GapMind for catabolism of small carbon sources

 

Protein WP_108358584.1 in Limnohabitans curvus MWH-C5

Annotation: NCBI__GCF_003063475.1:WP_108358584.1

Length: 354 amino acids

Source: GCF_003063475.1 in NCBI

Candidate for 72 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-cellobiose catabolism gtsD hi Sugar ABC transporter ATP-binding protein (characterized, see rationale) 76% 99% 525 ABC transporter for D-Glucosamine, ATPase component 53% 349.7
D-glucose catabolism gtsD hi Sugar ABC transporter ATP-binding protein (characterized, see rationale) 76% 99% 525 ABC transporter for D-Glucosamine, ATPase component 53% 349.7
lactose catabolism gtsD hi Sugar ABC transporter ATP-binding protein (characterized, see rationale) 76% 99% 525 ABC transporter for D-Glucosamine, ATPase component 53% 349.7
D-maltose catabolism gtsD hi Sugar ABC transporter ATP-binding protein (characterized, see rationale) 76% 99% 525 ABC transporter for D-Glucosamine, ATPase component 53% 349.7
sucrose catabolism gtsD hi Sugar ABC transporter ATP-binding protein (characterized, see rationale) 76% 99% 525 ABC transporter for D-Glucosamine, ATPase component 53% 349.7
trehalose catabolism gtsD hi Sugar ABC transporter ATP-binding protein (characterized, see rationale) 76% 99% 525 ABC transporter for D-Glucosamine, ATPase component 53% 349.7
D-xylose catabolism gtsD hi ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 54% 94% 362.8 ABC transporter for D-Glucosamine, ATPase component 53% 349.7
D-glucosamine (chitosamine) catabolism SM_b21216 med ABC transporter for D-Glucosamine, ATPase component (characterized) 53% 99% 349.7 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
D-galactose catabolism PfGW456L13_1897 med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 51% 94% 346.7 ABC transporter for D-Glucosamine, ATPase component 53% 349.7
D-maltose catabolism thuK 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) 48% 95% 317 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
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) 48% 95% 317 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
sucrose catabolism thuK 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) 48% 95% 317 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
trehalose catabolism thuK 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) 48% 95% 317 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 56% 79% 314.3 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 53% 85% 310.5 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 53% 85% 310.5 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
D-mannitol catabolism mtlK med ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) 46% 97% 310.1 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
D-maltose catabolism malK1 med 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) 49% 95% 309.3 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
D-cellobiose catabolism SMc04256 med ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 49% 96% 308.9 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
D-maltose catabolism malK_Aa med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 48% 91% 307.4 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
lactose catabolism lacK med ABC transporter for Lactose, ATPase component (characterized) 46% 99% 303.5 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 47% 96% 301.2 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Sorbitol, ATPase component (characterized) 47% 97% 301.2 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
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) 47% 94% 300.8 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 47% 95% 296.6 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 45% 99% 286.2 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
D-maltose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 45% 98% 285.4 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
sucrose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 45% 98% 285.4 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
trehalose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 45% 98% 285.4 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
D-maltose catabolism malK med ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 45% 98% 284.6 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
L-arabinose catabolism xacK med Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 45% 95% 283.9 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
D-cellobiose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 48% 86% 276.2 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
D-glucose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 48% 86% 276.2 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
lactose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 48% 86% 276.2 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
D-maltose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 48% 86% 276.2 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
sucrose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 48% 86% 276.2 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
trehalose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 48% 86% 276.2 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 45% 94% 271.6 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
xylitol catabolism HSERO_RS17020 med ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 43% 85% 270.4 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
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) 42% 99% 266.5 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
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) 42% 99% 266.5 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
putrescine catabolism potA med spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 42% 87% 236.1 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 39% 91% 218.8 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
glycerol catabolism glpT lo ABC transporter for Glycerol, ATPase component 2 (characterized) 36% 94% 214.2 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 84% 206.5 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 84% 206.5 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 84% 206.5 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 84% 206.5 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 84% 206.5 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 84% 206.5 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 84% 206.5 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 84% 206.5 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 78% 200.7 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 78% 200.7 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 78% 200.7 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 78% 200.7 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 36% 88% 194.1 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
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) 32% 87% 173.3 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 37% 66% 172.6 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
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) 35% 99% 149.8 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
L-glutamate catabolism gltL 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) 35% 99% 149.8 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtM (characterized) 35% 98% 141 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 35% 100% 136.3 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 35% 100% 136.3 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 32% 93% 136 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
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) 31% 93% 129.4 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
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) 31% 93% 129.4 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
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) 31% 93% 129.4 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
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) 31% 93% 129.4 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
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) 31% 93% 129.4 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
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) 31% 93% 129.4 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8
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) 32% 76% 125.2 ABC transporter for D-Glucose-6-Phosphate, ATPase component 54% 362.8

Sequence Analysis Tools

View WP_108358584.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MSSALKISGIRKCFGQGDNTVEVLKRIDIDVAPGEFLILVGPSGCGKSTLLNIIAGLEEP
TEGSISIGNKNVVGVPPAQRDIAMVFQSYALYPTMSVAENIGFALEIRKVPKAERQARIA
EVAAMLQIEHLLDRRPSQLSGGQRQRVAMGRALARNPQLFLFDEPLSNLDAKLRVEMRAE
IKRLHLLSGITSVYVTHDQVEAMTLGSRIAVMKGGVLQQLGTPDEIYNRPANTYVATFIG
SPTMNLIEGRVSGTEHFMIAGAQLSLMAPNHSDTPTLLGLRPEHIRLSDAAQWRGVVNLV
EPTGADTYVVVDTSAGKVTVRAAPQTLVRPGDSVGLEIQAEHVTWFDQASGLRL

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