GapMind for catabolism of small carbon sources

 

Protein PfGW456L13_1799 in Pseudomonas fluorescens GW456-L13

Annotation: Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)

Length: 351 amino acids

Source: pseudo13_GW456_L13 in FitnessBrowser

Candidate for 32 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
trehalose catabolism thuK med Trehalose import ATP-binding protein SugC; EC 7.5.2.- (characterized) 44% 93% 263.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 268.5
D-maltose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 46% 89% 261.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 268.5
D-maltose catabolism thuK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 46% 89% 261.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 268.5
sucrose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 46% 89% 261.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 268.5
trehalose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 46% 89% 261.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 268.5
D-maltose catabolism malK med ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 43% 96% 260 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 268.5
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) 46% 88% 252.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 268.5
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) 46% 88% 252.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 268.5
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) 46% 88% 252.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 268.5
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) 46% 88% 252.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 268.5
D-mannitol catabolism mtlK med ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) 42% 96% 252.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 268.5
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) 46% 88% 252.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 268.5
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) 46% 88% 252.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 268.5
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) 46% 88% 252.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 268.5
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) 46% 88% 252.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 268.5
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-sorbitol, ATPase component (characterized) 45% 90% 252.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 268.5
D-cellobiose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 45% 83% 248.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 268.5
D-glucose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 45% 83% 248.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 268.5
lactose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 45% 83% 248.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 268.5
lactose catabolism lacK med ABC transporter for Lactose, ATPase component (characterized) 47% 82% 248.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 268.5
D-maltose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 45% 83% 248.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 268.5
sucrose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 45% 83% 248.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 268.5
trehalose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 45% 83% 248.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 268.5
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 42% 87% 243.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 268.5
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 43% 95% 240.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 268.5
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 43% 95% 240.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 268.5
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 46% 80% 238.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 268.5
xylitol catabolism HSERO_RS17020 med ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 40% 81% 237.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 268.5
trehalose catabolism malK med 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) 43% 88% 231.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 268.5
L-alanine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 32% 100% 129.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 268.5
L-serine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 32% 100% 129.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 268.5
L-threonine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 32% 100% 129.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 268.5

Sequence Analysis Tools

View PfGW456L13_1799 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

MSGLILENVEKHYGSACAVKDVNLHLPEGKLVCFLGPSGCGKTTLLRMIAGLETLSGGEI
RLDGEDIGHTPAHLRNFGMVFQSLALFPHMTVGENIAYPLKLRGVSKADQQARVVELLEL
IQLQAMINRPVAKLSGGQRQRVAIARAIANHPKILLLDEPLSALDAKLRESMQVEIRQLQ
QRLNITTIMVTHDQREAMTMADIVVVLGEHKVQQVGTPIEIYRHPANEFVADFIGSGNIF
PATVLGNGKVSLPGGDALQVPICSSIVVGEKVKMLIRPEDLQLSAPQATAGNRLLGKVTF
VRDIGATIETTVECSGVSFTALSTPCQGFGLSVGHPVSVTLPVEACRVLGA

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