Rv2680 Still unknown · low auto-curated
H37Rv Rv2680 · MTBC0 mtbc0_002854 ·
210 aa · 3018520–3019152 (+) ·
RefSeq NP_217196.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF3000 domain-containing protein |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF3000. Function unknown. Foldseek best (non-significant) hit: 8any-assembly1_f Human mitochondrial ribosome in complex with LRPPRC, (prob 0.44, TM 0.39). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O86317
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)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Protein of unknown function (DUF3000) |
| Orthologous group | 2AIF4 |
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, 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
DUF3000 | PF11452.14 | 4.0e-72 | 23–202 | Protein of unknown function (DUF3000) |
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 88.0 (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 |
|---|---|---|---|---|
8any-assembly1_f |
0.44 | 0.39 | 6.8e-02 | 8any-assembly1_f Human mitochondrial ribosome in complex with LRPPRC, SLIRP, A-site, P-site, E-site tRNAs and mRNA |
5aj4-assembly1_AJ |
0.38 | 0.39 | 1.4e-01 | 5aj4-assembly1_AJ Structure of the 55S mammalian mitoribosome. |
6bok-assembly1_RA |
0.28 | 0.33 | 1.1e-01 | 6bok-assembly1_RA E. coli release factor 1 (containing deletion 302-304) bound to the 70S ribosome |
3fzb-assembly1_H |
0.25 | 0.40 | 2.0e-01 | 3fzb-assembly1_H Crystal structure of the tail terminator protein from phage lambda (gpU-WT) |
7nqh-assembly1_AJ |
0.21 | 0.39 | 4.3e-01 | 7nqh-assembly1_AJ 55S mammalian mitochondrial ribosome with mtRF1a and P-site tRNAMet |
6vmi-assembly1_f |
0.21 | 0.41 | 4.8e-01 | 6vmi-assembly1_f Structure of the human mitochondrial ribosome-EF-G1 complex (ClassIII) |
9d94-assembly1_If |
0.16 | 0.41 | 5.8e-01 | 9d94-assembly1_If Mycobacteriophage Bxb1 portal and connector assembly - Composite map and model |
8pk0-assembly1_f |
0.16 | 0.41 | 6.1e-01 | 8pk0-assembly1_f human mitoribosomal large subunit assembly intermediate 1 with GTPBP10-GTPBP7 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: echA15 (enoyl-CoA hydratase EchA15), high confidence from genomic context alone (score 753 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) |
|---|---|---|---|---|
Rv2681 hyp |
hypothetical protein | 974 | 975 ctx | neighborhood:882 coexpression:744 |
Rv2676c hemQ hyp |
hypothetical protein | 822 | 822 ctx | neighborhood:694 cooccurence:434 |
Rv2679 echA15 |
enoyl-CoA hydratase EchA15 | 753 | 753 ctx | neighborhood:747 |
Rv2413c hyp |
hypothetical protein | 738 | 739 ctx | cooccurence:738 |
Rv2256c hyp |
hypothetical protein | 743 | 733 ctx | cooccurence:728 |
Rv2050 rbpA |
RNA polymerase-binding protein RbpA | 733 | 733 ctx | cooccurence:733 |
Rv2219 |
transmembrane protein | 711 | 712 ctx | cooccurence:710 |
Rv2677c hemY |
protoporphyrinogen oxidase | 703 | 703 ctx | neighborhood:694 |
Rv2678c hemE |
uroporphyrinogen decarboxylase | 698 | 698 ctx | neighborhood:694 |
Rv2699c hyp |
hypothetical protein | 680 | 680 ctx | cooccurence:680 |
Rv2708c hyp |
hypothetical protein | 670 | 671 ctx | cooccurence:669 |
Rv2169c |
transmembrane protein | 670 | 670 ctx | cooccurence:670 |
Rv1830 |
HTH-type transcriptional regulator | 642 | 643 ctx | cooccurence:634 |
Rv2146c |
transmembrane protein | 641 | 641 ctx | cooccurence:637 |
Rv1087A |
Rv1087A, len: 106 aa (fragment). Conserved hypothetical protein, highly similar to C-terminus of near ORF O53434|YA86_MYCTU|Rv1086|MT1118|MT | 637 | 637 ctx | cooccurence:637 |
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: DUF3000 domain-containing protein
- Pfam (hmmscan --cut_ga): DUF3000 PF11452.14 (E=4e-72)
- Foldseek best: 8any-assembly1_f Human mitochondrial ribosome in complex with LRPPRC, SLIRP, A-s (prob 0.44, E=7e-02, TM=0.39)
- (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_217196.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF3000 (PF11452.14)
- 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
2AIF4 - Curated reference: UniProt O86317 (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 88.0, confident)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
53 functional partner(s); context anchor
echA15 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002854|Rv2680| MTSAGDDAERSDEEERRLTSAEPALFREAVAAMNAVTVRPEIELGPIRPPQRLAPYSYALGAEIKHPELDVIPERSEGDAFGRLIMLYDPDGSDAWDGTIRLVAYVQADLDSSEAVDPLLPEVAWSWLVDALTARTDQVRALGGTVTATTSVRYGDISGPPRAHQLELRASWTATTPDLGAHVQAFCDVLEHAAGLPPAGVTDLGSRSRA