GapMind for catabolism of small carbon sources

 

Protein 3608018 in Dinoroseobacter shibae DFL-12

Annotation: Dshi_1425 aldehyde dehydrogenase (RefSeq)

Length: 484 amino acids

Source: Dino in FitnessBrowser

Candidate for 30 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-phenylalanine catabolism pad-dh med phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized) 45% 98% 407.5 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 49% 432.6
4-hydroxybenzoate catabolism adh med Putative aldehyde dehydrogenase FUS7; Fusarin biosynthesis protein 7; EC 1.2.1.3 (characterized) 41% 95% 342.8 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 49% 432.6
2'-deoxyinosine catabolism adh med Putative aldehyde dehydrogenase FUS7; Fusarin biosynthesis protein 7; EC 1.2.1.3 (characterized) 41% 95% 342.8 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 49% 432.6
2-deoxy-D-ribose catabolism adh med Putative aldehyde dehydrogenase FUS7; Fusarin biosynthesis protein 7; EC 1.2.1.3 (characterized) 41% 95% 342.8 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 49% 432.6
ethanol catabolism adh med Putative aldehyde dehydrogenase FUS7; Fusarin biosynthesis protein 7; EC 1.2.1.3 (characterized) 41% 95% 342.8 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 49% 432.6
L-threonine catabolism adh med Putative aldehyde dehydrogenase FUS7; Fusarin biosynthesis protein 7; EC 1.2.1.3 (characterized) 41% 95% 342.8 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 49% 432.6
thymidine catabolism adh med Putative aldehyde dehydrogenase FUS7; Fusarin biosynthesis protein 7; EC 1.2.1.3 (characterized) 41% 95% 342.8 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 49% 432.6
L-tryptophan catabolism adh med Putative aldehyde dehydrogenase FUS7; Fusarin biosynthesis protein 7; EC 1.2.1.3 (characterized) 41% 95% 342.8 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 49% 432.6
L-arginine catabolism gabD lo succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] (characterized) 39% 96% 310.1 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 49% 432.6
L-citrulline catabolism gabD lo succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] (characterized) 39% 96% 310.1 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 49% 432.6
putrescine catabolism gabD lo succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] (characterized) 39% 96% 310.1 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 49% 432.6
L-fucose catabolism aldA lo NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 38% 97% 309.3 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 49% 432.6
L-rhamnose catabolism aldA lo NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 38% 97% 309.3 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 49% 432.6
L-threonine catabolism aldA lo NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 38% 97% 309.3 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 49% 432.6
L-arginine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 96% 298.9 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 49% 432.6
L-citrulline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 96% 298.9 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 49% 432.6
L-lysine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 96% 298.9 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 49% 432.6
L-proline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 96% 298.9 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 49% 432.6
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 36% 97% 292 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 49% 432.6
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 36% 97% 292 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 49% 432.6
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 32% 98% 265.8 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 49% 432.6
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 32% 98% 265.8 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 49% 432.6
L-isoleucine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 30% 97% 216.1 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 49% 432.6
myo-inositol catabolism mmsA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 30% 97% 216.1 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 49% 432.6
propionate catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 30% 97% 216.1 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 49% 432.6
L-threonine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 30% 97% 216.1 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 49% 432.6
L-valine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 30% 97% 216.1 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 49% 432.6
L-lysine catabolism amaB lo Alpha-aminoadipic semialdehyde dehydrogenase; Alpha-AASA dehydrogenase; Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Betaine aldehyde dehydrogenase; Delta1-piperideine-6-carboxylate dehydrogenase; P6c dehydrogenase; EC 1.2.1.31; EC 1.2.1.3; EC 1.2.1.8 (characterized) 32% 90% 214.9 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 49% 432.6
L-arginine catabolism astD lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 33% 90% 191 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 49% 432.6
L-citrulline catabolism astD lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 33% 90% 191 aromatic aldehyde dehydrogenase (EC 1.2.1.67; EC 1.2.1.29) 49% 432.6

Sequence Analysis Tools

View 3608018 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

MNVQTGFAQDVRVDFTGPYRHAINGALVDSAGSFEVFNPATDEVVAHAPNASRDQVEQAI
AAAKAAQPGWAALSQDERGAYIAAYADALDAHKQELITLLTTEQGKPRHSMATTEVEYAI
FWVREVAKRRLEDEVIEDTPEHTVKVAHTPLGVVGAITPWNFPVLLGLWKIAPCLVTGNT
MVMKPSPYTPLCTLRFGEIAQQVFPAGVLNVVAGGNEQGAWLTEHPDIAKISFTGSTATG
RKVMASSSCNLKRITLELGGNDPAILLPGTDYKPLIPTLFDAAYGNSGQWCIAVKRLYVH
ESLYDDFLRDFVAHAAEKTVGNGMDPNTDLGPIQNKMQYGKLKDLFADVKAQGLSVPLGG
EIPDGPGNFVPITIVDNPPKDSRVVREEPFGPILPIIKWSDLDEVVRDANDTEFGLAASV
WGPDRDTAIGVANRLEAGTVWVNEIHIHGIDIPFGGHKQSGMGVENGQEGLKEFTNTKTY
MFRK

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