miaA Resolved · high auto-curated
H37Rv Rv2727c · MTBC0 mtbc0_002901 ·
314 aa · 3062240–3063184 (-) ·
RefSeq NP_217243.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | tRNA delta(2)-isopentenylpyrophosphate transferase |
|---|---|
| MTBC0 PGAP re-annotation | tRNA (adenosine(37)-N6)-dimethylallyltransferase MiaA |
| Revised (this work) | TRNA (adenosine(37)-N6)-dimethylallyltransferase MiaA. Pfam: IPPT (PF01715.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJW1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | tRNA dimethylallyltransferase |
| EC (curated) |
EC 2.5.1.75
|
| Curated function | Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in tRNAs that read codons beginning with uridine, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | miaA |
| eggNOG description | Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in tRNAs that read codons beginning with uridine, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A) |
| Orthologous group | COG0324 |
| EC number |
EC 2.5.1.75
|
| KEGG orthology |
K00791
|
| KEGG pathways |
map00908, map01100, map01110
|
| Gene Ontology (32) |
GO:0003674, GO:0003824, GO:0006139, GO:0006396, GO:0006399, GO:0006400, GO:0006725, GO:0006807, GO:0008033, GO:0008150, GO:0008152, GO:0009451 +20 more
|
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 | 1.003 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 8 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 |
|---|---|---|---|---|
IPPT | PF01715.24 | 6.9e-79 | 40–283 | IPP transferase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: hflX (GTP-binding protein HflX), high confidence from genomic context alone (score 875 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2728c hyp |
hypothetical protein | 889 | 889 ctx | neighborhood:882 |
Rv2725c hflX |
GTP-binding protein HflX | 904 | 875 ctx | neighborhood:733 coexpression:551 |
Rv2726c dapF |
diaminopimelate epimerase | 850 | 850 ctx | neighborhood:849 |
Rv2733c miaB |
(dimethylallyl)adenosine tRNA methylthiotransferase | 939 | 812 ctx | fusion:725 textmining:691 |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 829 | 666 ctx | cooccurence:530 textmining:511 |
Rv2165c rsmH |
rRNA small subunit methyltransferase H | 656 | 612 | coexpression:417 |
Rv2729c |
integral membrane protein | 604 | 588 ctx | neighborhood:558 |
Rv1409 ribG |
bifunctional riboflavin biosynthesis diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino) uracil reductas | 579 | 579 | coexpression:421 |
Rv2731 hyp |
hypothetical protein | 568 | 568 ctx | neighborhood:506 |
Rv2343c dnaG |
DNA primase | 611 | 555 | coexpression:405 |
Rv3610c ftsH |
zinc metalloprotease FtsH | 598 | 545 | coexpression:423 |
Rv2554c ruvX |
Holliday junction resolvase | 545 | 545 | coexpression:508 |
Rv3433c nnr |
bifunctional ADP-dependent (S)-NAD(P)H-hydrate dehydratase/NAD(P)H-hydrate epimerase | 635 | 499 | |
Rv2724c fadE20 |
acyl-CoA dehydrogenase FadE20 | 489 | 489 ctx | neighborhood:489 |
Rv3418c groES |
chaperonin GroES | 487 | 488 |
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: tRNA delta(2)-isopentenylpyrophosphate transferase
- MTBC0 PGAP product: tRNA (adenosine(37)-N6)-dimethylallyltransferase MiaA
- Pfam (hmmscan --cut_ga): IPPT PF01715.24 (E=7e-79)
- (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_217243.1)
- Domains: Pfam-A via hmmscan --cut_ga — IPPT (PF01715.24)
- 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
COG0324 - Curated reference: UniProt P9WJW1 (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 —
61 functional partner(s); context anchor
hflX - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002901|Rv2727c|miaA MRPLAIIGPTGAGKSQLALDVAARLGARVSVEIVNADAMQLYRGMDIGTAKLPVSERRGIPHHQLDVLDVTETATVARYQRAAAADIEAIAARGAVPVVVGGSMLYVQSLLDDWSFPATDPSVRARWERRLAEVGVDRLHAELARRDPAAAAAILPTDARRTVRALEVVELTGQPFAASAPRIGAPRWDTVIVGLDCQTTILDERLARRTDLMFDQGLVEEVRTLLRNGLREGVTASRALGYAQVIAALDAGAGADMMRAAREQTYLGTRRYVRRQRSWFRRDHRVHWLDAGVASSPDRARLVDDAVRLWRHVT