GapMind for catabolism of small carbon sources

 

Protein PfGW456L13_3155 in Pseudomonas fluorescens GW456-L13

Annotation: L-Proline/Glycine betaine transporter ProP

Length: 429 amino acids

Source: pseudo13_GW456_L13 in FitnessBrowser

Candidate for 3 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-proline catabolism proP med Glycine betaine/proline/ectoine/pipecolic acid transporter OusA; Osmoprotectant uptake system A (characterized) 37% 87% 305.1 Inner membrane metabolite transport protein YhjE 39% 263.1
2-oxoglutarate (alpha-ketoglutarate) catabolism kgtP lo Alpha-ketoglutarate permease of the major facilitator superfamily protein (characterized, see rationale) 35% 89% 240.4 Glycine betaine/proline/ectoine/pipecolic acid transporter OusA; Osmoprotectant uptake system A 37% 305.1
citrate catabolism citA lo Citrate-proton symporter; Citrate carrier protein; Citrate transporter; Citrate utilization determinant; Citrate utilization protein A (characterized) 34% 97% 237.7 Glycine betaine/proline/ectoine/pipecolic acid transporter OusA; Osmoprotectant uptake system A 37% 305.1

Sequence Analysis Tools

View PfGW456L13_3155 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: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

VIVAAGIGNFVEWFDFAVYGFLATTIAQQFFPSGDASAALLKTFAVFAVAFAFRPLGGIF
FGMLGDRIGRKRTLAMTILLMAGATTLIGLLPTYAAIGVMAPILLSLIRCAQGFSAGGEY
AGACAYLMEHAPSDKRAWYGSFIPVSTFSAFAAAAVVAYALEASLSAEAMGSWGWRLPFL
IAAPLGLVGLYLRWKLDETPAFQAVTQEHAVAHSPLKETLRNHGAAICCLGAFVSLTALS
FYMFTTYFATYLQVAGGLSRATALLVSLIALLFAAAICPLAGLYSDRVGRRVTVMTACAL
LIVVVYPSFLMASSGSFAASIVGVMLLAIGAVLCGVVTAALLSETFPTRTRYTASAITYN
MAYTLFGGTAPLVATWLISTTGSNLSPAFYLIAIALLALAGGLALPETSRISLHDVAAQE
KAEGVGASA

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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