| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-proline catabolism | opuBA | med | BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) | 49% | 72% | 214.9 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| L-histidine catabolism | hutV | med | ABC transporter for L-Histidine, ATPase component (characterized) | 44% | 81% | 174.9 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| 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) | 40% | 81% | 162.2 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| putrescine catabolism | potA | lo | PotG aka B0855, component of Putrescine porter (characterized) | 43% | 63% | 178.3 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| L-proline catabolism | proV | lo | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 43% | 55% | 176.8 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| 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) | 41% | 65% | 168.7 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| 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) | 41% | 65% | 168.7 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| D-mannitol catabolism | mtlK | lo | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) | 40% | 70% | 166.8 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 39% | 67% | 162.5 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 40% | 71% | 161.4 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 39% | 64% | 161.4 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 40% | 71% | 161.4 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 38% | 63% | 160.6 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| lactose catabolism | lacK | lo | ABC transporter for Lactose, ATPase component (characterized) | 41% | 65% | 158.3 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 39% | 61% | 157.9 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 40% | 61% | 156.4 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 40% | 63% | 156.4 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| D-cellobiose catabolism | msiK | lo | MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized) | 39% | 63% | 155.2 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| D-maltose catabolism | malK | lo | ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) | 38% | 63% | 155.2 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 39% | 65% | 153.7 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| D-maltose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 38% | 68% | 151.4 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 40% | 62% | 151 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 40% | 61% | 148.7 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 39% | 61% | 148.7 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| D-maltose catabolism | malK_Sm | lo | MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) | 38% | 65% | 147.5 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| trehalose catabolism | malK | lo | MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) | 38% | 65% | 147.5 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| L-arginine catabolism | artP | lo | Arginine transport ATP-binding protein ArtM (characterized) | 38% | 98% | 146.4 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| D-alanine catabolism | Pf6N2E2_5405 | lo | ABC transporter for D-Alanine, ATPase component (characterized) | 37% | 93% | 145.6 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 36% | 69% | 144.4 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| L-asparagine catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 36% | 90% | 143.7 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| L-aspartate catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 36% | 90% | 143.7 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| L-glutamate catabolism | gltL | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 36% | 90% | 143.7 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| 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) | 35% | 92% | 142.1 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| 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) | 35% | 92% | 142.1 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| 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) | 35% | 92% | 142.1 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| 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) | 35% | 92% | 142.1 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| 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) | 35% | 92% | 142.1 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| 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) | 35% | 92% | 142.1 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| L-asparagine catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 35% | 97% | 140.2 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| L-aspartate catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 35% | 97% | 140.2 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| 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) | 35% | 91% | 139.8 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| D-glucosamine (chitosamine) catabolism | AO353_21725 | lo | ABC transporter for D-Glucosamine, putative ATPase component (characterized) | 34% | 94% | 134.4 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| L-tryptophan catabolism | ecfA1 | lo | Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) | 33% | 79% | 120.9 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| L-tryptophan catabolism | ecfA2 | lo | Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) | 35% | 76% | 118.6 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| D-cellobiose catabolism | TM0027 | lo | TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) | 32% | 87% | 110.2 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
| D-cellobiose catabolism | cbtD | lo | CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) | 32% | 65% | 108.2 | Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA | 52% | 248.8 |
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