GapMind for catabolism of small carbon sources

 

Protein PfGW456L13_1910 in Pseudomonas fluorescens GW456-L13

Annotation: FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1910

Length: 562 amino acids

Source: pseudo13_GW456_L13 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% 89% 259.2 long-chain-fatty-acid-CoA ligase (EC 6.2.1.3) 78% 923.3
2-deoxy-D-ribose catabolism aacS lo Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized) 32% 89% 259.2 long-chain-fatty-acid-CoA ligase (EC 6.2.1.3) 78% 923.3
L-leucine catabolism aacS lo Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized) 32% 89% 259.2 long-chain-fatty-acid-CoA ligase (EC 6.2.1.3) 78% 923.3
L-phenylalanine catabolism aacS lo Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized) 32% 89% 259.2 long-chain-fatty-acid-CoA ligase (EC 6.2.1.3) 78% 923.3
L-tyrosine catabolism aacS lo Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized) 32% 89% 259.2 long-chain-fatty-acid-CoA ligase (EC 6.2.1.3) 78% 923.3
phenylacetate catabolism paaK lo phenylacetate-CoA ligase (EC 6.2.1.30) (characterized) 31% 96% 216.9 long-chain-fatty-acid-CoA ligase (EC 6.2.1.3) 78% 923.3
L-phenylalanine catabolism paaK lo phenylacetate-CoA ligase (EC 6.2.1.30) (characterized) 31% 96% 216.9 long-chain-fatty-acid-CoA ligase (EC 6.2.1.3) 78% 923.3
4-hydroxybenzoate catabolism acs lo isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized) 30% 64% 147.5 long-chain-fatty-acid-CoA ligase (EC 6.2.1.3) 78% 923.3
L-lactate catabolism acs lo isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized) 30% 64% 147.5 long-chain-fatty-acid-CoA ligase (EC 6.2.1.3) 78% 923.3
acetate catabolism acs lo isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized) 30% 64% 147.5 long-chain-fatty-acid-CoA ligase (EC 6.2.1.3) 78% 923.3
2'-deoxyinosine catabolism acs lo isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized) 30% 64% 147.5 long-chain-fatty-acid-CoA ligase (EC 6.2.1.3) 78% 923.3
2-deoxy-D-ribose catabolism acs lo isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized) 30% 64% 147.5 long-chain-fatty-acid-CoA ligase (EC 6.2.1.3) 78% 923.3
ethanol catabolism acs lo isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized) 30% 64% 147.5 long-chain-fatty-acid-CoA ligase (EC 6.2.1.3) 78% 923.3
L-threonine catabolism acs lo isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized) 30% 64% 147.5 long-chain-fatty-acid-CoA ligase (EC 6.2.1.3) 78% 923.3
thymidine catabolism acs lo isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized) 30% 64% 147.5 long-chain-fatty-acid-CoA ligase (EC 6.2.1.3) 78% 923.3
L-tryptophan catabolism acs lo isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized) 30% 64% 147.5 long-chain-fatty-acid-CoA ligase (EC 6.2.1.3) 78% 923.3

Sequence Analysis Tools

View PfGW456L13_1910 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

Fitness BLAST: loading...

Sequence

MQPDFWNDKRPAGVPLDIDLGAYKSVIEVFERSCKKFADRPAFSNMGVTLTYAELERQSA
AFAGYLQAHTDLVAGDRIAVQMPNVLHYPIAVFGALRAGLIVVNTNPLYTAREMRHQFKD
SGARALVYLNMFGQKVQEVLPDTDIQYLIEAKMGDLMPAAKGWLVNTVVSKVKKMVPDYS
LPQAVSFKSALRMGRGLGIKPLKVGLDDIAVLQYTGGTTGLAKGAMLTHGNLVANMQQAR
ACLGQFGSDGQPLLREGQEVMIAPLPLYHIYAFTANCMCMMVTGNHNVLITNPRDIAGFI
KELKNWRFSALLGLNTLFVALMDHPDFKTLDFSSLKLTNSGGTALVKATAERWEQLTGCR
ITEGYGLTETSPVACTNPYGDQSRIGTVGLPVPGTTLKVINDDGVEQPLGERGELCIKGP
QIMKGYWQKPDATAEVLDAEGWFKSGDIAVIDPDGFVRIVDRKKDMIIVSGFNVYPNEIE
DVVMAHPNVANCAVIGVPDERSGEAVKLFVVAREAGVSLEELKAYCKENFTAYKVPKHIV
LRESLPMTPVGKILRRELRDIA

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 (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