Rv2119 Family assigned · medium auto-curated
H37Rv Rv2119 · MTBC0 mtbc0_002251 ·
278 aa · 2405649–2406485 (+) ·
RefSeq NP_216635.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | RecB family exonuclease |
| Revised (this work) | RecB family exonuclease. Pfam: PDDEXK_1 (PF12705.14). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O33254
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | PD-(D/E)XK endonuclease-like domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | recB |
| eggNOG description | RecB family |
| Orthologous group | COG2887 |
| KEGG orthology |
K07465
|
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 | 0.528 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 3 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 |
|---|---|---|---|---|
PDDEXK_1 | PF12705.14 | 6.1e-40 | 14–260 | PD-(D/E)XK nuclease superfamily |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: trmI (tRNA (adenine(58)-N(1))-methyltransferase), high confidence from genomic context alone (score 786 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) |
|---|---|---|---|---|
Rv2118c trmI |
tRNA (adenine(58)-N(1))-methyltransferase | 785 | 786 ctx | neighborhood:785 |
Rv3202c adnA |
ATP-dependent DNA helicase | 585 | 586 | |
Rv3259 hyp |
hypothetical protein | 582 | 582 ctx | cooccurence:582 |
Rv3416 whiB3 |
redox-responsive transcriptional regulator WhiB3 | 551 | 551 ctx | cooccurence:550 |
Rv0949 uvrD1 |
ATP-dependent DNA helicase UvrD | 548 | 481 | |
Rv3662c hyp |
hypothetical protein | 478 | 479 ctx | cooccurence:460 |
Rv2610c pimA |
alpha-(1-2)-phosphatidylinositol mannosyltransferase | 456 | 457 ctx | cooccurence:455 |
Rv0058 dnaB |
replicative DNA helicase | 484 | 456 | coexpression:409 |
Rv2097c pafA |
proteasome accessory factor PafA | 477 | 443 | |
Rv2028c |
universal stress protein | 438 | 438 ctx | cooccurence:438 |
Rv3198c uvrD2 |
ATP-dependent DNA helicase UvrD | 417 | 418 | |
Rv3363c hyp |
hypothetical protein | 416 | 417 ctx | cooccurence:415 |
Rv2112c dop |
pup deamidase/depupylase | 436 | 415 | |
Rv2593c ruvA |
Holliday junction ATP-dependent DNA helicase RuvA | 500 | 409 | coexpression:409 |
Rv2594c ruvC |
crossover junction endodeoxyribonuclease RuvC | 403 | 266 |
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: RecB family exonuclease
- Pfam (hmmscan --cut_ga): PDDEXK_1 PF12705.14 (E=6e-40)
- (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_216635.1)
- Domains: Pfam-A via hmmscan --cut_ga — PDDEXK_1 (PF12705.14)
- 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
COG2887 - Curated reference: UniProt O33254 (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 —
19 functional partner(s); context anchor
trmI - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002251|Rv2119| MADQPDPPTPRPALSPSRATDFKQCPLLYRFRAIDRLPEATSAAQLRGSVVHAALEQLYGLPAGLRSPDTARSLVQRAWDQMVAAEPELAGELDPGQPTQLLEDARALVSGYYRLEDPTRFDPQCCEQRVEVELADGTLLRGYIDRIDVAATGELRVVDYKTGKAPPAARALAEFKAMFQMKFYAVALFRSRGVPPTRLRLIYLADGQLLDYSPDRDELLRFEKTLMAIWRAIQSAGETGDFRPNPSRLCDWCPHQQRCPAFGGTPPPYPGWPTEPAA