Rv0210 Still unknown · low
H37Rv Rv0210 · MTBC0 mtbc0_000224 ·
492 aa · 250472–251950 (+) ·
RefSeq NP_214724.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Conserved hypothetical protein; no Pfam domain above threshold. Foldseek gives only a low-TM (0.21) partial match to Mtb IniA, not conclusive. Uncharacterised. |
Curated reference (UniProt)
| UniProt |
P96392
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Transmembrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | An essential GTPase that binds both GDP and GTP, with rapid nucleotide exchange. Plays a role in 16S rRNA processing and 30S ribosomal subunit biogenesis and possibly also in cell cycle regulation and energy metabolism |
| Orthologous group | COG1159 |
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 | 1.182 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 8 missense, 1 nonsense, 3 frameshift |
| Disruption | 4 distinct premature-stop/frameshift site(s); most common in 0.45% of strains (658) · convergent |
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 |
|---|---|---|---|---|
6j73-assembly2_B |
1.00 | 0.21 | 2.4e-08 sig | 6j73-assembly2_B Crystal structure of IniA from Mycobacterium smegmatis |
6j72-assembly1_A |
1.00 | 0.20 | 2.7e-07 sig | 6j72-assembly1_A Crystal structure of IniA from Mycobacterium smegmatis with GTP bound |
6j73-assembly1_A |
1.00 | 0.20 | 2.2e-07 sig | 6j73-assembly1_A Crystal structure of IniA from Mycobacterium smegmatis |
1mky-assembly1_A |
1.00 | 0.46 | 4.4e-03 sig | 1mky-assembly1_A Structural Analysis of the Domain Interactions in Der, a Switch Protein Containing Two GTPase Domains |
4aur-assembly1_A |
1.00 | 0.22 | 2.1e-05 sig | 4aur-assembly1_A LeoA bacterial dynamin GTPase from ETEC |
4dcu-assembly1_A |
0.97 | 0.40 | 5.0e-02 | 4dcu-assembly1_A Crystal Structure of B. subtilis EngA in complex with GDP |
4tql-assembly2_B |
0.54 | 0.32 | 4.3e-01 | 4tql-assembly2_B Computationally designed three helix bundle |
3zx6-assembly1_A |
0.54 | 0.29 | 2.5e-01 | 3zx6-assembly1_A Structure of Hamp(AF1503)-Tsr fusion - Hamp (A291V) mutant |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: trmB (tRNA (guanine-N(7)-)-methyltransferase), 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) |
|---|---|---|---|---|
Rv0209 hyp |
hypothetical protein | 976 | 976 ctx | neighborhood:882 coexpression:806 |
Rv0208c trmB |
tRNA (guanine-N(7)-)-methyltransferase | 801 | 801 ctx | neighborhood:775 |
Rv0207c hyp |
hypothetical protein | 775 | 775 ctx | neighborhood:775 |
Rv2474c hyp |
hypothetical protein | 750 | 750 ctx | cooccurence:750 |
Rv3413c rsdA |
anti-sigma-D factor RsdA | 746 | 746 ctx | cooccurence:746 |
Rv2687c |
antibiotic ABC transporter permease | 739 | 739 ctx | cooccurence:739 |
Rv2686c |
antibiotic ABC transporter permease | 734 | 735 ctx | cooccurence:734 |
Rv1978 hyp |
hypothetical protein | 732 | 733 ctx | cooccurence:732 |
Rv0206c mmpL3 |
transmembrane transport protein MmpL3 | 722 | 722 ctx | neighborhood:721 |
Rv1182 papA3 |
acyltransferase papA3 | 716 | 717 ctx | cooccurence:715 |
Rv0479c |
membrane protein | 703 | 704 ctx | cooccurence:703 |
Rv3824c papA1 |
acyltransferase | 686 | 686 ctx | cooccurence:686 |
Rv2743c hyp |
hypothetical protein | 673 | 674 ctx | cooccurence:672 |
Rv3405c |
HTH-type transcriptional regulator | 666 | 667 ctx | cooccurence:663 |
Rv3527 hyp |
hypothetical protein | 652 | 652 ctx | cooccurence:652 |
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
- MTBC0 PGAP product: 'hypothetical protein'
- Pfam: none above threshold
- Foldseek on the ESMFold model: only a partial, low-TM match -- inconclusive
ESM Atlas signal (exploratory)
Ancestral protein hash 2615589eb7f7c6d74965a0ad7a605c15 ·
10 ESM-space neighbours (max similarity 0.923).
SAE features are orienting indices, not validated domains.
| # | Index | Activation | Interpretation |
|---|---|---|---|
| 1 | 6012 |
1.42 | Post-GTPase helical scaffolds |
| 2 | 11893 |
1.33 | Dynamin helical stalk/paddle |
| 3 | 2174 |
1.29 | P-loop GTPase coupling helix |
| 4 | 8885 |
1.17 | Coiled-coil machine head domains |
| 5 | 11953 |
1.16 | GTPase-flanking coiled-coil scaffolds |
| 6 | 5138 |
1.16 | Canonical P-loop GTPase G-domain |
| 7 | 4409 |
1.13 | G-domain Walker A P-loop |
| 8 | 1965 |
1.09 | Transmembrane helical hairpins and anchors |
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_214724.1)
- 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
COG1159 - Curated reference: UniProt P96392 (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 93.2, very high)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
80 functional partner(s); context anchor
trmB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000224|Rv0210| MIRAASDDPAGVDELVAAIAPGLAGLGLPVINRREVVLVTGPWLAGVSGVRAALAERLPQRRFVETAELGPGDAPVAVVFVVSAATALTESDCVLLDTAAEHTDAVVAVVSKIDVHRGWRDVLTSNRDRLAARASRYARVPWVGAAAAPELGEPYLDDLVAAIQKQLADPAVARRNMLRAWESRLLMVARRFDGDAQSAGRRARVDALRQQRRTVLRQGRQSKSEHTIALRAQIQHARVKLSYFARNRCSLLRVELQEHVAGLSRKDIARFAAYTRGRVQEVVAEVGEGAVAHLADVAQLLGVPVQPPVLENLPAVLPTVVAPPLTSRRLEIRLTTLLGAGFGLGIALTLSRLVAGLTPGLAASGMVAGVAIGLAVTAWVVNARALLHDRVVVDRWTGEVTASLRSVVEQLVATRVVAVETLLSTAISERDDAENARVADQVSIIDGELREHAVAAARAAALRDREMPAVRAALEAVRAELGEPGTPTTGLF