Finding step aroP for L-tryptophan catabolism in Gallaecimonas xiamenensis 3-C-1
No candidates for aroP: tryptophan:H+ symporter AroP
GapMind classifies a step as low confidence even if it does not find any candidates. You can still try to find candidates by using Curated BLAST (which searches the 6-frame translation) or by text search of the annotations (which may indicate weak homology, under 30% identity or 50% coverage, that GapMind does not consider). See the links below.
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 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 A0A0N9WG97: SubName: Full=Amino acid permease {ECO:0000313|EMBL:ALI00611.1};
- UniProt sequence Q4KIP0: SubName: Full=Aromatic amino acid transport protein AroP {ECO:0000313|EMBL:AAY96158.1};
- Ignore hits to A2RMP5 when looking for 'other' hits (Aromatic amino acid permease FywP)
- Ignore hits to AO356_18530 when looking for 'other' hits (L-tyrosine transporter)
- Comment: AO353_05930 (A0A0N9WG97) from Pseudomonas fluorescens FW300-N2E3 is related to aroP and is specifically improtant for tryptophan utilization (although more so if Trp is the nitrogen source). PfGW456L13_4291 (A0A293QSB2) from P. fluorescens GW4560-L13 is related to aroP and is specifically important for tryptophan utilization. Unfortunately A0A293QSB2 is no longer in UniProt; the closest remaining sequence is Q4KIP0 (only 87% identical). FywP (A2RMP5) may well be a tryptophan transporter as well, so ignore.
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