Rv0822c Family assigned · medium auto-curated
H37Rv Rv0822c · MTBC0 mtbc0_000871 ·
684 aa · 917324–919378 (-) ·
RefSeq NP_215337.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | LCP family protein |
| Revised (this work) | LCP family protein. Pfam: LytR_cpsA_psr (PF03816.20), LytR_C (PF13399.12). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6WZI4
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | cell envelope-related transcriptional attenuator |
| Orthologous group | COG1316 |
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 | 0.512 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
LytR_cpsA_psr | PF03816.20 | 1.8e-40 | 254–428 | LytR_cpsA_psr family |
LytR_C | PF13399.12 | 7.8e-17 | 557–641 | LytR cell envelope-related transcriptional attenuator |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: dusB (tRNA-dihydrouridine synthase), medium confidence from genomic context alone (score 673 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) |
|---|---|---|---|---|
Rv1171 hyp |
hypothetical protein | 711 | 712 ctx | cooccurence:709 |
Rv0823c dusB |
tRNA-dihydrouridine synthase | 673 | 673 ctx | neighborhood:569 |
Rv3847 hyp |
hypothetical protein | 672 | 672 ctx | cooccurence:671 |
Rv0821c phoY2 |
phosphate-transport system transcriptional regulator PhoY2 | 654 | 654 ctx | neighborhood:649 |
Rv3202c adnA |
ATP-dependent DNA helicase | 650 | 651 ctx | cooccurence:634 |
Rv0048c |
membrane protein | 649 | 649 ctx | cooccurence:649 |
Rv0875c hyp |
hypothetical protein | 633 | 633 ctx | cooccurence:628 |
Rv3779 |
transmembrane protein | 616 | 616 ctx | cooccurence:610 |
Rv3840 |
transcriptional regulator | 952 | 601 ctx | cooccurence:533 textmining:886 |
Rv3662c hyp |
hypothetical protein | 568 | 569 ctx | cooccurence:566 |
Rv2709 |
transmembrane protein | 542 | 543 ctx | cooccurence:540 |
Rv2164c hyp |
hypothetical protein | 541 | 542 ctx | cooccurence:539 |
Rv0825c hyp |
hypothetical protein | 533 | 533 ctx | neighborhood:532 |
Rv3435c |
transmembrane protein | 528 | 528 ctx | cooccurence:527 |
Rv0517 |
acyltransferase | 506 | 488 ctx | cooccurence:485 |
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: LCP family protein
- Pfam (hmmscan --cut_ga): LytR_cpsA_psr PF03816.20 (E=2e-40), LytR_C PF13399.12 (E=8e-17)
- (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_215337.1)
- Domains: Pfam-A via hmmscan --cut_ga — LytR_cpsA_psr (PF03816.20), LytR_C (PF13399.12)
- 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
COG1316 - Curated reference: UniProt I6WZI4 (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 —
51 functional partner(s); context anchor
dusB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000871|Rv0822c| MSDGESAAPWARLSESAFPDGVDRWITVPPATWVAAQGPRDTQNVGCHATGAVSVADLIARLGPAFPDLPTHRHVAPEPEPSGRGPKVPDDADDQQDTEAIAIPAHSLEFLSELPDLRAANYPRADHARREPELPGKQLTGSARVRPLRIRRTSPAPAKPAPNSGRRPMVLAARSLAALFAALALALTGGAWQWSASKNSRLNMVSALDPHSGDIVNPSGQHGDENFLLVGMDSRAGANANIGAGDAEDAGGARSDTVMLVNIPASRERVVAVSFPRDLAITPIQCEAWNPETGKYGPIYDEKTGTMGPRLVYTETKLNSAFSFGGPKCLVKVIQKLSGLSINRFIAIDFVGFARMVEALGGVEVCSTTPLRDYELGTVLEHAGRQVIDGPTALNYVRARQVTTESNGDYGRIKRQQLFLSSLLRSMISTDTLFNLSRLNNVVNMFIGNSYVDNVKTKDLVELGRSLQHMAAGHVTFVTVPTGITDQNGDEPPRTSDMKALFTAIIDDDPLPLENDHNAQRLGNTPSTPPTTTKKAPQAGLTNEIQHQQVTTTSPKEVTVQVSNSTGQAGLATTATDQLKRNGFNVMAPDDYPSSLLATTVFFSPGNEQAAATVAAVFGQSKIERVTGIGQLVQVVLGQDFSAVRAPLPSGSTVSVQISRNSSSPPTKLPEDLTVTNAADTTCE