GapMind for catabolism of small carbon sources

 

Protein BPHYT_RS23175 in Burkholderia phytofirmans PsJN

Annotation: BPHYT_RS23175 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase

Length: 497 amino acids

Source: BFirm in FitnessBrowser

Candidate for 17 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism kauB hi 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 65% 99% 647.1 aldehyde dehydrogenase 56% 548.9
L-arginine catabolism puuC hi 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 65% 99% 647.1 aldehyde dehydrogenase 56% 548.9
L-citrulline catabolism puuC hi 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 65% 99% 647.1 aldehyde dehydrogenase 56% 548.9
putrescine catabolism puuC hi 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 65% 99% 647.1 aldehyde dehydrogenase 56% 548.9
L-arginine catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 54% 100% 534.3 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 65% 647.1
L-arginine catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 54% 100% 534.3 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 65% 647.1
L-citrulline catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 54% 100% 534.3 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 65% 647.1
L-citrulline catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 54% 100% 534.3 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 65% 647.1
putrescine catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 54% 100% 534.3 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 65% 647.1
putrescine catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 54% 100% 534.3 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 65% 647.1
L-phenylalanine catabolism pad-dh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 47% 92% 424.9 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 65% 647.1
L-fucose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 44% 95% 369.8 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 65% 647.1
L-rhamnose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 44% 95% 369.8 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 65% 647.1
L-threonine catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 44% 95% 369.8 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 65% 647.1
L-tryptophan catabolism nbaE med aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 41% 95% 334.3 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 65% 647.1
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized) 34% 94% 212.2 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 65% 647.1
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized) 34% 94% 212.2 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 65% 647.1

Sequence Analysis Tools

View BPHYT_RS23175 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

MDKKSFAFWQDKAATLSIEGRAFIDGEYRDAEGGRTFDCLSPIDGKLLAKVADSGAADVD
AAVAAARRAFDSGVWSGLNPRQRKAVLLRWAASIREHMDELALLETLDAGKPIADTTSVD
VPGAAYCVEWFAEAIDKIGGEVAPADHHLLGLVTREPIGVVAAVVPWNFPILMASWKFGP
ALAAGNSVVLKPSEKSPLTAIRLAQLALDAGIPAGVFNVVPGAGEPGKLLALHQDVDCLA
FTGSTNVGKLIMQYAGQSNLKRVWLELGGKSPNIVMPDCPDMDRAANAAAGAIFYNMGEM
CTAGSRLLVHRDIKDVFIDKLIAAARSYTPGNPLDPDTSMGAIVDKVQLERVLGYIEAGR
AEAKLLLGGARVKEDTGGFYIEPTIFEIPGSGAKVAREEIFGPVLSVITFDTVEEAIRIA
NDSEYGLAAAVWTSNLTTAHEVSRKLRAGTVWVNCYDEGGDMNFPFGGYKQSGNGRDKSL
HALEKYTELKSTLVRLR

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