Rv3714c Family assigned · medium auto-curated
H37Rv Rv3714c · MTBC0 mtbc0_003937 ·
296 aa · 4183052–4183942 (-) ·
RefSeq NP_218231.1
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 |
O69681
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Cullin, a subunit of E3 ubiquitin ligase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | Psort location Cytoplasmic, score |
| Orthologous group | COG5340 |
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 | 0.637 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 9 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 | 1.7e-05 | 78–185 | AbiEi antitoxin C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: recR (recombination protein RecR), medium confidence from genomic context alone (score 636 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) |
|---|---|---|---|---|
Rv3585 radA |
DNA repair protein RadA | 791 | 791 | coexpression:791 |
Rv3586 disA |
DNA integrity scanning protein DisA | 730 | 730 | coexpression:730 |
Rv3715c recR |
recombination protein RecR | 635 | 636 ctx | neighborhood:632 |
Rv3716c hyp |
hypothetical protein | 627 | 627 ctx | neighborhood:625 |
Rv3859c gltB |
glutamate synthase large subunit | 522 | 522 | coexpression:515 |
Rv3776 hyp |
hypothetical protein | 478 | 479 ctx | cooccurence:451 |
Rv2100 hyp |
hypothetical protein | 473 | 474 ctx | cooccurence:447 |
Rv0393 hyp |
hypothetical protein | 471 | 471 ctx | cooccurence:467 |
Rv1702c hyp |
hypothetical protein | 448 | 448 ctx | cooccurence:412 |
Rv0515 hyp |
hypothetical protein | 446 | 447 | |
Rv0767c |
HTH-type transcriptional regulator | 445 | 445 ctx | cooccurence:443 |
Rv3810 pirG |
cell surface protein | 442 | 443 ctx | cooccurence:440 |
Rv3717 hyp |
hypothetical protein | 431 | 432 ctx | neighborhood:425 |
Rv3497c mce4C |
Mce family protein Mce4C | 430 | 261 | |
Rv0290 eccD3 |
ESX-3 secretion system protein EccD | 525 | 205 | textmining:428 |
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=2e-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_218231.1)
- 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
COG5340 - Curated reference: UniProt O69681 (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 —
21 functional partner(s); context anchor
recR - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003937|Rv3714c| MLISRMSVRSASMSVMGDVFIGSEAITAGRLTRHELQRWYQPMFRGVYVSRRSVPTLWDRTVGAWLATRRHGVIAGNAASALHGAQWVDVDVAIELISPTTRPQHGLVIRRETLCDDEITRVVGLPVTTLARTAYDLGRHLSRGEAVARLDALMRATPFSRDDVLLLAKRHAGARGVRRLRDVLPLVDGGAASPKETWLRLLLIDAGLPVPTTQIPVVHRWRNVGVLDMGWEKYMVAAEYDGDQHRSDRGRYVKDQRRLRKLAELGWIVIRVIAEDNPDDVVNRVRAALLARGWRP