Rv3669 Family assigned · medium auto-curated
H37Rv Rv3669 · MTBC0 mtbc0_003888 ·
172 aa · 4134657–4135175 (+) ·
RefSeq NP_218186.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane protein |
|---|---|
| MTBC0 PGAP re-annotation | phage holin family protein |
| Revised (this work) | Phage holin family protein. Pfam: Phage_holin_3_6 (PF07332.17). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O69637
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable conserved transmembrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Putative Actinobacterial Holin-X, holin superfamily III |
| Orthologous group | 2DPPE |
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 | 0.355 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 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 |
|---|---|---|---|---|
Phage_holin_3_6 | PF07332.17 | 4.6e-32 | 32–145 | Putative Actinobacterial Holin-X, holin superfamily III |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ephE (epoxide hydrolase EphE), high confidence from genomic context alone (score 900 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3670 ephE |
epoxide hydrolase EphE | 900 | 900 ctx | neighborhood:881 |
Rv3668c |
protease | 733 | 733 ctx | neighborhood:693 |
Rv3207c hyp |
hypothetical protein | 691 | 691 ctx | cooccurence:691 |
Rv1417 |
membrane protein | 655 | 655 ctx | cooccurence:655 |
Rv0862c hyp |
hypothetical protein | 596 | 596 ctx | cooccurence:596 |
Rv3311 hyp |
hypothetical protein | 595 | 595 ctx | cooccurence:589 |
Rv3259 hyp |
hypothetical protein | 567 | 568 ctx | cooccurence:546 |
Rv2049c hyp |
hypothetical protein | 564 | 565 ctx | cooccurence:562 |
Rv2170 |
GCN5-like N-acetyltransferase | 562 | 563 ctx | cooccurence:561 |
Rv3438 hyp |
hypothetical protein | 551 | 551 ctx | cooccurence:548 |
Rv3256c hyp |
hypothetical protein | 545 | 545 ctx | cooccurence:545 |
Rv3662c hyp |
hypothetical protein | 539 | 539 ctx | cooccurence:426 |
Rv3212 hyp |
hypothetical protein | 538 | 521 ctx | cooccurence:519 |
Rv1698 mctB |
copper transporter MctB | 514 | 515 ctx | cooccurence:512 |
Rv0556 |
transmembrane protein | 505 | 506 ctx | cooccurence:503 |
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: transmembrane protein
- MTBC0 PGAP product: phage holin family protein
- Pfam (hmmscan --cut_ga): Phage_holin_3_6 PF07332.17 (E=5e-32)
- (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_218186.1)
- Domains: Pfam-A via hmmscan --cut_ga — Phage_holin_3_6 (PF07332.17)
- 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
2DPPE - Curated reference: UniProt O69637 (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
ephE - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003888|Rv3669| MSKIDRKNGVPSTLTTIPLADPHAGPAEPSIGDLIKDATTQMSTLVRAEVELARAEITRDVKKGLTGSVFFISSLVVGFYSTFFFFFFVAELLDTWIWRWVAFLLVFAIMVVVTAVLALLGFLKVRRIRGPRQTIASVKETRTALTPGHDKTPVTPKPVTSDRATPVDPSGW