GapMind for catabolism of small carbon sources

 

Finding step proY for L-proline catabolism in Pseudomonas putida KT2440

5 candidates for proY: proline:H+ symporter

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
med PP_5031 proline (histidine) APC transporter Proline-specific permease (ProY) (characterized) 60% 98% 566.2 histidine permease 83% 779.6
med PP_1059 Uncharacterized amino acid permease YtnA Proline-specific permease (ProY) (characterized) 57% 95% 524.6 L-alanine and D-alanine permease 90% 859.8
med PP_0284 gamma-aminobutyrate permease GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP (characterized) 52% 97% 459.9 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 71% 632.1
med PP_4106 gamma-aminobutyrate permease GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP (characterized) 50% 97% 449.5 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 61% 545.4
med PP_0927 aromatic amino acid transport protein Proline-specific permease (ProY) (characterized) 44% 98% 382.9 Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan 69% 642.5

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 proY

Or cluster all characterized proY 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