GapMind for catabolism of small carbon sources

 

Protein PfGW456L13_4204 in Pseudomonas fluorescens GW456-L13

Annotation: ABC transporter, ATP-binding protein

Length: 329 amino acids

Source: pseudo13_GW456_L13 in FitnessBrowser

Candidate for 15 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
putrescine catabolism potA hi spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 46% 84% 271.6 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.5
D-mannitol catabolism mtlK med SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 45% 89% 248.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 271.6
D-cellobiose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 81% 202.2 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 271.6
D-galactose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 81% 202.2 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 271.6
D-glucose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 81% 202.2 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 271.6
lactose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 81% 202.2 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 271.6
D-maltose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 81% 202.2 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 271.6
D-mannose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 81% 202.2 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 271.6
sucrose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 81% 202.2 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 271.6
trehalose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 81% 202.2 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 271.6
sucrose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 40% 94% 222.2 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 271.6
L-isoleucine catabolism natE lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 33% 84% 114 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 271.6
L-leucine catabolism natE lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 33% 84% 114 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 271.6
L-proline catabolism natE lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 33% 84% 114 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 271.6
L-valine catabolism natE lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 33% 84% 114 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 271.6

Sequence Analysis Tools

View PfGW456L13_4204 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

MSYVSVQHLQKSFAGTTVFSDINCEIQKGEFVTLLGPSGCGKSTLLRCIAGLTSVDGGKI
LLDGADIVPVSPQKRGIGMVFQSYALFPNMTVEQNVAFGLRMQKVNADDSRKRVAEVLKL
VELNDFAARYPHQLSGGQCQRVALARSLVTRPRLLLLDEPLSALDARIRKHLREQIRQIQ
RELGLTTIFVTHDQEEALTMSDRIFLMNQGKIVQSGDAETLYTAPVDVFAAGFIGNYNLL
DADSASKLLQRPINKRIAIRPEAIELSLDGELDAQVRSHSLLGNVIRYRVEARGVELVVD
VLNRSAADLHPDGQRLALSIDPTALCEVA

This GapMind analysis is from Sep 17 2021. 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 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