GapMind for catabolism of small carbon sources

 

Protein 6938545 in Shewanella amazonensis SB2B

Annotation: Sama_2648 aldehyde dehydrogenase (RefSeq)

Length: 498 amino acids

Source: SB2B in FitnessBrowser

Candidate for 36 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) 75% 100% 777.7 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) 58% 580.1
L-arginine catabolism puuC hi 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 75% 100% 777.7 aldehyde dehydrogenase 56% 553.5
L-citrulline catabolism puuC hi 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 75% 100% 777.7 aldehyde dehydrogenase 56% 553.5
putrescine catabolism puuC hi 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 75% 100% 777.7 aldehyde dehydrogenase 56% 553.5
L-arginine catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 58% 98% 580.1 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 75% 777.7
L-arginine catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 58% 98% 580.1 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 75% 777.7
L-citrulline catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 58% 98% 580.1 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 75% 777.7
L-citrulline catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 58% 98% 580.1 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 75% 777.7
putrescine catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 58% 98% 580.1 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 75% 777.7
putrescine catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 58% 98% 580.1 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 75% 777.7
L-phenylalanine catabolism pad-dh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 46% 92% 417.2 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 75% 777.7
L-fucose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 43% 95% 377.5 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 75% 777.7
L-rhamnose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 43% 95% 377.5 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 75% 777.7
L-threonine catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 43% 95% 377.5 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 75% 777.7
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 38% 97% 344.4 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 75% 777.7
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 38% 97% 344.4 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 75% 777.7
L-tryptophan catabolism nbaE lo aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 37% 95% 307.4 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 75% 777.7
L-arabinose catabolism xacF lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 38% 97% 297.7 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 75% 777.7
D-galacturonate catabolism dopDH lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 38% 97% 297.7 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 75% 777.7
D-glucuronate catabolism dopDH lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 38% 97% 297.7 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 75% 777.7
D-xylose catabolism dopDH lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 38% 97% 297.7 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 75% 777.7
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 36% 99% 291.2 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 75% 777.7
L-arginine catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 35% 96% 283.9 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 75% 777.7
L-citrulline catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 35% 96% 283.9 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 75% 777.7
L-lysine catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 35% 96% 283.9 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 75% 777.7
L-proline catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 35% 96% 283.9 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 75% 777.7
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 32% 98% 245.7 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 75% 777.7
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 32% 98% 245.7 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 75% 777.7
L-isoleucine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 34% 95% 241.1 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 75% 777.7
myo-inositol catabolism mmsA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 34% 95% 241.1 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 75% 777.7
propionate catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 34% 95% 241.1 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 75% 777.7
L-threonine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 34% 95% 241.1 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 75% 777.7
L-valine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 34% 95% 241.1 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 75% 777.7
L-valine catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 97% 238.8 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 75% 777.7
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 33% 94% 204.1 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 75% 777.7
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 33% 94% 204.1 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 75% 777.7

Sequence Analysis Tools

View 6938545 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

MSTPQSRSEWEAMAQRLEINGRAFINGHYCDAVGKETFDCISPVDGRLLTQVASCQQADA
DIAVANARAVFESGVWSLQSPVKRKKVMIRFAELLEAHADELALLETLDMGKPIAHSKAV
DVAGAARAIRWSGEAIDKIYDELAPTPHNEIGMITREPVGVVAAIVPWNFPMLMACWKLG
PALATGNSVVLKPSEKSPLTAIRMAQLAKEAGLPDGVLNVLPGFGHTVGQALALHMDVDT
LVFTGSTKIAKQLMVYAGQSNMKRVWLEAGGKSPNIVFNDAPDLKAAAEAAASAIAFNQG
EVCTAGSRLLVESGVKDELIKLIVKEMEAWQPGHPLDPATTCGAVVDKQQLDTVLGYIKA
GHDEGAKLMCGGSQVLAETGGVYVAPTVFDGVTNQMKIAREEIFGPVMSVITFDGMDEAV
AIANDTIYGLAAGVWTSDISKAHKTAKALRSGMVWINHYDGGDMTAPFGGYKQSGNGRDK
SLHAFEKYTEVKATWIAL

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