Rv2100 Still unknown · low auto-curated
H37Rv Rv2100 · MTBC0 - ·
550 aa · 2358389–2360041 (+) ·
RefSeq NP_216616.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF222. Function unknown. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WLJ3
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Uncharacterized protein Rv2100 |
UniProt still lists this protein as Uncharacterized protein Rv2100; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
V Defense mechanisms
|
|---|---|
| eggNOG description | HNH endonuclease |
| Orthologous group | COG1403 |
| Gene Ontology (8) |
GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0016020, GO:0030312, GO:0044464, GO:0071944
|
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 | 0.598 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 10 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.12% of strains (174) · 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 |
|---|---|---|---|---|
DUF222 | PF02720.23 | 3.2e-53 | 66–321 | Domain of unknown function (DUF222) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: PE_PGRS36 (PE-PGRS family protein PE_PGRS36; Rv2098c, (MTCY49.38c), len: 434 aa. PE_PGRS36,Member of the Mycobacterium tuberculosis PE family, PGRS sub), medium confidence from genomic context alone (score 646 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) |
|---|---|---|---|---|
Rv3074 hyp |
hypothetical protein | 927 | 800 | coexpression:730 textmining:652 |
Rv3776 hyp |
hypothetical protein | 801 | 800 | coexpression:798 |
Rv1765c hyp |
hypothetical protein | 771 | 771 ctx | cooccurence:759 |
Rv2015c hyp |
hypothetical protein | 769 | 770 ctx | cooccurence:761 |
Rv0094c hyp |
hypothetical protein | 732 | 733 ctx | cooccurence:677 |
Rv1148c hyp |
hypothetical protein | 942 | 717 ctx | cooccurence:680 textmining:805 |
Rv3467 hyp |
hypothetical protein | 706 | 707 ctx | cooccurence:677 |
Rv1587c hyp |
hypothetical protein | 703 | 704 ctx | cooccurence:695 |
Rv1945 hyp |
hypothetical protein | 939 | 701 ctx | cooccurence:684 textmining:805 |
Rv1128c hyp |
hypothetical protein | 936 | 686 ctx | cooccurence:681 textmining:805 |
Rv1073 hyp |
hypothetical protein | 651 | 651 ctx | cooccurence:647 |
Rv2098c PE_PGRS36 |
PE-PGRS family protein PE_PGRS36; Rv2098c, (MTCY49.38c), len: 434 aa. PE_PGRS36,Member of the Mycobacterium tuberculosis PE family, PGRS sub | 646 | 646 ctx | neighborhood:505 |
Rv0756c hyp |
hypothetical protein | 604 | 605 ctx | cooccurence:599 |
Rv1157c hyp |
hypothetical protein | 595 | 595 ctx | cooccurence:593 |
Rv2721c hyp |
hypothetical protein | 591 | 591 ctx | cooccurence:591 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): hypothetical protein
- Pfam (hmmscan --cut_ga): DUF222 PF02720.23 (E=3e-53)
- (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_216616.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF222 (PF02720.23)
- 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
COG1403 - Curated reference: UniProt P9WLJ3 (SwissProt, reviewed; Inferred from homology)
- 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 —
56 functional partner(s); context anchor
PE_PGRS36 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2100| MAGALFEPSFAAAHPAGLLRRPVTRTVVLSVAATSIAHMFEISLPDPTELCRSDDGALVAAIEDCARVEAAASARRLSAIAELTGRRTGADQRADWACDFWDCAAAEVAAALTISHGKASGQMHLSLALNRLPQVAALFLAGHLGARLFSIIAWRTYLVRDPHALSLLDAALAEHAGAWGPLSAPKLEKAIDSWIDRYDPGALRRSRISARTRDLCIGDPDEDAGTAALWGRLYATDAAMLDRRLTEMAHGVCEDDPRTLAQRRADALGALAAGADHLACGCGKPDCPSGAGNDERAAGVVIHVVADASALDAQPDPHLSGDEPPSRPLTPETTLFEALTPDPEPDPPATHAPAELITTGGGVVPAPLLAELIRGGATISQVRHPGDLAAEPHYRPSAKLAEFVRMRDLTCRFPGCDVPAEFCDIDHSAPWPLGPTHPSNLKCACRKHHLLKTFWTGWRDVQLPDGTVIWTAPNGHTYTTHPGSRIFFPTWHTTTAELPQTSTAAVNVDARGLMMPRRRRTRAAELAHRINAERALNDAYMAERNKPPSF