Rv3678A Family assigned · low auto-curated · to review
H37Rv Rv3678A · MTBC0 - ·
53 aa · 4118530–4118691 (-) ·
RefSeq YP_178004.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | No Pfam domain above threshold; Foldseek indicates a fold similar to 8i0t-assembly1_C The cryo-EM structure of human Bact-III complex (prob 1.00, TM 0.82). Structure-based, putative. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed (flagged for human review).
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
I6X824
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | DUF4177 domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Domain of unknown function (DUF4177) |
| Orthologous group | 2E3JZ |
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)
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 73.0 (confident). 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 |
|---|---|---|---|---|
8i0t-assembly1_C |
1.00 | 0.82 | 2.1e-01 | 8i0t-assembly1_C The cryo-EM structure of human Bact-III complex |
8i0w-assembly1_C |
1.00 | 0.82 | 2.1e-01 | 8i0w-assembly1_C The cryo-EM structure of human C complex |
6ahd-assembly1_C |
1.00 | 0.81 | 2.5e-01 | 6ahd-assembly1_C The Cryo-EM Structure of Human Pre-catalytic Spliceosome (B complex) at 3.8 angstrom resolution |
3jb9-assembly1_B |
1.00 | 0.79 | 3.2e-01 | 3jb9-assembly1_B Cryo-EM structure of the yeast spliceosome at 3.6 angstrom resolution |
6icz-assembly1_C |
0.99 | 0.81 | 3.6e-01 | 6icz-assembly1_C Cryo-EM structure of a human post-catalytic spliceosome (P complex) at 3.0 angstrom |
5a9x-assembly1_A |
0.99 | 0.77 | 3.4e-01 | 5a9x-assembly1_A Structure of GDP bound BipA |
8h6e-assembly1_5C |
0.99 | 0.81 | 4.3e-01 | 8h6e-assembly1_5C Cryo-EM structure of human exon-defined spliceosome in the late pre-B state. |
4zck-assembly1_A |
0.99 | 0.80 | 5.1e-01 | 4zck-assembly1_A Crystal Structure of C-terminal Fragment of Escherichia coli BipA/TypA |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3677c (beta lactamase), high confidence from genomic context alone (score 869 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) |
|---|---|---|---|---|
Rv3678c hyp |
hypothetical protein | 875 | 875 ctx | neighborhood:867 |
Rv3677c |
beta lactamase | 869 | 869 ctx | neighborhood:867 |
Rv3679 |
anion transporter ATPase | 785 | 785 ctx | neighborhood:783 |
Rv3680 |
anion transporter ATPase | 785 | 785 ctx | neighborhood:783 |
Rv1211 hyp |
hypothetical protein | 773 | 773 ctx | cooccurence:770 |
Rv3597c lsr2 |
iron-regulated H-NS-like protein | 484 | 484 ctx | cooccurence:481 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): hypothetical protein
- Foldseek best: 8i0t-assembly1_C The cryo-EM structure of human Bact-III complex (prob 1.00, E=2e-01, TM=0.82)
- (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 YP_178004.1)
- 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
2E3JZ - Curated reference: UniProt I6X824 (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 73.0, confident)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
6 functional partner(s); context anchor
Rv3677c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3678A| MTQPTAWEYATVPLLTHATKQILDQWGADGWELVAVLPGPTGEQHVAYLKRPK