GapMind for catabolism of small carbon sources

 

Protein WP_011604557.1 in Frankia alni ACN14a

Annotation: NCBI__GCF_000058485.1:WP_011604557.1

Length: 487 amino acids

Source: GCF_000058485.1 in NCBI

Candidate for 39 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 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 45% 93% 407.9 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 46% 426.8
2'-deoxyinosine catabolism adh med Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 45% 93% 407.9 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 46% 426.8
2-deoxy-D-ribose catabolism adh med Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 45% 93% 407.9 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 46% 426.8
ethanol catabolism adh med Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 45% 93% 407.9 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 46% 426.8
L-threonine catabolism adh med Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 45% 93% 407.9 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 46% 426.8
thymidine catabolism adh med Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 45% 93% 407.9 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 46% 426.8
L-tryptophan catabolism adh med Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 45% 93% 407.9 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 46% 426.8
L-phenylalanine catabolism pad-dh med phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39) (characterized) 44% 96% 374.8 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 46% 426.8
L-fucose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 44% 92% 372.5 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 46% 426.8
L-rhamnose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 44% 92% 372.5 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 46% 426.8
L-threonine catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 44% 92% 372.5 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 46% 426.8
L-arginine catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 44% 91% 369.8 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 46% 426.8
L-citrulline catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 44% 91% 369.8 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 46% 426.8
putrescine catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 44% 91% 369.8 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 46% 426.8
L-arginine catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 40% 93% 352.1 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 46% 426.8
L-arginine catabolism puuC med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 40% 93% 352.1 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 46% 426.8
L-citrulline catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 40% 93% 352.1 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 46% 426.8
L-citrulline catabolism puuC med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 40% 93% 352.1 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 46% 426.8
putrescine catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 40% 93% 352.1 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 46% 426.8
putrescine catabolism puuC med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 40% 93% 352.1 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 46% 426.8
L-arginine catabolism kauB med gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 42% 95% 340.9 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 46% 426.8
4-hydroxybenzoate catabolism praB lo aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 40% 95% 325.1 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 46% 426.8
L-tryptophan catabolism nbaE lo aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 40% 95% 325.1 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 46% 426.8
L-tryptophan catabolism praB lo aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 40% 95% 325.1 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 46% 426.8
L-arginine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 39% 92% 313.9 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 46% 426.8
L-citrulline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 39% 92% 313.9 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 46% 426.8
L-lysine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 39% 92% 313.9 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 46% 426.8
L-proline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 39% 92% 313.9 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 46% 426.8
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 37% 95% 303.9 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 46% 426.8
L-arabinose catabolism xacF lo Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 37% 95% 287.7 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 46% 426.8
D-galacturonate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 37% 95% 287.7 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 46% 426.8
D-glucuronate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 37% 95% 287.7 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 46% 426.8
D-xylose catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 37% 95% 287.7 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 46% 426.8
L-isoleucine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 93% 241.9 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 46% 426.8
myo-inositol catabolism mmsA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 93% 241.9 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 46% 426.8
propionate catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 93% 241.9 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 46% 426.8
L-threonine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 93% 241.9 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 46% 426.8
L-valine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 93% 241.9 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 46% 426.8
L-lysine catabolism amaB lo L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale) 31% 99% 214.9 (Z)-2-((N-methylformamido)methylene)-5-hydroxybutyrolactone dehydrogenase; MFMB dehydrogenase; EC 1.2.1.- 46% 426.8

Sequence Analysis Tools

View WP_011604557.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MTTTVTMRIGAERRAGTTTFDSIDPYTGEAWATVAEASRADVDDAVAAARAAFDGGEWSK
LSGRERGRLMRRLAAVIEEHADELGLAETRDNGKLLREMGGQVRSLSAWYEYYAGLADKI
DGRVVDTGRPDYFGFVTREPIGVVGAVLPWNSPLLLLTFKIAPALAAGCTIVAKPSEQAP
VSILKFADLFEEAGFPPGVFNTVSGASREVGEWLVGHPGVDRVSFTGSEITGAAVAAAAA
KHLAPVTLELGGKSANIVFPDADLAAASNGLIAGIFAAAGQTCIAGSRALVHADVYEEVV
ARVAERAARIRLGDPKDPETEMGPICFPGQHEKIRRFVAQAKEQGADIVGGGGDGGLGGL
FFEPTIVANVTNDAMVCQEEIFGPVLSVLRFSSEEEAIAIANDSRYGLAAGIWTADIRRA
FRMTKALRVGTVWVNAYRTLNYAMPFGGIKSSGFGRENGTEGLHEYLQEKAVWIETTGAT
RDPFVLG

This GapMind analysis is from Apr 09 2024. 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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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