argR Resolved · high auto-curated
H37Rv Rv1657 · MTBC0 mtbc0_001766 ·
170 aa · 1882884–1883396 (+) ·
RefSeq NP_216173.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | arginine repressor |
|---|---|
| MTBC0 PGAP re-annotation | arginine repressor |
| Revised (this work) | Arginine repressor. Pfam: Arg_repressor (PF01316.28), Arg_repressor_C (PF02863.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPY9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Arginine repressor |
| Curated function | Regulates arginine biosynthesis genes. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | argR |
| eggNOG description | Regulates arginine biosynthesis genes |
| Orthologous group | COG1438 |
| KEGG orthology |
K03402
|
| Gene Ontology (53) |
GO:0000976, GO:0001067, GO:0001130, GO:0001216, GO:0003674, GO:0003676, GO:0003677, GO:0003690, GO:0003700, GO:0005488, GO:0005575, GO:0006355 +41 more
|
Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are computed annotations, not manual curation; cross-check against the primary literature before treating a specific reaction as established.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 0.26 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 2 missense, 0 nonsense, 0 frameshift |
pN/pS from segregating SNPs (singletons removed) normalised by possible sites. Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene). A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a convergent one (many independent alleles) is typical of resistance loss-of-function.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
Arg_repressor | PF01316.28 | 1.3e-25 | 16–85 | Arginine repressor, DNA binding domain |
Arg_repressor_C | PF02863.24 | 1.5e-24 | 102–167 | Arginine repressor, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: argJ (bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase), high confidence from genomic context alone (score 998 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1653 argJ |
bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase | 999 | 998 ctx | neighborhood:881 coexpression:985 textmining:931 |
Rv1654 argB |
acetylglutamate kinase | 999 | 996 ctx | neighborhood:881 coexpression:968 textmining:931 |
Rv1655 argD |
acetylornithine aminotransferase | 998 | 988 ctx | neighborhood:882 coexpression:905 textmining:915 |
Rv1658 argG |
argininosuccinate synthase | 997 | 988 ctx | neighborhood:879 coexpression:908 textmining:799 |
Rv1656 argF |
ornithine carbamoyltransferase | 997 | 987 ctx | neighborhood:882 coexpression:892 textmining:804 |
Rv1652 argC |
N-acetyl-gamma-glutamyl-phoshate reductase | 997 | 986 ctx | neighborhood:881 coexpression:888 textmining:811 |
Rv1659 argH |
argininosuccinate lyase | 994 | 981 ctx | neighborhood:783 coexpression:915 textmining:735 |
Rv1661 pks7 |
polyketide synthase | 627 | 611 ctx | neighborhood:588 |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 684 | 561 ctx | neighborhood:544 |
Rv1649 pheS |
phenylalanine--tRNA ligase subunit alpha | 607 | 548 ctx | neighborhood:544 |
Rv1647 |
adenylate cyclase | 520 | 521 ctx | neighborhood:518 |
Rv1651c PE_PGRS30 |
PE-PGRS family protein PE_PGRS30 | 498 | 498 ctx | neighborhood:498 |
Rv3859c gltB |
glutamate synthase large subunit | 629 | 478 ctx | neighborhood:475 |
Rv2322c rocD1 |
Rv2322c, (MTCY3G12.12), len: 221 aa. Probable rocD1,ornithine aminotransferase, highly similar to N-terminal region of other ornithine amino | 535 | 465 | coexpression:426 |
Rv2321c rocD2 |
Rv2321c, (MTCY3G12.13), len: 181 aa. Probable rocD2,ornithine aminotransferase, highly similar to C-terminal region of other ornithine amino | 534 | 464 | coexpression:425 |
STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression, experimental, database, text-mining) into a 0–1000 score. The ctx badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion, phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with the operon context and the primary literature before assigning a function.
Evidence
- Legacy H37Rv annotation: arginine repressor
- MTBC0 PGAP product: arginine repressor
- Pfam (hmmscan --cut_ga): Arg_repressor PF01316.28 (E=1e-25), Arg_repressor_C PF02863.24 (E=1e-24)
- (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)
Sources
- Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
- Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_216173.1)
- Domains: Pfam-A via hmmscan --cut_ga — Arg_repressor (PF01316.28), Arg_repressor_C (PF02863.24)
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021,
doi:10.1093/molbev/msab293), eggNOG 5.0 DB
(Huerta-Cepas et al. 2019) — OG
COG1438 - Curated reference: UniProt P9WPY9 (SwissProt, reviewed; Evidence at protein level)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
42 functional partner(s); context anchor
argJ - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001766|Rv1657|argR MSRAKAAPVAGPEVAANRAGRQARIVAILSSAQVRSQNELAALLAAEGIEVTQATLSRDLEELGAVKLRGADGGTGIYVVPEDGSPVRGVSGGTDRMARLLGELLVSTDDSGNLAVLRTPPGAAHYLASAIDRAALPQVVGTIAGDDTILVVAREPTTGAQLAGMFENLR