Rv1278 Family assigned · medium auto-curated
H37Rv Rv1278 · MTBC0 mtbc0_001368 ·
875 aa · 1436397–1439024 (+) ·
RefSeq NP_215794.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | AAA family ATPase |
| Revised (this work) | AAA family ATPase. Pfam: AAA_15 (PF13175.13), AAA_27 (PF13514.13), AAA_23 (PF13476.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WM41
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv1278 |
UniProt still lists this protein as Uncharacterized protein Rv1278; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| eggNOG description | AAA domain |
| Orthologous group | COG0419 |
| Gene Ontology (10) |
GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0008150, GO:0016020, GO:0030312, GO:0040007, GO:0044464, GO:0071944
|
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 | 0.736 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 10 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 |
|---|---|---|---|---|
AAA_15 | PF13175.13 | 5.3e-10 | 1–63 | AAA ATPase domain |
AAA_27 | PF13514.13 | 7.0e-08 | 1–61 | AAA domain |
AAA_23 | PF13476.13 | 4.2e-07 | 5–72 | AAA domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1279 (GMC-type oxidoreductase), high confidence from genomic context alone (score 969 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) |
|---|---|---|---|---|
Rv1277 hyp |
hypothetical protein | 999 | 1000 ctx | neighborhood:881 cooccurence:774 coexpression:926 experimental:928 database:844 |
Rv1279 |
GMC-type oxidoreductase | 968 | 969 ctx | neighborhood:853 coexpression:796 |
Rv1629 polA |
DNA polymerase I | 952 | 919 | experimental:432 database:844 textmining:430 |
Rv3646c topA |
DNA topoisomerase I | 895 | 879 | database:654 |
Rv2737c recA |
recombinase A | 859 | 816 | experimental:421 database:635 |
Rv2090 |
5'-3' exonuclease | 829 | 807 | experimental:432 database:652 |
Rv2115c mpa |
proteasome-associated ATPase | 796 | 788 | experimental:782 |
Rv1276c hyp |
hypothetical protein | 743 | 743 ctx | neighborhood:740 |
Rv2529 hyp |
hypothetical protein | 769 | 736 | database:615 |
Rv2301 cut2 |
cutinase | 716 | 717 ctx | cooccurence:401 database:544 |
Rv1747 |
ABC transporter ATP-binding protein/permease | 717 | 700 | database:579 |
Rv1334 mec |
[CysO | 711 | 700 | database:611 |
Rv1329c dinG |
ATP-dependent helicase DinG | 709 | 698 | database:639 |
Rv3062 ligB |
DNA ligase | 714 | 683 | database:611 |
Rv0938 ligD |
multifunctional non-homologous end joining DNA repair protein/ATP dependent DNA ligase LigD | 763 | 680 | database:611 |
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: AAA family ATPase
- Pfam (hmmscan --cut_ga): AAA_15 PF13175.13 (E=5e-10), AAA_27 PF13514.13 (E=7e-08), AAA_23 PF13476.13 (E=4e-07)
- (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_215794.1)
- Domains: Pfam-A via hmmscan --cut_ga — AAA_15 (PF13175.13), AAA_27 (PF13514.13), AAA_23 (PF13476.13)
- 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
COG0419 - Curated reference: UniProt P9WM41 (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 —
128 functional partner(s); context anchor
Rv1279 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001368|Rv1278| MKLHRLALTNYRGIAHRDVEFPDHGVVVVCGANEIGKSSMVEALDLLLEYKDRSTKKEVKQVKPTNADVGSEVIAEISSGPYRFVYRKRFHKRCETELTVLAPRREQLTGDEAHERVRTMLAETVDTELWHAQRVLQAASTAAVDLSGCDALSRALDLAAGDDAALSGTESLLIERIEAEYARYFTPTGRPTGEWSAAVSRLAAAEAAVADCAAAVAEVDDGVRRHTELTEQVAELSQQLLAHQLRLEAARVAAEKIAAITDDAREAKLIATAAAATSGASTAAHAGRLGLLTEIDTRTAAVVAAEAKARQAADEQATARAEAEACDAALTEATQVLTAVRLRAESARRTLDQLADCEEADRLAARLARIDDIEGDRDRVCAELSAVTLTEELLSRIERAAAAVDRGGAQLASISAAVEFTAAVDIELGVGDQRVSLSAGQSWSVTATGPTEVKVPGVLTARIVPGATALDFQAKYAAAQQELADALAAGEVADLAAARSADLCRRELLSRRDQLTATLAGLCGDEQVDQLRSRLEQLCAGQPAELDLVSTDTATARAELDAVEAARIAAEKDCETRRQIAAGAARRLAETSTRATVLQNAAAAESAELGAAMTRLACERASVGDDELAAKAEADLRVLQTAEQRVIDLADELAATAPDAVAAELAEAADAVELLRERHDEAIRALHEVGVELSVFGTQGRKGKLDAAETEREHAASHHARVGRRARAARLLRSVMARHRDTTRLRYVEPYRAELHRLGRPVFGPSFEVEVDTDLRIRSRTLDDRTVPYECLSGGAKEQLGILARLAGAALVAKEDAVPVLIDDALGFTDPERLAKMGEVFDTIGADGQVIVLTCSPTRYGGVKGAHRIDLDAIQ