GapMind for catabolism of small carbon sources

 

Protein N515DRAFT_0481 in Dyella japonica UNC79MFTsu3.2

Annotation: N515DRAFT_0481 2-oxoisovalerate dehydrogenase E1 component

Length: 755 amino acids

Source: Dyella79 in FitnessBrowser

Candidate for 4 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-isoleucine catabolism bkdB med 3-methyl-2-oxobutanoate dehydrogenase subunit beta; Branched-chain alpha-ketoacid dehydrogenase E1 component subunit beta; BCKADH E1-beta; EC 1.2.4.4 (characterized) 35% 90% 162.2
L-leucine catabolism bkdB med 3-methyl-2-oxobutanoate dehydrogenase subunit beta; Branched-chain alpha-ketoacid dehydrogenase E1 component subunit beta; BCKADH E1-beta; EC 1.2.4.4 (characterized) 35% 90% 162.2
L-valine catabolism bkdB med 3-methyl-2-oxobutanoate dehydrogenase subunit beta; Branched-chain alpha-ketoacid dehydrogenase E1 component subunit beta; BCKADH E1-beta; EC 1.2.4.4 (characterized) 35% 90% 162.2
L-phenylalanine catabolism PPDCbeta lo Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale) 33% 96% 142.1 3-methyl-2-oxobutanoate dehydrogenase subunit beta; Branched-chain alpha-ketoacid dehydrogenase E1 component subunit beta; BCKADH E1-beta; EC 1.2.4.4 35% 162.2

Sequence Analysis Tools

View N515DRAFT_0481 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

MTALPFSLSARHKGFNRAEIVDQNFIEFVQLWQGHARAAPRDGEAVLPGSALDAQGFRDL
LESQLISRHLDLMARVLRVQNKVFYTIGSSGHEGNAMVARLTRHTDPAFLHYRSGGFMAE
RFRKLPGMDPVMDSALSFAASMEDPASGGRHKVWGSKPLWVLPQTSTIASHLPKAFGTAV
AIEQARRIGHPLPVPQDSIAICSFGDASSNHATAQTAFNAAAWTAYQKLPAPVLFVCEDN
GIGISVKTPSGWIANNFRQRPDLDYFHADGLDLAEGYGQVREAVEHCRRTRRPTFLHLRT
TRVMGHAGTDFEIEWRSVDELFALEATDPLLRSAEIALASGLYTRESLLALYEATRKQCF
AAAEEADRRPRLGTLAEVMKPLAPYTPAAVKAEAERADYAARRAEVFGGEDKLPEKQAPR
HLAIQIGQALHEVMAKYPESLLFGEDVALKGGVYTVTKGLFKTFKGNRVFNTLLDETVIL
GLAQGYANMGMLPMPEIQYLAYFHNACDQIRGEACSLQFFSNDQYRNPLVMRVAALGYQK
GFGGHFHNDNSIAALRDIPGLVVGCPSRGDDAAAMLRTLMALAKVDGRVCAFLEPIALYM
TKDLYEAGDGQWQFAYPAPGEALPLGEGRVYEQDADDLVVFTFGNGVPMALRAAREIEKK
HGWRTRVVDLRWLAPLNDKFIAGQARNARRILVLDEGRRSAGVGEGIITAIVEGGCGATP
LQRVVGADTYTPLAGAALLVLPGEAEIVAAAERML

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