GapMind for catabolism of small carbon sources

 

Protein BWI76_RS10695 in Klebsiella michiganensis M5al

Annotation: BWI76_RS10695 aldehyde dehydrogenase PuuC

Length: 495 amino acids

Source: Koxy in FitnessBrowser

Candidate for 25 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism gabD hi 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 82% 100% 824.7 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 60% 589.7
L-arginine catabolism patD hi 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 82% 100% 824.7 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 60% 589.7
L-arginine catabolism puuC hi 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 82% 100% 824.7 aldehyde dehydrogenase 53% 499.2
L-citrulline catabolism gabD hi 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 82% 100% 824.7 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 60% 589.7
L-citrulline catabolism patD hi 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 82% 100% 824.7 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 60% 589.7
L-citrulline catabolism puuC hi 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 82% 100% 824.7 aldehyde dehydrogenase 53% 499.2
putrescine catabolism gabD hi 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 82% 100% 824.7 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 60% 589.7
putrescine catabolism patD hi 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 82% 100% 824.7 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 60% 589.7
putrescine catabolism puuC hi 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 82% 100% 824.7 aldehyde dehydrogenase 53% 499.2
L-arginine catabolism kauB med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 60% 99% 589.7 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) 82% 824.7
L-phenylalanine catabolism pad-dh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 42% 92% 387.1 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) 82% 824.7
L-fucose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 42% 96% 379 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) 82% 824.7
L-rhamnose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 42% 96% 379 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) 82% 824.7
L-threonine catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 42% 96% 379 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) 82% 824.7
4-hydroxybenzoate catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 41% 100% 364.8 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) 82% 824.7
L-tryptophan catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 41% 100% 364.8 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) 82% 824.7
L-tryptophan catabolism nbaE med aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 43% 95% 340.5 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) 82% 824.7
L-isoleucine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 33% 96% 245.7 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) 82% 824.7
myo-inositol catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 33% 96% 245.7 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) 82% 824.7
propionate catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 33% 96% 245.7 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) 82% 824.7
L-threonine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 33% 96% 245.7 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) 82% 824.7
L-valine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 33% 96% 245.7 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) 82% 824.7
L-valine catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 33% 96% 245.7 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) 82% 824.7
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized) 33% 93% 206.5 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) 82% 824.7
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized) 33% 93% 206.5 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) 82% 824.7

Sequence Analysis Tools

View BWI76_RS10695 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

MDFHNLAYWQQKARELTIETRLFINGEYSAAADNSVFATIDPAAQQTLAEVARGKKADVD
RAVQAARGVFDRGDWSQASPAQRKAVLTKFADLMDAHREELALLETLDTGKPIRHSLRDD
IPGAARAIRWYAEAIDKVYGEVAPTGGNELAMIVREPIGVIAAVVPWNFPLLLACWKLGP
ALASGNSVVLKPSEKSPLTALRLAGLAKQAGLPDGVFNVVSGFGHEAGQALALHPDVEVI
TFTGSTRTAKQLLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQKAVNATAGGIFYNQGQ
VCIAGTRLLLEESIADRFLDLLKEQAKGWQPGNPLDPNTTMGMLIDNTHADSVHSFIRAG
EAHSTLLLDGRKNPWPAAVGPTIFVDVDPASPLSQEEIFGPVLVVTRFKNEEQALALAND
SRYGLGAAVWTRDLSRAHRVSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHAL
EKFTELKTIWIALES

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