miaB Resolved · high auto-curated
H37Rv Rv2733c · MTBC0 mtbc0_002907 ·
512 aa · 3067401–3068939 (-) ·
RefSeq NP_217249.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | (dimethylallyl)adenosine tRNA methylthiotransferase |
|---|---|
| MTBC0 PGAP re-annotation | tRNA (N6-isopentenyl adenosine(37)-C2)-methylthiotransferase MiaB |
| Revised (this work) | TRNA (N6-isopentenyl adenosine(37)-C2)-methylthiotransferase MiaB. Pfam: UPF0004 (PF00919.27), Radical_SAM (PF04055.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WK05
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase |
| EC (curated) |
EC 2.8.4.3
|
| Curated function | Catalyzes the methylthiolation of N6-(dimethylallyl)adenosine (i(6)A), leading to the formation of 2-methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | miaB |
| eggNOG description | Catalyzes the methylthiolation of N6- (dimethylallyl)adenosine (i(6)A), leading to the formation of 2- methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine |
| Orthologous group | COG0621 |
| EC number |
EC 2.8.4.3
|
| KEGG orthology |
K06168
|
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 | 0.906 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
UPF0004 | PF00919.27 | 1.3e-29 | 27–125 | Uncharacterized protein family UPF0004 |
Radical_SAM | PF04055.28 | 5.9e-29 | 172–348 | Radical SAM superfamily |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2732c (transmembrane protein), high confidence from genomic context alone (score 882 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2732c |
transmembrane protein | 882 | 882 ctx | neighborhood:882 |
Rv2727c miaA |
tRNA delta(2)-isopentenylpyrophosphate transferase | 939 | 812 ctx | fusion:725 textmining:691 |
Rv2880c |
Rv2880c, (MTCY274.11c), len: 275 aa. Conserved hypothetical protein, highly similar in N-terminus to others e.g. O86754|SC6A9.22c hypothetic | 760 | 669 ctx | cooccurence:534 |
Rv2783c gpsI |
bifunctional guanosine pentaphosphate synthetase/polyribonucleotide nucleotidyltransferase | 719 | 644 ctx | cooccurence:522 |
Rv2879c rlmN |
Conserved hypothetical protein; Specifically methylates position 2 of adenine 2503 in 23S rRNA and position 2 of adenine 37 in tRNAs; Belong | 734 | 633 ctx | cooccurence:483 |
Rv1340 rphA |
ribonuclease PH | 615 | 616 | experimental:608 |
Rv1229c mrp |
multiple resistance/pH adaptation protein | 655 | 549 ctx | cooccurence:545 |
Rv1407 fmu |
16S rRNA m5C967 methyltransferase | 716 | 537 | coexpression:430 textmining:413 |
Rv2444c rne |
ribonuclease E | 551 | 533 | |
Rv2903c lepB |
signal peptidase | 518 | 518 | coexpression:418 |
Rv2372c rsmE |
rRNA small subunit methyltransferase E | 515 | 461 | |
Rv2404c lepA |
GTP-binding protein LepA | 453 | 453 | coexpression:408 |
Rv1299 prfA |
peptide chain release factor PrfA | 572 | 441 | coexpression:423 |
Rv2388c hemN |
oxygen-independent coproporphyrinogen III oxidase | 509 | 438 | |
Rv2734 hyp |
hypothetical protein | 425 | 426 ctx | neighborhood:426 |
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: (dimethylallyl)adenosine tRNA methylthiotransferase
- MTBC0 PGAP product: tRNA (N6-isopentenyl adenosine(37)-C2)-methylthiotransferase MiaB
- Pfam (hmmscan --cut_ga): UPF0004 PF00919.27 (E=1e-29), Radical_SAM PF04055.28 (E=6e-29)
- (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_217249.1)
- Domains: Pfam-A via hmmscan --cut_ga — UPF0004 (PF00919.27), Radical_SAM (PF04055.28)
- 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
COG0621 - Curated reference: UniProt P9WK05 (SwissProt, reviewed; 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)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
41 functional partner(s); context anchor
Rv2732c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002907|Rv2733c|miaB MVAHDAAAGVTGEGAGPPVRRAPARTYQVRTYGCQMNVHDSERLAGLLEAAGYRRATDGSEADVVVFNTCAVRENADNRLYGNLSHLAPRKRANPDMQIAVGGCLAQKDRDAVLRRAPWVDVVFGTHNIGSLPTLLERARHNKVAQVEIAEALQQFPSSLPSSRESAYAAWVSISVGCNNSCTFCIVPSLRGREVDRSPADILAEVRSLVNDGVLEVTLLGQNVNAYGVSFADPALPRNRGAFAELLRACGDIDGLERVRFTSPHPAEFTDDVIEAMAQTRNVCPALHMPLQSGSDRILRAMRRSYRAERYLGIIERVRAAIPHAAITTDLIVGFPGETEEDFAATLDVVRRARFAAAFTFQYSKRPGTPAAQLDGQLPKAVVQERYERLIALQEQISLEANRALVGQAVEVLVATGEGRKDTVTARMSGRARDGRLVHFTAGQPRVRPGDVITTKVTEAAPHHLIADAGVLTHRRTRAGDAHTAGQPGRAVGLGMPGVGLPVSAAKPGGCR