Rv2529 Family assigned · medium auto-curated
H37Rv Rv2529 · MTBC0 - ·
463 aa · 2852875–2854266 (+) ·
RefSeq NP_217045.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains ERCC4 (PF02732.22), Lsr2_DNA-bd (PF23359.2) domain(s); putative function inferred from the domain architecture. |
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 |
P95024
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ERCC4 domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| eggNOG description | ERCC4 domain |
| Orthologous group | COG1948 |
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 | 0.746 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 8 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.48% of strains (693) · 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 |
|---|---|---|---|---|
ERCC4 | PF02732.22 | 1.9e-14 | 277–399 | ERCC4 domain |
Lsr2_DNA-bd | PF23359.2 | 4.5e-08 | 427–460 | Lsr2 DNA-binding domain |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3646c topA |
DNA topoisomerase I | 964 | 953 | experimental:883 database:615 |
Rv1629 polA |
DNA polymerase I | 969 | 951 | experimental:662 database:844 textmining:412 |
Rv1252c lprE |
lipoprotein LprE | 946 | 945 | experimental:864 database:607 |
Rv2090 |
5'-3' exonuclease | 891 | 876 | experimental:662 database:622 |
Rv0641 rplA |
50S ribosomal protein L1 | 843 | 826 | experimental:473 database:683 |
Rv2737c recA |
recombinase A | 851 | 806 | experimental:528 database:594 |
Rv2101 helZ |
helicase HelZ | 825 | 791 | experimental:475 database:617 |
Rv2116 lppK |
lipoprotein LppK | 782 | 773 | experimental:459 database:594 |
Rv0002 dnaN |
DNA polymerase III subunit beta | 781 | 772 | experimental:459 database:594 |
Rv1947 hyp |
hypothetical protein | 786 | 771 | database:610 |
Rv1278 hyp |
hypothetical protein | 769 | 736 | database:615 |
Rv1277 hyp |
hypothetical protein | 767 | 730 | database:615 |
Rv1329c dinG |
ATP-dependent helicase DinG | 771 | 718 | database:664 |
Rv2729c |
integral membrane protein | 714 | 704 | database:516 |
Rv1179c hyp |
hypothetical protein | 707 | 687 | database:610 |
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): ERCC4 PF02732.22 (E=2e-14), Lsr2_DNA-bd PF23359.2 (E=4e-08)
- (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_217045.1)
- Domains: Pfam-A via hmmscan --cut_ga — ERCC4 (PF02732.22), Lsr2_DNA-bd (PF23359.2)
- 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
COG1948 - Curated reference: UniProt P95024 (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 — 114 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2529| MHLAHRVASSRDTPSSSATPNAVSGSASNAADRPCLVRPPTAPPWAHGPRLRRDPTGGGSTPSIVLSRSTDRSKDGHRIVPAGARKSGVRASTGRLPSTRKTTRSPDCRPSASRTAFGTVTCPFDVTMGSSECLLHRCRTPPVPSHSVELLVAANPAEDSRLPYLIRLPVGAGLVFATSDVWPRTKALYCHRLDIADWPADPVVVDRVELRSCSRRGAAIDVVAARARENRSQLVHTMARGRQVVFWQSPKTRKQSRPGVRTPTARAAGIPELHIVVDAHERYPYTFADKPAKTTREALPCGDYGLKVAGQLVAAVERKALADLTSGVLNGNLKYQLTELAALPRAAVVVEDRYSEIFAHSFARPTAIADGLAELQIGFPNVPIVFCQTRKLAQEYTYRYLAAALTWFVDDADATTVFEPAAAEPEPSSAELRAWAKSVGLPVSDRGRLRPQILQAWRAAHPR