Rv1277 Family assigned · medium auto-curated
H37Rv Rv1277 · MTBC0 - ·
417 aa · 1426164–1427417 (+) ·
RefSeq NP_215793.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains Metallophos (PF00149.34) 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 |
Q50699
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Nuclease SbcCD subunit D |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | sbcD |
| eggNOG description | DNA repair exonuclease |
| Orthologous group | COG0420 |
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 | 0.146 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 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 |
|---|---|---|---|---|
Metallophos | PF00149.34 | 2.1e-09 | 35–201 | Calcineurin-like phosphoesterase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1279 (GMC-type oxidoreductase), high confidence from genomic context alone (score 889 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) |
|---|---|---|---|---|
Rv1278 hyp |
hypothetical protein | 999 | 1000 ctx | neighborhood:881 cooccurence:774 coexpression:926 experimental:928 database:844 |
Rv1629 polA |
DNA polymerase I | 989 | 980 | experimental:836 database:844 textmining:494 |
Rv2090 |
5'-3' exonuclease | 937 | 930 | experimental:777 database:652 |
Rv1329c dinG |
ATP-dependent helicase DinG | 930 | 919 | experimental:771 database:639 |
Rv1279 |
GMC-type oxidoreductase | 889 | 889 ctx | neighborhood:853 |
Rv2737c recA |
recombinase A | 908 | 853 | experimental:449 database:635 textmining:406 |
Rv2196 qcrB |
ubiquinol-cytochrome C reductase cytochrome subunit B | 796 | 785 | experimental:784 |
Rv3646c topA |
DNA topoisomerase I | 846 | 784 | database:654 |
Rv1276c hyp |
hypothetical protein | 742 | 742 ctx | neighborhood:740 |
Rv2529 hyp |
hypothetical protein | 767 | 730 | database:615 |
Rv1527c pks5 |
polyketide synthase | 736 | 720 | experimental:404 database:511 |
Rv2933 ppsC |
phthiocerol synthesis polyketide synthase type I PpsC | 736 | 720 | experimental:404 database:511 |
Rv3825c pks2 |
phthioceranic/hydroxyphthioceranic acid synthase | 736 | 720 | experimental:404 database:511 |
Rv2940c mas |
multifunctional mycocerosic acid synthase | 736 | 720 | experimental:404 database:511 |
Rv2048c pks12 |
polyketide synthase | 735 | 719 | experimental:404 database:511 |
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): Metallophos PF00149.34 (E=2e-09)
- (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_215793.1)
- Domains: Pfam-A via hmmscan --cut_ga — Metallophos (PF00149.34)
- 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
COG0420 - Curated reference: UniProt Q50699 (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 —
141 functional partner(s); context anchor
Rv1279 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1277| MSPRPGPAGRGPAPCRCADLHSLCVDSHALRRDGMRFLHTADWQLGMTRHFLAGDAQPRYSAARRDAVAGLKALAADVGAEFVVVAGDVFEHNQLAPQIVGQSLEAMRVIGLPVYLLPGNHDPLDASSVYTSTLFRAERPDNVVVLDRAGVHEVRPGVQIVAAPWRSKAPTTDPVAEVLAGLPTDAAIRLLVAHGGVDALDPDHDKPSLIRLAALDDALTRQAIHYVALGDKHSLTQVGSSGRVWYSGAPEVTNFDDVEPDPGHVLVVDIDESDPRHPVTVDARRIGRWRFVTLHHQVDTSRDIADLDLNLDLMTDKDRTVVRLALTGSLTVTDRAALDTCLDKYARLFAWLGLWERHTDLAVIPVDAEFTDLGIGGFAAAAVDELVATARGGDDESAVDAQAALALLLRLADRGAA