Finding step potA for putrescine catabolism in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Finding step potA for putrescine catabolism in Burkholderia phytofirmans PsJN

5 candidates for potA: putrescine ABC transporter, ATPase component (PotA/PotG)

Score	Gene	Description	Similar to	Id.	Cov.	Bits	Other hit	Other id.	Other bits
hi	BPHYT_RS11445	putrescine/spermidine ABC transporter ATP-binding protein	PotG aka B0855, component of Putrescine porter (characterized)	55%	98%	408.3	Maltose-transporting ATPase (EC 3.6.3.19)	42%	261.9
hi	BPHYT_RS23145	putrescine/spermidine ABC transporter ATP-binding protein	PotG aka B0855, component of Putrescine porter (characterized)	55%	99%	404.4	CP4-6 prophage; ABC transporter ATP-binding protein AfuC	41%	257.3
med	BPHYT_RS02505	spermidine/putrescine ABC transporter ATPase	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)	46%	89%	280.4	Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter	44%	279.6
med	BPHYT_RS09400	spermidine/putrescine ABC transporter ATPase	PotG aka B0855, component of Putrescine porter (characterized)	42%	95%	266.2	Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized	46%	278.5
med	BPHYT_RS22015	spermidine/putrescine ABC transporter ATPase	spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)	48%	75%	261.9	CP4-6 prophage; ABC transporter ATP-binding protein AfuC	46%	265.0

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.

Also see fitness data for the candidates

Definition of step potA

Curated sequence P31134: PotG aka B0855, component of Putrescine porter. putrescine ABC transporter ATP binding subunit (EC 7.6.2.16). putrescine ABC transporter ATP binding subunit (EC 7.6.2.16)
Curated sequence CH_024626: spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31. Spermidine/putrescine import ATP-binding protein PotA; EC 7.6.2.11. Spermidine/putrescine import ATP-binding protein PotA aka B1126, component of Polyamine (putrescine/spermidine) uptake porter. spermidine preferential ABC transporter ATP binding subunit (EC 7.6.2.11; EC 7.6.2.16). spermidine preferential ABC transporter ATP binding subunit (EC 7.6.2.11; EC 7.6.2.16)
Curated sequence Q97Q42: Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD
Comment: 4-part ABC transporters include E. coli potABCD or potGHIF, which are related to each other, and a related system, also named potABCD, from Streptococcus pneuomoniae.

Or cluster all characterized potA proteins

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

Downloads

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

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:

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