Finding step argT for L-lysine catabolism in Collimonas arenae Ter10
4 candidates for argT: L-lysine ABC transporter, substrate-binding component ArgT
| Score | Gene | Description | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| lo | CAter10_RS04095 | basic amino acid ABC transporter substrate-binding protein | ABC transporter for L-Lysine, periplasmic substrate-binding component (characterized) | 34% | 96% | 140.2 | Basic amino acid uptake transporter, BgtAB | 42% | 150.2 |
| lo | CAter10_RS14910 | cystine ABC transporter substrate-binding protein | Putative amino-acid binding periplasmic protein (characterized, see rationale) | 36% | 87% | 138.3 | L-cystine-binding protein FliY; CBP; Protein FliY; Sulfate starvation-induced protein 7; SSI7 | 43% | 205.3 |
| lo | CAter10_RS04100 | basic amino acid ABC transporter substrate-binding protein | Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter periplasmic binding protein, 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) | 35% | 91% | 136.7 | Basic amino acid uptake transporter, BgtAB | 36% | 145.6 |
| lo | CAter10_RS04105 | basic amino acid ABC transporter substrate-binding protein | Putative amino-acid binding periplasmic protein (characterized, see rationale) | 30% | 93% | 123.2 | Glutamine ABC transporter permease and substrate binding protein protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity | 36% | 153.3 |
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 argT
- Curated sequence CH_003045: lysine/arginine/ornithine ABC transporter, periplasmic lysine/arginine/ornithine-binding protein ArgT. Lysine/arginine/ornithine-binding periplasmic protein; LAO-binding protein
- Curated sequence P09551: ArgT aka B2310, 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 periplasmic binding protein (EC 7.4.2.1)
- Curated sequence Q9HU31: Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter periplasmic binding protein, 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 AO356_05495: ABC transporter for L-Lysine, periplasmic substrate-binding component
- Curated sequence AO356_09900: ABC transporter for L-Lysine, periplasmic substrate-binding component
- Curated sequence Pf6N2E2_2958: ABC transporter for L-Lysine, periplasmic substrate-binding component
- UniProt sequence Q92PA9: SubName: Full=Putative amino-acid binding periplasmic protein {ECO:0000313|EMBL:CAC46449.1};
- UniProt sequence Q88GX4: SubName: Full=Amino acid ABC transporter, periplasmic binding protein {ECO:0000313|EMBL:AAN69193.1};
- Comment: In E. coli and Salmonella, the ABC transporter has a lysine/arginine specific binding protein (argT), two permease subunits (hisQM, which are similar to each other), and an ATPase subunit (hisP). Pseudomonas aeruginosa has a homologous lysine transporter, PA5152-PA5155, as do various strains of Pseudomonas fluorescens. In P. putida, a similar system was identified using fitness data (argT = PP_3593 = Q88GX4; hisQ = PP_3594 = Q88GX3; hisM = PP_3595 = Q88GX2; hisP = PP_3597 = Q88GX0). In S. meliloti, a similar substrate-binding protein was identified using fitness data (SMc00140 = Q92PA9), but the ATPase subunit was not found (it might be shared with other systems).
Or cluster all characterized argT proteins
This GapMind analysis is from Sep 24 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 (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