Rv3524 Family assigned · medium auto-curated
H37Rv Rv3524 · MTBC0 mtbc0_003740 ·
343 aa · 3984432–3985463 (+) ·
RefSeq NP_218041.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | NHL repeat-containing protein |
| Revised (this work) | NHL repeat-containing protein. Pfam: NHL (PF01436.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6X7J6
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable conserved membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | NHL repeat |
| Orthologous group | COG3391 |
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 | 0.071 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 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 |
|---|---|---|---|---|
NHL | PF01436.28 | 3.3e-06 | 272–298 | NHL repeat |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: PE_PGRS23 (PE-PGRS family protein PE_PGRS23), medium confidence from genomic context alone (score 690 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1243c PE_PGRS23 |
PE-PGRS family protein PE_PGRS23 | 690 | 690 ctx | cooccurence:649 |
Rv2383c mbtB |
phenyloxazoline synthase | 668 | 668 | coexpression:657 |
Rv2194 qcrC |
ubiquinol-cytochrome C reductase cytochrome subunit C | 672 | 652 | experimental:622 |
Rv3523 ltp3 |
lipid carrier protein | 638 | 637 ctx | neighborhood:636 |
Rv2853 PE_PGRS48 |
PE-PGRS family protein PE_PGRS48 | 612 | 612 ctx | cooccurence:560 |
Rv0124 PE_PGRS2 |
PE-PGRS family protein PE_PGRS2 | 606 | 607 ctx | cooccurence:554 |
Rv3522 ltp4 |
lipid transfer protein | 601 | 601 ctx | neighborhood:600 |
Rv3533c PPE62 |
PPE family protein PPE62 | 600 | 601 ctx | cooccurence:598 |
Rv3521 hyp |
hypothetical protein | 570 | 570 ctx | neighborhood:570 |
Rv1135c PPE16 |
PPE family protein PPE16 | 559 | 560 ctx | cooccurence:557 |
Rv3558 PPE64 |
PPE family protein PPE64 | 556 | 556 ctx | cooccurence:554 |
Rv0755c PPE12 |
PPE family protein PPE12 | 540 | 540 ctx | cooccurence:539 |
Rv3159c PPE53 |
PPE family protein PPE53 | 524 | 524 ctx | cooccurence:523 |
Rv1157c hyp |
hypothetical protein | 523 | 524 | coexpression:421 |
Rv1918c PPE35 |
PPE family protein PPE35 | 521 | 522 ctx | cooccurence:520 |
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: membrane protein
- MTBC0 PGAP product: NHL repeat-containing protein
- Pfam (hmmscan --cut_ga): NHL PF01436.28 (E=3e-06)
- (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_218041.1)
- Domains: Pfam-A via hmmscan --cut_ga — NHL (PF01436.28)
- 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
COG3391 - Curated reference: UniProt I6X7J6 (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 —
40 functional partner(s); context anchor
PE_PGRS23 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003740|Rv3524| MVKFTPDSQTSVLRAGKCSGTLSPSRSRLQRGSWPVDSERRRYGWPRNRRTLAITGAAVVVVVTLAAIGYLIFEPKISGSSTSRQAASPTTPSPPSQVVVPIDLWNPDGVTVDLADAVYVADSGHKRLLKLPAGSNTPTTLPFTDTIGPGGVAVNSNRDVYVIDEDSHHVLKLAAGIEPPVELPFGSLGDAHGLAVDRSDSVYVVDYDNAKVLKLPPGADTPTELPFVGLDHPYDVAVDGAGTVYVTDSGHNRVVALTAGSATPVHLPFADLSFPAGVTVDRDDSVYVADLNNNRVLKLAAGSNAQSQLPFTGLFSPTDVAVDNDGAVYVIDFYNRMLKLPTA