GapMind for catabolism of small carbon sources

 

Protein WP_013820725.1 in Methylomonas methanica MC09

Annotation: NCBI__GCF_000214665.1:WP_013820725.1

Length: 240 amino acids

Source: GCF_000214665.1 in NCBI

Candidate for 71 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
putrescine catabolism potA lo PotG aka B0855, component of Putrescine porter (characterized) 41% 57% 170.2 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 37% 168.7
D-maltose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 40% 63% 167.5 PotG aka B0855, component of Putrescine porter 41% 170.2
sucrose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 40% 63% 167.5 PotG aka B0855, component of Putrescine porter 41% 170.2
trehalose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 40% 63% 167.5 PotG aka B0855, component of Putrescine porter 41% 170.2
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 38% 61% 166 PotG aka B0855, component of Putrescine porter 41% 170.2
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 41% 59% 165.2 PotG aka B0855, component of Putrescine porter 41% 170.2
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 63% 164.9 PotG aka B0855, component of Putrescine porter 41% 170.2
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 63% 164.9 PotG aka B0855, component of Putrescine porter 41% 170.2
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 63% 164.9 PotG aka B0855, component of Putrescine porter 41% 170.2
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 63% 164.9 PotG aka B0855, component of Putrescine porter 41% 170.2
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 63% 164.9 PotG aka B0855, component of Putrescine porter 41% 170.2
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 63% 164.9 PotG aka B0855, component of Putrescine porter 41% 170.2
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 63% 164.9 PotG aka B0855, component of Putrescine porter 41% 170.2
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 63% 164.9 PotG aka B0855, component of Putrescine porter 41% 170.2
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 57% 162.9 PotG aka B0855, component of Putrescine porter 41% 170.2
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 57% 162.9 PotG aka B0855, component of Putrescine porter 41% 170.2
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 57% 162.9 PotG aka B0855, component of Putrescine porter 41% 170.2
D-maltose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 57% 162.9 PotG aka B0855, component of Putrescine porter 41% 170.2
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 57% 162.9 PotG aka B0855, component of Putrescine porter 41% 170.2
D-mannitol catabolism mtlK lo ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) 42% 58% 162.9 PotG aka B0855, component of Putrescine porter 41% 170.2
sucrose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 57% 162.9 PotG aka B0855, component of Putrescine porter 41% 170.2
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 57% 162.9 PotG aka B0855, component of Putrescine porter 41% 170.2
trehalose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 57% 162.9 PotG aka B0855, component of Putrescine porter 41% 170.2
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 57% 162.9 PotG aka B0855, component of Putrescine porter 41% 170.2
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 40% 64% 159.5 PotG aka B0855, component of Putrescine porter 41% 170.2
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtM (characterized) 39% 93% 158.7 PotG aka B0855, component of Putrescine porter 41% 170.2
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 37% 56% 158.3 PotG aka B0855, component of Putrescine porter 41% 170.2
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 41% 61% 157.9 PotG aka B0855, component of Putrescine porter 41% 170.2
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% 59% 157.5 PotG aka B0855, component of Putrescine porter 41% 170.2
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 39% 58% 156.4 PotG aka B0855, component of Putrescine porter 41% 170.2
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 39% 64% 156 PotG aka B0855, component of Putrescine porter 41% 170.2
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 93% 156 PotG aka B0855, component of Putrescine porter 41% 170.2
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 93% 156 PotG aka B0855, component of Putrescine porter 41% 170.2
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 39% 64% 156 PotG aka B0855, component of Putrescine porter 41% 170.2
L-glutamate catabolism gltL lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 93% 156 PotG aka B0855, component of Putrescine porter 41% 170.2
L-asparagine catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 36% 95% 154.8 PotG aka B0855, component of Putrescine porter 41% 170.2
