Rv0481c Family assigned · low
H37Rv Rv0481c · MTBC0 mtbc0_000506 ·
174 aa · 573353–573877 (-) ·
RefSeq NP_214995.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF2505 domain-containing protein |
| Revised (this work) | DUF2505; ESMFold matches a START-like / Ups1 lipid-transfer fold (PDB 5JQM); putative lipid-binding protein. |
Curated reference (UniProt)
| UniProt |
P9WKV5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv0481c |
UniProt still lists this protein as Uncharacterized protein Rv0481c; 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 (DUF2505) |
| Orthologous group | 2ED3C |
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, 3 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 |
|---|---|---|---|---|
DUF2505 | PF10698.16 | 1.7e-45 | 7–170 | Protein of unknown function (DUF2505) |
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 95.8 (very high). 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 |
|---|---|---|---|---|
5jqm-assembly1_B |
1.00 | 0.66 | 2.4e-07 sig | 5jqm-assembly1_B Crystal Structure of Phosphatidic acid Transporter Ups1/Mdm35 Void of Bound Phospholipid from Saccharomyces Cerevisiae at 1.5 Angstroms Resolution |
8ag0-assembly1_A |
1.00 | 0.63 | 1.0e-07 sig | 8ag0-assembly1_A Crystal structure of mutant PRELID3a-TRIAP1 complex - R53E |
2d4r-assembly1_A |
1.00 | 0.69 | 3.7e-07 sig | 2d4r-assembly1_A Crystal structure of TTHA0849 from Thermus thermophilus HB8 |
6cay-assembly1_A |
1.00 | 0.76 | 4.5e-06 sig | 6cay-assembly1_A Crystal structure of the first StART-like domain of Ysp2p/Lam2p in its apo and ergosterol-bound state. |
5jqm-assembly1_C |
1.00 | 0.64 | 8.3e-07 sig | 5jqm-assembly1_C Crystal Structure of Phosphatidic acid Transporter Ups1/Mdm35 Void of Bound Phospholipid from Saccharomyces Cerevisiae at 1.5 Angstroms Resolution |
5jqm-assembly1_A |
1.00 | 0.65 | 1.8e-06 sig | 5jqm-assembly1_A Crystal Structure of Phosphatidic acid Transporter Ups1/Mdm35 Void of Bound Phospholipid from Saccharomyces Cerevisiae at 1.5 Angstroms Resolution |
6byd-assembly1_A |
1.00 | 0.76 | 6.0e-05 sig | 6byd-assembly1_A Crystal structure of the second StART domain of yeast Lam4 |
6v8j-assembly4_D |
1.00 | 0.60 | 2.0e-06 sig | 6v8j-assembly4_D Crystal structure of Ara h 8.0201 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0479c (membrane protein), high confidence from genomic context alone (score 877 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) |
|---|---|---|---|---|
Rv0479c |
membrane protein | 876 | 877 ctx | neighborhood:741 cooccurence:544 |
Rv0483 lprQ |
lipoprotein LprQ | 809 | 809 ctx | neighborhood:734 |
Rv0482 murB |
UDP-N-acetylenolpyruvoylglucosamine reductase | 792 | 792 ctx | neighborhood:790 |
Rv0996 |
transmembrane protein | 767 | 768 ctx | cooccurence:767 |
Rv0556 |
transmembrane protein | 764 | 765 ctx | cooccurence:764 |
Rv1109c hyp |
hypothetical protein | 764 | 765 ctx | cooccurence:764 |
Rv3212 hyp |
hypothetical protein | 760 | 761 ctx | cooccurence:754 |
Rv2091c |
membrane protein | 750 | 750 ctx | cooccurence:750 |
Rv2446c |
integral membrane protein | 747 | 747 ctx | cooccurence:747 |
Rv0480c |
amidohydrolase | 744 | 745 ctx | neighborhood:741 |
Rv0475 hbhA |
heparin binding hemagglutinin HbhA | 743 | 743 ctx | cooccurence:741 |
Rv3850 hyp |
hypothetical protein | 742 | 743 ctx | cooccurence:741 |
Rv3438 hyp |
hypothetical protein | 741 | 742 ctx | cooccurence:740 |
Rv0358 hyp |
hypothetical protein | 739 | 739 ctx | cooccurence:738 |
Rv0863 hyp |
hypothetical protein | 735 | 735 ctx | cooccurence:735 |
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: DUF2505 domain-containing protein
- Pfam: DUF2505 PF10698.16
- Foldseek best: 5jqm-assembly1_B Crystal Structure of Phosphatidic acid Transporter Ups1/Mdm35 V (prob 1.00, E=2e-07, TM=0.66)
- (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_214995.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF2505 (PF10698.16)
- 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
2ED3C - Curated reference: UniProt P9WKV5 (SwissProt, reviewed; 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 95.8, very high)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
95 functional partner(s); context anchor
Rv0479c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000506|Rv0481c| MPRSFDMSADYEGSVEEVHRAFYEADYWKARLAETPVDVATLESIRVGGDSGDDGTIEVVTLQMVRSHNLPGLVTQLHRGDLSVRREETWGPVKEGIATASIAGSIVDAPVNLWGTAVLSPIPESGGSRMTLQVTIQVRIPFIGGKLERLIGTQLSQLVTIEQRFTTLWITNNV