Rv2514c Family assigned · low auto-curated
H37Rv Rv2514c · MTBC0 mtbc0_002677 ·
153 aa · 2853767–2854228 (-) ·
RefSeq NP_217030.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF4411 family protein |
| Revised (this work) | DUF4411 family protein. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6Y0Y0
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | DUF4411 family protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Domain of unknown function (DUF4411) |
| Orthologous group | COG1487 |
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 | 0.952 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 3 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 |
|---|---|---|---|---|
DUF4411 | PF14367.13 | 4.7e-45 | 3–153 | Domain of unknown function (DUF4411) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1371 (membrane protein), high confidence from genomic context alone (score 707 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2515c hyp |
hypothetical protein | 998 | 994 ctx | neighborhood:882 cooccurence:774 coexpression:802 textmining:803 |
Rv1371 |
membrane protein | 707 | 707 ctx | cooccurence:703 |
Rv2608 PPE42 |
PPE family protein PPE42 | 644 | 644 ctx | cooccurence:639 |
Rv2939 papA5 |
phthiocerol/phthiodiolone dimycocerosyl transferase | 640 | 640 ctx | cooccurence:638 |
Rv2516c hyp |
hypothetical protein | 514 | 515 ctx | neighborhood:513 |
Rv2517c hyp |
hypothetical protein | 514 | 515 ctx | neighborhood:513 |
Rv0878c PPE13 |
PPE family protein PPE13 | 440 | 440 ctx | cooccurence:435 |
Rv0300 vapB2 |
antitoxin VapB2 | 433 | 434 | experimental:412 |
Rv1917c PPE34 |
PPE family protein PPE34 | 412 | 413 | |
Rv2601A vapB41 |
antitoxin VapB41 | 429 | 407 | |
Rv1952 vapB14 |
antitoxin VapB14 | 429 | 407 | |
Rv1270c lprA |
lipoprotein LprA | 400 | 401 | |
Rv2017 |
transcriptional regulator | 664 | 78 | textmining:651 |
Rv0268c hyp |
hypothetical protein | 868 | 63 | textmining:865 |
Rv0366c hyp |
hypothetical protein | 662 | 56 | textmining:657 |
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: hypothetical protein
- MTBC0 PGAP product: DUF4411 family protein
- Pfam (hmmscan --cut_ga): DUF4411 PF14367.13 (E=5e-45)
- (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_217030.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF4411 (PF14367.13)
- 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
COG1487 - Curated reference: UniProt I6Y0Y0 (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 —
27 functional partner(s); context anchor
Rv1371 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002677|Rv2514c| MLYSFDTSAILNGRRDLFRPAVFRSLWGRVEDAISAGQIRSVDEVQRELARRDDDAKRWADGQTGLFCPLDEQIQQAARHILRLHPNMVRQGGRRSAADPFVIALAMVNNATVVTQETASGNIEKPRIPDVCDALGVPWLTLMGYIEAQGWTF