Rv3143 Resolved · medium auto-curated
H37Rv Rv3143 · MTBC0 mtbc0_003341 ·
133 aa · 3532356–3532757 (+) ·
RefSeq NP_217659.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | response regulator |
|---|---|
| MTBC0 PGAP re-annotation | response regulator |
| Revised (this work) | Response regulator. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGL7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized response regulatory protein Rv3143 |
UniProt still lists this protein as Uncharacterized response regulatory protein Rv3143; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
T Signal transduction mechanisms
|
|---|---|
| eggNOG description | response regulator |
| Orthologous group | COG0784 |
| Gene Ontology (6) |
GO:0005575, GO:0005618, GO:0005623, GO:0030312, GO:0044464, GO:0071944
|
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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 0 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: nuoJ (NADH-quinone oxidoreductase subunit J), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3154 nuoJ |
NADH-quinone oxidoreductase subunit J | 999 | 999 ctx | cooccurence:695 experimental:997 |
Rv3151 nuoG |
NADH-quinone oxidoreductase subunit G | 999 | 999 ctx | cooccurence:740 experimental:997 |
Rv3147 nuoC |
NADH-quinone oxidoreductase subunit C | 999 | 999 ctx | cooccurence:705 experimental:997 |
Rv3153 nuoI |
NADH-quinone oxidoreductase subunit I | 998 | 999 ctx | cooccurence:516 experimental:997 |
Rv3146 nuoB |
NADH-quinone oxidoreductase subunit B | 998 | 998 ctx | neighborhood:473 experimental:997 |
Rv3145 nuoA |
NADH-quinone oxidoreductase subunit A | 998 | 998 ctx | neighborhood:477 experimental:997 |
Rv3149 nuoE |
NADH-quinone oxidoreductase subunit E | 950 | 949 ctx | cooccurence:524 experimental:870 |
Rv3148 nuoD |
NADH-quinone oxidoreductase subunit D | 959 | 926 | experimental:870 textmining:478 |
Rv3150 nuoF |
NADH-quinone oxidoreductase subunit F | 922 | 920 | experimental:870 |
Rv3158 nuoN |
NADH-quinone oxidoreductase subunit N | 916 | 913 | experimental:870 |
Rv3156 nuoL |
NADH-quinone oxidoreductase subunit L | 914 | 911 | experimental:870 |
Rv3157 nuoM |
NADH-quinone oxidoreductase subunit M | 897 | 897 | experimental:870 |
Rv3155 nuoK |
NADH-quinone oxidoreductase subunit K | 901 | 896 | experimental:870 |
Rv3152 nuoH |
NADH-quinone oxidoreductase subunit H | 896 | 896 | experimental:870 |
Rv3692 moxR2 |
methanol dehydrogenase transcriptional regulator MoxR | 798 | 798 | coexpression:798 |
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: response regulator
- MTBC0 PGAP product: response regulator
- (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_217659.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
COG0784 - Curated reference: UniProt P9WGL7 (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 —
64 functional partner(s); context anchor
nuoJ - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003341|Rv3143| MPDSSTALRILVYSDNVQTRERVMRALGKRLHPDLPDLTYVEVATGPMVIRQMDRGGIDLAILDGEATPTGGMGIAKQLKDELASCPPILVLTGRPDDTWLASWSRAEAAVPHPVDPIVLGRTVLSLLRAPAH