Rv2415c Family assigned · medium auto-curated
H37Rv Rv2415c · MTBC0 mtbc0_002571 ·
297 aa · 2737159–2738052 (-) ·
RefSeq NP_216931.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | ComEA family DNA-binding protein |
| Revised (this work) | ComEA family DNA-binding protein. Pfam: SLBB (PF10531.16), HHH_3 (PF12836.14), HHH (PF00633.30). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71728
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Helix-hairpin-helix DNA-binding motif class 1 domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | comEA |
| eggNOG description | TIGRFAM Competence protein ComEA, helix-hairpin-helix |
| Orthologous group | COG1555 |
| KEGG orthology |
K02237
|
| KEGG modules |
M00429
|
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 | 1.369 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 7 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 |
|---|---|---|---|---|
SLBB | PF10531.16 | 8.0e-09 | 139–193 | SLBB domain |
HHH_3 | PF12836.14 | 7.7e-20 | 234–296 | Helix-hairpin-helix motif |
HHH | PF00633.30 | 2.7e-08 | 238–263 | Helix-hairpin-helix motif |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: eis (enhanced intracellular survival protein), high confidence from genomic context alone (score 865 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) |
|---|---|---|---|---|
Rv2414c hyp |
hypothetical protein | 922 | 898 ctx | neighborhood:869 |
Rv2416c eis |
enhanced intracellular survival protein | 865 | 865 ctx | neighborhood:429 coexpression:774 |
Rv2413c hyp |
hypothetical protein | 836 | 830 ctx | neighborhood:829 |
Rv1988 erm(37) |
23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(37) | 740 | 741 | coexpression:732 |
Rv1257c |
oxidoreductase | 732 | 733 | coexpression:732 |
Rv2551c hyp |
hypothetical protein | 729 | 646 | coexpression:645 |
Rv2421c nadD |
nicotinate-nucleotide adenylyltransferase | 543 | 543 | |
Rv0017c rodA |
cell division protein RodA | 521 | 503 | |
Rv1258c tap |
multidrug-efflux transporter | 474 | 474 | coexpression:474 |
Rv2420c rsfS hyp |
hypothetical protein | 467 | 467 | |
Rv3840 |
transcriptional regulator | 453 | 453 ctx | cooccurence:414 |
Rv2478c hyp |
hypothetical protein | 567 | 433 | coexpression:417 |
Rv0648 |
alpha-mannosidase | 430 | 430 | coexpression:430 |
Rv2417c |
DegV domain-containing protein | 424 | 425 ctx | neighborhood:420 |
Rv0054 ssb |
single-strand DNA-binding protein | 560 | 424 | coexpression:408 |
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: ComEA family DNA-binding protein
- Pfam (hmmscan --cut_ga): SLBB PF10531.16 (E=8e-09), HHH_3 PF12836.14 (E=8e-20), HHH PF00633.30 (E=3e-08)
- (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_216931.1)
- Domains: Pfam-A via hmmscan --cut_ga — SLBB (PF10531.16), HHH_3 (PF12836.14), HHH (PF00633.30)
- 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
COG1555 - Curated reference: UniProt P71728 (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 —
24 functional partner(s); context anchor
eis - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002571|Rv2415c| MRTELPAERLQRRLGAVPDIDSHAASAHLDPEPHDPTDDGPDHDEPRDDPNSLLPRWLPDTSRGQGWADRIRADPGRAGAVALAVIAALAVLVTVFTLIRDRTEPVMSAKLPPVEPVSPTNPRSSASPGSPDRSGLPVVVSVVGLVHTPGLVTLAPGARIADALQAAGGAVDGADTVGLNMARQLGDGEQIVVGLAPPSGQPRVLGSSVGAGTPGPAGTSGTATTGPKTAPKTAEVLDLNTATVEQLDALPGIGPVTAAAIVAWRQRNGRFTSVDQLADVDGIGPARLDKLRNLVRV