component (characterized) | 34% | 86% | 137.1 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
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) | 37% | 75% | 128.6 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 34% | 56% | 128.6 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 33% | 61% | 127.9 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
L-histidine catabolism | Ac3H11_2560 | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 34% | 86% | 127.1 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
L-histidine catabolism | hutV | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 35% | 79% | 126.3 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 33% | 60% | 124.4 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
lactose catabolism | lacK | lo | LacK, component of Lactose porter (characterized) | 34% | 59% | 124.4 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
putrescine catabolism | potA | lo | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) | 33% | 56% | 124 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
D-maltose catabolism | malK | lo | ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) | 33% | 58% | 121.7 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
D-maltose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 34% | 63% | 121.7 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
trehalose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 34% | 63% | 121.7 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 30% | 56% | 117.5 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 34% | 60% | 115.5 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 34% | 60% | 115.5 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
D-mannitol catabolism | mtlK | lo | ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) | 32% | 59% | 114.4 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 33% | 58% | 109.4 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 33% | 58% | 109.4 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 33% | 58% | 109.4 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
D-maltose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 33% | 58% | 109.4 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 33% | 58% | 109.4 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
sucrose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 33% | 58% | 109.4 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 33% | 58% | 109.4 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
trehalose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 33% | 58% | 109.4 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 33% | 58% | 109.4 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
glycerol catabolism | glpS | lo | ABC transporter for Glycerol, ATPase component 1 (characterized) | 31% | 52% | 90.9 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 202.2 |
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