Rv0455c Family assigned · low
H37Rv Rv0455c · MTBC0 mtbc0_000477 ·
148 aa · 548740–549186 (-) ·
RefSeq NP_214969.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF5078 domain-containing protein |
| Revised (this work) | DUF5078; structure solved (PDB 8DRI, Rv0455c); fold characterised, function not established. |
Curated reference (UniProt)
| UniProt |
O53740
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 | Domain of unknown function (DUF5078) |
| Orthologous group | 2ARRN |
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 |
|---|---|---|---|---|
DUF5078 | PF16877.11 | 5.1e-54 | 33–147 | Domain of unknown function (DUF5078) |
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 85.0 (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 |
|---|---|---|---|---|
8dri-assembly2_B |
1.00 | 0.93 | 1.7e-15 sig | 8dri-assembly2_B Structure of Rv0455c from Mycobacterium tuberculosis |
7ref-assembly2_B |
1.00 | 0.86 | 3.9e-10 sig | 7ref-assembly2_B Structure of MS3494 from Mycobacterium smegmatis |
7ohp-assembly1_b |
0.02 | 0.23 | 7.0e+00 | 7ohp-assembly1_b Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL25 expression shut down, population A |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: echA2 (enoyl-CoA hydratase EchA2), high confidence from genomic context alone (score 796 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) |
|---|---|---|---|---|
Rv0456c echA2 |
enoyl-CoA hydratase EchA2 | 796 | 796 ctx | neighborhood:795 |
Rv0457c |
peptidase | 635 | 636 ctx | neighborhood:635 |
Rv0397A hyp |
hypothetical protein | 461 | 461 ctx | neighborhood:461 |
Rv0559c hyp |
hypothetical protein | 665 | 73 | textmining:654 |
Rv0338c |
iron-sulfur-binding reductase | 662 | 68 | textmining:653 |
Rv0489 gpm1 |
2,3-bisphosphoglycerate-dependent phosphoglycerate mutase | 443 | 55 | textmining:435 |
Rv0511 hemD |
uroporphyrin-III C-methyltransferase | 516 | 52 | textmining:511 |
Rv0677c mmpS5 |
membrane protein MmpS5 | 520 | 50 | textmining:516 |
Rv0676c mmpL5 |
transmembrane transport protein MmpL5 | 514 | 50 | textmining:510 |
Rv0560c |
benzoquinone methyltransferase | 434 | 47 | textmining:431 |
Rv1127c ppdK |
pyruvate, phosphate dikinase PpdK | 505 | 46 | textmining:503 |
Rv1338 murI |
glutamate racemase | 425 | 46 | textmining:422 |
Rv2047c hyp |
hypothetical protein | 657 | 42 | textmining:657 |
Rv1085c |
hemolysin-like protein | 652 | 41 | textmining:652 |
Rv1432 |
dehydrogenase | 630 | 41 | textmining:630 |
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: DUF5078 domain-containing protein
- Pfam: DUF5078 PF16877.11
- Foldseek best: 8dri-assembly2_B Structure of Rv0455c from Mycobacterium tuberculosis (prob 1.00, E=2e-15, TM=0.93)
- (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_214969.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF5078 (PF16877.11)
- 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
2ARRN - Curated reference: UniProt O53740 (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 85.0, confident)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
15 functional partner(s); context anchor
echA2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000477|Rv0455c| MSRLSSILRAGAAFLVLGIAAATFPQSAAADSTEDFPIPRRMIATTCDAEQYLAAVRDTSPVYYQRYMIDFNNHANLQQATINKAHWFFSLSPAERRDYSEHFYNGDPLTFAWVNHMKIFFNNKGVVAKGTEVCNGYPAGDMSVWNWA