Rv3258c Still unknown · low auto-curated
H37Rv Rv3258c · MTBC0 - ·
163 aa · 3638811–3639302 (-) ·
RefSeq NP_217775.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF3499. Function unknown. Foldseek best (non-significant) hit: 6wwa-assembly2_Y Crystal structure of human SHLD2-SHLD3-REV7 complex (prob 0.02, TM 0.13). |
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 |
O53351
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | DUF3499 domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Protein of unknown function (DUF3499) |
| Orthologous group | 2C7XW |
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.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
DUF3499 | PF12005.14 | 1.4e-45 | 22–160 | Protein of unknown function (DUF3499) |
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 85.8 (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 |
|---|---|---|---|---|
6wwa-assembly2_Y |
0.02 | 0.13 | 3.8e+00 | 6wwa-assembly2_Y Crystal structure of human SHLD2-SHLD3-REV7 complex |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0007 (membrane protein), high confidence from genomic context alone (score 707 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) |
|---|---|---|---|---|
Rv3259 hyp |
hypothetical protein | 806 | 806 ctx | neighborhood:777 |
Rv3587c |
membrane protein | 798 | 798 | coexpression:798 |
Rv0129c fbpC |
diacylglycerol acyltransferase/mycolyltransferase Ag85C | 740 | 740 | coexpression:740 |
Rv0007 |
membrane protein | 707 | 707 ctx | cooccurence:703 |
Rv2256c hyp |
hypothetical protein | 698 | 687 ctx | cooccurence:670 |
Rv1024 |
membrane protein | 668 | 668 ctx | cooccurence:666 |
Rv2917 hyp |
hypothetical protein | 660 | 660 ctx | cooccurence:660 |
Rv3260c whiB2 |
transcriptional regulator WhiB2 | 657 | 658 | coexpression:449 |
Rv3257c pmmA |
phosphomannomutase PmmA | 629 | 630 ctx | neighborhood:618 |
Rv3255c manA |
mannose-6-phosphate isomerase | 641 | 624 ctx | neighborhood:618 |
Rv3256c hyp |
hypothetical protein | 622 | 623 ctx | neighborhood:618 |
Rv2146c |
transmembrane protein | 558 | 559 ctx | cooccurence:552 |
Rv2033c hyp |
hypothetical protein | 528 | 528 ctx | cooccurence:505 |
Rv0430 hyp |
hypothetical protein | 522 | 504 | |
Rv0538 |
membrane protein | 499 | 500 ctx | cooccurence:495 |
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): DUF3499 PF12005.14 (E=1e-45)
- Foldseek best: 6wwa-assembly2_Y Crystal structure of human SHLD2-SHLD3-REV7 complex (prob 0.02, E=4e+00, TM=0.13)
- (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_217775.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF3499 (PF12005.14)
- 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
2C7XW - Curated reference: UniProt O53351 (TrEMBL, unreviewed; Predicted)
- Model confidence: ESMFold per-residue pLDDT (mean 85.8, confident)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
29 functional partner(s); context anchor
Rv0007 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3258c| MRVSGASAALVHDSLSVVNVPRRCCRPGCPHYAVATLTFVYSDSTAVIGPLATAREPHSWDLCVGHAGRITAPRGWELVRHAGPLPSHPDEDDLVALADAVREGGPSAGRRHHPGGNGAPLHGFDDFPAAATGAPTGGGVLAPPEPGAGRRRGHLRVLPDPAD