GapMind for catabolism of small carbon sources

 

Protein PP_3817 in Pseudomonas putida KT2440

Annotation: PP_3817 Polyamine ABC transporter, ATP-binding protein

Length: 382 amino acids

Source: Putida in FitnessBrowser

Candidate for 25 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) 43% 94% 267.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 52% 320.5
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) 41% 91% 241.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 52% 320.5
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) 41% 91% 241.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 52% 320.5
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) 41% 91% 241.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 52% 320.5
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) 41% 91% 241.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 52% 320.5
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) 41% 91% 241.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 52% 320.5
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) 41% 91% 241.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 52% 320.5
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) 41% 91% 241.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 52% 320.5
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) 41% 91% 241.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 52% 320.5
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) 41% 91% 241.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 52% 320.5
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) 41% 91% 241.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 52% 320.5
D-galactose catabolism PfGW456L13_1897 med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 42% 89% 237.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 52% 320.5
D-mannitol catabolism mtlK med ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) 40% 89% 235.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 52% 320.5
D-xylose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 43% 76% 226.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 52% 320.5
lactose catabolism lacK med ABC transporter for Lactose, ATPase component (characterized) 43% 78% 221.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 52% 320.5
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 40% 92% 234.6 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 52% 320.5
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 38% 92% 229.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 52% 320.5
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) 38% 92% 226.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 52% 320.5
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) 38% 92% 226.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 52% 320.5
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 37% 100% 222.6 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 52% 320.5
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) 38% 93% 221.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 52% 320.5
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 40% 84% 214.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 52% 320.5
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 39% 86% 214.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 52% 320.5
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 39% 86% 214.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 52% 320.5
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 39% 86% 214.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 52% 320.5

Sequence Analysis Tools

View PP_3817 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

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

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MSAVIKDNAHGKTLVSLRGLNKHYGDFTAVDNLDLEIQDGEFLTFLGSSGSGKSTTLSML
AGFETPSSGEILVDGQSLVNVPPHKRDIGMVFQRYSLFPHLNVRDNIAFPLAIRKLGAAE
TAKRVDAMLKLVQLEQFAHRKPSQMSGGQQQRVAIARALVYEPRILLMDEPLGALDKKLR
EDLQDELRQLHRRLGITIVYVTHDQEEAMRLSQRIAIFSHGKIVGLGTGYDLYQNPPNAF
VASFLGNSNFLRIKASSNGAGSFEGQPVAIRLTPGLAASQDALIMVRPEKAVAMSAEQAM
REPLPAGWNEVTAKVGEVLFLGESQTCHVVTAGGTELTVKALSAAGMPMQPGDSVKVRWA
VADACIYTEWAESDLSKSAGAH

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 preprint 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