Rv1312 Still unknown · low
H37Rv Rv1312 · MTBC0 mtbc0_001404 ·
147 aa · 1476727–1477170 (+) ·
RefSeq NP_215828.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF2550 domain-containing protein |
| Revised (this work) | DUF2550; Foldseek best hit (PH domain, TM 0.46) not conclusive. Function unknown. |
Curated reference (UniProt)
| UniProt |
P9WM29
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv1312 |
UniProt still lists this protein as Uncharacterized protein Rv1312; 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 (DUF2550) |
| Orthologous group | 2E6YX |
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) pseudogene candidate
| pN/pS | 0.173 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 1 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 10.67% of strains (15493) · clonal |
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 |
|---|---|---|---|---|
DUF2550 | PF10739.16 | 3.6e-40 | 11–139 | Protein of unknown function (DUF2550) |
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 93.0 (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 |
|---|---|---|---|---|
5l81-assembly1_A |
1.00 | 0.46 | 1.2e-03 sig | 5l81-assembly1_A Crystal structure of the PH domain of murine kindlin-3 |
3voq-assembly1_B |
1.00 | 0.57 | 5.8e-03 sig | 3voq-assembly1_B Crystal structure of the pleckstrin homology domain of human Sin1, a TORC2 subunit |
7lc1-assembly2_D |
1.00 | 0.53 | 3.2e-03 sig | 7lc1-assembly2_D Crystal Structure of KRAS4b (GMPPNP-bound) in complex with the RBD-PH domains of SIN1 |
5l81-assembly2_B |
1.00 | 0.59 | 1.3e-02 | 5l81-assembly2_B Crystal structure of the PH domain of murine kindlin-3 |
3voq-assembly1_A |
1.00 | 0.54 | 9.6e-03 sig | 3voq-assembly1_A Crystal structure of the pleckstrin homology domain of human Sin1, a TORC2 subunit |
6nf1-assembly1_A |
1.00 | 0.58 | 1.5e-02 | 6nf1-assembly1_A Vav1 inhibited by an allosteric inhibitor: Vav1 inhibitors block GEF activity |
3bji-assembly1_A |
1.00 | 0.58 | 2.2e-02 | 3bji-assembly1_A Structural Basis of Promiscuous Guanine Nucleotide Exchange by the T-Cell Essential Vav1 |
6new-assembly1_A |
1.00 | 0.59 | 2.7e-02 | 6new-assembly1_A Apo structure of the activated truncation of Vav1 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: atpC (ATP synthase subunit epsilon), high confidence from genomic context alone (score 881 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) |
|---|---|---|---|---|
Rv1311 atpC |
ATP synthase subunit epsilon | 881 | 881 ctx | neighborhood:881 |
Rv1309 atpG |
ATP synthase subunit gamma | 812 | 812 ctx | neighborhood:812 |
Rv1308 atpA |
ATP synthase subunit alpha | 812 | 812 ctx | neighborhood:812 |
Rv1310 atpD |
ATP synthase subunit beta | 812 | 812 ctx | neighborhood:812 |
Rv1305 atpE |
ATP synthase subunit C | 737 | 738 ctx | neighborhood:738 |
Rv3268 hyp |
hypothetical protein | 697 | 697 ctx | cooccurence:697 |
Rv1307 atpH |
ATP synthase subunit b/delta | 632 | 632 ctx | neighborhood:632 |
Rv3244c lpqB |
lipoprotein LpqB | 632 | 632 ctx | cooccurence:632 |
Rv2712c hyp |
hypothetical protein | 612 | 612 ctx | cooccurence:612 |
Rv1306 atpF |
ATP synthase subunit B | 603 | 603 ctx | neighborhood:603 |
Rv2342 hyp |
hypothetical protein | 545 | 545 ctx | cooccurence:545 |
Rv3910 murJ |
peptidoglycan biosynthesis protein | 630 | 534 ctx | cooccurence:534 |
Rv0862c hyp |
hypothetical protein | 497 | 497 ctx | cooccurence:497 |
Rv1304 atpB |
ATP synthase subunit A | 494 | 494 ctx | neighborhood:494 |
Rv2518c ldtB |
L,D-transpeptidase LdtB | 493 | 493 ctx | cooccurence:493 |
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: DUF2550 domain-containing protein
- Pfam: DUF2550 PF10739.16
- Foldseek best: 5l81-assembly1_A Crystal structure of the PH domain of murine kindlin-3 (prob 1.00, E=1e-03, TM=0.46)
- (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_215828.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF2550 (PF10739.16)
- 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
2E6YX - Curated reference: UniProt P9WM29 (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 93.0, very high)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
37 functional partner(s); context anchor
atpC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001404|Rv1312| MSAPMIGMVVLVVVLGLAVLALSYRLWKLRQGGTAGIMRDIPAVGGHGWRHGVIRYRGGEAAFYRLSSLRLWPDRRLSRRGVEIISRRAPRGDEFDIMTDEIVVVELCDSTQDRRVGYEIALDRGALTAFLSWLESRPSPRARRRSM