Rv2884 Family assigned · medium auto-curated
H37Rv Rv2884 · MTBC0 - ·
252 aa · 3193393–3194151 (+) ·
RefSeq NP_217400.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Transcriptional regulator. Pfam: GlnR_1st (PF21695.4), Trans_reg_C (PF00486.35). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
I6X5M3
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable transcriptional regulatory protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K TranscriptionT Signal transduction mechanisms
|
|---|---|
| eggNOG description | Transcriptional regulatory protein, C terminal |
| Orthologous group | COG0745 |
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 | 0.356 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 4 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 |
|---|---|---|---|---|
GlnR_1st | PF21695.4 | 4.3e-33 | 21–130 | Transcription regulator GlnR, N-terminal domain |
Trans_reg_C | PF00486.35 | 7.8e-25 | 161–232 | Transcriptional regulatory protein, C terminal |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0600c (two component sensor kinase HK1), high confidence from genomic context alone (score 872 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0600c |
two component sensor kinase HK1 | 877 | 872 ctx | cooccurence:710 |
Rv1032c trcS |
two component sensor histidine kinase TrcS | 806 | 795 ctx | cooccurence:526 |
Rv3764c tcrY |
two component sensor kinase TcrY | 798 | 786 ctx | cooccurence:504 |
Rv0490 senX3 |
two component sensor histidine kinase SenX3 | 865 | 781 ctx | cooccurence:617 textmining:410 |
Rv1027c kdpE |
transcriptional regulator KdpE | 739 | 740 ctx | cooccurence:725 |
Rv0982 mprB |
two component histidine-protein kinase/phosphatase MprB | 738 | 729 | |
Rv0902c prrB |
two component sensor histidine kinase PrrB | 730 | 719 | |
Rv0758 phoR |
two component system response sensor kinase PhoR | 800 | 716 ctx | cooccurence:500 |
Rv0601c |
two component sensor kinase HK2 | 672 | 660 | |
Rv3245c mtrB |
two component sensory histidine kinase MtrB | 644 | 597 | |
Rv3365c hyp |
hypothetical protein | 593 | 578 | |
Rv2998A |
Rv2998A, len: 67 aa. Probable conserved hypothetical protein, (possibly gene fragment), highly similar to central part of two-component sens | 592 | 577 | |
Rv2883c pyrH |
uridylate kinase | 560 | 547 ctx | neighborhood:484 |
Rv3645 |
transmembrane protein | 547 | 519 | |
Rv1028c kdpD |
sensor protein KdpD | 564 | 512 | experimental:417 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): transcriptional regulator
- Pfam (hmmscan --cut_ga): GlnR_1st PF21695.4 (E=4e-33), Trans_reg_C PF00486.35 (E=8e-25)
- (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_217400.1)
- Domains: Pfam-A via hmmscan --cut_ga — GlnR_1st (PF21695.4), Trans_reg_C (PF00486.35)
- 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
COG0745 - Curated reference: UniProt I6X5M3 (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 —
39 functional partner(s); context anchor
Rv0600c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2884| MPTGPTTGKWHPHEVWRYLLEVLLLTDEADLESALPELESFAQSVQRAPLDDPGAAKGADADVAIIDARADLAAARRVCRRLTTSAPALAVVAVVAPANFVAVDGDWIFDDVLLNAAGGAELQARLRLAITRRRSTLAGTLQFGDLVLHPASYTASLGDRDLGLTLTEFKLMNFLVQHAGRAFTRTRLMREVWGYECHGRIRTVDVHVRRLRAKLGAEHESMIDTVRGVGYMAVTPPQPRWIISESILNRCK