Rv1762c Family assigned · medium auto-curated
H37Rv Rv1762c · MTBC0 mtbc0_001877 ·
262 aa · 2013446–2014234 (-) ·
RefSeq NP_216278.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | heavy metal-binding domain-containing protein |
| Revised (this work) | Heavy metal-binding domain-containing protein. Pfam: YbjQ_1 (PF01906.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06797
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Encapsulin nanocompartment protein Rv1762c |
| Curated function | Cargo protein of a type 1 encapsulin nanocompartment possibly involved in protection against oxidative stress. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Belongs to the UPF0145 family |
| Orthologous group | COG0393 |
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 | 0.207 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 1 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.92% of strains (1340) · 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 |
|---|---|---|---|---|
YbjQ_1 | PF01906.24 | 1.1e-08 | 161–244 | Putative heavy-metal-binding |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: gltB (glutamate synthase large subunit), medium confidence from genomic context alone (score 544 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) |
|---|---|---|---|---|
Rv1761c hyp |
hypothetical protein | 887 | 887 ctx | neighborhood:881 |
Rv1775 hyp |
hypothetical protein | 553 | 553 ctx | cooccurence:553 |
Rv3859c gltB |
glutamate synthase large subunit | 544 | 544 ctx | neighborhood:544 |
Rv2113 |
integral membrane protein | 532 | 532 ctx | cooccurence:532 |
Rv3903c cpnT hyp |
hypothetical protein | 507 | 507 ctx | cooccurence:507 |
Rv0538 |
membrane protein | 500 | 501 ctx | cooccurence:500 |
Rv0090 |
membrane protein | 485 | 485 ctx | cooccurence:483 |
Rv2729c |
integral membrane protein | 461 | 461 ctx | cooccurence:458 |
Rv0143c |
transmembrane protein | 452 | 452 ctx | cooccurence:421 |
Rv2412 rpsT |
30S ribosomal protein S20 | 412 | 413 | coexpression:413 |
Rv2986c hupB |
DNA-binding protein HU | 407 | 407 | coexpression:405 |
Rv2856 nicT |
nickel-transport integral membrane protein NicT | 401 | 401 ctx | cooccurence:401 |
Rv2577 hyp |
hypothetical protein | 400 | 400 ctx | cooccurence:400 |
Rv1763 |
Rv1763, (MTCY28.29), len: 108 aa. Putative Transposase for IS6110 (fragment), identical to many other Mycobacterium tuberculosis IS6110 tran | 917 | 393 | textmining:870 |
Rv1764 |
Putative transposase; Rv1764, (MTCY28.30), len: 328 aa. Putative Transposase for IS6110 insertion element. Identical to many other M. tuberc | 891 | 393 | textmining:829 |
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: heavy metal-binding domain-containing protein
- Pfam (hmmscan --cut_ga): YbjQ_1 PF01906.24 (E=1e-08)
- (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_216278.1)
- Domains: Pfam-A via hmmscan --cut_ga — YbjQ_1 (PF01906.24)
- 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
COG0393 - Curated reference: UniProt O06797 (SwissProt, reviewed; 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 —
22 functional partner(s); context anchor
gltB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001877|Rv1762c| MQSSSLDPVASERLSHAEKSFTSDLSINEFALLHGAGFEPIELVMGVSVYHVGFQFSGMRQQQELGVLTEATYRARWNAMARMQAEADALKADGIVGVRLNWRHHGEGGEHLEFMAVGTAVRYTAKPGAFRRPNGQAFSSHLSGQDMVTLLRSGFAPVAFVMGNCVFHIAVQGFMQTLRQIGRNMEMPQWTQGNYQARELAMSRMQSEAERDGATGVVGVHFAISNYAWGVHTVEFYTAGTAVRRTGSGETITPSFVLPMDS