GapMind for catabolism of small carbon sources

 

Protein PP_1722 in Pseudomonas putida KT2440

Annotation: PP_1722 ABC transporter, ATP-binding protein

Length: 329 amino acids

Source: Putida in FitnessBrowser

Candidate for 11 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% 86% 278.5 Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized 45% 258.1
D-mannitol catabolism mtlK med SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 46% 88% 249.6 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 278.5
lactose catabolism lacK med ABC transporter for Lactose, ATPase component (characterized) 41% 97% 234.2 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 278.5
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Sorbitol, ATPase component (characterized) 40% 97% 227.6 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 278.5
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 42% 76% 221.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 278.5
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 43% 87% 218.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 278.5
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 51% 58% 229.6 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 278.5
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 46% 69% 228.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 278.5
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 49% 66% 227.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 278.5
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 37% 92% 219.2 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 278.5
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 34% 96% 184.1 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 46% 278.5

Sequence Analysis Tools

View PP_1722 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

MSFVSVQKLQKSYAGSPVFERIDCHIERGEFVTLLGPSGCGKSTLLRCIAGLTSVDSGQI
LLDGHDIVPLSPQKRGIGMVFQSYALFPNMTVEQNVAFGLRMQKVKADESQLRVREVLEL
VELGKFAGRYPHQLSGGQCQRVALARSLVTRPRLLLLDEPLSALDARIRKHLREQIRAIQ
RELGLTTIFVTHDQEEALTMSDRIFLMNQGRIVQSGDAETLYTAPVDLFAAGFIGNYNLL
DADSASRLLQRPVASRLAIRPESITLGEHGELDAEVRSHSLLGNVIRYRVRVREVELVVD
VLNRSPADLHADGKRVSVSIDPTALREVA

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