GapMind for catabolism of small carbon sources

 

Protein BPHYT_RS34305 in Burkholderia phytofirmans PsJN

Annotation: BPHYT_RS34305 succinate-semialdehyde dehydrogenase

Length: 479 amino acids

Source: BFirm in FitnessBrowser

Candidate for 11 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism davD hi Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 63% 99% 629
L-citrulline catabolism davD hi Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 63% 99% 629
L-lysine catabolism davD hi Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 63% 99% 629
L-proline catabolism davD hi Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 63% 99% 629
L-arginine catabolism gabD hi succinate-semialdehyde dehydrogenase (NAD+) (EC 1.2.1.24) (characterized) 63% 99% 613.2
L-citrulline catabolism gabD hi succinate-semialdehyde dehydrogenase (NAD+) (EC 1.2.1.24) (characterized) 63% 99% 613.2
putrescine catabolism gabD hi succinate-semialdehyde dehydrogenase (NAD+) (EC 1.2.1.24) (characterized) 63% 99% 613.2
L-phenylalanine catabolism pad-dh med phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized) 41% 98% 323.9 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 63% 629.0
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 39% 97% 323.9 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 63% 629.0
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 39% 97% 323.9 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 63% 629.0
L-lysine catabolism amaB lo Alpha-aminoadipic semialdehyde dehydrogenase; Alpha-AASA dehydrogenase; Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Betaine aldehyde dehydrogenase; Delta1-piperideine-6-carboxylate dehydrogenase; P6c dehydrogenase; EC 1.2.1.31; EC 1.2.1.3; EC 1.2.1.8 (characterized) 30% 86% 223.4 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 63% 629.0

Sequence Analysis Tools

View BPHYT_RS34305 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

MNEFLRTGHFIGGEWYEGADTYAVLNPATGEVVAHVAKGGAAETAQAIAAAERAFPAWRA
LTAKERSARVKRWGELMLENRDALAELLTLEQGKPLAEARGEVGYAASFFEWFAEEAKRA
YGDVIPSPNPNAKIIVTREPVGVVAAITPWNFPLAMITRKAGPALAAGCTMVLKPSEETP
LSAFALAVLAAKAGIPPGVFNIVSGDAVAIGGALTESDVVRKLSFTGSTRVGKLLAKQSA
DTLKKLSLELGGNAPFIVFDDADLDAAVQGAMASKFRNTGQTCVCVNRFYVQDGIYDAFT
SALTQAVRKMRVGNALQGEVEQGPLINQAALKKVETHVADALQKGAKILTGGKPHTLGGT
FYEPTVLADADNSMLIAGEETFGPVAACFRFKTEAEAIEAANDTPFGLSAYFYTRDLARA
WRVGEALESGMVGINEGIVSTEVAPFGGVKQSGLGREGSKYGLDEYTELKYMMMGGLGR

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