Rv3675 Still unknown · low auto-curated
H37Rv Rv3675 · MTBC0 mtbc0_003894 ·
125 aa · 4139832–4140209 (+) ·
RefSeq NP_218192.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Conserved hypothetical protein; no recognised domain. Function unknown. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6YCQ7
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Possible membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2AXWZ |
|---|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: nth (endonuclease III), high confidence from genomic context alone (score 779 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3674c nth |
endonuclease III | 855 | 779 ctx | neighborhood:779 |
Rv3671c marP |
serine protease | 742 | 697 ctx | neighborhood:697 |
Rv3673c |
membrane-anchored thioredoxin-like protein | 704 | 653 ctx | neighborhood:653 |
Rv3676 crp |
cAMP receptor protein | 585 | 585 ctx | neighborhood:580 |
Rv3672c hyp |
hypothetical protein | 489 | 489 ctx | neighborhood:487 |
Rv1690 lprJ |
lipoprotein LprJ | 535 | 212 | textmining:435 |
Rv3354 hyp |
hypothetical protein | 526 | 70 | textmining:512 |
Rv1855c |
oxidoreductase | 514 | 50 | textmining:510 |
Rv3355c |
integral membrane protein | 517 | 47 | textmining:514 |
Rv3346c |
transmembrane protein | 441 | 47 | textmining:438 |
Rv3677c |
beta lactamase | 631 | 44 | textmining:630 |
Rv0191 |
MFS-type transporter | 615 | 41 | textmining:615 |
Rv0446c |
transmembrane protein | 514 | 41 | textmining:514 |
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: hypothetical protein
- (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_218192.1)
- 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
2AXWZ - Curated reference: UniProt I6YCQ7 (TrEMBL, unreviewed; Predicted)
- 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
nth - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003894|Rv3675| MFTLLVSWLLVACVPGLLMLATLGLGRLERFLARDTVTATDVAEFLEQAEAVDVHTLARNGMPEALDYLHRRQARRITDSPPLGSGAGPRYAGPLFVTDLDSPVEPPRHGQPNPQFRTARHANHV