GapMind for catabolism of small carbon sources

 

Protein WP_028489030.1 in Thiothrix lacustris DSM 21227

Annotation: NCBI__GCF_000621325.1:WP_028489030.1

Length: 348 amino acids

Source: GCF_000621325.1 in NCBI

Candidate for 79 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-sorbitol (glucitol) catabolism mtlK hi ABC transporter for D-Sorbitol, ATPase component (characterized) 66% 98% 426.4 ABC transporter for D-Maltose and D-Trehalose, ATPase component 55% 359.4
D-maltose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 55% 99% 359.4 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
D-maltose catabolism thuK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 55% 99% 359.4 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
sucrose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 55% 99% 359.4 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
trehalose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 55% 99% 359.4 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
D-mannitol catabolism mtlK med SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 56% 100% 349 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 54% 100% 344.4 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 54% 100% 344.4 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
sucrose catabolism thuK med ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 54% 100% 344 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
trehalose catabolism thuK med ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 54% 100% 344 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
D-cellobiose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 53% 99% 340.5 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
D-glucose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 53% 99% 340.5 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
lactose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 53% 99% 340.5 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
D-maltose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 53% 99% 340.5 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
sucrose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 53% 99% 340.5 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
trehalose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 53% 99% 340.5 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 52% 100% 337.8 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
lactose catabolism lacK med LacK, component of Lactose porter (characterized) 53% 100% 325.1 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
D-maltose catabolism malK med Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 48% 100% 314.7 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
D-cellobiose catabolism msiK med 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) 50% 95% 313.2 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
D-cellobiose catabolism gtsD med 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) 47% 99% 302 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
D-glucose catabolism gtsD med 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) 47% 99% 302 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
lactose catabolism gtsD med 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) 47% 99% 302 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
D-maltose catabolism gtsD med 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) 47% 99% 302 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
D-mannose catabolism TT_C0211 med 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) 47% 99% 302 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
sucrose catabolism gtsD med 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) 47% 99% 302 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
trehalose catabolism gtsD med 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) 47% 99% 302 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 51% 88% 297.4 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 47% 98% 288.9 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
D-xylose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 45% 95% 288.5 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
D-galactose catabolism PfGW456L13_1897 med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 45% 95% 288.1 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
L-arabinose catabolism xacK med Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 47% 94% 285 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
D-maltose catabolism malK_Sm med 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) 46% 98% 282.7 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
trehalose catabolism malK med 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) 46% 98% 282.7 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
D-maltose catabolism malK_Aa med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 48% 84% 280.4 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 48% 87% 280 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
D-glucosamine (chitosamine) catabolism SM_b21216 med ABC transporter for D-Glucosamine, ATPase component (characterized) 43% 100% 270.8 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 42% 96% 262.7 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
xylitol catabolism HSERO_RS17020 med ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 47% 79% 259.6 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
D-cellobiose catabolism SMc04256 med ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 43% 96% 259.2 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
putrescine catabolism potA med Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) 41% 85% 244.2 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 45% 86% 241.9 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
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) 58% 67% 280.8 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
glycerol catabolism glpT lo ABC transporter for Glycerol, ATPase component 2 (characterized) 38% 82% 206.8 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 96% 201.1 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 96% 201.1 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 96% 201.1 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 96% 201.1 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 96% 201.1 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 96% 201.1 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 96% 201.1 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 96% 201.1 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 79% 195.7 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 79% 195.7 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 79% 195.7 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 79% 195.7 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 35% 88% 186.4 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
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% 73% 168.7 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 38% 56% 159.1 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
L-glutamate catabolism gltL lo GluA aka CGL1950, component of Glutamate porter (characterized) 36% 98% 156.8 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 98% 154.8 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 98% 154.8 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 34% 91% 153.7 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 34% 91% 153.7 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
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) 38% 81% 152.9 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
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) 38% 81% 152.9 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 35% 92% 151.8 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
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) 36% 91% 151 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
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% 148.7 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
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% 148.7 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
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% 148.7 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
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% 148.7 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
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% 148.7 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
L-asparagine catabolism aatP lo PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized) 37% 89% 145.2 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
L-aspartate catabolism aatP lo PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized) 37% 89% 145.2 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 35% 97% 142.9 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 33% 86% 110.9 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
citrate catabolism fecE lo iron(III) dicitrate transport ATP-binding protein FecE (characterized) 31% 91% 98.2 ABC transporter for D-Sorbitol, ATPase component 66% 426.4
D-ribose catabolism rbsA lo ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized) 30% 51% 97.8 ABC transporter for D-Sorbitol, ATPase component 66% 426.4

Sequence Analysis Tools

View WP_028489030.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MAFLELKNVDKYYGKLHAIKQVSLEIQSGEFIVFVGPSGCGKSTLLRMIAGLEVINGGQL
ILDGRDITEVPPSQRDLAMVFQSYALYPHMTVEENMSFALRLAKVDPAIIQEKVKMAADK
LNLTAYLQRTPKALSGGQRQRVAIGRSIVRSPKVFLFDEPLSNLDAALRGNTRVEIASLH
RELGATTVYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDQPINRFVARFIGMPQMN
VAPASLFGQFPAQVAEVGIRPEHLQMVSPEDGLLAGKVVLVEALGNETLVHVRPDKVQLE
EPLIVRLYGRTTVHVGDRVGLKWDDSKHIHYFDTKGMRLTHMTQGAAA

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

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.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

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).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory