Rv1404 Family assigned · medium auto-curated
H37Rv Rv1404 · MTBC0 mtbc0_001505 ·
160 aa · 1589935–1590417 (+) ·
RefSeq NP_215920.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | MarR family transcriptional regulator |
| Revised (this work) | MarR family transcriptional regulator. Pfam: MarR_2 (PF12802.14), MarR (PF01047.29). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71672
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable transcriptional regulatory protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | MarR family |
| Orthologous group | COG1846 |
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 | 0.093 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 1 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 |
|---|---|---|---|---|
MarR_2 | PF12802.14 | 3.3e-10 | 42–100 | MarR family |
MarR | PF01047.29 | 4.2e-18 | 43–100 | MarR family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1403c (methyltransferase), medium confidence from genomic context alone (score 580 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1403c |
methyltransferase | 900 | 580 ctx | neighborhood:574 textmining:773 |
Rv1619 hyp |
hypothetical protein | 538 | 519 ctx | cooccurence:517 |
Rv2060 |
integral membrane protein | 475 | 447 | |
Rv0678 mmpR5 hyp |
hypothetical protein | 474 | 326 | |
Rv0194 |
multidrug ABC transporter ATPase/permease | 576 | 257 | textmining:454 |
Rv1407 fmu |
16S rRNA m5C967 methyltransferase | 566 | 175 | textmining:497 |
Rv1405c |
methyltransferase | 887 | 166 | textmining:870 |
Rv0880 |
HTH-type transcriptional regulator | 789 | 162 | textmining:759 |
Rv3291c lrpA |
transcriptional regulator LrpA | 820 | 84 | textmining:812 |
Rv0560c |
benzoquinone methyltransferase | 739 | 52 | textmining:737 |
Rv1986 lysE |
amino acid transporter | 428 | 50 | textmining:423 |
Rv1185c fadD21 |
fatty-acid--CoA ligase FadD21 | 415 | 50 | textmining:410 |
Rv0193c hyp |
hypothetical protein | 870 | 46 | textmining:870 |
Rv2887 |
HTH-type transcriptional regulator | 870 | 44 | textmining:870 |
Rv0195 |
two component transcriptional regulator | 456 | 44 | textmining:455 |
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: MarR family transcriptional regulator
- Pfam (hmmscan --cut_ga): MarR_2 PF12802.14 (E=3e-10), MarR PF01047.29 (E=4e-18)
- (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_215920.1)
- Domains: Pfam-A via hmmscan --cut_ga — MarR_2 (PF12802.14), MarR (PF01047.29)
- 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
COG1846 - Curated reference: UniProt P71672 (TrEMBL, unreviewed; 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 —
15 functional partner(s); context anchor
Rv1403c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001505|Rv1404| MMPTEYPATAEESVDVITDALLTASRLLVAISAHSIAQVDENITIPQFRTLVILSNHGPINLATLATLLGVQPSATGRMVDRLVGAELIDRLPHPTSRRELLAALTKRGRDVVRQVTEHRRTEIARIVEQMAPAERHGLVRALTAFTEAGGEPDARYEIE