GapMind for catabolism of small carbon sources

 

Protein GFF1133 in Marinobacter adhaerens HP15

Annotation: HP15_1111 betaine aldehyde dehydrogenase

Length: 493 amino acids

Source: Marino in FitnessBrowser

Candidate for 22 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism praB hi 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 83% 100% 850.1 retinal dehydrogenase (EC 1.2.1.36) 45% 432.2
L-tryptophan catabolism praB hi 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 83% 100% 850.1 retinal dehydrogenase (EC 1.2.1.36) 45% 432.2
L-tryptophan catabolism nbaE med aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 75% 95% 728.4 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 83% 850.1
4-hydroxybenzoate catabolism adh med 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 43% 99% 421.8 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 83% 850.1
2'-deoxyinosine catabolism adh med 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 43% 99% 421.8 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 83% 850.1
2-deoxy-D-ribose catabolism adh med 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 43% 99% 421.8 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 83% 850.1
ethanol catabolism adh med 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 43% 99% 421.8 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 83% 850.1
L-threonine catabolism adh med 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 43% 99% 421.8 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 83% 850.1
thymidine catabolism adh med 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 43% 99% 421.8 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 83% 850.1
L-tryptophan catabolism adh med 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 43% 99% 421.8 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 83% 850.1
L-arginine catabolism patD lo 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 38% 94% 342.8 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 83% 850.1
L-citrulline catabolism patD lo 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 38% 94% 342.8 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 83% 850.1
putrescine catabolism patD lo 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 38% 94% 342.8 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 83% 850.1
L-phenylalanine catabolism pad-dh lo phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39) (characterized) 38% 97% 340.1 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 83% 850.1
L-arginine catabolism gabD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 39% 96% 338.2 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 83% 850.1
L-arginine catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 39% 96% 338.2 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 83% 850.1
L-citrulline catabolism gabD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 39% 96% 338.2 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 83% 850.1
L-citrulline catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 39% 96% 338.2 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 83% 850.1
putrescine catabolism gabD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 39% 96% 338.2 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 83% 850.1
putrescine catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 39% 96% 338.2 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 83% 850.1
L-arginine catabolism astD lo Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized) 31% 95% 194.5 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 83% 850.1
L-citrulline catabolism astD lo Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized) 31% 95% 194.5 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 83% 850.1

Sequence Analysis Tools

View GFF1133 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

MKPGKAAMKEIKHHINGQYVSSCSSRLFDNVNPANGKIISKVHEAGREEVDAAVKAARAA
LRGPWGKMTLDERTSILHKVADGINARFDEFLEGECLDTGKPKSMASHIDIPRGAANFKV
FADMIKNVPTESFEMPTPDGTGALNYAVRRPKGVIGVISPWNLPLLLMTWKVGPALACGN
TVVVKPSEETPTTTTLLGEVMKEAGVPDGVFNVVHGFGGDSAGAFLTEHPQVDGITFTGE
IGTGEVIMKAAAKGIRDISLELGGKNAGVVFADCDIDKAIEGTMRSAFANCGQVCLGTER
VYVERSIFDEFVGRLKEAAEGMKIGPPDDAEADMGPLVSLNHREKVLSYYQKAVDDGATV
VTGGGVPEMPEALAGGAWVQPTIWTGLPEDSAVITDEIFGPCCHIRPFDTEEEAIELANS
LPYGLASAIWSENITRAHRVAGQIEAGIIWVNSWFLRDLRTPFGGSKQSGIGREGGVHSL
EFYTEMKNICVKL

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