GapMind for catabolism of small carbon sources

 

Protein GFF2136 in Pseudomonas simiae WCS417

Annotation: PS417_10895 AMP-dependent synthetase

Length: 566 amino acids

Source: WCS417 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
propionate catabolism prpE med Acyl-coenzyme A synthetase ACSM3, mitochondrial; Acyl-CoA synthetase medium-chain family member 3; Butyrate--CoA ligase 3; Butyryl-coenzyme A synthetase 3; Middle-chain acyl-CoA synthetase 3; Propionate--CoA ligase; Protein SA homolog; EC 6.2.1.2; EC 6.2.1.17 (characterized) 39% 93% 398.7 medium-chain acyl-CoA ligase (EC 6.2.1.2) 39% 386.0
4-hydroxybenzoate catabolism acs med 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized) 41% 94% 379.8 Acyl-coenzyme A synthetase ACSM3, mitochondrial; Acyl-CoA synthetase medium-chain family member 3; Butyrate--CoA ligase 3; Butyryl-coenzyme A synthetase 3; Middle-chain acyl-CoA synthetase 3; Propionate--CoA ligase; Protein SA homolog; EC 6.2.1.2; EC 6.2.1.17 39% 398.7
L-lactate catabolism acs med 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized) 41% 94% 379.8 Acyl-coenzyme A synthetase ACSM3, mitochondrial; Acyl-CoA synthetase medium-chain family member 3; Butyrate--CoA ligase 3; Butyryl-coenzyme A synthetase 3; Middle-chain acyl-CoA synthetase 3; Propionate--CoA ligase; Protein SA homolog; EC 6.2.1.2; EC 6.2.1.17 39% 398.7
acetate catabolism acs med 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized) 41% 94% 379.8 Acyl-coenzyme A synthetase ACSM3, mitochondrial; Acyl-CoA synthetase medium-chain family member 3; Butyrate--CoA ligase 3; Butyryl-coenzyme A synthetase 3; Middle-chain acyl-CoA synthetase 3; Propionate--CoA ligase; Protein SA homolog; EC 6.2.1.2; EC 6.2.1.17 39% 398.7
2'-deoxyinosine catabolism acs med 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized) 41% 94% 379.8 Acyl-coenzyme A synthetase ACSM3, mitochondrial; Acyl-CoA synthetase medium-chain family member 3; Butyrate--CoA ligase 3; Butyryl-coenzyme A synthetase 3; Middle-chain acyl-CoA synthetase 3; Propionate--CoA ligase; Protein SA homolog; EC 6.2.1.2; EC 6.2.1.17 39% 398.7
2-deoxy-D-ribose catabolism acs med 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized) 41% 94% 379.8 Acyl-coenzyme A synthetase ACSM3, mitochondrial; Acyl-CoA synthetase medium-chain family member 3; Butyrate--CoA ligase 3; Butyryl-coenzyme A synthetase 3; Middle-chain acyl-CoA synthetase 3; Propionate--CoA ligase; Protein SA homolog; EC 6.2.1.2; EC 6.2.1.17 39% 398.7
ethanol catabolism acs med 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized) 41% 94% 379.8 Acyl-coenzyme A synthetase ACSM3, mitochondrial; Acyl-CoA synthetase medium-chain family member 3; Butyrate--CoA ligase 3; Butyryl-coenzyme A synthetase 3; Middle-chain acyl-CoA synthetase 3; Propionate--CoA ligase; Protein SA homolog; EC 6.2.1.2; EC 6.2.1.17 39% 398.7
L-threonine catabolism acs med 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized) 41% 94% 379.8 Acyl-coenzyme A synthetase ACSM3, mitochondrial; Acyl-CoA synthetase medium-chain family member 3; Butyrate--CoA ligase 3; Butyryl-coenzyme A synthetase 3; Middle-chain acyl-CoA synthetase 3; Propionate--CoA ligase; Protein SA homolog; EC 6.2.1.2; EC 6.2.1.17 39% 398.7
thymidine catabolism acs med 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized) 41% 94% 379.8 Acyl-coenzyme A synthetase ACSM3, mitochondrial; Acyl-CoA synthetase medium-chain family member 3; Butyrate--CoA ligase 3; Butyryl-coenzyme A synthetase 3; Middle-chain acyl-CoA synthetase 3; Propionate--CoA ligase; Protein SA homolog; EC 6.2.1.2; EC 6.2.1.17 39% 398.7
L-tryptophan catabolism acs med 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized) 41% 94% 379.8 Acyl-coenzyme A synthetase ACSM3, mitochondrial; Acyl-CoA synthetase medium-chain family member 3; Butyrate--CoA ligase 3; Butyryl-coenzyme A synthetase 3; Middle-chain acyl-CoA synthetase 3; Propionate--CoA ligase; Protein SA homolog; EC 6.2.1.2; EC 6.2.1.17 39% 398.7
4-hydroxybenzoate catabolism hcl lo Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized) 32% 92% 204.9 Acyl-coenzyme A synthetase ACSM3, mitochondrial; Acyl-CoA synthetase medium-chain family member 3; Butyrate--CoA ligase 3; Butyryl-coenzyme A synthetase 3; Middle-chain acyl-CoA synthetase 3; Propionate--CoA ligase; Protein SA homolog; EC 6.2.1.2; EC 6.2.1.17 39% 398.7

Sequence Analysis Tools

View GFF2136 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 and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MTQPFLAARDFLLAHRTDYATAVRDFRWPQLGEFNWALDYFDAMAEGNPADALWIVEEDG
SEQRYSFQQLAARSNQVANHLRALGVNRGDRVLLMLGNDVALWDTMLAAFKLGAVVIPAT
ALLNPDDLRDRIERGQVRHVVVGEAHVHKFAGLAQGCSRICVGSAPAGWVAHNAAFEYPE
QFEAQGRTLATDPMLLYFTSGTTSKPKMVLHSHQSYPVGHLSTMYWIGLQPGDLHLNISS
PGWAKHAWSCLFAPWNAGACIFIHNVARFSAPALLSALERYGVTSLCAPPTVWRMLIQED
LASYRPRLSLRELVGAGEPLNPEIIEQIQQAWGLPLRDGFGQSETTALVGNTPGQLLKPG
SMGRPLPGYQVALLDPDGIPGNEGEVALPLDVRPLGLMLCYEDSPEKTAEVMRDGYYRTG
DTAQIDADGYITFVGRADDVFKASDYRISPFELESALIEHPAVMEVAVVPSPDPLRLAVP
KAFLILAHDEPGSAALAQHILAFAREHLAPYKRVRRIEFVTELPKTISGKIRRVELRQME
VLRRQGDTRGEHEHFEEDFVRPTAES

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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, the preprint on GapMind for carbon sources, 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