L-aspartate catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 36% 95% 154.8 PotG aka B0855, component of Putrescine porter 41% 170.2
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 39% 60% 153.7 PotG aka B0855, component of Putrescine porter 41% 170.2
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 39% 60% 153.7 PotG aka B0855, component of Putrescine porter 41% 170.2
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 39% 60% 153.7 PotG aka B0855, component of Putrescine porter 41% 170.2
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 39% 60% 153.7 PotG aka B0855, component of Putrescine porter 41% 170.2
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 38% 58% 153.3 PotG aka B0855, component of Putrescine porter 41% 170.2
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 34% 60% 153.3 PotG aka B0855, component of Putrescine porter 41% 170.2
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 36% 65% 151 PotG aka B0855, component of Putrescine porter 41% 170.2
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) 38% 88% 150.6 PotG aka B0855, component of Putrescine porter 41% 170.2
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) 36% 55% 148.7 PotG aka B0855, component of Putrescine porter 41% 170.2
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) 36% 55% 148.7 PotG aka B0855, component of Putrescine porter 41% 170.2
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 37% 55% 147.5 PotG aka B0855, component of Putrescine porter 41% 170.2
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 34% 67% 146.4 PotG aka B0855, component of Putrescine porter 41% 170.2
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) 39% 54% 145.6 PotG aka B0855, component of Putrescine porter 41% 170.2
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 36% 57% 144.1 PotG aka B0855, component of Putrescine porter 41% 170.2
L-histidine catabolism hisP lo Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 34% 92% 143.7 PotG aka B0855, component of Putrescine porter 41% 170.2
L-lysine catabolism hisP lo Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 34% 92% 143.7 PotG aka B0855, component of Putrescine porter 41% 170.2
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) 36% 56% 142.9 PotG aka B0855, component of Putrescine porter 41% 170.2
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) 36% 56% 142.9 PotG aka B0855, component of Putrescine porter 41% 170.2
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) 36% 56% 142.9 PotG aka B0855, component of Putrescine porter 41% 170.2
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) 36% 56% 142.9 PotG aka B0855, component of Putrescine porter 41% 170.2
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) 36% 56% 142.9 PotG aka B0855, component of Putrescine porter 41% 170.2
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) 36% 56% 142.9 PotG aka B0855, component of Putrescine porter 41% 170.2
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) 36% 56% 142.9 PotG aka B0855, component of Putrescine porter 41% 170.2
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 35% 89% 142.1 PotG aka B0855, component of Putrescine porter 41% 170.2
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 35% 89% 142.1 PotG aka B0855, component of Putrescine porter 41% 170.2
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 37% 52% 141.4 PotG aka B0855, component of Putrescine porter 41% 170.2
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 38% 59% 138.7 PotG aka B0855, component of Putrescine porter 41% 170.2
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 32% 91% 137.5 PotG aka B0855, component of Putrescine porter 41% 170.2
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 31% 64% 137.1 PotG aka B0855, component of Putrescine porter 41% 170.2
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 33% 59% 132.1 PotG aka B0855, component of Putrescine porter 41% 170.2
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 33% 59% 127.5 PotG aka B0855, component of Putrescine porter 41% 170.2
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 35% 76% 120.2 PotG aka B0855, component of Putrescine porter 41% 170.2
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 31% 86% 119.8 PotG aka B0855, component of Putrescine porter 41% 170.2
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 32% 57% 118.2 PotG aka B0855, component of Putrescine porter 41% 170.2

Sequence Analysis Tools

View WP_013820725.1 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

MIQVKNLFKSYADNRVLENVSIELERGKVLAILGPSGCGKTTLLRLLAGFEKPNQGEISK
DGRILSSESFCLVPAKRDLAMIFQELALWPHMTVFQNVAFAAKKLAMSKTSRVELIYGIL
EKVSLLRYAKCFPSDLSGGERQRLAIARAIITNPDILLMDEPFNNLDPITKSDVVDLIRS
LNINTNMTIIYATHNFDEILNFADRIVVMNRGGFIQDIGKQGFLNFSNMDLLDWYKTCLL

This GapMind analysis is from Apr 09 2024. 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