GapMind for catabolism of small carbon sources

 

Protein GFF2074 in Phaeobacter inhibens BS107

Annotation: PGA1_c21070 betaine aldehyde dehydrogenase BetB

Length: 488 amino acids

Source: Phaeo 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-fucose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 41% 94% 345.1 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 69% 693.7
L-rhamnose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 41% 94% 345.1 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 69% 693.7
L-threonine catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 41% 94% 345.1 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 69% 693.7
L-arginine catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 41% 96% 321.6 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 69% 693.7
L-citrulline catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 41% 96% 321.6 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 69% 693.7
putrescine catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 41% 96% 321.6 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 69% 693.7
L-phenylalanine catabolism pad-dh lo phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39) (characterized) 39% 97% 330.5 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 69% 693.7
L-arginine catabolism kauB lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 40% 96% 319.3 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 69% 693.7
L-arginine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 40% 96% 319.3 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 69% 693.7
L-citrulline catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 40% 96% 319.3 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 69% 693.7
putrescine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 40% 96% 319.3 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 69% 693.7
L-arginine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 98% 314.3 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 69% 693.7
L-citrulline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 98% 314.3 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 69% 693.7
L-lysine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 98% 314.3 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 69% 693.7
L-proline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 98% 314.3 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 69% 693.7
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 34% 94% 213.4 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 69% 693.7
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 34% 94% 213.4 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 69% 693.7

Sequence Analysis Tools

View GFF2074 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

MQQFQQYIGGVFSDGSARFESRDPASGEVWAMMPEARASDVEAAVAAARAAFHAPDWAGM
TATGRGKLLYRLADLIAENAETLAQLETRDTGKIIRETSAQIAYVADYYRYYAGLADKIE
GAHLPIDKPDMEVWLRREPLGVVAAVVPWNSQLFLAAVKIGPALAAGCTVVLKASEEAPA
PLLEFARIFDQAGFPRGVLNVITGFGADCGAVLTAHPGIDHIAFTGGPDTARHVVRNSAE
NLASTSLELGGKSPFIVFEDVDIDSAVNAQVSAIFAATGQSCVAGSRLIISNQIKAQFLH
RLKEKAENIRIGAPELPETEVGPLCTDAQMRRAVELVAASLAAGARIVTGGQPLEGEGNF
FPPTILDCSEAPEAPCLREEFFGPVLSVCGFDTEAEALALANDTAHGLASGVFTRDLTRA
HRMIRGIRAGIVWVNTYRAVSPIAPFGGQGLSGHGREGGLQAALDYTRVKTVWLRTSDDP
IPDPFVMR

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