Rv2972c Family assigned · medium auto-curated
H37Rv Rv2972c · MTBC0 mtbc0_003157 ·
237 aa · 3348198–3348911 (-) ·
RefSeq NP_217488.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | HNH endonuclease family protein |
| Revised (this work) | HNH endonuclease family protein. Pfam: GmrSD_C (PF07510.17). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6X5W6
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible conserved membrane or exported protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| eggNOG description | Protein of unknown function (DUF1524) |
| Orthologous group | COG2356 |
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 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 |
|---|---|---|---|---|
GmrSD_C | PF07510.17 | 4.3e-15 | 89–224 | GmrSD restriction endonucleases, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: recG (ATP-dependent DNA helicase RecG), high confidence from genomic context alone (score 929 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) |
|---|---|---|---|---|
Rv2973c recG |
ATP-dependent DNA helicase RecG | 929 | 929 ctx | neighborhood:881 coexpression:431 |
Rv2974c hyp |
hypothetical protein | 809 | 809 ctx | neighborhood:800 |
Rv2975c hyp |
hypothetical protein | 801 | 801 ctx | neighborhood:800 |
Rv3923c rnpA |
ribonuclease P protein component | 684 | 685 | coexpression:684 |
Rv3211 rhlE |
ATP-dependent RNA helicase RhlE | 600 | 575 | database:477 |
Rv1253 deaD |
ATP-dependent RNA helicase DeaD | 595 | 570 | database:477 |
Rv3859c gltB |
glutamate synthase large subunit | 617 | 544 ctx | neighborhood:544 |
Rv2390c hyp |
hypothetical protein | 520 | 502 | |
Rv1814 erg3 |
membrane-bound C-5 sterol desaturase | 497 | 498 | coexpression:498 |
Rv1362c |
membrane protein | 459 | 439 | |
Rv1363c |
membrane protein | 459 | 439 | |
Rv1972 |
Mce associated membrane protein | 458 | 437 | |
Rv0199 |
membrane protein | 457 | 437 | |
Rv1973 |
Mce associated membrane protein | 457 | 437 | |
Rv0178 |
Mce associated membrane protein | 457 | 437 |
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: HNH endonuclease family protein
- Pfam (hmmscan --cut_ga): GmrSD_C PF07510.17 (E=4e-15)
- (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_217488.1)
- Domains: Pfam-A via hmmscan --cut_ga — GmrSD_C (PF07510.17)
- 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
COG2356 - Curated reference: UniProt I6X5W6 (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 —
29 functional partner(s); context anchor
recG - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003157|Rv2972c| MNRRTLLWLSAIAALALVVAYQTLGSSAGRHADEFAARAGVPTVQPGADVLAGIAVLPKRIHRYDYRRSAFGHPWDDRNDAPGGHNGCDTRDDILDRDLVDKTYVSIKRCPNAVATGTLRDPYTNTTVAFQRGASVGQSVQIDHIVPLSYAWDMGAYRWPNSERMRFANDPANLLAVQGQANQDKGDSPPAQWMPPNKAFACQYAMQFIAVLRGYSLPVDQPSSDVLRQAAATCPTG