GapMind for catabolism of small carbon sources

 

Protein BPHYT_RS22430 in Burkholderia phytofirmans PsJN

Annotation: BPHYT_RS22430 succinate-semialdehyde dehydrogenase

Length: 486 amino acids

Source: BFirm in FitnessBrowser

Candidate for 21 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) 70% 100% 693.7 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 68% 683.7
L-citrulline catabolism davD hi Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 70% 100% 693.7 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 68% 683.7
L-lysine catabolism davD hi Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 70% 100% 693.7 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 68% 683.7
L-proline catabolism davD hi Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 70% 100% 693.7 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 68% 683.7
L-arginine catabolism gabD med NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 68% 100% 677.2 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 68% 683.7
L-citrulline catabolism gabD med NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 68% 100% 677.2 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 68% 683.7
putrescine catabolism gabD med NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 68% 100% 677.2 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 68% 683.7
4-hydroxybenzoate catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 56% 92% 551.6 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 70% 693.7
2'-deoxyinosine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 56% 92% 551.6 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 70% 693.7
2-deoxy-D-ribose catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 56% 92% 551.6 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 70% 693.7
ethanol catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 56% 92% 551.6 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 70% 693.7
L-threonine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 56% 92% 551.6 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 70% 693.7
thymidine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 56% 92% 551.6 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 70% 693.7
L-tryptophan catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 56% 92% 551.6 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 70% 693.7
L-arabinose catabolism xacF med 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) 42% 100% 370.5 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 70% 693.7
D-galacturonate catabolism dopDH med 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) 42% 100% 370.5 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 70% 693.7
D-glucuronate catabolism dopDH med 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) 42% 100% 370.5 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 70% 693.7
D-xylose catabolism dopDH med 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) 42% 100% 370.5 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 70% 693.7
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 37% 96% 322 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 70% 693.7
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 37% 96% 322 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 70% 693.7
L-lysine catabolism amaB lo Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale) 33% 87% 221.9 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 70% 693.7

Sequence Analysis Tools

View BPHYT_RS22430 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

MTTLSLKDPSLLKSHAYIAGEWQGADDGTTFEVKNPATGETIATVPRMGTAETRRAIDTA
NAAWPAWRATTAKQRAVILRKWHDLMMENADDLAKILTTEQGKPLAEAKGEIQYAASFLE
WFAEEGKRVNGDTIPTPASDKRIVVTKEPIGVCAAITPWNFPAAMITRKVGPALAAGCPI
IVKPAEATPLSALALAVLAERAGVPRGVFNVVTGEPKAIGAEMTGNPIVRKLSFTGSTPV
GRLLMAQCAPTVKKVSLELGGNAPFIVFDDADLDAAVAGAIASKYRNSGQTCVCTNRFYV
HDKVYDAFAEKLRVAVEQLKVGRGTEDGVTQGPLINDAAVLKVESHIEDALAKGARIVTG
GKRHALGHGFFEPTVLADVTPAMKVARDETFGPLAPLFRFSSDEEVIRLANDTEFGLASY
FYSRDIGRVWRVAEALEYGMVGINTGLISNEVAPFGGVKQSGLGREGSHYGIDDYVVIKY
LCVGGI

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