GapMind for catabolism of small carbon sources

 

Finding step opuBA for L-proline catabolism in Herbaspirillum seropedicae SmR1

4 candidates for opuBA: proline ABC transporter, ATPase component OpuBA/BusAA

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
med HSERO_RS08545 glycine/betaine ABC transporter ATP-binding protein BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) 49% 76% 255.4 ABC-type quaternary amine transporter (EC 7.6.2.9) 68% 521.9
med HSERO_RS03005 ABC transporter ATP-binding protein BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) 41% 73% 181.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 48% 250.8
lo HSERO_RS11145 sulfate ABC transporter ATP-binding protein BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) 40% 72% 176.4 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 46% 270.8
lo HSERO_RS05415 spermidine/putrescine ABC transporter ATPase BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) 38% 76% 174.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 46% 312.4

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

Also see fitness data for the candidates

Definition of step opuBA

Or cluster all characterized opuBA proteins

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