GapMind for catabolism of small carbon sources

 

Protein GFF4164 in Pseudomonas stutzeri RCH2

Annotation: FitnessBrowser__psRCH2:GFF4164

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

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

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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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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