Rv1716 Family assigned · medium auto-curated
H37Rv Rv1716 · MTBC0 - ·
276 aa · 1943576–1944406 (+) ·
RefSeq NP_216232.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains Cyclase (PF04199.20) 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 |
O53929
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Cyclase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | Putative cyclase |
| Orthologous group | COG1878 |
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 | 0.787 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 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 |
|---|---|---|---|---|
Cyclase | PF04199.20 | 4.9e-37 | 17–168 | Putative cyclase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadB3 (3-hydroxybutyryl-CoA dehydrogenase FadB), high confidence from genomic context alone (score 985 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) |
|---|---|---|---|---|
Rv1717 hyp |
hypothetical protein | 992 | 993 ctx | neighborhood:882 cooccurence:615 coexpression:853 |
Rv1715 fadB3 |
3-hydroxybutyryl-CoA dehydrogenase FadB | 984 | 985 ctx | neighborhood:881 coexpression:860 |
Rv1714 |
oxidoreductase | 997 | 984 ctx | neighborhood:881 coexpression:828 textmining:870 |
Rv1718 hyp |
hypothetical protein | 977 | 978 ctx | neighborhood:808 coexpression:860 |
Rv1719 |
transcriptional regulator | 903 | 904 ctx | neighborhood:798 |
Rv3728 |
membrane protein | 791 | 791 | coexpression:785 |
Rv1775 hyp |
hypothetical protein | 580 | 580 ctx | cooccurence:573 |
Rv1713 engA |
GTPase Der | 549 | 549 ctx | neighborhood:520 |
Rv1712 cmk |
cytidylate kinase | 535 | 535 ctx | neighborhood:520 |
Rv1711 |
RNA pseudouridine synthase | 511 | 511 ctx | neighborhood:489 |
Rv1710 scpB |
segregation and condensation protein ScpB | 496 | 496 ctx | neighborhood:489 |
Rv1708 |
initiation inhibitor protein | 492 | 492 ctx | neighborhood:489 |
Rv1709 scpA |
segregation and condensation protein ScpA | 484 | 484 ctx | neighborhood:476 |
Rv1773c |
transcriptional regulator | 478 | 479 ctx | cooccurence:453 |
Rv1937 |
oxygenase | 469 | 449 ctx | cooccurence:410 |
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): Cyclase PF04199.20 (E=5e-37)
- (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_216232.1)
- Domains: Pfam-A via hmmscan --cut_ga — Cyclase (PF04199.20)
- 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
COG1878 - Curated reference: UniProt O53929 (TrEMBL, unreviewed; Predicted)
- 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 —
16 functional partner(s); context anchor
fadB3 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1716| MTFAWPLGAAESTLEFYDLSHPWGHGAPAWPYFEDVQIERLHGMAKSRVLTQKITTVMHSGTHIDAPAHVVEGTPFLDEIPLSAFFGTGVVVSIPKGKWGMVTAEDLQNATPDIRPGDIVVVNTGWHHKYADSAEYYAYSPGFDKKAGEWFAAKGVKAVGTDTQALDHPLATAIAPHSPAEAQGGLLPWAVREYEAQTGRKVLDDFPDWEPCHRAILSQGIYGFENVGGDLDKVTGKRVTFAAFPWRWVGGDGCIVRLVAIVDPTGSYRIETGKAV