Rv2559c Resolved · high auto-curated
H37Rv Rv2559c · MTBC0 mtbc0_002727 ·
452 aa · 2902116–2903474 (-) ·
RefSeq NP_217075.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | replication-associated recombination protein A |
| Revised (this work) | Replication-associated recombination protein A. Pfam: RuvB_N (PF05496.19), Sigma54_activ_2 (PF14532.13), AAA (PF00004.36), AAA_5 (PF07728.21), AAA_assoc_2 (PF16193.12), MgsA_C (PF12002.14). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WQN1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized AAA domain-containing protein Rv2559c |
UniProt still lists this protein as Uncharacterized AAA domain-containing protein Rv2559c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | rarA |
| eggNOG description | aaa ATPase |
| Orthologous group | COG2256 |
| KEGG orthology |
K07478
|
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 | 0.253 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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 |
|---|---|---|---|---|
RuvB_N | PF05496.19 | 1.6e-12 | 35–153 | Holliday junction DNA helicase RuvB P-loop domain |
Sigma54_activ_2 | PF14532.13 | 3.6e-06 | 66–177 | Sigma-54 interaction domain |
AAA | PF00004.36 | 1.8e-14 | 68–171 | ATPase family associated with various cellular activities (AAA) |
AAA_5 | PF07728.21 | 5.3e-08 | 68–159 | AAA domain (dynein-related subfamily) |
AAA_assoc_2 | PF16193.12 | 5.7e-25 | 202–277 | AAA C-terminal domain |
MgsA_C | PF12002.14 | 1.8e-67 | 278–443 | MgsA AAA+ ATPase C terminal |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2560 hyp |
hypothetical protein | 773 | 774 ctx | neighborhood:773 |
Rv2566 hyp |
hypothetical protein | 600 | 600 ctx | neighborhood:599 |
Rv2438c nadE |
glutamine-dependent NAD(+) synthetase | 579 | 576 | coexpression:489 |
Rv2847c cysG |
multifunctional uroporphyrin-III C-methyltransferase/precorrin-2 oxidase/ferrochelatase | 411 | 412 | |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 408 | 409 | |
Rv2116 lppK |
lipoprotein LppK | 439 | 406 | experimental:404 |
Rv2603c |
transcriptional regulator | 405 | 406 | |
Rv0002 dnaN |
DNA polymerase III subunit beta | 438 | 405 | experimental:404 |
Rv2592c ruvB |
Holliday junction ATP-dependent DNA helicase RuvB | 461 | 404 | |
Rv1537 dinX |
DNA polymerase IV | 428 | 391 | |
Rv3056 dinP |
DNA polymerase IV 2 | 405 | 366 | |
Rv2101 helZ |
helicase HelZ | 425 | 341 | |
Rv2593c ruvA |
Holliday junction ATP-dependent DNA helicase RuvA | 415 | 326 | |
Rv1901 cinA |
competence damage-inducible protein CinA | 471 | 306 | |
Rv1629 polA |
DNA polymerase I | 574 | 287 | textmining:428 |
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: replication-associated recombination protein A
- Pfam (hmmscan --cut_ga): RuvB_N PF05496.19 (E=2e-12), Sigma54_activ_2 PF14532.13 (E=4e-06), AAA PF00004.36 (E=2e-14), AAA_5 PF07728.21 (E=5e-08), AAA_assoc_2 PF16193.12 (E=6e-25), MgsA_C PF12002.14 (E=2e-67)
- (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_217075.1)
- Domains: Pfam-A via hmmscan --cut_ga — RuvB_N (PF05496.19), Sigma54_activ_2 (PF14532.13), AAA (PF00004.36), AAA_5 (PF07728.21), AAA_assoc_2 (PF16193.12), MgsA_C (PF12002.14)
- 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
COG2256 - Curated reference: UniProt P9WQN1 (SwissProt, reviewed; 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 — 15 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002727|Rv2559c| MPEAVSDGLFDVPGVPMTSGHDLGASAGAPLAVRMRPASLDEVVGQDHLLAPGSPLRRLVEGSGVASVILYGPPGSGKTTLAALISQATGRRFEALSALSAGVKEVRAVIENSRKALLHGEQTVLFIDEVHRFSKTQQDALLSAVEHRVVLLVAATTENPSFSVVAPLLSRSLILQLRPLTAEDTRAVVQRAIDDPRGLGRAVAVAPEAVDLLVQLAAGDARRALTALEVAAEAAQAAGELVSVQTIERSVDKAAVRYDRDGDQHYDVVSAFIKSVRGSDVDAALHYLARMLVAGEDPRFIARRLMILASEDIGMADPSALQVAVAAAQTVALIGMPEAQLTLAHATIHLATAPKSNAVTTALAAAMNDIKAGKAGLVPAHLRDGHYSGAAALGNAQGYKYSHDDPDGVVAQQYPPDELVDVDYYRPTGRGGEREIAGRLDRLRAIIRKKRG