Rv3196 Family assigned · low
H37Rv Rv3196 · MTBC0 - ·
299 aa · 3565788–3566687 (+) ·
RefSeq NP_217712.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Probable ThiF/MoeB/E1-family adenylyltransferase of undetermined substrate; NOT a YcaO heterocyclase. RefSeq leaves it 'hypothetical protein'. A strong Foldseek hit to the cyanobactin heterocyclase TruD (4bs9, query-normalised TM-score 0.72) is a normalised-TM-score artefact: the alignment covers only the N-terminal scaffold (TruD residues 3-321), stops before the YcaO catalytic domain, and the target-normalised TM-score is 0.33 (~38% coverage); none of the YcaO catalytic residues lies in the aligned region. HHpred re-routes it (>=99.9%) to standalone adenylyltransferases (MccB, PaaA) and the ThiF/MoeB/E1-like adenylation superfamily, within which the CxxC pair (C208/C211) matches the MoeB-type zinc motif. A RiPP role is independently improbable (no precursor-peptide cassette, maturation protease, or TfuA in H37Rv). A worked example of the normalised-TM-score trap. |
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 |
O53342
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Cyclodehydratase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| eggNOG description | UBA ThiF-type NAD FAD binding protein |
| Orthologous group | COG0476 |
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 5 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 93.2 (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 |
|---|---|---|---|---|
4bs9-assembly1_A-2 |
1.00 | 0.63 | 4.6e-13 sig | 4bs9-assembly1_A-2 Structure of the heterocyclase TruD |
4v1t-assembly1_B |
1.00 | 0.65 | 1.5e-12 sig | 4v1t-assembly1_B Heterocyclase in complex with substrate and Cofactor |
3h9g-assembly2_D |
1.00 | 0.59 | 5.0e-12 sig | 3h9g-assembly2_D Crystal structure of E. coli MccB + MccA-N7isoASN |
3h5n-assembly1_D |
1.00 | 0.60 | 9.1e-12 sig | 3h5n-assembly1_D Crystal structure of E. coli MccB + ATP |
4v1v-assembly1_B |
1.00 | 0.60 | 6.4e-12 sig | 4v1v-assembly1_B Heterocyclase in complex with substrate and Cofactor |
3h5n-assembly1_B |
1.00 | 0.60 | 9.1e-12 sig | 3h5n-assembly1_B Crystal structure of E. coli MccB + ATP |
6om4-assembly2_B |
1.00 | 0.61 | 1.9e-11 sig | 6om4-assembly2_B The structure of Microcin C7 biosynthetic enzyme MccB in complex with N-formylated MccA |
3h5r-assembly1_B |
1.00 | 0.57 | 4.7e-12 sig | 3h5r-assembly1_B Crystal structure of E. coli MccB + Succinimide |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2609c (membrane protein), medium confidence from genomic context alone (score 648 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) |
|---|---|---|---|---|
Rv3446c hyp |
hypothetical protein | 824 | 816 | coexpression:734 |
Rv3323c moaX |
MoaD-MoaE fusion protein MoaX | 835 | 812 | coexpression:444 experimental:473 |
Rv3195 hyp |
hypothetical protein | 803 | 803 ctx | neighborhood:802 |
Rv3448 eccD4 |
ESX-4 secretion system protein EccD4 | 788 | 789 | coexpression:754 |
Rv3449 mycP4 |
membrane-anchored mycosin | 771 | 771 | coexpression:771 |
Rv0416 thiS |
sulfur carrier protein ThiS | 715 | 698 | coexpression:450 experimental:455 |
Rv3415c hyp |
hypothetical protein | 679 | 679 ctx | cooccurence:678 |
Rv3119 moaE1 |
molybdopterin synthase catalytic subunit 1 | 693 | 678 | coexpression:434 |
Rv0866 moaE2 |
molybdopterin synthase catalytic subunit 2 | 693 | 677 | coexpression:432 |
Rv3025c iscS |
cysteine desulfurase | 691 | 672 | database:615 |
Rv0417 thiG |
thiazole synthase | 675 | 655 | coexpression:643 |
Rv2609c |
membrane protein | 648 | 648 ctx | cooccurence:625 |
Rv0434 hyp |
hypothetical protein | 657 | 644 | database:595 |
Rv1973 |
Mce associated membrane protein | 629 | 616 | database:466 |
Rv2301 cut2 |
cutinase | 608 | 594 | database:464 |
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
- RefSeq: hypothetical protein
- Foldseek hit to TruD (4bs9) is a normalised-TM-score artefact: qtmscore 0.72 vs ttmscore 0.33 (~38% coverage); YcaO catalytic domain NOT in the aligned region
- HHpred re-routes >=99.9% to ThiF/MoeB/E1 adenylyltransferase superfamily (MccB, PaaA); CxxC (C208/C211) = MoeB-type Zn motif
- RiPP / heterocyclase role excluded (no precursor cassette / protease / TfuA / second YcaO in H37Rv)
- Scaffold-of-fold caution; conserved in >99.98% of ~250,724 genomes
- Curated against the companion dark-enzymes re-annotation (Guyeux 2026)
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_217712.1)
- 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
COG0476 - Curated reference: UniProt O53342 (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 93.2, very high)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
91 functional partner(s); context anchor
Rv2609c - Primary literature: Guyeux C (2026). Structure-guided functional hypotheses for uncharacterised enzymes of Mycobacterium tuberculosis in preparation. doi:10.5281/zenodo.20571950
Ancestral MTBC0 protein sequence
>H37Rv|Rv3196| MSARSVAPSQVMRRAASALYSLNPAMPVLLRPDGAVQVGWDPRRAVLVRPPRGLTATGLAALLRSMRSPIPITELQRQAAERGLVDGDAMANLVAQLVGAGVATPLANPGNLDSRRRAASIRVHGRGPLSDLLVQALRCSGARIRHSSQPHAAVTPAGVDLVVLSDYLVADPHMVRDLHTERVPHLPVRVRDGTGMVGPLVVPGVTSCLGCADLHRSDRDAAWPAIAAQLRDTVGVADRATLLATAALALSQVNRVIAAVRGQEATPEPPSALNTTLEFDLNAGSIVARQWTRHPRCFC