Rv3517 Family assigned · medium auto-curated
H37Rv Rv3517 · MTBC0 mtbc0_003733 ·
279 aa · 3977108–3977947 (+) ·
RefSeq NP_218034.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Contains AbiEi_1 (PF09407.17) 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.
Curated reference (UniProt)
| UniProt |
O53562
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Cullin, a subunit of E3 ubiquitin ligase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Protein conserved in bacteria |
| Orthologous group | COG2852 |
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 | 0.462 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 4 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 |
|---|---|---|---|---|
AbiEi_1 | PF09407.17 | 2.6e-05 | 62–167 | AbiEi antitoxin C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: echA19 (enoyl-CoA hydratase EchA19), medium confidence from genomic context alone (score 550 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) |
|---|---|---|---|---|
Rv3516 echA19 |
enoyl-CoA hydratase EchA19 | 907 | 550 ctx | neighborhood:548 textmining:803 |
Rv2345 |
transmembrane protein | 524 | 524 ctx | cooccurence:524 |
Rv3859c gltB |
glutamate synthase large subunit | 522 | 523 | coexpression:516 |
Rv2100 hyp |
hypothetical protein | 518 | 519 ctx | cooccurence:493 |
Rv3776 hyp |
hypothetical protein | 518 | 519 ctx | cooccurence:501 |
Rv0393 hyp |
hypothetical protein | 499 | 500 ctx | cooccurence:495 |
Rv0767c |
HTH-type transcriptional regulator | 473 | 474 ctx | cooccurence:471 |
Rv3202c adnA |
ATP-dependent DNA helicase | 454 | 455 | coexpression:423 |
Rv3668c |
protease | 426 | 426 ctx | cooccurence:417 |
Rv0515 hyp |
hypothetical protein | 422 | 423 ctx | cooccurence:411 |
Rv3515c fadD19 |
acyl-CoA synthetase | 423 | 422 ctx | neighborhood:415 |
Rv0336 hyp |
hypothetical protein | 421 | 422 ctx | cooccurence:410 |
Rv3492c |
Mce associated protein | 407 | 408 ctx | cooccurence:403 |
Rv1179c hyp |
hypothetical protein | 806 | 72 | textmining:800 |
Rv3738c PPE66 |
PPE family protein PPE66 | 667 | 62 | textmining:660 |
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: hypothetical protein
- Pfam (hmmscan --cut_ga): AbiEi_1 PF09407.17 (E=3e-05)
- (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_218034.1)
- Domains: Pfam-A via hmmscan --cut_ga — AbiEi_1 (PF09407.17)
- 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
COG2852 - Curated reference: UniProt O53562 (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 —
21 functional partner(s); context anchor
echA19 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003733|Rv3517| MIEPFLGSEAIASGALTRHRLRSAYATIHPDVYVSPGADLTAWSRAQAAWLWSRRRGVIAGQSAAAMHGAKWVDARQAAELLYDHRRPPAGIHTWSDRVADDEIQPISGMNTTTPARTALDLARRYPVGKAVAAIDALARATDLKLADVEMLAERYRGSRGIRNARIALDLVDPGAESPRETWLRLLLIRAGFPRPQTQIPVYDEYGQLVAVIDMGWAGIKVGVDYEGDHHRTDRRTFNKDIKRAEALTELGWTDVRVTVEDTEGGIIWRVSAAWQRRT