Rv2828A Still unknown · low auto-curated
H37Rv Rv2828A · MTBC0 - ·
89 aa · 3136330–3136599 (-) ·
RefSeq YP_007411535.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF2277. Function unknown. Foldseek best (non-significant) hit: 5wi4-assembly1_C CRYSTAL STRUCTURE OF DYNLT1/TCTEX-1 IN COMPLEX WITH A (prob 0.20, TM 0.63). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
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 |
I6YAC9
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | DUF2277 domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Uncharacterized conserved protein (DUF2277) |
| Orthologous group | COG5552 |
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 | 0.406 · 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
DUF2277 | PF10041.15 | 1.5e-33 | 1–84 | Uncharacterized conserved protein (DUF2277) |
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 81.7 (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 |
|---|---|---|---|---|
5wi4-assembly1_C |
0.20 | 0.63 | 5.9e+00 | 5wi4-assembly1_C CRYSTAL STRUCTURE OF DYNLT1/TCTEX-1 IN COMPLEX WITH ARHGEF2 |
8glv-assembly1_AR |
0.18 | 0.52 | 3.9e+00 | 8glv-assembly1_AR 96-nm repeat unit of doublet microtubules from Chlamydomonas reinhardtii flagella |
5wi4-assembly1_A |
0.18 | 0.64 | 6.6e+00 | 5wi4-assembly1_A CRYSTAL STRUCTURE OF DYNLT1/TCTEX-1 IN COMPLEX WITH ARHGEF2 |
5wi4-assembly1_B |
0.16 | 0.63 | 7.0e+00 | 5wi4-assembly1_B CRYSTAL STRUCTURE OF DYNLT1/TCTEX-1 IN COMPLEX WITH ARHGEF2 |
8bqs-assembly1_Eh |
0.16 | 0.66 | 8.8e+00 | 8bqs-assembly1_Eh Cryo-EM structure of the I-II-III2-IV2 respiratory supercomplex from Tetrahymena thermophila |
8glv-assembly1_MK |
0.15 | 0.62 | 7.4e+00 | 8glv-assembly1_MK 96-nm repeat unit of doublet microtubules from Chlamydomonas reinhardtii flagella |
3g80-assembly1_A |
0.11 | 0.40 | 6.2e+00 | 3g80-assembly1_A Nodamura virus protein b2, RNA-binding domain |
2ctw-assembly1_A |
0.09 | 0.41 | 5.6e+00 | 2ctw-assembly1_A Solution structure of J-domain from mouse DnaJ subfamily C menber 5 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapB22 (antitoxin VapB22), high confidence from genomic context alone (score 787 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) |
|---|---|---|---|---|
Rv2828c hyp |
hypothetical protein | 802 | 801 ctx | neighborhood:801 |
Rv2830c vapB22 |
antitoxin VapB22 | 786 | 787 ctx | neighborhood:787 |
Rv2829c vapC22 |
ribonuclease VapC22 | 786 | 787 ctx | neighborhood:787 |
Rv2831 echA16 |
enoyl-CoA hydratase EchA16 | 772 | 772 ctx | neighborhood:772 |
Rv3731 ligC |
DNA ligase C | 657 | 657 ctx | cooccurence:657 |
Rv1156 hyp |
hypothetical protein | 615 | 615 ctx | cooccurence:615 |
Rv2570 hyp |
hypothetical protein | 478 | 478 ctx | cooccurence:478 |
Rv0269c hyp |
hypothetical protein | 465 | 465 ctx | cooccurence:464 |
Rv3730c ligD hyp |
hypothetical protein | 456 | 456 ctx | cooccurence:455 |
Rv0938 ligD |
multifunctional non-homologous end joining DNA repair protein/ATP dependent DNA ligase LigD | 431 | 431 ctx | cooccurence:431 |
Rv2826c hyp |
hypothetical protein | 424 | 424 ctx | neighborhood:424 |
Rv2827c hyp |
hypothetical protein | 424 | 424 ctx | neighborhood:424 |
Rv0421c hyp |
hypothetical protein | 411 | 411 |
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
- Pfam (hmmscan --cut_ga): DUF2277 PF10041.15 (E=2e-33)
- Foldseek best: 5wi4-assembly1_C CRYSTAL STRUCTURE OF DYNLT1/TCTEX-1 IN COMPLEX WITH ARHGEF2 (prob 0.20, E=6e+00, TM=0.63)
- (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_007411535.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF2277 (PF10041.15)
- 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
COG5552 - Curated reference: UniProt I6YAC9 (TrEMBL, unreviewed; Predicted)
- 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 81.7, confident)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
13 functional partner(s); context anchor
vapB22 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2828A| MCRNITELRGLQPPATPVEIAAAARQYVRKVSGITHPSAATAEAFEAAVAEVTATTTRLLDALPPRRQPPKTVPPLRRPDVAARLAGSR