Rv1066 Family assigned · medium auto-curated
H37Rv Rv1066 · MTBC0 mtbc0_001146 ·
131 aa · 1195337–1195732 (+) ·
RefSeq NP_215582.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | rhodanese-like domain-containing protein |
| Revised (this work) | Rhodanese-like domain-containing protein. Pfam: Rhodanese (PF00581.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53414
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Rhodanese domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| eggNOG description | sulfurtransferase |
| Orthologous group | COG0607 |
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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
Rhodanese | PF00581.26 | 4.0e-08 | 23–116 | Rhodanese-like domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lpqV (lipoprotein LpqV), medium confidence from genomic context alone (score 600 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) |
|---|---|---|---|---|
Rv1065 hyp |
hypothetical protein | 996 | 996 ctx | neighborhood:836 fusion:615 cooccurence:631 coexpression:860 |
Rv3846 sodA |
superoxide dismutase | 634 | 612 | experimental:573 |
Rv1064c lpqV |
lipoprotein LpqV | 600 | 600 ctx | neighborhood:597 |
Rv2367c ybeY |
endoribonuclease | 583 | 584 | experimental:573 |
Rv3456c rplQ |
50S ribosomal protein L17 | 517 | 517 | experimental:466 |
Rv3268 hyp |
hypothetical protein | 514 | 514 | |
Rv3443c rplM |
50S ribosomal protein L13 | 509 | 509 | experimental:453 |
Rv0710 rpsQ |
30S ribosomal protein S17 | 508 | 509 | experimental:476 |
Rv2442c rplU |
50S ribosomal protein L21 | 497 | 498 | experimental:466 |
Rv0701 rplC |
50S ribosomal protein L3 | 491 | 492 | experimental:450 |
Rv0640 rplK |
50S ribosomal protein L11 | 491 | 492 | experimental:461 |
Rv0715 rplX |
50S ribosomal protein L24 | 483 | 484 | experimental:453 |
Rv0723 rplO |
50S ribosomal protein L15 | 481 | 482 | experimental:453 |
Rv1063c |
NTE family protein | 474 | 474 ctx | neighborhood:472 |
Rv2643 arsC |
arsenic-transport integral membrane protein ArsC | 468 | 445 |
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: rhodanese-like domain-containing protein
- Pfam (hmmscan --cut_ga): Rhodanese PF00581.26 (E=4e-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_215582.1)
- Domains: Pfam-A via hmmscan --cut_ga — Rhodanese (PF00581.26)
- 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
COG0607 - Curated reference: UniProt O53414 (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 —
43 functional partner(s); context anchor
lpqV - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001146|Rv1066| MSRIDRVLEAARRRYRRLAADQVPEAARRGAVLVDIRPQAQRAREGEVPGALVIERNVLEWRCDPTSDARLPQAVDDDVEWVILCSEGYTSSLAAASLLDLGLHRATDVVGGYRALAAGGVLAELGGAVGG