GapMind for catabolism of small carbon sources

 

Protein N515DRAFT_1736 in Dyella japonica UNC79MFTsu3.2

Annotation: N515DRAFT_1736 3-oxoacid CoA-transferase

Length: 451 amino acids

Source: Dyella79 in FitnessBrowser

Candidate for 16 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
2-deoxy-D-ribonate catabolism atoA hi acetyl-CoA:acetoacetate CoA transferase, A subunit (EC 2.8.3.8) (characterized) 67% 99% 321.2
2-deoxy-D-ribose catabolism atoA hi acetyl-CoA:acetoacetate CoA transferase, A subunit (EC 2.8.3.8) (characterized) 67% 99% 321.2
L-leucine catabolism atoA hi acetyl-CoA:acetoacetate CoA transferase, A subunit (EC 2.8.3.8) (characterized) 67% 99% 321.2
L-phenylalanine catabolism atoA hi acetyl-CoA:acetoacetate CoA transferase, A subunit (EC 2.8.3.8) (characterized) 67% 99% 321.2
L-tyrosine catabolism atoA hi acetyl-CoA:acetoacetate CoA transferase, A subunit (EC 2.8.3.8) (characterized) 67% 99% 321.2
2-deoxy-D-ribonate catabolism atoD hi acetyl-CoA:acetoacetate CoA transferase, B subunit (EC 2.8.3.8) (characterized) 73% 96% 290.4
2-deoxy-D-ribose catabolism atoD hi acetyl-CoA:acetoacetate CoA transferase, B subunit (EC 2.8.3.8) (characterized) 73% 96% 290.4
L-leucine catabolism atoD hi acetyl-CoA:acetoacetate CoA transferase, B subunit (EC 2.8.3.8) (characterized) 73% 96% 290.4
L-phenylalanine catabolism atoD hi acetyl-CoA:acetoacetate CoA transferase, B subunit (EC 2.8.3.8) (characterized) 73% 96% 290.4
L-tyrosine catabolism atoD hi acetyl-CoA:acetoacetate CoA transferase, B subunit (EC 2.8.3.8) (characterized) 73% 96% 290.4
4-hydroxybenzoate catabolism pcaI hi 3-oxoadipate CoA-transferase subunit A; EC 2.8.3.6 (characterized) 46% 94% 205.3
L-tryptophan catabolism pcaI hi 3-oxoadipate CoA-transferase subunit A; EC 2.8.3.6 (characterized) 46% 94% 205.3
4-hydroxybenzoate catabolism pcaJ hi 3-oxoadipate CoA-transferase (subunit 1/2) (EC 2.8.3.6) (characterized) 49% 94% 190.3
L-tryptophan catabolism pcaJ hi 3-oxoadipate CoA-transferase (subunit 1/2) (EC 2.8.3.6) (characterized) 49% 94% 190.3
L-lysine catabolism ctfB med Butyrate--acetoacetate CoA-transferase subunit B; Short=Coat B; EC 2.8.3.9 (characterized, see rationale) 46% 95% 208.4 3-oxoacid CoA-transferase (EC 2.8.3.5) 56% 520.8
L-lysine catabolism ctfA lo Butyrate--acetoacetate CoA-transferase subunit A; Short=Coat A; EC 2.8.3.9 (characterized, see rationale) 40% 93% 160.6 3-oxoacid CoA-transferase (EC 2.8.3.5) 56% 520.8

Sequence Analysis Tools

View N515DRAFT_1736 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

MDKVYASAAQALDGLLFDDMTIAAGGFGLCGIPENLIAALLAAGTKGLTIVGNNAGVDDF
GMGPLLKTRQVKRVYASYVGENKEFERQVLAGELELHLVPQGTLAEKLRAGGAGIPGFYT
RTAFGTKLAEGKETKVFDGKEYVLEEAIHADVSIVKAWKGDRLGNLVFRKTARNFNPMIA
TCGKLCVAEVEELVEVGTLEPDQVHVPGIYVDRIIQGPSYEKRIEFRTVAGANTGKESPL
RTAMAQRAAKELRDGFYVNLGIGIPTLVANFIPAGIDVTLQSENGLLGIGPFPDDAHVDP
DLINAGKQTITTLPGSSFFSSAESFAMIRGGHIDLSILGGLEVSCTGDLANWMVPGKMVK
GPGGAMDLVSGVKRVVVLMEHTAKDGSPKIKNQCDLPLTGQQVVDLIITDLCVFEVEKGK
GLTLIELQEGVTVEEVKAKTGCDFAVASTLG

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