GapMind for catabolism of small carbon sources

 

Protein CA265_RS19585 in Pedobacter sp. GW460-11-11-14-LB5

Annotation: CA265_RS19585 pyruvate dehydrogenase

Length: 562 amino acids

Source: Pedo557 in FitnessBrowser

Candidate for 3 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-isoleucine catabolism bkdC lo Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized) 33% 100% 208 Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial; 70 kDa mitochondrial autoantigen of primary biliary cirrhosis; PBC; Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex; Pyruvate dehydrogenase complex component E2; PDC-E2; PDCE2; EC 2.3.1.12 38% 350.9
L-leucine catabolism bkdC lo Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized) 33% 100% 208 Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial; 70 kDa mitochondrial autoantigen of primary biliary cirrhosis; PBC; Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex; Pyruvate dehydrogenase complex component E2; PDC-E2; PDCE2; EC 2.3.1.12 38% 350.9
L-valine catabolism bkdC lo Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized) 33% 100% 208 Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial; 70 kDa mitochondrial autoantigen of primary biliary cirrhosis; PBC; Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex; Pyruvate dehydrogenase complex component E2; PDC-E2; PDCE2; EC 2.3.1.12 38% 350.9

Sequence Analysis Tools

View CA265_RS19585 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

MADVIKMPKMSDTMTEGVLAKWHKKVGDKVKSGDVLAEVETDKATMDMESYWDGTLLYVG
VEEGTAVPVDAIMAVIGKEGEDYKAALEAEQSGSQESGSPKSERKDEAPKAEEKKEEAPA
QGGGLSEEELAAKGVTVIRMPLLSDTMTEGVIAEWHKKVGDKVKDDDVLADVETDKATME
VMGYATGTLLHIGVEKGAAAKVNGIIAIVGPEGTDVSGILAGGSAPAPKAESAEAPKAEK
SATVAEIETPRTSSCGTTTDNGDSRVKASPLAKKIAKDKGIDLAQVAGSAEGGRIIKKDI
ENFKPSAAPAKAESASAPAAEKAAAPAPVIPQYVGEVKFTEAPVSQMRKVIAKRLAESLF
TAPHFYLTISIDMDNAMAARTAINAVAPVKVSFNDIVIKAVAVALKKHPAVNSSWGGDKI
RFNEHTNIGVAMAVEDGLLVPVVRFADGKSLSHISAEVKDFGGKAKAKKLQPADWEGSTF
TVSNLGMFGIDEFTSIINSPDGAILSVGAIQQVPVVKNGAVVPGNVMKLTLGCDHRVVDG
ATGAQFLQTLKGLLEEPIRLLA

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