Rv3242c Family assigned · low auto-curated
H37Rv Rv3242c · MTBC0 mtbc0_003450 ·
213 aa · 3643713–3644354 (-) ·
RefSeq NP_217759.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | ComF family protein |
| Revised (this work) | ComF family protein. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O05887
TrEMBL · unreviewed
· Inferred from homology
|
|---|---|
| UniProt name | Phosphoribosyltransferase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | pyrE_1 |
| eggNOG description | phosphoribosyltransferase |
| Orthologous group | COG1040 |
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 | 1.199 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mtrB (two component sensory histidine kinase MtrB), high confidence from genomic context alone (score 712 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) |
|---|---|---|---|---|
Rv2894c xerC |
tyrosine recombinase XerC | 902 | 902 | coexpression:902 |
Rv1364c |
sigma factor regulatory protein | 892 | 889 | coexpression:874 |
Rv3754 tyrA |
prephenate dehydrogenase TyrA | 833 | 821 | coexpression:821 |
Rv2584c apt |
adenine phosphoribosyltransferase | 808 | 808 | coexpression:808 |
Rv2677c hemY |
protoporphyrinogen oxidase | 787 | 788 | coexpression:776 |
Rv3332 nagA |
N-acetylglucosamine-6-phosphate deacetylase NagA | 785 | 786 | coexpression:772 |
Rv3781 rfbE |
O-antigen/lipopolysaccharide ABC transporter ATP-binding protein RfbE | 776 | 777 | coexpression:777 |
Rv1354c hyp |
hypothetical protein | 746 | 735 | coexpression:649 |
Rv3243c hyp |
hypothetical protein | 724 | 725 ctx | neighborhood:717 |
Rv3245c mtrB |
two component sensory histidine kinase MtrB | 711 | 712 ctx | neighborhood:595 |
Rv3244c lpqB |
lipoprotein LpqB | 681 | 681 ctx | neighborhood:630 |
Rv2896c dprA hyp |
hypothetical protein | 753 | 678 | coexpression:509 |
Rv2414c hyp |
hypothetical protein | 689 | 594 | coexpression:428 |
Rv3246c mtrA |
two component DNA-binding response regulator MtrA | 593 | 578 ctx | neighborhood:556 |
Rv3296 lhr |
ATP-dependent helicase | 574 | 575 | coexpression:575 |
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: ComF family protein
- (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_217759.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
COG1040 - Curated reference: UniProt O05887 (TrEMBL, unreviewed; Inferred from homology)
- 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 —
53 functional partner(s); context anchor
mtrB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003450|Rv3242c| MLDLVLPLECGGCGAPATRWCAACAAELSVAAGEPHVVSPRVDPQVPVFALGRYAGVRRQAILAMKEHGRRDLVAPLACALIVGVDHLLSWGMLENPLTMVPAPTRRWAARRRGGDPVSRMARIAGATLGRHHDVTVVPALRMRALARDSVGLGASARERNITGRVLLRGQRPRNEVVLVDDIITTGATARESVRVLQAAGVRVGAVLAVAAA