Finding step artQ for L-arginine catabolism in Pseudomonas fluorescens GW456-L13
5 candidates for artQ: L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ)
| Score | Gene | Description | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| hi | PfGW456L13_1965 | Arginine/ornithine ABC transporter, permease protein AotQ | ABC transporter for L-Arginine, permease component 1 (characterized) | 97% | 100% | 438 | | | |
| hi | PfGW456L13_3700 | Arginine/ornithine ABC transporter, permease protein AotQ | L-Arginine ABC transporter, permease component 2 (characterized) | 78% | 100% | 365.5 | | | |
| hi | PfGW456L13_378 | Arginine ABC transporter, permease protein ArtQ | Probable permease of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) | 67% | 99% | 325.5 | | | |
| hi | PfGW456L13_4636 | Histidine ABC transporter, permease protein HisQ (TC 3.A.1.3.1) | ABC transporter for L-Arginine, permease component 2 (characterized) | 66% | 98% | 294.3 | | | |
| hi | PfGW456L13_384 | Histidine ABC transporter, permease protein HisQ (TC 3.A.1.3.1) | ABC transporter for L-Arginine, permease component 2 (characterized) | 65% | 98% | 282.7 | | | |
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 artQ
- Curated sequence Q9HU30: Probable permease of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR
- Curated sequence CH_107317: arginine/ornithine transport protein. AotQ, component of Arginine/ornithine (but not lysine) porter
- Curated sequence P0A2I9: Histidine transport system permease protein HisQ. Histidine transport system permease protein HisQ aka STM2353, component of Histidine/arginine/lysine/ornithine porter (Heuveling et al. 2014). In contrast to some homologous homodimeric systems, the heterodimeric histidine transporter of Salmonella enterica Typhimurium
- Curated sequence P0AE34: Arginine ABC transporter permease protein ArtQ. Arginine transport system permease protein ArtQ aka B0862, component of Arginine porter. L-arginine ABC transporter membrane subunit ArtQ (EC 7.4.2.1). L-arginine ABC transporter membrane subunit ArtQ (EC 7.4.2.1)
- Curated sequence P52094: Histidine transport system permease protein HisQ. Histidine transport system permease protein HisQ, component of Histidine/Arginine/Lysine (basic amino acid) uptake porter, HisJ/ArgT/HisP/HisM/HisQ [R, R, C, M, M, respectively] (Gilson et al. 1982). HisJ binds L-His (preferred), but 1-methyl-L-His and 3-methyl-L-His also bind, while the dipeptide carnosine binds weakly; D-histidine and the histidine degradation products, histamine, urocanic acid and imidazole do not bind. L-Arg, homo-L-Arg, and post-translationally modified methylated Arg-analogs also bind with the exception of symmetric dimethylated-L-Arg. L-Lys and L-Orn show weaker interactions with HisJ and methylated and acetylated Lys variants show poor binding.The carboxylate groups of these amino acids and their variants are essential. lysine/arginine/ornithine ABC transporter / histidine ABC transporter, membrane subunit HisQ (EC 7.4.2.1)
- Curated sequence BPHYT_RS07675: ABC transporter for L-Arginine, permease component 2
- Curated sequence GFF4244: ABC transporter for L-Arginine, permease component 1
- Curated sequence Pf1N1B4_3432: ABC transporter for L-Arginine and L-Citrulline, permease component 1
- Curated sequence AO353_03050: ABC transporter for L-Arginine and L-Citrulline, permease component 2
- Curated sequence AO356_18705: L-Arginine ABC transporter, permease component 2
- Curated sequence Pf6N2E2_5661: L-Arginine ABC transporter, permease protein AotQ
- Ignore hits to AO356_09905 when looking for 'other' hits (ABC transporter for L-Lysine, permease component 1)
- Ignore hits to Pf6N2E2_2959 when looking for 'other' hits (ABC transporter for L-Lysine, permease component 1)
- Ignore hits to AO356_05500 when looking for 'other' hits (ABC transporter for L-Lysine, permease component 1)
- Comment: Ignore closely related lysine transporters in P. fluorescens (which may well transport arginine; AO356_09905 has a subtle defect in arginine utilization)
Or cluster all characterized artQ proteins
This GapMind analysis is from Apr 09 2024. 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 (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