Rv2618 Family assigned · low auto-curated · to review
H37Rv Rv2618 · MTBC0 - ·
225 aa · 2946434–2947111 (+) ·
RefSeq NP_217134.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | No Pfam domain above threshold; Foldseek indicates a fold similar to 6cmv-assembly3_F Crystal structure of Archaeal Biofilm Regulator (AbfR2) from Su (prob 1.00, TM 0.57). Structure-based, putative. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed (flagged for human review).
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 |
O06195
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Transcriptional regulator |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | transcriptional regulator |
| Orthologous group | COG2345 |
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 | 1.104 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 3 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 91.7 (very high). A confident model makes the fold comparison meaningful.
Best matches against the PDB, ranked by Foldseek homology probability. A high probability / TM-score suggests a shared fold; unless flagged sig (E < 0.01) these are fold hypotheses, not assignments.
| Target | Prob | TM | E-value | Description |
|---|---|---|---|---|
6cmv-assembly3_F |
1.00 | 0.57 | 2.0e-04 sig | 6cmv-assembly3_F Crystal structure of Archaeal Biofilm Regulator (AbfR2) from Sulfolobus acidocaldarius |
1q1h-assembly1_A |
1.00 | 0.80 | 1.8e-02 | 1q1h-assembly1_A An extended winged helix domain in general transcription factor E/IIE alpha |
3r0a-assembly1_A |
1.00 | 0.69 | 5.4e-03 sig | 3r0a-assembly1_A Possible transcriptional regulator from Methanosarcina mazei Go1 (gi 21227196) |
6pln-assembly2_B |
1.00 | 0.63 | 3.4e-03 sig | 6pln-assembly2_B X-ray crystal structure of Pyrococcus furiosus general transcription factor TFE-alpha |
3f21-assembly1_A |
1.00 | 0.72 | 1.8e-02 | 3f21-assembly1_A Crystal structure of Zalpha in complex with d(CACGTG) |
1ku9-assembly1_B |
1.00 | 0.49 | 1.5e-03 sig | 1ku9-assembly1_B X-ray Structure of a Methanococcus jannaschii DNA-Binding Protein: Implications for Antibiotic Resistance in Staphylococcus aureus |
6xjf-assembly3_C |
1.00 | 0.69 | 2.0e-02 | 6xjf-assembly3_C X-ray crystal structure of Pyrococcus furiosus general transcription factor TFE-alpha (SeMet labeled protein) |
2d1h-assembly1_B |
1.00 | 0.65 | 3.3e-02 | 2d1h-assembly1_B Crystal structure of ST1889 protein from thermoacidophilic archaeon Sulfolobus tokodaii |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2617c (transmembrane protein), high confidence from genomic context alone (score 873 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) |
|---|---|---|---|---|
Rv2617c |
transmembrane protein | 873 | 873 ctx | neighborhood:581 cooccurence:706 |
Rv2428 ahpC |
alkyl hydroperoxide reductase subunit AhpC | 499 | 500 | coexpression:481 |
Rv2359 zur |
zinc uptake regulation protein | 457 | 458 | coexpression:440 |
Rv1909c furA |
ferric uptake regulation protein FurA | 456 | 457 | coexpression:439 |
Rv3887c eccD2 |
ESX-2 secretion system protein EccD | 448 | 448 ctx | cooccurence:448 |
Rv1156 hyp |
hypothetical protein | 442 | 442 ctx | cooccurence:442 |
Rv3153 nuoI |
NADH-quinone oxidoreductase subunit I | 438 | 438 | experimental:431 |
Rv3191c |
transposase | 434 | 41 | textmining:434 |
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
- Foldseek best: 6cmv-assembly3_F Crystal structure of Archaeal Biofilm Regulator (AbfR2) from Su (prob 1.00, E=2e-04, TM=0.57)
- (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_217134.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
COG2345 - Curated reference: UniProt O06195 (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)
- Model confidence: ESMFold per-residue pLDDT (mean 91.7, very high)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
8 functional partner(s); context anchor
Rv2617c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2618| MDPVRRQLYQFVCSQSMPVSRDQAADAVGIPRHQAKFHLDRLTAEGLLDTEYARLTGRSGPGAGRTAKLYRRAGRDIALSLPQREYELAGRLMAAAIVLSATTGEPTVEVLNRIAHDYGQAMGAAATTRPPADPAAALELTLDVLRKYGYEPRRPAGPGDDEVELVNCPFHALAREQTELACNMNHALITGVADALAPHSPAVRLAPGPARCCVVLKRCSAHDPE