Rv1907c Still unknown · low auto-curated
H37Rv Rv1907c · MTBC0 - ·
215 aa · 2153235–2153882 (-) ·
RefSeq NP_216423.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF4262. Function unknown. Foldseek best (non-significant) hit: 4q3o-assembly4_H Crystal structure of MGS-MT1, an alpha/beta hydrolase (prob 0.04, TM 0.35). |
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 |
L0TAY1
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | DUF4262 domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Domain of unknown function (DUF4262) |
| Orthologous group | 2C8CM |
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) pseudogene candidate
| pN/pS | 1.008 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 6 missense, 0 nonsense, 3 frameshift |
| Disruption | 3 distinct premature-stop/frameshift site(s); most common in 12.15% of strains (17644) · 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 |
|---|---|---|---|---|
DUF4262 | PF14081.12 | 1.5e-31 | 83–197 | Domain of unknown function (DUF4262) |
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 79.1 (confident). 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 |
|---|---|---|---|---|
4q3o-assembly4_H |
0.04 | 0.35 | 2.7e+00 | 4q3o-assembly4_H Crystal structure of MGS-MT1, an alpha/beta hydrolase enzyme from a Lake Matapan deep-sea metagenome library |
6mrs-assembly1_A |
0.03 | 0.25 | 1.6e+00 | 6mrs-assembly1_A De novo designed protein Peak6 |
7z5u-assembly1_A |
0.03 | 0.41 | 6.6e+00 | 7z5u-assembly1_A Crystal structure of the peptidase domain of collagenase G from Clostridium histolyticum in complex with a hydroxamate-based inhibitor |
2qg7-assembly2_D |
0.03 | 0.28 | 3.0e+00 | 2qg7-assembly2_D Plasmodium vivax ethanolamine kinase Pv091845 |
6cib-assembly6_F |
0.02 | 0.31 | 6.2e+00 | 6cib-assembly6_F The structure of YcaO from Methanopyrus kandleri bound with AMPPCP and Mg2+ |
4uoi-assembly4_F |
0.02 | 0.39 | 9.5e+00 | 4uoi-assembly4_F Unexpected structure for the N-terminal domain of Hepatitis C virus envelope glycoprotein E1 |
3aac-assembly1_B |
0.02 | 0.41 | 7.9e+00 | 3aac-assembly1_B Small heat shock protein hsp14.0 with the mutations of I120F and I122F in the form II crystal |
4q05-assembly1_B |
0.02 | 0.20 | 1.6e+00 | 4q05-assembly1_B Crystal structure of an esterase E25 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: katG (catalase-peroxidase), high confidence from genomic context alone (score 945 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) |
|---|---|---|---|---|
Rv1908c katG |
catalase-peroxidase | 957 | 945 ctx | neighborhood:805 coexpression:731 |
Rv0330c hyp |
hypothetical protein | 727 | 727 ctx | cooccurence:719 |
Rv1909c furA |
ferric uptake regulation protein FurA | 831 | 712 ctx | neighborhood:698 textmining:438 |
Rv0093c |
membrane protein | 637 | 638 ctx | cooccurence:636 |
Rv0034 hyp |
hypothetical protein | 605 | 606 ctx | cooccurence:600 |
Rv2209 |
integral membrane protein | 602 | 603 ctx | cooccurence:600 |
Rv2775 |
GCN5-like N-acetyltransferase | 588 | 589 ctx | cooccurence:588 |
Rv0355c PPE8 |
PPE family protein PPE8 | 578 | 578 ctx | cooccurence:576 |
Rv3350c PPE56 |
PPE family protein PPE56 | 575 | 575 ctx | cooccurence:574 |
Rv3347c PPE55 |
PPE family protein PPE55 | 569 | 569 ctx | cooccurence:567 |
Rv1004c |
membrane protein | 566 | 567 ctx | cooccurence:562 |
Rv1752 hyp |
hypothetical protein | 566 | 566 ctx | cooccurence:564 |
Rv1452c PE_PGRS28 |
PE-PGRS family protein PE_PGRS28 | 558 | 558 ctx | cooccurence:558 |
Rv2305 hyp |
hypothetical protein | 556 | 556 ctx | cooccurence:556 |
Rv2490c PE_PGRS43 |
PE-PGRS family protein PE_PGRS43 | 552 | 552 ctx | cooccurence:552 |
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
- Pfam (hmmscan --cut_ga): DUF4262 PF14081.12 (E=1e-31)
- Foldseek best: 4q3o-assembly4_H Crystal structure of MGS-MT1, an alpha/beta hydrolase enzyme fr (prob 0.04, E=3e+00, TM=0.35)
- (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_216423.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF4262 (PF14081.12)
- 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
2C8CM - Curated reference: UniProt L0TAY1 (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 79.1, confident)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
64 functional partner(s); context anchor
katG - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1907c| MIGPARRSTTTRRSTPRADRLAGCWCLPGAICQTPRAWWSQARRDGDDETGMRRKGAEMCWMCDHPEATAEEYLDEVYGIMLMHGWAVQHVECERRPFAYTVGLTRRGLPELVVTGLSPRRGQRLLNIAARRALVGDLLTPGMQTTLPAGPLVETVQVTHPDAHLYCAIAIFGDKVTALQLVWADRRGRWPWAADFDEGRGTQPVLGMRATRRSA