Rv1719 Family assigned · medium auto-curated
H37Rv Rv1719 · MTBC0 mtbc0_001829 ·
259 aa · 1957656–1958435 (+) ·
RefSeq NP_216235.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | IclR family transcriptional regulator |
| Revised (this work) | IclR family transcriptional regulator. Pfam: HTH_IclR (PF09339.17), HTH_23 (PF13384.13), MarR_2 (PF12802.14), DUF7343 (PF24034.2), HTH_24 (PF13412.13), HTH_Crp_2 (PF13545.13), MarR (PF01047.29), IclR_C (PF01614.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71977
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | HTH-type transcriptional regulator Rv1719 |
| Curated function | Binds to the upstream region of Rv1714 and probably modulates the expression of the downstream gene(s). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | Bacterial regulatory proteins, crp family |
| Orthologous group | COG1414 |
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 | 0.563 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 6 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 |
|---|---|---|---|---|
HTH_IclR | PF09339.17 | 1.4e-13 | 16–63 | IclR helix-turn-helix domain |
HTH_23 | PF13384.13 | 6.1e-06 | 18–62 | Homeodomain-like domain |
MarR_2 | PF12802.14 | 5.3e-11 | 19–65 | MarR family |
DUF7343 | PF24034.2 | 3.4e-07 | 21–63 | Domain of unknown function (DUF7343) |
HTH_24 | PF13412.13 | 9.4e-11 | 22–62 | Winged helix-turn-helix DNA-binding |
HTH_Crp_2 | PF13545.13 | 6.1e-09 | 22–68 | Crp-like helix-turn-helix domain |
MarR | PF01047.29 | 2.7e-07 | 22–64 | MarR family |
IclR_C | PF01614.25 | 1.3e-54 | 81–249 | Bacterial transcriptional regulator IclR C-terminal |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadB3 (3-hydroxybutyryl-CoA dehydrogenase FadB), high confidence from genomic context alone (score 953 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1715 fadB3 |
3-hydroxybutyryl-CoA dehydrogenase FadB | 953 | 953 ctx | neighborhood:798 coexpression:750 |
Rv1718 hyp |
hypothetical protein | 935 | 935 ctx | neighborhood:867 coexpression:449 |
Rv1716 hyp |
hypothetical protein | 903 | 904 ctx | neighborhood:798 |
Rv1714 |
oxidoreductase | 884 | 884 ctx | neighborhood:798 |
Rv1717 hyp |
hypothetical protein | 784 | 785 ctx | neighborhood:698 |
Rv0264c hyp |
hypothetical protein | 710 | 711 | coexpression:656 |
Rv0494 |
HTH-type transcriptional regulator | 719 | 704 ctx | cooccurence:645 |
Rv3263 |
DNA methylase | 687 | 687 | coexpression:687 |
Rv0263c hyp |
hypothetical protein | 658 | 658 | coexpression:646 |
Rv1776c |
transcriptional regulator | 590 | 580 | coexpression:580 |
Rv1713 engA |
GTPase Der | 539 | 539 ctx | neighborhood:531 |
Rv3903c cpnT hyp |
hypothetical protein | 513 | 495 | |
Rv1712 cmk |
cytidylate kinase | 489 | 490 ctx | neighborhood:482 |
Rv0165c mce1R |
transcriptional regulator Mce1R | 498 | 479 ctx | cooccurence:456 |
Rv0043c |
HTH-type transcriptional regulator | 483 | 463 |
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: transcriptional regulator
- MTBC0 PGAP product: IclR family transcriptional regulator
- Pfam (hmmscan --cut_ga): HTH_IclR PF09339.17 (E=1e-13), HTH_23 PF13384.13 (E=6e-06), MarR_2 PF12802.14 (E=5e-11), DUF7343 PF24034.2 (E=3e-07), HTH_24 PF13412.13 (E=9e-11), HTH_Crp_2 PF13545.13 (E=6e-09), MarR PF01047.29 (E=3e-07), IclR_C PF01614.25 (E=1e-54)
- (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_216235.1)
- Domains: Pfam-A via hmmscan --cut_ga — HTH_IclR (PF09339.17), HTH_23 (PF13384.13), MarR_2 (PF12802.14), DUF7343 (PF24034.2), HTH_24 (PF13412.13), HTH_Crp_2 (PF13545.13), MarR (PF01047.29), IclR_C (PF01614.25)
- 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
COG1414 - Curated reference: UniProt P71977 (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 —
29 functional partner(s); context anchor
fadB3 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001829|Rv1719| MSAEEQDTRSGGIQVIARAAELLRVLQAHPGGLSQAEIGERVGMARSTVSRILNALEDEGLVASRGARGPYRLGPEITRMATTVRLGVVTEMHPFLTELSRELDETVDLSILDGDRADVVDQVVPPQRLRAVSAVGESFPLYCCANGKALLAALPPERQARALPSRLAPLTANTITDRAALRDELNRIRVDGVAYDREEQTEGICAVGAVLRGVSVELVAVSVPVPAQRFYGREAELAGALLAWVSKVDAWFNGTEDRK