Rv3355c Still unknown · low auto-curated
H37Rv Rv3355c · MTBC0 mtbc0_003570 ·
97 aa · 3796222–3796515 (-) ·
RefSeq NP_217872.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | integral membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF3017 domain-containing protein |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF3017. 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 |
O50384
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable integral membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Protein of unknown function (DUF3017) |
| Orthologous group | 2DRQP |
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 | 0.396 · 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 |
|---|---|---|---|---|
DUF3017 | PF11222.14 | 1.5e-21 | 17–89 | Protein of unknown function (DUF3017) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: folD (bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase), high confidence from genomic context alone (score 882 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3356c folD |
bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase | 882 | 882 ctx | neighborhood:881 |
Rv3359 |
oxidoreductase | 739 | 739 ctx | neighborhood:738 |
Rv3357 relJ |
antitoxin RelJ | 556 | 557 ctx | neighborhood:557 |
Rv3358 relK |
toxin RelK | 556 | 557 ctx | neighborhood:557 |
Rv1343c lprD |
lipoprotein LprD | 521 | 522 ctx | cooccurence:519 |
Rv0556 |
transmembrane protein | 520 | 521 ctx | cooccurence:519 |
Rv0817c lmeA hyp |
hypothetical protein | 502 | 503 ctx | cooccurence:501 |
Rv3794 embA |
arabinosyltransferase A | 495 | 495 ctx | cooccurence:492 |
Rv3850 hyp |
hypothetical protein | 492 | 493 ctx | cooccurence:490 |
Rv3438 hyp |
hypothetical protein | 490 | 491 ctx | cooccurence:489 |
Rv1166 lpqW |
monoacyl phosphatidylinositol tetramannoside-binding protein LpqW | 487 | 487 ctx | cooccurence:484 |
Rv0383c ttfA hyp |
hypothetical protein | 477 | 477 ctx | cooccurence:477 |
Rv3244c lpqB |
lipoprotein LpqB | 475 | 475 ctx | cooccurence:472 |
Rv3795 embB |
arabinosyltransferase B | 470 | 471 ctx | cooccurence:468 |
Rv0412c glnX |
membrane protein | 467 | 468 ctx | cooccurence:465 |
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: integral membrane protein
- MTBC0 PGAP product: DUF3017 domain-containing protein
- Pfam (hmmscan --cut_ga): DUF3017 PF11222.14 (E=1e-21)
- (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_217872.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF3017 (PF11222.14)
- 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
2DRQP - Curated reference: UniProt O50384 (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 —
33 functional partner(s); context anchor
folD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003570|Rv3355c| MTVRAVFRRTVGAQWPILLVGSIFAVGFVLAGANFWRRGALLIGIGVGVAAVLRLVLSEERAGLLVVRSKGIDFVTTVTVAAAMVYIASTIDPLGTG