Finding step aroP for L-phenylalanine catabolism in Lactobacillus silagei IWT126
5 candidates for aroP: L-phenylalanine:H+ symporter AroP
Score | Gene | Description | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
med | CES79_RS01925 | amino acid permease | Aromatic amino acid transport protein AroP (characterized, see rationale) | 41% | 96% | 371.3 | D-serine/D-alanine/glycine transporter | 48% | 411.0 |
med | CES79_RS11280 | amino acid permease | Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs (characterized) | 41% | 95% | 363.6 | Serine transporter, SerP2 or YdgB, of 459 aas and 12 TMSs (Trip et al. 2013). Transports L-alanine (Km = 20 μM), D-alanine (Km = 38 μM), L-serine, D-serine (Km = 356 μM) and glycine (Noens and Lolkema 2015). The encoding gene is adjacent to the one encoding SerP1 (TC# 2.A.3.1.21) | 45% | 400.2 |
med | CES79_RS03490 | amino acid permease | Aromatic amino acid transport protein AroP (characterized, see rationale) | 40% | 94% | 346.7 | L-alanine and D-alanine permease | 46% | 416.4 |
med | CES79_RS10735 | amino acid permease | Aromatic amino acid transport protein AroP (characterized, see rationale) | 40% | 96% | 342 | L-alanine and D-alanine permease | 44% | 386.7 |
lo | CES79_RS01340 | amino acid permease | Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) | 36% | 86% | 314.3 | Lysine permease LysP | 61% | 607.1 |
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 aroP
- Curated sequence P15993: Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan. aromatic amino acid:H+ symporter AroP. aromatic amino acid:H+ symporter AroP
- Curated sequence F2HN33: Transporter for phenylalainine, tyrosine and tryptophan of 449 aas and 12 TMSs, FywP or YsjA
- Curated sequence P24207: Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs. phenylalanine:H+ symporter PheP. phenylalanine:H+ symporter PheP
- Curated sequence Q2VQZ4: Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids)
- Curated sequence Q46065: Aromatic amino acid permease, AroP
- UniProt sequence A0A0C4YP23: SubName: Full=Aromatic amino acid transport protein AroP {ECO:0000313|EMBL:AJG24240.1};
- Ignore hits to A2RMP5 when looking for 'other' hits (Aromatic amino acid permease FywP)
- Comment: RR42_RS33495 from Cupriavidus basilensis FW507-4G11 (A0A0C4YP23) is the phenylalanine transporter. Ignore A2RMP5, an ortholog from another Lactococcus.
Or cluster all characterized aroP proteins
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Links
Downloads
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:
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