GapMind for catabolism of small carbon sources

 

Protein GFF5028 in Pseudomonas simiae WCS417

Annotation: PS417_25760 spermidine/putrescine ABC transporter ATP-binding protein

Length: 370 amino acids

Source: WCS417 in FitnessBrowser

Candidate for 40 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 PotG aka B0855, component of Putrescine porter (characterized) 47% 85% 272.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8
D-maltose catabolism malK med Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 44% 83% 254.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8
D-maltose catabolism malK_Aa med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 47% 75% 251.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 47% 78% 249.6 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8
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) 43% 94% 248.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8
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) 43% 94% 248.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8
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) 43% 94% 248.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8
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) 43% 94% 248.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8
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) 43% 94% 248.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8
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) 43% 94% 248.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8
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) 43% 94% 248.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8
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) 43% 94% 248.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8
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) 43% 94% 248.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8
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) 43% 94% 248.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8
lactose catabolism lacK med LacK, component of Lactose porter (characterized) 43% 82% 245 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8
D-mannitol catabolism mtlK med ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) 41% 86% 243.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8
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) 44% 87% 242.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8
D-xylose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 44% 84% 239.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 41% 93% 238 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8
D-sorbitol (glucitol) catabolism mtlK med MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) 40% 81% 237.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8
L-arabinose catabolism xacK med Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 45% 79% 234.6 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8
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) 43% 78% 231.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8
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) 43% 78% 231.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8
D-galactose catabolism PfGW456L13_1897 med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 44% 77% 228.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8
xylitol catabolism HSERO_RS17020 med ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 41% 73% 226.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8
L-proline catabolism opuBA med 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) 41% 75% 191.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 40% 91% 233.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 40% 91% 233.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 40% 91% 233.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 37% 97% 228.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 40% 96% 228.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 39% 91% 221.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 89% 206.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 89% 206.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 89% 206.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 89% 206.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 89% 206.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 89% 206.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 89% 206.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 89% 206.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 310.8

Sequence Analysis Tools

View GFF5028 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MSEVDSNDVLVSFRGVQKSYDGENLIVKDLNLEIRKGEFLTLLGPSGSGKTTSLMMLAGF
ETPTAGEIQLAGRSINNVPPHKRDIGMVFQNYALFPHMTVAENLAFPLSVRALSKTDISE
RVKRVLSMVQLDAFAQRYPAQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREHM
QMEIKHLHQRLGVTVVYVTHDQGEALTMSDRVAVFHQGEIQQIAAPRTLYEEPKNTFVAN
FIGENNRLNGRLHSHSGERCVVELARGEKVEALAVNVGQVGGPVTLSVRPERVSLNGSSE
SCVNRFSGRVAEFIYLGDHVRVRLEVCGKADFFVKQPIAELDPALAVGDVVPIGWQVEHV
RALDPLLEAN

This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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