Protein Pf6N2E2_1468 in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Protein Pf6N2E2_1468 in Pseudomonas fluorescens FW300-N2E2

Annotation: NAD-dependent formate dehydrogenase beta subunit

Length: 519 amino acids

Source: pseudo6_N2E2 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
4-hydroxybenzoate catabolism	bamH	lo	Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)	38%	79%	341.3	NAD-dependent formate dehydrogenase, beta subunit	63%	666.8
phenylacetate catabolism	bamH	lo	Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)	38%	79%	341.3	NAD-dependent formate dehydrogenase, beta subunit	63%	666.8
L-phenylalanine catabolism	bamH	lo	Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)	38%	79%	341.3	NAD-dependent formate dehydrogenase, beta subunit	63%	666.8

Sequence Analysis Tools

View Pf6N2E2_1468 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

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

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MLTLCIPRDSVARAVGADKVADALALEAERRQLPLTVLRTSSRGLYWLEPLVELESAGVR
LGFGPVTPADVPGLLDALTGDPGSHPLALGPVEAIPYLKSQQRLLFARAGITQPLSLDDY
RAQGGFQGLARSIQMDGADVVASVLDSGLRGRGGAAFPAGIKWRTVRDAVGAQKYVVCNA
DEGDSGTFADRMLMEGDPFLLIEGMIIAGLAVGATMGYIYVRSEYPAAISTLNDALRIAR
DAGYLGANVSGSGRTFDIEVRVGAGAYICGEETALLESLEGKRGTVRAKPPLPAIQGLFG
LPTLVHNVVTLASVPIILEKGAQFYRDFGMGRSLGTMPFQLAGNVRQGGLVERAFGLSLR
ELVEGYGGGTASGRPLKAAQVGGPLGAWVPPSQFDTPLDYEAFAAMGAMLGHGGVVVADD
SLDMAQMARFALQFCAEESCGKCTPCRIGSTRGVEVVDRLIASTEAGARQEQALLLQDLC
DTLQYGSLCALGGMTSYPVASALKHFPADFGLATTEADQ

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources