GapMind for catabolism of small carbon sources

 

Protein Pf6N2E2_1879 in Pseudomonas fluorescens FW300-N2E2

Annotation: Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)

Length: 511 amino acids

Source: pseudo6_N2E2 in FitnessBrowser

Candidate for 16 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
2-deoxy-D-ribonate catabolism aacS lo Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized) 32% 94% 253.1 acyl-CoA ligase 35% 281.6
2-deoxy-D-ribose catabolism aacS lo Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized) 32% 94% 253.1 acyl-CoA ligase 35% 281.6
L-leucine catabolism aacS lo Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized) 32% 94% 253.1 acyl-CoA ligase 35% 281.6
L-phenylalanine catabolism aacS lo Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized) 32% 94% 253.1 acyl-CoA ligase 35% 281.6
L-tyrosine catabolism aacS lo Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized) 32% 94% 253.1 acyl-CoA ligase 35% 281.6
phenylacetate catabolism paaK lo medium-chain acyl-CoA ligase (EC 6.2.1.2); phenylacetate-CoA ligase (EC 6.2.1.30) (characterized) 33% 62% 166.8 acyl-CoA ligase 35% 281.6
L-phenylalanine catabolism paaK lo medium-chain acyl-CoA ligase (EC 6.2.1.2); phenylacetate-CoA ligase (EC 6.2.1.30) (characterized) 33% 62% 166.8 acyl-CoA ligase 35% 281.6
4-hydroxybenzoate catabolism acs lo isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized) 31% 64% 151.4 acyl-CoA ligase 35% 281.6
L-lactate catabolism acs lo isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized) 31% 64% 151.4 acyl-CoA ligase 35% 281.6
acetate catabolism acs lo isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized) 31% 64% 151.4 acyl-CoA ligase 35% 281.6
2'-deoxyinosine catabolism acs lo isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized) 31% 64% 151.4 acyl-CoA ligase 35% 281.6
2-deoxy-D-ribose catabolism acs lo isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized) 31% 64% 151.4 acyl-CoA ligase 35% 281.6
ethanol catabolism acs lo isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized) 31% 64% 151.4 acyl-CoA ligase 35% 281.6
L-threonine catabolism acs lo isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized) 31% 64% 151.4 acyl-CoA ligase 35% 281.6
thymidine catabolism acs lo isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized) 31% 64% 151.4 acyl-CoA ligase 35% 281.6
L-tryptophan catabolism acs lo isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized) 31% 64% 151.4 acyl-CoA ligase 35% 281.6

Sequence Analysis Tools

View Pf6N2E2_1879 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

MEHSIGNWVGRSAARFGNKPAIIFEGKYWSFLDIDVQSSRLAASLESMGVKREDVVSIYS
PNSPEWIITYYAILKIGAIVNPLNTMLTAREAAFAIKNCGAVAVFSTSDKLLALQEHIGP
TEVISLISFDGITVAGMRHFNLLVDANVAVREYPVTGIQKDDISTIGYTSGTTGQPKGAV
LSHRCILTNVSMTATMHLRTASDIAVSALPLSHVYGNVVMNSAIAYGMTLVLHKTFDAEA
ILSSIQIYGATLLEGVPTMYIYLLNCPNLGAYDVSSLTRCTVGGQMMPYTAMENVERALG
CRLLELWGMTELGGLGTTHSLYGERRLGSIGVALPHLEARIAQLELDGDALPLGEIGELQ
IRGPVVMKHYLGRPDATAETKTDEGWLRTGDLARMDSEGFIYIVDRLKDMFITAGFNIYP
AELERVIAEHPSVAMVAVGSVLDEIKGELAKAYIVPKTGYEIDIQQIERHCRDRLAAYKV
PRLFQIVEDLPKTSSGKVMRRMLRQIFESKL

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