Rv1115 Still unknown · low auto-curated
H37Rv Rv1115 · MTBC0 mtbc0_001197 ·
232 aa · 1248627–1249325 (+) ·
RefSeq NP_215631.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Conserved hypothetical protein; no recognised domain. Function unknown. Foldseek best (non-significant) hit: 8gra-assembly1_G Structure of Type VI secretion system cargo delivery (prob 0.01, TM 0.14). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06567
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Possible exported protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| eggNOG description | NLP P60 protein |
| Orthologous group | COG0791 |
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 | 2.065 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 6 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 88.1 (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 |
|---|---|---|---|---|
8gra-assembly1_G |
0.01 | 0.14 | 7.8e+00 | 8gra-assembly1_G Structure of Type VI secretion system cargo delivery vehicle Hcp-VgrG-PAAR |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapB32 (antitoxin VapB32), medium confidence from genomic context alone (score 478 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) |
|---|---|---|---|---|
Rv1116 hyp |
hypothetical protein | 515 | 516 ctx | neighborhood:505 |
Rv1113 vapB32 |
antitoxin VapB32 | 478 | 478 ctx | neighborhood:472 |
Rv1114 vapC32 |
ribonuclease VapC32 | 478 | 477 ctx | neighborhood:472 |
Rv1111c hyp |
hypothetical protein | 902 | 281 | textmining:870 |
Rv3094c hyp |
hypothetical protein | 516 | 52 | textmining:511 |
Rv0987 |
adhesion component ABC transporter permease | 514 | 50 | textmining:510 |
Rv1500 pimF |
glycosyltransferase | 696 | 47 | textmining:695 |
Rv1811 mgtC |
Mg2+ transport P-type ATPase MgtC | 401 | 46 | |
Rv1145 mmpL13a |
transmembrane transport protein | 512 | 44 | textmining:511 |
Rv3407 vapB47 |
antitoxin VapB47 | 440 | 44 | textmining:439 |
Rv3447c eccC4 |
ESX-4 secretion system protein EccC4 | 864 | 41 | textmining:864 |
Rv0104 hyp |
hypothetical protein | 803 | 41 | textmining:803 |
Rv1396c PE_PGRS25 |
PE-PGRS family protein PE_PGRS25 | 652 | 41 | textmining:652 |
Rv1088 PE9 |
PE family protein PE9 | 651 | 41 | textmining:651 |
Rv0232 |
transcriptional regulator | 627 | 41 | textmining:627 |
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: hypothetical protein
- MTBC0 PGAP product: hypothetical protein
- Foldseek best: 8gra-assembly1_G Structure of Type VI secretion system cargo delivery vehicle Hc (prob 0.01, E=8e+00, TM=0.14)
- (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_215631.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
COG0791 - Curated reference: UniProt O06567 (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 88.1, confident)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
17 functional partner(s); context anchor
vapB32 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001197|Rv1115| MISTTRIDFLWILSVAFASMIALATLLTLINQVVGTPYIPGGDSPAGTDCSELASWVSNAATARPVFGDRFNTGNEEAALAARGFQQGTAPNALVIGWNGHHTAVTLPDGTPVSSGEGGGVRVGGGGAYQPKFTHHMYLPMDVDAGEDQPPAPDEPVTAVDDVEPEMPAPCPTQRPPVTPRHNLCNKLRTMPGALSAALAAAAPVWPAPISGCRGFSTSLLAKRNHPVIVGK