Rv2491 Family assigned · medium auto-curated
H37Rv Rv2491 · MTBC0 mtbc0_002653 ·
207 aa · 2829555–2830178 (+) ·
RefSeq NP_217007.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | TIGR00725 family protein |
| Revised (this work) | TIGR00725 family protein. Pfam: LDcluster4 (PF18306.7). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6XEF6
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | TIGR00725 family protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | cytokinin biosynthetic process |
| Orthologous group | COG1611 |
| EC number |
EC 3.2.2.10
|
| KEGG orthology |
K06966
|
| KEGG pathways |
map00230, map00240
|
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 | 2.006 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 5 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.20% of strains (292) · clonal |
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 |
|---|---|---|---|---|
LDcluster4 | PF18306.7 | 1.4e-38 | 27–152 | SLOG cluster4 family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapC38 (ribonuclease VapC38), medium confidence from genomic context alone (score 619 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) |
|---|---|---|---|---|
Rv2492 hyp |
hypothetical protein | 967 | 967 ctx | neighborhood:882 coexpression:731 |
Rv2494 vapC38 |
ribonuclease VapC38 | 619 | 619 ctx | neighborhood:619 |
Rv2493 vapB38 |
antitoxin VapB38 | 619 | 619 ctx | neighborhood:619 |
Rv0570 nrdZ |
vitamin B12-dependent ribonucleoside-diphosphate reductase | 430 | 431 | coexpression:413 |
Rv3051c nrdE |
ribonucleoside-diphosphate reductase subunit alpha | 426 | 427 | coexpression:409 |
Rv3048c nrdF2 |
ribonucleoside-diphosphate reductase subunit beta NrdF2 | 418 | 418 | coexpression:408 |
Rv0233 nrdB |
ribonucleoside-diphosphate reductase subunit beta NrdB | 417 | 418 | coexpression:407 |
Rv1981c nrdF1 |
ribonucleoside-diphosphate reductase subunit beta NrdF1 | 416 | 417 | coexpression:406 |
Rv1094 desA2 |
acyl-ACP desaturase DesA | 408 | 408 | coexpression:402 |
Rv0824c desA1 |
acyl-ACP desaturase DesA | 406 | 406 | coexpression:400 |
Rv3846 sodA |
superoxide dismutase | 403 | 92 | |
Rv0808 purF |
amidophosphoribosyltransferase | 820 | 85 | textmining:812 |
Rv2883c pyrH |
uridylate kinase | 656 | 47 | textmining:654 |
Rv1205 log hyp |
hypothetical protein | 809 | 44 | textmining:809 |
Rv2017 |
transcriptional regulator | 631 | 44 | textmining:630 |
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: TIGR00725 family protein
- Pfam (hmmscan --cut_ga): LDcluster4 PF18306.7 (E=1e-38)
- (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_217007.1)
- Domains: Pfam-A via hmmscan --cut_ga — LDcluster4 (PF18306.7)
- 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
COG1611 - Curated reference: UniProt I6XEF6 (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 —
15 functional partner(s); context anchor
vapC38 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002653|Rv2491| MVDTSAPASRLDTDPRRAHVSLSKHPYQIGVFGSGTIGPRVYELAYQVGAEIAKQGHILISGGMTGTMEASSRGASDADGLVVGVLPGDKFTDGNAYSTIKILSGMQFARNYITGLSCHGAIVVGGSSGAYEEARRVWEGRGPVVVLANSGSPTGASAQMLSMQEIFGVAFPEDKPKPWRVFSAATPAESVSLVIGLIRKGYAQHEP