Rv3231c Still unknown · low auto-curated
H37Rv Rv3231c · MTBC0 mtbc0_003440 ·
169 aa · 3630506–3631015 (-) ·
RefSeq NP_217748.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF6912. Function unknown. Foldseek best (non-significant) hit: 8zm3-assembly1_C Cryo-EM strcuture of Cas5-HNH Cascade,apo-Conf2 (prob 0.03, TM 0.35). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O05876
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2DRWJ |
|---|
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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 0 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 |
|---|---|---|---|---|
DUF6912 | PF21853.2 | 2.2e-58 | 3–166 | Family of unknown function (DUF6912) |
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 82.5 (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 |
|---|---|---|---|---|
8zm3-assembly1_C |
0.03 | 0.35 | 7.1e+00 | 8zm3-assembly1_C Cryo-EM strcuture of Cas5-HNH Cascade,apo-Conf2 |
2rgi-assembly1_B |
0.02 | 0.31 | 6.2e+00 | 2rgi-assembly1_B Crystal structure of Ca2+-free S100A2 at 1.6 A resolution |
6bnl-assembly2_E |
0.02 | 0.28 | 3.3e+00 | 6bnl-assembly2_E Crystal structure of TCR-MHC-like molecule |
6ihv-assembly1_A |
0.02 | 0.16 | 8.9e-01 | 6ihv-assembly1_A Crystal structure of bacterial serine phosphatase bearing R161E mutation |
7rno-assembly1_A |
0.01 | 0.22 | 5.1e+00 | 7rno-assembly1_A Model of the Ac-6-FP/hpMR1/bB2m/TAPBPR complex from integrated docking, NMR and restrained MD |
3gmq-assembly1_A |
0.01 | 0.20 | 5.8e+00 | 3gmq-assembly1_A Structure of mouse CD1d expressed in SF9 cells, no ligand added |
3tvm-assembly2_E |
0.01 | 0.19 | 5.1e+00 | 3tvm-assembly2_E Structure of the mouse CD1d-SMC124-iNKT TCR complex |
4pj8-assembly1_A |
0.01 | 0.23 | 7.6e+00 | 4pj8-assembly1_A Structure of human MR1-5-OP-RU in complex with human MAIT TRBV20 TCR |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ppk2 (polyphosphate kinase), high confidence from genomic context alone (score 882 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) |
|---|---|---|---|---|
Rv3232c ppk2 |
polyphosphate kinase | 975 | 882 ctx | neighborhood:881 textmining:803 |
Rv2170 |
GCN5-like N-acetyltransferase | 770 | 771 ctx | cooccurence:770 |
Rv3230c |
stearoyl-CoA 9-desaturase electron transfer protein | 952 | 769 ctx | neighborhood:768 textmining:803 |
Rv3233c |
Rv3233c, (MTCY20B11.08c), len: 196 aa. Possible triacylglycerol synthase (See Daniel et al., 2004), similar to C-terminus of Q9RIU8|SCM11.13 | 908 | 744 ctx | neighborhood:740 textmining:658 |
Rv3234c tgs3 |
diacyglycerol O-acyltransferase | 906 | 742 ctx | neighborhood:740 textmining:652 |
Rv0948c |
chorismate mutase | 730 | 730 ctx | cooccurence:722 |
Rv3311 hyp |
hypothetical protein | 722 | 723 ctx | cooccurence:721 |
Rv3412 hyp |
hypothetical protein | 717 | 717 ctx | cooccurence:716 |
Rv1332 |
transcriptional regulator | 711 | 711 ctx | cooccurence:707 |
Rv3229c desA3 |
stearoyl-CoA 9-desaturase | 710 | 710 ctx | neighborhood:709 |
Rv3657c |
membrane protein | 699 | 699 ctx | cooccurence:691 |
Rv3605c hyp |
hypothetical protein | 669 | 669 ctx | cooccurence:669 |
Rv2179c |
3'-5' exoribonuclease | 664 | 664 ctx | cooccurence:664 |
Rv3259 hyp |
hypothetical protein | 651 | 651 ctx | cooccurence:650 |
Rv2744c 35kd_ag hyp |
hypothetical protein | 640 | 640 ctx | cooccurence:637 |
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: hypothetical protein
- Pfam (hmmscan --cut_ga): DUF6912 PF21853.2 (E=2e-58)
- Foldseek best: 8zm3-assembly1_C Cryo-EM strcuture of Cas5-HNH Cascade,apo-Conf2 (prob 0.03, E=7e+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_217748.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF6912 (PF21853.2)
- 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
2DRWJ - Curated reference: UniProt O05876 (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 82.5, confident)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
73 functional partner(s); context anchor
ppk2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003440|Rv3231c| MTQVYIPATLAMLQRLVADGALWPVNGTAFAVTPTLRESYAEGDDEELAEVALREAALASLRLLAADIGATADALPPRRAVLAAEVDDATYRPDLDDAVVRLAGPITIDQVVAAYVDNAGAEPAVMAAIAVIDAADLGDEDAELVVGDAQDHDLAWYANQELPFLLDLL