GapMind for catabolism of small carbon sources

 

Protein WP_048081400.1 in Methanobacterium veterum MK4

Annotation: NCBI__GCF_000745485.1:WP_048081400.1

Length: 348 amino acids

Source: GCF_000745485.1 in NCBI

Candidate for 63 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
putrescine catabolism potA med spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 45% 72% 233.8 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 46% 73% 208 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 43% 71% 205.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
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) 40% 89% 241.1 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
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) 40% 89% 241.1 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
D-cellobiose catabolism gtsD 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) 38% 87% 237.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
D-glucose catabolism gtsD 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) 38% 87% 237.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
lactose catabolism gtsD 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) 38% 87% 237.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
D-maltose catabolism gtsD 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) 38% 87% 237.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
D-maltose 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) 38% 87% 237.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
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) 38% 87% 237.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
sucrose catabolism gtsD 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) 38% 87% 237.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
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) 38% 87% 237.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
trehalose catabolism gtsD 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) 38% 87% 237.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 36% 90% 230.7 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 39% 78% 221.9 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
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% 79% 219.5 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
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% 79% 219.5 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 36% 87% 216.1 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 99% 214.5 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 99% 214.5 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 99% 214.5 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 99% 214.5 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 99% 214.5 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 99% 214.5 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 99% 214.5 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 99% 214.5 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 90% 213.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 90% 213.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 90% 213.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 90% 213.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
D-maltose catabolism malK lo ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 33% 85% 213 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 36% 85% 211.1 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 35% 97% 211.1 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 36% 85% 211.1 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 36% 85% 211.1 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 36% 82% 208 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 36% 80% 207.6 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 36% 93% 206.8 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 36% 93% 206.8 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 35% 83% 205.7 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 34% 87% 200.7 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 39% 74% 200.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 36% 86% 198.7 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
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) 34% 80% 198 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 83% 195.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 83% 195.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 83% 195.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 83% 195.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 83% 195.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 83% 195.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 39% 72% 194.1 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
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) 37% 77% 192.2 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 41% 64% 191.8 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 34% 96% 191.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
glycerol catabolism glpT lo ABC transporter for Glycerol, ATPase component 2 (characterized) 31% 90% 170.2 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 38% 60% 166.8 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 38% 80% 154.8 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 32% 84% 153.7 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
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) 36% 81% 150.6 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 40% 83% 142.5 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
D-alanine catabolism AZOBR_RS08250 lo Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 32% 88% 99.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2
L-proline catabolism AZOBR_RS08250 lo Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 32% 88% 99.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 358.2

Sequence Analysis Tools

View WP_048081400.1 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

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Sequence

MIRIENLSNDWKEFKINNINLQVEDSEYFIILGPSGSGKTMLLELIAGMWPLDSGKIYMD
NKDITTLPPEKRGIGFVYQNYMLFPHKTVFENIAFGLKVRKVRDEEIKTRVKEMMDLLKI
SHLADRLPRTLSGGEQQRTALARALIIYPKILLMDEPLSALDRKTRDELMQELKEIHRKF
DVTLVHVTHNFDEALMLADRIAIMRNGEISQVGTSTEIFRHPADKFVADFVGAENIIEGT
AKKDGERLTIIDTGNISIYSTEQKQGHVHITVRPEDIILSTQKVETSARNVFKGSIRGIV
DTGALIKLTIDVGEPLVVFLTRQSFLDMELNIGKSVWTYFKATAVHVF

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