GapMind for catabolism of small carbon sources

 

Protein GFF3382 in Phaeobacter inhibens BS107

Annotation: PGA1_c34350 acetyl-CoA acetyltransferase PhbA

Length: 391 amino acids

Source: Phaeo in FitnessBrowser

Candidate for 19 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism atoB hi Acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized) 60% 99% 464.2
L-arginine catabolism atoB hi Acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized) 60% 99% 464.2
L-citrulline catabolism atoB hi Acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized) 60% 99% 464.2
2-deoxy-D-ribonate catabolism atoB hi Acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized) 60% 99% 464.2
2-deoxy-D-ribose catabolism atoB hi Acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized) 60% 99% 464.2
L-leucine catabolism atoB hi Acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized) 60% 99% 464.2
L-lysine catabolism atoB hi Acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized) 60% 99% 464.2
phenylacetate catabolism atoB hi Acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized) 60% 99% 464.2
L-phenylalanine catabolism atoB hi Acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized) 60% 99% 464.2
L-proline catabolism atoB hi Acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized) 60% 99% 464.2
L-tyrosine catabolism atoB hi Acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized) 60% 99% 464.2
L-isoleucine catabolism fadA hi Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized) 59% 100% 459.1
L-isoleucine catabolism fadA hi acetyl-CoA C-acyltransferase (EC 2.3.1.16) (TIGR01930) 100% 439.4
4-hydroxybenzoate catabolism paaJ2 med subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized) 48% 100% 350.5 Acetyl-CoA C-acetyltransferase (EC 2.3.1.9) 60% 464.2
4-hydroxybenzoate catabolism pcaF med subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized) 48% 100% 350.5 Acetyl-CoA C-acetyltransferase (EC 2.3.1.9) 60% 464.2
phenylacetate catabolism paaJ2 med subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized) 48% 100% 350.5 Acetyl-CoA C-acetyltransferase (EC 2.3.1.9) 60% 464.2
L-phenylalanine catabolism paaJ2 med subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized) 48% 100% 350.5 Acetyl-CoA C-acetyltransferase (EC 2.3.1.9) 60% 464.2
L-tryptophan catabolism pcaF med subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized) 48% 100% 350.5 Acetyl-CoA C-acetyltransferase (EC 2.3.1.9) 60% 464.2
phenylacetate catabolism paaJ1 med 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale) 46% 100% 330.1 Acetyl-CoA C-acetyltransferase (EC 2.3.1.9) 60% 464.2
L-phenylalanine catabolism paaJ1 med 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale) 46% 100% 330.1 Acetyl-CoA C-acetyltransferase (EC 2.3.1.9) 60% 464.2

Sequence Analysis Tools

View GFF3382 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

MTDIVILDGARTAIGTFGGSLAGTTPIDLATVASKAAMERSGVAPEQIGNVVFGHVINTE
PRDMYLSRVAAMQAGIPNGTPAMNVNRLCGSGAQAIVSGIQSLMLGDAEFALTGGAENMS
RSPFIVPSARWGQKMGDARALDMMLGALNCPFGTGHMGVTAENVADEHDITRAQMDEFAL
ASQTRAAAAIEAGYFASQITPVEVKVKRDMVPFDVDEHPKASTLETLGGLKAVFKKDGRV
TAGNASGINDGAAAIVMATADAARQAGLKPKARILGYAHAGVRPEVMGIGPVPAVQNLLK
KTGLSASDFDVVESNEAFAAQALAVNKELGLDPAKVNPNGGAIALGHPVGATGAIITLKT
LYELERIGGSKGLITMCIGGGQGIALAIERL

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