Rv2164c Still unknown · low auto-curated
H37Rv Rv2164c · MTBC0 mtbc0_002300 ·
384 aa · 2454449–2455603 (-) ·
RefSeq NP_216680.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Conserved hypothetical protein; no recognised domain. Function unknown. Foldseek best (non-significant) hit: 8j07-assembly1_c2 96nm repeat of human respiratory doublet microtubule (prob 0.04, TM 0.14). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06213
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable conserved proline rich membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
D Cell cycle control, cell division, chromosome partitioning
|
|---|---|
| eggNOG description | Essential cell division protein. May link together the upstream cell division proteins, which are predominantly cytoplasmic, with the downstream cell division proteins, which are predominantly periplasmic |
| Orthologous group | COG2919 |
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 | 0.953 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 12 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 70.3 (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 |
|---|---|---|---|---|
8j07-assembly1_c2 |
0.04 | 0.14 | 2.1e+00 | 8j07-assembly1_c2 96nm repeat of human respiratory doublet microtubule and associated axonemal complexes |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pbpB (penicillin-binding membrane protein PbpB), high confidence from genomic context alone (score 979 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) |
|---|---|---|---|---|
Rv2163c pbpB |
penicillin-binding membrane protein PbpB | 988 | 979 ctx | neighborhood:881 coexpression:806 textmining:475 |
Rv2151c ftsQ |
cell division protein FtsQ | 931 | 922 ctx | neighborhood:544 experimental:829 |
Rv2165c rsmH |
rRNA small subunit methyltransferase H | 969 | 910 ctx | neighborhood:882 textmining:673 |
Rv2166c mraZ |
transcriptional regulator MraZ | 978 | 837 ctx | neighborhood:816 textmining:876 |
Rv0538 |
membrane protein | 772 | 773 ctx | cooccurence:767 |
Rv3909 hyp |
hypothetical protein | 771 | 772 ctx | cooccurence:769 |
Rv3835 hyp |
hypothetical protein | 923 | 770 ctx | cooccurence:766 textmining:680 |
Rv2709 |
transmembrane protein | 770 | 770 ctx | cooccurence:769 |
Rv3658c |
transmembrane protein | 748 | 749 ctx | cooccurence:748 |
Rv3903c cpnT hyp |
hypothetical protein | 747 | 748 ctx | cooccurence:746 |
Rv2843 hyp |
hypothetical protein | 746 | 747 ctx | cooccurence:743 |
Rv2939 papA5 |
phthiocerol/phthiodiolone dimycocerosyl transferase | 742 | 743 ctx | cooccurence:742 |
Rv0007 |
membrane protein | 729 | 729 ctx | cooccurence:723 |
Rv1111c hyp |
hypothetical protein | 724 | 725 ctx | cooccurence:722 |
Rv0339c iniR |
transcriptional regulator | 723 | 723 ctx | cooccurence:719 |
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
- Foldseek best: 8j07-assembly1_c2 96nm repeat of human respiratory doublet microtubule and assoc (prob 0.04, E=2e+00, TM=0.14)
- (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_216680.1)
- 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
COG2919 - Curated reference: UniProt O06213 (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 70.3, confident)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
100 functional partner(s); context anchor
pbpB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002300|Rv2164c| MRAKREAPKSRSSDRRRRADSPAAATRRTTTNSAPSRRIRSRAGKTSAPGRQARVSRPGPQTSPMLSPFDRPAPAKNTSQAKARAKARKAKAPKLVRPTPMERLAARLTSIDLRPRTLANKVPFVVLVIGSLGVGLGLTLWLSTDAAERSYQLSNARERTRMLQQHKEALERDVREAASAPALAEAARRQGMIPTRDTAHLVQDPDGNWVVVGTPKPADGVPPPPLNTKLPEDPPPPPKPAAVPLEVPVRVTPGPDDPAPPARSGPEVLVRTPDGTATLGGATHLPTQAGPQLPGPVPIPGAPGPMPAPPLGAVPSPAPAENPVPLQVGAAPPAGLPGPAPVAATPGLSGGSQPMVAPPAPVPANGEQFGPVTAPVPTAPGAPR