GapMind for catabolism of small carbon sources

 

Protein WP_011867836.1 in Methanococcus maripaludis C5

Annotation: NCBI__GCF_000016125.1:WP_011867836.1

Length: 312 amino acids

Source: GCF_000016125.1 in NCBI

Candidate for 61 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
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) 43% 63% 199.1 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
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) 43% 63% 199.1 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
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) 39% 67% 195.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
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) 39% 67% 195.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
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) 39% 67% 195.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
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) 39% 67% 195.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
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) 39% 67% 195.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
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) 39% 67% 195.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
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) 39% 67% 195.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
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) 39% 67% 195.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
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) 39% 67% 195.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 39% 60% 190.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 44% 63% 189.1 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 42% 56% 185.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 38% 68% 184.5 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 41% 56% 182.2 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 38% 88% 181.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
D-mannitol catabolism mtlK lo ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) 41% 63% 181 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 32% 95% 177.6 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 32% 95% 177.6 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) 41% 63% 177.2 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 42% 60% 176 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 38% 66% 174.1 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 38% 66% 174.1 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 38% 66% 174.1 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 36% 69% 171.8 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 38% 53% 170.6 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 62% 170.2 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 62% 170.2 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 62% 170.2 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 62% 170.2 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 62% 170.2 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 62% 170.2 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 34% 78% 167.9 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
putrescine catabolism potA lo PotG aka B0855, component of Putrescine porter (characterized) 35% 81% 167.5 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
trehalose catabolism malK lo MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized) 37% 65% 167.5 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
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% 57% 166.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 39% 54% 141.7 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 31% 71% 140.2 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
L-alanine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 34% 84% 109.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
L-histidine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 34% 84% 109.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
L-leucine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 34% 84% 109.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
L-proline catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 34% 84% 109.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
L-serine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 34% 84% 109.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
L-threonine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 34% 84% 109.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
L-isoleucine catabolism livF lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 32% 81% 101.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
L-leucine catabolism livF lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 32% 81% 101.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
L-valine catabolism livF lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 32% 81% 101.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
myo-inositol catabolism PGA1_c07320 lo Inositol transport system ATP-binding protein (characterized) 35% 78% 100.1 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
L-phenylalanine catabolism livF lo high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) 31% 98% 95.9 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
D-fructose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 33% 86% 94.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
D-mannose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 33% 86% 94.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
D-ribose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 33% 86% 94.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
sucrose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 33% 86% 94.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
L-proline catabolism HSERO_RS00895 lo ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 30% 97% 92.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
D-cellobiose catabolism mglA lo glucose transporter, ATPase component (characterized) 34% 76% 85.9 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
D-glucose catabolism mglA lo glucose transporter, ATPase component (characterized) 34% 76% 85.9 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
lactose catabolism mglA lo glucose transporter, ATPase component (characterized) 34% 76% 85.9 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
D-maltose catabolism mglA lo glucose transporter, ATPase component (characterized) 34% 76% 85.9 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
sucrose catabolism mglA lo glucose transporter, ATPase component (characterized) 34% 76% 85.9 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4
trehalose catabolism mglA lo glucose transporter, ATPase component (characterized) 34% 76% 85.9 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 52% 260.4

Sequence Analysis Tools

View WP_011867836.1 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

MLKLEKLCKSWKEFQLKSVNLDIDDNYCILLGPSGAGKSVIIQCITGILKPDSGRIYFDG
EDITDIPPEKRNFGYVPQNYALFPHMNVYNNIAYGMKLRKCPKLEIEKKITEIAEFLKIT
HILNRKPTTLSGGEQQRVAIARALVLDPKILLLDEPTSALDTNIKENVISELKRIGELVP
IIHITHDFVEAKTLGNQIAILINGELNDFGDSEIFKTPKNEKIANFLGYNVITEEKESFA
VAPEEIFVKKHDDTDNGEYIKGKVESLVDFGYYKKVSVNINETVVKTITDGENPVNVGDI
VSIKYKRKVPIN

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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