Finding step fadA for L-isoleucine catabolism in Saccharomonospora cyanea NA-134

GapMind for catabolism of small carbon sources

Finding step fadA for L-isoleucine catabolism in Saccharomonospora cyanea NA-134

5 candidates for fadA: 2-methylacetoacetyl-CoA thiolase

Score	Gene	Description	Similar to	Id.	Cov.	Bits	Other hit	Other id.	Other bits
hi	SACCYDRAFT_RS20715	acetyl-CoA C-acyltransferase	acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)	45%	100%	303.5	Beta-ketoadipyl CoA thiolase (EC 2.3.1.-)	41%	279.3
med	SACCYDRAFT_RS20715	acetyl-CoA C-acyltransferase	acetyl-CoA C-acyltransferase (EC 2.3.1.16) (TIGR01930)		100%	462.3	Beta-ketoadipyl CoA thiolase (EC 2.3.1.-)	41%	279.3
hi	SACCYDRAFT_RS18430	acetyl-CoA C-acetyltransferase	Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)	55%	99%	390.2
hi	SACCYDRAFT_RS18430	acetyl-CoA C-acetyltransferase	acetyl-CoA C-acyltransferase (EC 2.3.1.16) (TIGR01930)		100%	453.2
hi	SACCYDRAFT_RS13890	acetyl-CoA C-acyltransferase	Steroid 3-ketoacyl-CoA thiolase; Acetyl-CoA acetyltransferase FadA5; Beta-ketoacyl-CoA thiolase; EC 2.3.1.16 (characterized)	50%	99%	366.7	3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223	42%	248.8
med	SACCYDRAFT_RS19680	acetyl-CoA acetyltransferase	3-ketoacyl-CoA thiolase FadA; Acetyl-CoA acyltransferase; Beta-ketothiolase; Fatty acid oxidation complex subunit beta; EC 2.3.1.16 (characterized)	42%	99%	287.7	Putative acyltransferase Rv0859; EC 2.3.1.-	79%	640.6
med	SACCYDRAFT_RS19680	acetyl-CoA acetyltransferase	acetyl-CoA C-acyltransferase (EC 2.3.1.16) (TIGR01930)		100%	446.3	Putative acyltransferase Rv0859; EC 2.3.1.-	79%	640.6
med	SACCYDRAFT_RS07515	acetyl-CoA C-acyltransferase	subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)	51%	100%	364.4	3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223	52%	376.7
med	SACCYDRAFT_RS07515	acetyl-CoA C-acyltransferase	acetyl-CoA C-acyltransferase (EC 2.3.1.16) (TIGR01930)		100%	438.3	3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223	52%	376.7

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

GapMind searches the predicted proteins for candidates by using ublast (a fast alternative to protein BLAST) to find similarities to characterized proteins or by using HMMer to find similarities to enzyme models (usually from TIGRFams). For alignments to characterized proteins (from ublast), scores of 44 bits correspond to an expectation value (E) of about 0.001.

Definition of step fadA

Curated proteins or TIGRFams with EC 2.3.1.16 (search)
Ignore hits to items matching 2.3.1.9 when looking for 'other' hits
Comment: 2.3.1.9 is a similar reaction, acetoacetyl-CoA thiolase

Or cluster all characterized fadA proteins

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources