Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
L-glutamate catabolism | gltL | med | GluA aka CGL1950, component of Glutamate porter (characterized) | 42% | 86% | 159.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
L-asparagine catabolism | bgtA | med | ATPase (characterized, see rationale) | 43% | 84% | 159.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
L-aspartate catabolism | bgtA | med | ATPase (characterized, see rationale) | 43% | 84% | 159.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
L-arginine catabolism | artP | med | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- (characterized) | 43% | 85% | 156.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
L-histidine catabolism | aapP | med | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 41% | 85% | 155.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
L-histidine catabolism | hisP | med | histidine transport ATP-binding protein hisP (characterized) | 40% | 88% | 153.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
L-lysine catabolism | hisP | med | histidine transport ATP-binding protein hisP (characterized) | 40% | 88% | 153.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
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% | 59% | 168.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
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% | 59% | 168.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 40% | 60% | 165.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
L-histidine catabolism | PA5503 | lo | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 38% | 66% | 162.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 42% | 63% | 162.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 42% | 63% | 162.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 42% | 63% | 162.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 42% | 63% | 162.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 42% | 63% | 162.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 42% | 63% | 162.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 42% | 63% | 162.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 42% | 63% | 162.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
D-cellobiose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 39% | 62% | 161.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
D-glucose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 39% | 62% | 161.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
lactose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 39% | 62% | 161.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
D-maltose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 39% | 62% | 161.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
sucrose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 39% | 62% | 161.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
trehalose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 39% | 62% | 161.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
L-asparagine catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 39% | 83% | 154.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
L-aspartate catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 39% | 83% | 154.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
D-maltose catabolism | malK | lo | ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) | 39% | 58% | 151.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
D-mannose catabolism | TT_C0211 | lo | Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 40% | 58% | 151.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
sucrose catabolism | thuK | lo | Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 40% | 58% | 151.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 39% | 64% | 151 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
L-asparagine catabolism | aatP | lo | ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) | 39% | 88% | 150.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
L-aspartate catabolism | aatP | lo | ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) | 39% | 88% | 150.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
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% | 84% | 149.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
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% | 84% | 149.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
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% | 84% | 149.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
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% | 84% | 149.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
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% | 84% | 149.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 38% | 57% | 148.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 39% | 55% | 148.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 38% | 66% | 148.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 39% | 58% | 147.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
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) | 37% | 87% | 147.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
L-asparagine catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 37% | 89% | 147.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
L-aspartate catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 37% | 89% | 147.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 40% | 59% | 145.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
D-alanine catabolism | Pf6N2E2_5405 | lo | ABC transporter for D-Alanine, ATPase component (characterized) | 38% | 86% | 144.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 39% | 66% | 144.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 39% | 66% | 144.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 38% | 56% | 144.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 36% | 55% | 143.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 36% | 55% | 143.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 36% | 55% | 143.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 36% | 55% | 143.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
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) | 39% | 55% | 142.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
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) | 39% | 55% | 142.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 37% | 55% | 142.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
putrescine catabolism | potA | lo | Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) | 37% | 55% | 142.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 38% | 60% | 141.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
L-proline catabolism | opuBA | lo | 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) | 38% | 67% | 141 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
L-histidine catabolism | BPHYT_RS24015 | lo | ABC transporter related (characterized, see rationale) | 37% | 86% | 139.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 37% | 65% | 138.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
L-histidine catabolism | Ac3H11_2560 | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 39% | 75% | 137.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
L-tryptophan catabolism | ecfA2 | lo | Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) | 40% | 77% | 137.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
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) | 35% | 58% | 136.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
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) | 38% | 83% | 132.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
L-citrulline catabolism | AO353_03040 | lo | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 33% | 91% | 131.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
D-glucosamine (chitosamine) catabolism | AO353_21725 | lo | ABC transporter for D-glucosamine, ATPase component (characterized) | 35% | 85% | 130.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
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) | 31% | 88% | 118.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
glycerol catabolism | glpS | lo | GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) | 35% | 54% | 112.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
glycerol catabolism | glpT | lo | GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) | 30% | 63% | 112.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 45% | 220.7 |
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