Rv0611c Still unknown · low
H37Rv Rv0611c · MTBC0 mtbc0_000643 ·
73 aa · 709513–709734 (-) ·
RefSeq NP_215125.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF4926 domain-containing protein |
| Revised (this work) | Conserved hypothetical; function unknown. Structure-based hint rejected: weak fold echo (SH3 beta-barrel, eukaryotic); function unknown. |
Curated reference (UniProt)
| UniProt |
I6XVR9
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | DUF4926 domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Domain of unknown function (DUF4926) |
| Orthologous group | 2EHRH |
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 | 0.741 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 2 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 |
|---|---|---|---|---|
DUF4926 | PF16277.12 | 1.1e-21 | 4–59 | Domain of unknown function (DUF4926) |
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 70.1 (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 |
|---|---|---|---|---|
1wfw-assembly1_A |
1.00 | 0.60 | 1.2e-02 | 1wfw-assembly1_A Solution structure of SH3 domain of mouse Kalirin-9a protein |
8bnv-assembly1_A |
1.00 | 0.69 | 2.1e-02 | 8bnv-assembly1_A Crystal structure of Pif1 from Deferribacter desulfuricans in apo from |
3gpl-assembly2_B |
1.00 | 0.66 | 7.6e-02 | 3gpl-assembly2_B Crystal structure of the ternary complex of RecD2 with DNA and ADPNP |
3e1s-assembly1_A |
0.99 | 0.67 | 1.8e-01 | 3e1s-assembly1_A Structure of an N-terminal truncation of Deinococcus radiodurans RecD2 |
2kgt-assembly1_A |
0.98 | 0.63 | 1.1e-01 | 2kgt-assembly1_A Solution structure of SH3 domain of PTK6 |
2ke9-assembly1_A |
0.98 | 0.63 | 1.2e-01 | 2ke9-assembly1_A NMR solution structure of the CASKIN SH3 domain |
8b1t-assembly1_D |
0.97 | 0.53 | 6.8e-02 | 8b1t-assembly1_D RecBCD-DNA in complex with the phage protein Abc2 |
1v1c-assembly1_A |
0.89 | 0.62 | 3.6e-01 | 1v1c-assembly1_A Solution Structure of the SH3 domain of Obscurin |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapC24 (ribonuclease VapC24), medium confidence from genomic context alone (score 522 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) |
|---|---|---|---|---|
Rv0610c hyp |
hypothetical protein | 667 | 667 ctx | neighborhood:662 |
Rv0612 hyp |
hypothetical protein | 582 | 582 ctx | neighborhood:579 |
Rv0240 vapC24 |
ribonuclease VapC24 | 521 | 522 ctx | cooccurence:516 |
Rv2549c vapC20 |
ribonuclease VapC20 | 517 | 518 ctx | cooccurence:515 |
Rv1397c vapC10 |
ribonuclease VapC10 | 514 | 514 ctx | cooccurence:511 |
Rv0355c PPE8 |
PPE family protein PPE8 | 472 | 473 ctx | cooccurence:470 |
Rv3081 hyp |
hypothetical protein | 456 | 456 ctx | cooccurence:456 |
Rv3350c PPE56 |
PPE family protein PPE56 | 433 | 433 ctx | cooccurence:433 |
Rv3347c PPE55 |
PPE family protein PPE55 | 431 | 432 ctx | cooccurence:430 |
Rv2490c PE_PGRS43 |
PE-PGRS family protein PE_PGRS43 | 426 | 426 ctx | cooccurence:426 |
Rv1651c PE_PGRS30 |
PE-PGRS family protein PE_PGRS30 | 426 | 426 ctx | cooccurence:426 |
Rv0872c PE_PGRS15 |
PE-PGRS family protein PE_PGRS15 | 425 | 425 ctx | cooccurence:425 |
Rv1917c PPE34 |
PPE family protein PPE34 | 416 | 417 ctx | cooccurence:416 |
Rv2949c |
chorismate pyruvate-lyase | 414 | 415 ctx | cooccurence:411 |
Rv2209 |
integral membrane protein | 403 | 404 ctx | cooccurence:400 |
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
- Structural Foldseek hit not propagated -- weak fold echo (SH3 beta-barrel, eukaryotic); function unknown
- Reviewed against literature (extended structural cross-check, 2026-06-02)
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_215125.2)
- Domains: Pfam-A via hmmscan --cut_ga — DUF4926 (PF16277.12)
- 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
2EHRH - Curated reference: UniProt I6XVR9 (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 70.1, 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
vapC24 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000643|Rv0611c| MYAEHDVVVLTRDVPDKSLIAGDVGAVVGRYAAGGYEVDFTAANGCTVAVVTLAGDDIRPRRRREIPHVREVA