Rv2113 Family assigned · low auto-curated
H37Rv Rv2113 · MTBC0 mtbc0_002245 ·
397 aa · 2399893–2401086 (+) ·
RefSeq NP_216629.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | integral membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | integral membrane protein |
| Revised (this work) | Integral membrane protein. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O33248
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable integral membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 28ND6 |
|---|
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 | 1.322 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 7 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).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0538 (membrane protein), high confidence from genomic context alone (score 755 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2114 hyp |
hypothetical protein | 924 | 924 ctx | neighborhood:874 cooccurence:418 |
Rv0538 |
membrane protein | 755 | 755 ctx | cooccurence:752 |
Rv3903c cpnT hyp |
hypothetical protein | 745 | 746 ctx | cooccurence:743 |
Rv1775 hyp |
hypothetical protein | 740 | 741 ctx | cooccurence:740 |
Rv1963c mce3R |
transcriptional repressor Mce3R | 720 | 720 ctx | cooccurence:716 |
Rv1937 |
oxygenase | 682 | 682 ctx | cooccurence:679 |
Rv3732 hyp |
hypothetical protein | 679 | 680 ctx | cooccurence:678 |
Rv3788 hyp |
hypothetical protein | 673 | 674 ctx | cooccurence:667 |
Rv2761c hsdS |
type I restriction/modification system specificity determinant HsdS | 620 | 620 ctx | cooccurence:618 |
Rv2843 hyp |
hypothetical protein | 620 | 620 ctx | cooccurence:618 |
Rv0493c hyp |
hypothetical protein | 609 | 609 ctx | cooccurence:607 |
Rv0444c rskA |
anti-sigma-K factor RskA | 592 | 592 ctx | cooccurence:587 |
Rv2939 papA5 |
phthiocerol/phthiodiolone dimycocerosyl transferase | 591 | 592 ctx | cooccurence:588 |
Rv2112c dop |
pup deamidase/depupylase | 586 | 585 ctx | neighborhood:581 |
Rv1024 |
membrane protein | 573 | 574 ctx | cooccurence:571 |
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: integral membrane protein
- MTBC0 PGAP product: integral membrane protein
- (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_216629.1)
- 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
28ND6 - Curated reference: UniProt O33248 (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 —
37 functional partner(s); context anchor
Rv0538 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002245|Rv2113| MSLSVRRPPAARAAAIVEAESWFLKRGLPSVLTMRGRCRRLWPRSAPMLAAWAVVEGCLMAVFFVTDGGEVFISATPTTAQWVILALLAVALPLASLVGWLVSQISSGRGQAAVATMAVAFAAASDVIESGPIQLLRTAVVVGLVLLQTGCGVGSVLGWAVRMTLEHLATVGTLAVRALPIVLLTALVFFNTYVWLMAANINGERLTLAMVFLLAIAGAFVVSKTVERVRPLLRSTTVMPQGSQSLAGTPFATMGDPSPGFPLTRAERLNVVFLLAASQLVEILVVASVGAAIYLVLGMIILTPPLLREWTHYDSMTTTVLGMTFPAPDSLIRMCLFLGALTFMYISARAVDDAEYRAMFLDPLIDDLHTALLARNRYRNNVVTAPCAGVDAGHVDD