GapMind for catabolism of small carbon sources

 

Protein GFF4164 in Pseudomonas stutzeri RCH2

Annotation: Psest_4237 succinate-semialdehyde dehydrogenase

Length: 482 amino acids

Source: psRCH2 in FitnessBrowser

Candidate for 29 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism gabD hi NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 84% 100% 820.1
L-citrulline catabolism gabD hi NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 84% 100% 820.1
putrescine catabolism gabD hi NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 84% 100% 820.1
L-arginine catabolism davD hi Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 82% 100% 808.1
L-citrulline catabolism davD hi Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 82% 100% 808.1
L-lysine catabolism davD hi Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 82% 100% 808.1
L-proline catabolism davD hi Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 82% 100% 808.1
4-hydroxybenzoate catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 55% 91% 542 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 84% 820.1
2'-deoxyinosine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 55% 91% 542 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 84% 820.1
2-deoxy-D-ribose catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 55% 91% 542 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 84% 820.1
ethanol catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 55% 91% 542 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 84% 820.1
L-threonine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 55% 91% 542 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 84% 820.1
thymidine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 55% 91% 542 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 84% 820.1
L-tryptophan catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 55% 91% 542 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 84% 820.1
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) 43% 97% 376.3 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 84% 820.1
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) 43% 97% 376.3 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 84% 820.1
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) 43% 97% 376.3 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 84% 820.1
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) 43% 97% 376.3 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 84% 820.1
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 40% 98% 341.7 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 84% 820.1
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 40% 98% 341.7 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 84% 820.1
L-isoleucine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 96% 254.2 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 84% 820.1
myo-inositol catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 96% 254.2 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 84% 820.1
propionate catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 96% 254.2 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 84% 820.1
L-threonine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 96% 254.2 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 84% 820.1
L-valine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 96% 254.2 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 84% 820.1
L-valine catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 96% 254.2 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 84% 820.1
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% 88% 234.2 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 84% 820.1
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 34% 94% 220.7 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 84% 820.1
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 34% 94% 220.7 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 84% 820.1

Sequence Analysis Tools

View GFF4164 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

MQLKDTALFRQQAYIDGAWLDADSGQTISVNNPATGETLGTVPKMGAAETRRAIDAAERA
LPAWRDLTAKERSQKLRRWFELLMENQDDLGRLMTLEQGKPLAEAKGEIAYAASFIEWFA
EEAKRIYGDTIPGHQKDKRIIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVIK
PASQTPFSALAMVELAERAGIPKGVLSVVTGSAGDIGNELTANPKVRKISFTGSTEVGAK
LMEQCAPGIKKVSLELGGNAPFIVFDDADLDEAVKGAVQSKYRNAGQTCVCVNRIYVQDG
VYDTFAEKFQAAVAKLRVGNGLEEGTDLGPLIDDRAAAKVREHIEDAVAQGARLVAGGQA
HALGGSYFEPTVLVNVPDSAKVAKEETFGPLAPLFRFKDEADAIAKANDTEFGLASYFYA
RDLGRVFRVAEALEYGMVGINTGLISTEVAPFGGVKSSGLGREGSKYGIEDYLEIKYLCM
GI

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