Rv3104c Family assigned · medium auto-curated
H37Rv Rv3104c · MTBC0 mtbc0_003300 ·
308 aa · 3493216–3494142 (-) ·
RefSeq NP_217620.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane protein |
|---|---|
| MTBC0 PGAP re-annotation | mechanosensitive ion channel family protein |
| Revised (this work) | Mechanosensitive ion channel family protein. Pfam: MS_channel_1st (PF21088.3), MS_channel_2nd (PF00924.25), MS_channel_3rd (PF21082.3). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O05781
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible conserved transmembrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | mscS |
| eggNOG description | mechanosensitive ion channel |
| Orthologous group | COG0668 |
| KEGG orthology |
K22044
|
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 | 0.239 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 3 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.10% of strains (146) · clonal |
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 |
|---|---|---|---|---|
MS_channel_1st | PF21088.3 | 8.6e-09 | 89–129 | Mechanosensitive ion channel, transmembrane helices 2/3 |
MS_channel_2nd | PF00924.25 | 2.9e-18 | 131–200 | Mechanosensitive ion channel, beta-domain |
MS_channel_3rd | PF21082.3 | 1.8e-11 | 207–292 | Mechanosensitive ion channel MscS, C-terminal |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: prfB (peptide chain release factor PrfB), high confidence from genomic context alone (score 892 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3105c prfB |
peptide chain release factor PrfB | 892 | 892 ctx | neighborhood:881 |
Rv3103c hyp |
hypothetical protein | 883 | 882 ctx | neighborhood:882 |
Rv3106 fprA |
NADPH-ferredoxin reductase FprA | 780 | 780 ctx | neighborhood:780 |
Rv3102c ftsE |
cell division ATP-binding protein FtsE | 716 | 716 ctx | neighborhood:706 |
Rv3101c ftsX |
cell division protein FtsX | 706 | 706 ctx | neighborhood:702 |
Rv3100c smpB |
SsrA-binding protein | 686 | 685 ctx | neighborhood:682 |
Rv3099c hyp |
hypothetical protein | 637 | 637 ctx | neighborhood:635 |
Rv1832 gcvB |
glycine dehydrogenase | 617 | 618 | coexpression:618 |
Rv0260c |
transcriptional regulator | 425 | 189 | |
Rv3412 hyp |
hypothetical protein | 557 | 169 | textmining:489 |
Rv0985c mscL |
large-conductance ion mechanosensitive channel | 513 | 94 | textmining:485 |
Rv3665c dppB |
dipeptide ABC transporter permease DppB | 504 | 77 | textmining:485 |
Rv0067c |
transcriptional regulator | 489 | 53 | textmining:483 |
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: mechanosensitive ion channel family protein
- Pfam (hmmscan --cut_ga): MS_channel_1st PF21088.3 (E=9e-09), MS_channel_2nd PF00924.25 (E=3e-18), MS_channel_3rd PF21082.3 (E=2e-11)
- (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_217620.1)
- Domains: Pfam-A via hmmscan --cut_ga — MS_channel_1st (PF21088.3), MS_channel_2nd (PF00924.25), MS_channel_3rd (PF21082.3)
- 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
COG0668 - Curated reference: UniProt O05781 (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 —
13 functional partner(s); context anchor
prfB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003300|Rv3104c| MTTSGTVLATSIAQHWHNFWRGEIGDWILNRGLRIVMLLIAAVLAARFVTWLANRVTRRLDLGFTESDALVRSEATKHRQAVASVISWVSIVLIYVVVVYEVIDVLPVPVGALVGPAAVLGAALGFGAQRLVQDLLAGFFIIVEKQYGFGDLVELSMVGSPENAAGTVEDVTLRVTKLRSSEGEVFTVPNGNIVKSVNLSKDWARAVVDIPVPTSADLGRVNEVLHQECEHARHDSLLGELLLDEPTVMGVERIEVDTVTLRLVARTLPGKQFEAGRQLRVLVIRALTRAGIVTAADARAAVAESPEQ