GapMind for catabolism of small carbon sources

 

Protein GFF2135 in Phaeobacter inhibens BS107

Annotation: PGA1_c21670 betaine aldehyde dehydrogenase BetB

Length: 485 amino acids

Source: Phaeo in FitnessBrowser

Candidate for 42 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism adh med 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 53% 98% 490.7 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
L-arginine catabolism patD med 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 53% 98% 490.7 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
L-citrulline catabolism patD med 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 53% 98% 490.7 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
2'-deoxyinosine catabolism adh med 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 53% 98% 490.7 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
2-deoxy-D-ribose catabolism adh med 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 53% 98% 490.7 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
ethanol catabolism adh med 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 53% 98% 490.7 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
putrescine catabolism patD med 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 53% 98% 490.7 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
L-threonine catabolism adh med 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 53% 98% 490.7 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
thymidine catabolism adh med 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 53% 98% 490.7 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
L-tryptophan catabolism adh med 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 53% 98% 490.7 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
L-phenylalanine catabolism pad-dh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 44% 91% 380.2 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
L-arginine catabolism kauB med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 40% 96% 352.8 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
L-arginine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 40% 96% 352.8 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
L-citrulline catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 40% 96% 352.8 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
putrescine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 40% 96% 352.8 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 39% 98% 354.4 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 39% 98% 354.4 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
L-fucose catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 40% 95% 350.9 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
L-rhamnose catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 40% 95% 350.9 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
L-threonine catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 40% 95% 350.9 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
L-arabinose catabolism xacF lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 40% 98% 332.8 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
D-galacturonate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 40% 98% 332.8 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
D-glucuronate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 40% 98% 332.8 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
D-xylose catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 40% 98% 332.8 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
L-tryptophan catabolism nbaE lo aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 38% 94% 317 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
L-arginine catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 37% 97% 314.7 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
L-citrulline catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 37% 97% 314.7 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
L-lysine catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 37% 97% 314.7 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
L-proline catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 37% 97% 314.7 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 38% 99% 313.9 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
L-isoleucine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 98% 279.6 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
myo-inositol catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 98% 279.6 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
propionate catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 98% 279.6 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
L-threonine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 98% 279.6 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
L-valine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 98% 279.6 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
L-valine catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 98% 279.6 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 36% 92% 246.5 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 36% 92% 246.5 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 36% 92% 246.5 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 36% 92% 246.5 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 36% 92% 246.5 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7
L-lysine catabolism amaB lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized) 32% 85% 238.8 betaine aldehyde dehydrogenase (EC 1.2.1.8) 69% 658.7

Sequence Analysis Tools

View GFF2135 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 and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MTHPAQPKASHFINGEYVEDTAGTPIPVIYAATGEQIATVHAATPAIVEQALSTAKAAQK
AWARMTGTERGRILRRAADIMRERNHDLSVLETYDTGKPLQETLVADATSGADALEYFGG
LAASLTGEHIPLGEDWVYTKREALGLCVGIGAWNYPTQIACWKGAPALACGNSMVFKPSE
TTPLCALKVAEILIEAGAPAGVFNVVQGMGEVGGALVTDPRVDKVSLTGSVPTGKKVYAA
AAEGMKHVTMELGGKSPLIIFDDADIDNAVGGAINGNFYSSGQVCSNGTRVFVQKGIKEK
FLARLAERTGNAILGDPMDEATSFGPMVTENQMNIVLGYIEKGKEEGARLICGGRRADMD
GYFIEPTVFADVTDDMTIAREEIFGPVMSVLDFDTEEEVVARANDTEFGLSAGVFTKDFT
RAHRVIGNLEAGSCFINSYNDAPVEAPFGGVKASGVGRENSKEAIKHFSQVKSVYVRMGD
VEAAF

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, the preprint on GapMind for carbon sources, 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