Rv2975c Still unknown · low auto-curated
H37Rv Rv2975c · MTBC0 - ·
84 aa · 3331358–3331612 (-) ·
RefSeq NP_217491.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Conserved hypothetical protein; no recognised domain. Function unknown. Foldseek best (non-significant) hit: 6gj3-assembly1_F The baseplate complex from the type VI secretion syst (prob 0.18, TM 0.62). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
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 |
P95120
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | DhaL domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | dak3 |
| eggNOG description | glycerone kinase activity |
| Orthologous group | COG1461 |
| EC number |
EC 2.7.1.28, EC 2.7.1.29, EC 4.6.1.15
|
| KEGG orthology |
K00863, K07030
|
| KEGG pathways |
map00051, map00561, map00680, map01100, map01120, map01200, map04622
|
| KEGG modules |
M00344
|
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 | 0.344 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 1 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 61.67% of strains (89551) · reference-fixed |
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 58.2 (low). Low-confidence model: the fold may be unreliable, so treat these structural hits with caution.
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 |
|---|---|---|---|---|
6gj3-assembly1_F |
0.18 | 0.62 | 5.0e+00 | 6gj3-assembly1_F The baseplate complex from the type VI secretion system |
6e3y-assembly1_R |
0.18 | 0.62 | 5.3e+00 | 6e3y-assembly1_R Cryo-EM structure of the active, Gs-protein complexed, human CGRP receptor |
9avg-assembly1_Q |
0.18 | 0.46 | 1.9e+00 | 9avg-assembly1_Q Structure of human calcium-sensing receptor in complex with chimeric Gs (miniGis) protein in nanodiscs |
9asb-assembly1_Q |
0.15 | 0.48 | 2.7e+00 | 9asb-assembly1_Q Structure of human calcium-sensing receptor in complex with chimeric Gq (miniGisq) protein in nanodiscs |
9ayf-assembly1_Q |
0.13 | 0.45 | 2.9e+00 | 9ayf-assembly1_Q Structure of human calcium-sensing receptor in complex with Gi1 (miniGi1) protein in detergent |
8wpu-assembly1_B |
0.13 | 0.44 | 2.7e+00 | 8wpu-assembly1_B Human calcium-sensing receptor(CaSR) bound to cinacalcet in complex with Gq protein |
9axf-assembly1_Q |
0.11 | 0.45 | 4.2e+00 | 9axf-assembly1_Q Structure of human calcium-sensing receptor in complex with chimeric Gq (miniGisq) protein in detergent |
4nqi-assembly1_A |
0.08 | 0.41 | 5.0e+00 | 4nqi-assembly1_A Structure of the N-terminal I-BAR domain (1-259) of D.Discoideum IBARa |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: recG (ATP-dependent DNA helicase RecG), high confidence from genomic context alone (score 801 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) |
|---|---|---|---|---|
Rv2974c hyp |
hypothetical protein | 978 | 978 ctx | neighborhood:773 fusion:875 |
Rv2973c recG |
ATP-dependent DNA helicase RecG | 801 | 801 ctx | neighborhood:800 |
Rv2972c hyp |
hypothetical protein | 801 | 801 ctx | neighborhood:800 |
Rv2417c |
DegV domain-containing protein | 762 | 753 | experimental:652 |
Rv1081c |
membrane protein | 559 | 560 ctx | cooccurence:558 |
Rv3205c hyp |
hypothetical protein | 531 | 531 ctx | cooccurence:512 |
Rv2927c sepIVA hyp |
hypothetical protein | 511 | 512 ctx | cooccurence:445 |
Rv0948c |
chorismate mutase | 505 | 506 ctx | cooccurence:504 |
Rv2698 |
transmembrane protein | 497 | 498 ctx | cooccurence:495 |
Rv0556 |
transmembrane protein | 480 | 481 ctx | cooccurence:479 |
Rv2171 lppM |
lipoprotein LppM | 469 | 470 ctx | cooccurence:468 |
Rv0358 hyp |
hypothetical protein | 463 | 463 ctx | cooccurence:463 |
Rv1474c |
transcriptional regulator | 435 | 436 ctx | cooccurence:434 |
Rv2732c |
transmembrane protein | 431 | 432 ctx | cooccurence:426 |
Rv3647c hyp |
hypothetical protein | 429 | 430 ctx | cooccurence:426 |
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: 6gj3-assembly1_F The baseplate complex from the type VI secretion system (prob 0.18, E=5e+00, TM=0.62)
- (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_217491.1)
- 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
COG1461 - Curated reference: UniProt P95120 (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)
- Model confidence: ESMFold per-residue pLDDT (mean 58.2, low)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
20 functional partner(s); context anchor
recG - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2975c| MGTADRPLDASALRDWAHAVVSDLILHIDEINRLNVFPVADSDTGVNMLFTMRAAVVEADLHANSQADAEDVARVAAALAAGAR