Rv2709 Still unknown · low auto-curated
H37Rv Rv2709 · MTBC0 mtbc0_002883 ·
148 aa · 3044254–3044700 (+) ·
RefSeq NP_217225.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF3099 domain-containing protein |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF3099. Function unknown. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6YA25
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable conserved transmembrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Protein of unknown function (DUF3099) |
| Orthologous group | 2EGIC |
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 | 3.9 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 11 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 |
|---|---|---|---|---|
DUF3099 | PF11298.14 | 8.5e-28 | 33–104 | Protein of unknown function (DUF3099) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0007 (membrane protein), medium confidence from genomic context alone (score 682 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2708c hyp |
hypothetical protein | 820 | 820 ctx | neighborhood:788 |
Rv2164c hyp |
hypothetical protein | 770 | 770 ctx | cooccurence:769 |
Rv3909 hyp |
hypothetical protein | 751 | 751 ctx | cooccurence:751 |
Rv3835 hyp |
hypothetical protein | 749 | 749 ctx | cooccurence:741 |
Rv0007 |
membrane protein | 682 | 682 ctx | cooccurence:680 |
Rv2520c |
membrane protein | 679 | 679 ctx | cooccurence:679 |
Rv2710 sigB |
RNA polymerase sigma factor SigB | 678 | 678 ctx | neighborhood:676 |
Rv1209 hyp |
hypothetical protein | 669 | 669 ctx | cooccurence:669 |
Rv0339c iniR |
transcriptional regulator | 666 | 666 ctx | cooccurence:665 |
Rv1638A hyp |
hypothetical protein | 664 | 664 ctx | cooccurence:662 |
Rv2843 hyp |
hypothetical protein | 637 | 637 ctx | cooccurence:636 |
Rv2468c hyp |
hypothetical protein | 635 | 635 ctx | cooccurence:634 |
Rv1109c hyp |
hypothetical protein | 634 | 635 ctx | cooccurence:631 |
Rv1853 ureD |
urease accessory protein UreD | 629 | 629 ctx | cooccurence:629 |
Rv0343 iniC |
iIsoniazid inductible protein IniC | 624 | 625 ctx | cooccurence:619 |
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
- Legacy H37Rv annotation: transmembrane protein
- MTBC0 PGAP product: DUF3099 domain-containing protein
- Pfam (hmmscan --cut_ga): DUF3099 PF11298.14 (E=8e-28)
- (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_217225.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF3099 (PF11298.14)
- 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
2EGIC - Curated reference: UniProt I6YA25 (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)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
64 functional partner(s); context anchor
Rv0007 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002883|Rv2709| MWDSRVMKHGLRLGFNGQFDDFDDFDDKGRPVLITAAAPSYEVEHRTRVRKYLTLMAFRVPALILAAIAYGAWHNGLISLLIVAASVPLPWMAVLIANDRPPRRADEPRRFDVARRRIPLFPTAERPALEPRRQPAERSAPRGFADHG