Rv1000c Family assigned · medium auto-curated
H37Rv Rv1000c · MTBC0 - ·
205 aa · 1116531–1117148 (-) ·
RefSeq YP_177777.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains 2OG-FeII_Oxy_2 (PF13532.13) 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 |
L7N6A4
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Fe2OG dioxygenase domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| eggNOG description | DNA repair protein |
| Orthologous group | COG3145 |
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, 1 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.26% of strains (376) · 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 |
|---|---|---|---|---|
2OG-FeII_Oxy_2 | PF13532.13 | 7.5e-16 | 102–200 | 2OG-Fe(II) oxygenase superfamily |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: arcA (arginine deiminase), medium confidence from genomic context alone (score 679 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) |
|---|---|---|---|---|
Rv2573 |
2-dehydropantoate 2-reductase | 682 | 682 | coexpression:682 |
Rv1001 arcA |
arginine deiminase | 679 | 679 ctx | neighborhood:677 |
Rv0976c hyp |
hypothetical protein | 407 | 407 | coexpression:407 |
Rv1378c hyp |
hypothetical protein | 869 | 363 | textmining:804 |
Rv1317c alkA |
bifunctional regulatory protein/DNA repair enzyme AlkA | 622 | 329 | textmining:461 |
Rv3074 hyp |
hypothetical protein | 711 | 318 | textmining:594 |
Rv1148c hyp |
hypothetical protein | 434 | 237 | |
Rv1128c hyp |
hypothetical protein | 426 | 226 | |
Rv1945 hyp |
hypothetical protein | 424 | 224 | |
Rv2593c ruvA |
Holliday junction ATP-dependent DNA helicase RuvA | 420 | 210 | |
Rv2594c ruvC |
crossover junction endodeoxyribonuclease RuvC | 675 | 93 | textmining:657 |
Rv3395c hyp |
hypothetical protein | 813 | 91 | textmining:803 |
Rv2592c ruvB |
Holliday junction ATP-dependent DNA helicase RuvB | 424 | 91 | |
Rv2100 hyp |
hypothetical protein | 812 | 86 | textmining:803 |
Rv2720 lexA |
repressor LexA | 621 | 83 | textmining:605 |
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): 2OG-FeII_Oxy_2 PF13532.13 (E=7e-16)
- (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 YP_177777.1)
- Domains: Pfam-A via hmmscan --cut_ga — 2OG-FeII_Oxy_2 (PF13532.13)
- 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
COG3145 - Curated reference: UniProt L7N6A4 (TrEMBL, unreviewed; Predicted)
- 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 —
16 functional partner(s); context anchor
arcA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1000c| MCDKLGGVAIAVQGALFEHNERRQLGDGAFIDIRSGWLTGGEELLDALLSTVPWRAERRQMYDRVVDVPRLVSFHDLTIEDPPHPQLARMRRRLNDIYGGELGEPFTTAGLCYYRDGSDSVAWHGDTIGRGSTEDTMVAIVSLGATRVFALRPRGRGPSLRLPLAHGDLLVMGGSCQRTFEHAVPKTSAPTGPRVSIQFRPRDVR