Rv1780 Family assigned · low
H37Rv Rv1780 · MTBC0 mtbc0_001894 ·
187 aa · 2032710–2033273 (+) ·
RefSeq NP_216296.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | BPI/SPLUNC1-like lipid-binding fold (PDB 5I7L); putative lipid-binding protein. |
Curated reference (UniProt)
| UniProt |
O53931
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2ESGC |
|---|
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 | 0.34 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 1 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).
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 90.9 (very high). A confident model makes the fold comparison meaningful.
Best matches against the PDB, ranked by Foldseek homology probability. A high probability / TM-score suggests a shared fold; unless flagged sig (E < 0.01) these are fold hypotheses, not assignments.
| Target | Prob | TM | E-value | Description |
|---|---|---|---|---|
5i7l-assembly3_A |
1.00 | 0.60 | 4.8e-04 sig | 5i7l-assembly3_A Crystal Structure of SPLUNC1 Disulfide Mutant M2 (A48C, V253C) |
6baq-assembly3_C |
1.00 | 0.62 | 1.9e-03 sig | 6baq-assembly3_C Mus musculus BPIFA1 |
6baq-assembly1_A |
1.00 | 0.58 | 2.2e-03 sig | 6baq-assembly1_A Mus musculus BPIFA1 |
6baq-assembly2_B |
1.00 | 0.57 | 2.1e-03 sig | 6baq-assembly2_B Mus musculus BPIFA1 |
6baq-assembly8_H |
1.00 | 0.49 | 1.4e-03 sig | 6baq-assembly8_H Mus musculus BPIFA1 |
6baq-assembly6_F |
1.00 | 0.54 | 2.4e-03 sig | 6baq-assembly6_F Mus musculus BPIFA1 |
6baq-assembly7_G |
0.99 | 0.42 | 1.6e-03 sig | 6baq-assembly7_G Mus musculus BPIFA1 |
6baq-assembly5_E |
0.99 | 0.45 | 4.9e-03 sig | 6baq-assembly5_E Mus musculus BPIFA1 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lipE (lipase LipE), medium confidence from genomic context alone (score 644 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) |
|---|---|---|---|---|
Rv2042c hyp |
hypothetical protein | 757 | 757 ctx | cooccurence:725 |
Rv2342 hyp |
hypothetical protein | 756 | 756 ctx | cooccurence:755 |
Rv3707c hyp |
hypothetical protein | 670 | 670 ctx | cooccurence:670 |
Rv0817c lmeA hyp |
hypothetical protein | 668 | 668 ctx | cooccurence:668 |
Rv0466 hyp |
hypothetical protein | 653 | 653 ctx | cooccurence:652 |
Rv3775 lipE |
lipase LipE | 644 | 644 ctx | cooccurence:641 |
Rv1125 hyp |
hypothetical protein | 636 | 636 ctx | cooccurence:636 |
Rv0479c |
membrane protein | 627 | 628 ctx | cooccurence:624 |
Rv0185 hyp |
hypothetical protein | 615 | 615 ctx | cooccurence:615 |
Rv0356c hyp |
hypothetical protein | 589 | 589 ctx | cooccurence:589 |
Rv0383c ttfA hyp |
hypothetical protein | 571 | 571 ctx | cooccurence:571 |
Rv1610 |
membrane protein | 545 | 545 ctx | cooccurence:545 |
Rv1371 |
membrane protein | 540 | 540 ctx | cooccurence:540 |
Rv3035 hyp |
hypothetical protein | 527 | 527 ctx | cooccurence:526 |
Rv0184 hyp |
hypothetical protein | 524 | 524 ctx | cooccurence:524 |
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
- MTBC0 PGAP product: hypothetical protein
- Foldseek best: 5i7l-assembly3_A Crystal Structure of SPLUNC1 Disulfide Mutant M2 (A48C, V253C) (prob 1.00, E=5e-04, TM=0.60)
- (structure-only promotion reviewed by hand, 2026-06-01)
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_216296.1)
- 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
2ESGC - Curated reference: UniProt O53931 (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)
- Model confidence: ESMFold per-residue pLDDT (mean 90.9, very high)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
44 functional partner(s); context anchor
lipE - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001894|Rv1780| MQNHDYVTYEEFGRRFFEVAVTPDRVAAAFADIAGSEFAMEPISQGPGGIAKVSANVKIREPRVTRKLGDLITFVIHIPLSIDLLLDLRLDKQRFMVAGDIALRATARAAEPLLLIVDVAKPRPSDITVNVSSKSIRGEVLRILAGVDGEIRRFIAQYVSAEIDSPKSQAAQVINVAEQLDSTWSGP