GapMind for catabolism of small carbon sources

 

Protein H281DRAFT_02464 in Paraburkholderia bryophila 376MFSha3.1

Annotation: H281DRAFT_02464 betaine aldehyde dehydrogenase

Length: 489 amino acids

Source: Burk376 in FitnessBrowser

Candidate for 21 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism patD med 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 52% 97% 493 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 78% 758.4
L-citrulline catabolism patD med 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 52% 97% 493 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 78% 758.4
putrescine catabolism patD med 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 52% 97% 493 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 78% 758.4
L-arginine catabolism kauB med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 43% 96% 395.6 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 78% 758.4
L-arginine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 43% 96% 395.6 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 78% 758.4
L-citrulline catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 43% 96% 395.6 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 78% 758.4
putrescine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 43% 96% 395.6 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 78% 758.4
L-phenylalanine catabolism pad-dh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 43% 93% 393.7 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 78% 758.4
4-hydroxybenzoate catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 42% 97% 392.5 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 78% 758.4
L-tryptophan catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 42% 97% 392.5 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 78% 758.4
L-fucose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 40% 95% 363.6 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 78% 758.4
L-rhamnose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 40% 95% 363.6 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 78% 758.4
L-threonine catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 40% 95% 363.6 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 78% 758.4
L-tryptophan catabolism nbaE med 2-aminomuconic 6-semialdehyde dehydrogenase; Aminomuconate-semialdehyde dehydrogenase; EC 1.2.1.32 (characterized) 41% 99% 359.8 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 78% 758.4
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 39% 99% 337.4 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 78% 758.4
L-valine catabolism mmsA lo Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized) 36% 94% 272.7 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 78% 758.4
L-isoleucine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 98% 260.8 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 78% 758.4
myo-inositol catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 98% 260.8 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 78% 758.4
propionate catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 98% 260.8 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 78% 758.4
L-threonine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 98% 260.8 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 78% 758.4
L-valine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 98% 260.8 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 78% 758.4

Sequence Analysis Tools

View H281DRAFT_02464 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

MAVFATQRLYIGGTYVDATGGETFDTVDPANGETLATVQQASSADVDRAVQSAREGQREW
AALTGMQRSRILRRAVDILRERNDELAALETRDTGKPIAETQAVDIVTGADVIEYYAGLA
TAIEGQQIPLRPTSFVYTRREPLGVCAGIGAWNYPIQIACWKSAPALAAGNAMIFKPSEV
TPLSALKLAEIYTEAGVPPGVFNVVQGDGRVGAMLAAHPDIEKISFTGGVETGKKVMSMA
GASSLKEVTMELGGKSPLLVFDDANLERAADIAMSANFFSSGQVCTNGTRVFVQRSVLER
FEALVLERVKRIRVGAPGDASTNFGPLVSAAQLQKVLGYIDSGVQEGARLIAGGKRLSEG
HFGQGQYVEPTVFTGCHDDMRIVREEIFGPVMSILIFDNEDEAIERANRTAYGLAAGVVT
ENLARAHRVIHRLEAGICWINTWGESPAEMPVGGYKQSGVGRENGITTLEHYTRIKSVQV
ELGPYQPVF

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