tsaE Family assigned · medium auto-curated
H37Rv Rv3422c · MTBC0 mtbc0_003636 ·
168 aa · 3865130–3865636 (-) ·
RefSeq NP_217939.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | tRNA threonylcarbamoyladenosine biosynthesis protein |
|---|---|
| MTBC0 PGAP re-annotation | tRNA (adenosine(37)-N6)-threonylcarbamoyltransferase complex ATPase subunit type 1 TsaE |
| Revised (this work) | TRNA (adenosine(37)-N6)-threonylcarbamoyltransferase complex ATPase subunit type 1 TsaE. Pfam: TsaE (PF02367.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFS7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | tRNA threonylcarbamoyladenosine biosynthesis protein TsaE |
| Curated function | Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaD and TsaB. TsaE seems to play an indirect role in the t(6)A biosynthesis pathway, possibly in regulating the core enzymatic function of TsaD (By similarity). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | tsaE |
| eggNOG description | tRNA threonylcarbamoyladenosine modification |
| Orthologous group | COG0802 |
| KEGG orthology |
K06925
|
| Gene Ontology (2) |
GO:0008150, GO:0040007
|
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 | 0.38 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 1 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 |
|---|---|---|---|---|
TsaE | PF02367.24 | 8.8e-31 | 26–155 | Threonylcarbamoyl adenosine biosynthesis protein TsaE |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: alr (alanine racemase), high confidence from genomic context alone (score 992 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3421c tsaB hyp |
hypothetical protein | 999 | 996 ctx | neighborhood:881 coexpression:777 experimental:803 textmining:895 |
Rv3423c alr |
alanine racemase | 996 | 992 ctx | neighborhood:882 fusion:695 coexpression:730 textmining:542 |
Rv3419c gcp |
O-sialoglycoprotein endopeptidase | 999 | 990 ctx | neighborhood:881 coexpression:553 experimental:790 textmining:922 |
Rv3420c rimI |
ribosomal-protein-alanine acetyltransferase RimI | 985 | 889 ctx | neighborhood:881 textmining:876 |
Rv3433c nnr |
bifunctional ADP-dependent (S)-NAD(P)H-hydrate dehydratase/NAD(P)H-hydrate epimerase | 885 | 805 ctx | neighborhood:544 coexpression:412 textmining:438 |
Rv3432c gadB |
glutamate decarboxylase GadB | 620 | 620 ctx | neighborhood:544 |
Rv0408 pta |
phosphate acetyltransferase | 575 | 576 | coexpression:413 |
Rv1301 |
threonylcarbamoyl-AMP synthase | 650 | 543 | database:500 |
Rv3418c groES |
chaperonin GroES | 739 | 531 ctx | neighborhood:531 textmining:467 |
Rv2367c ybeY |
endoribonuclease | 523 | 523 ctx | cooccurence:474 |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 544 | 516 ctx | neighborhood:442 |
Rv2727c miaA |
tRNA delta(2)-isopentenylpyrophosphate transferase | 691 | 487 ctx | cooccurence:440 textmining:424 |
Rv2977c thiL |
thiamine-monophosphate kinase | 465 | 465 | coexpression:421 |
Rv3417c groEL1 |
chaperonin GroEL | 730 | 445 ctx | neighborhood:445 textmining:534 |
Rv3424c hyp |
hypothetical protein | 412 | 412 ctx | neighborhood:408 |
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 threonylcarbamoyladenosine biosynthesis protein
- MTBC0 PGAP product: tRNA (adenosine(37)-N6)-threonylcarbamoyltransferase complex ATPase subunit type 1 TsaE
- Pfam (hmmscan --cut_ga): TsaE PF02367.24 (E=9e-31)
- (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_217939.1)
- Domains: Pfam-A via hmmscan --cut_ga — TsaE (PF02367.24)
- 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
COG0802 - Curated reference: UniProt P9WFS7 (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 —
19 functional partner(s); context anchor
alr - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003636|Rv3422c|tsaE MSREGIRRRPKARAGLTGGGTATLPRVEDTLTLGSRLGEQLCAGDVVVLSGPLGAGKTVLAKGIAMAMDVEGPITSPTFVLARMHRPRRPGTPAMVHVDVYRLLDHNSADLLSELDSLDLDTDLEDAVVVVEWGEGLAERLSQRHLDVRLERVSHSDTRIATWSWGRS