GapMind for catabolism of small carbon sources

 

Protein Pf1N1B4_3234 in Pseudomonas fluorescens FW300-N1B4

Annotation: FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3234

Length: 400 amino acids

Source: pseudo1_N1B4 in FitnessBrowser

Candidate for 22 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism paaJ2 hi subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized) 89% 100% 704.1 acetyl-CoA C-acetyltransferase (EC 2.3.1.16) 47% 328.9
4-hydroxybenzoate catabolism paaJ2 med pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174) (TIGR02430) 100% 737 acetyl-CoA C-acetyltransferase (EC 2.3.1.16) 47% 328.9
4-hydroxybenzoate catabolism pcaF hi subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized) 89% 100% 704.1 Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) 66% 523.5
4-hydroxybenzoate catabolism pcaF med pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174) (TIGR02430) 100% 737 Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) 66% 523.5
phenylacetate catabolism paaJ2 hi subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized) 89% 100% 704.1 acetyl-CoA C-acetyltransferase (EC 2.3.1.16) 47% 328.9
phenylacetate catabolism paaJ2 med pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174) (TIGR02430) 100% 737 acetyl-CoA C-acetyltransferase (EC 2.3.1.16) 47% 328.9
L-phenylalanine catabolism paaJ2 hi subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized) 89% 100% 704.1 acetyl-CoA C-acetyltransferase (EC 2.3.1.16) 47% 328.9
L-phenylalanine catabolism paaJ2 med pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174) (TIGR02430) 100% 737 acetyl-CoA C-acetyltransferase (EC 2.3.1.16) 47% 328.9
L-tryptophan catabolism pcaF hi subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized) 89% 100% 704.1 Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) 66% 523.5
L-tryptophan catabolism pcaF med pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174) (TIGR02430) 100% 737 Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) 66% 523.5
L-isoleucine catabolism fadA hi subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized) 89% 100% 704.1 Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 85% 673.3
L-isoleucine catabolism fadA med acetyl-CoA C-acyltransferase (EC 2.3.1.16) (TIGR01930) 100% 443.1 Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 85% 673.3
phenylacetate catabolism paaJ1 hi 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale) 71% 100% 565.1 acetyl-CoA C-acetyltransferase (EC 2.3.1.16) 47% 328.9
L-phenylalanine catabolism paaJ1 hi 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale) 71% 100% 565.1 acetyl-CoA C-acetyltransferase (EC 2.3.1.16) 47% 328.9
4-hydroxybenzoate catabolism atoB med acetyl-CoA C-acetyltransferase [EC: 2.3.1.9] (characterized) 47% 100% 328.2 Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 85% 673.3
L-arginine catabolism atoB med acetyl-CoA C-acetyltransferase [EC: 2.3.1.9] (characterized) 47% 100% 328.2 Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 85% 673.3
L-citrulline catabolism atoB med acetyl-CoA C-acetyltransferase [EC: 2.3.1.9] (characterized) 47% 100% 328.2 Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 85% 673.3
2-deoxy-D-ribonate catabolism atoB med acetyl-CoA C-acetyltransferase [EC: 2.3.1.9] (characterized) 47% 100% 328.2 Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 85% 673.3
2-deoxy-D-ribose catabolism atoB med acetyl-CoA C-acetyltransferase [EC: 2.3.1.9] (characterized) 47% 100% 328.2 Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 85% 673.3
L-leucine catabolism atoB med acetyl-CoA C-acetyltransferase [EC: 2.3.1.9] (characterized) 47% 100% 328.2 Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 85% 673.3
L-lysine catabolism atoB med acetyl-CoA C-acetyltransferase [EC: 2.3.1.9] (characterized) 47% 100% 328.2 Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 85% 673.3
phenylacetate catabolism atoB med acetyl-CoA C-acetyltransferase [EC: 2.3.1.9] (characterized) 47% 100% 328.2 Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 85% 673.3
L-phenylalanine catabolism atoB med acetyl-CoA C-acetyltransferase [EC: 2.3.1.9] (characterized) 47% 100% 328.2 Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 85% 673.3
L-proline catabolism atoB med acetyl-CoA C-acetyltransferase [EC: 2.3.1.9] (characterized) 47% 100% 328.2 Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 85% 673.3
L-tyrosine catabolism atoB med acetyl-CoA C-acetyltransferase [EC: 2.3.1.9] (characterized) 47% 100% 328.2 Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 85% 673.3
4-hydroxybenzoate catabolism pimB med 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized) 41% 100% 249.6 subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) 89% 704.1
phenylacetate catabolism pimB med 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized) 41% 100% 249.6 subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) 89% 704.1
L-phenylalanine catabolism pimB med 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized) 41% 100% 249.6 subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) 89% 704.1

Sequence Analysis Tools

View Pf1N1B4_3234 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

MRDVYICDAIRTPIGRFGGGLSAVRADDLAAVPIKALMARNPSVDWSAVDEVFLGCANQA
GEDNRNVARMALLLAGLPETIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM
SRAPFVMGKADAAFSRNMKLEDTTIGWRFINPLMKAQYGVDAMPQTADNVADDYRISRAD
QDAFALRSQQRTAAAQAAGFFAEEIVEVRIAHKKGESVVTQDEHPRADTTLETLAKLKPV
NGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTARAKVLGMSSAGVAPRVMGIGPVP
AVRKLTERLGLAVSDFDVIELNEAFASQGLAVLRELGLADDSAQVNPNGGAIALGHPLGM
SGARLVLTALHQLEKTGGKKGLATMCVGVGQGLALAIERV

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