gcp Family assigned · medium auto-curated
H37Rv Rv3419c · MTBC0 mtbc0_003633 ·
344 aa · 3862994–3864028 (-) ·
RefSeq NP_217936.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | O-sialoglycoprotein endopeptidase |
|---|---|
| MTBC0 PGAP re-annotation | tRNA (adenosine(37)-N6)-threonylcarbamoyltransferase complex transferase subunit TsaD |
| Revised (this work) | TRNA (adenosine(37)-N6)-threonylcarbamoyltransferase complex transferase subunit TsaD. Pfam: TsaD (PF00814.32), HypF_C_2 (PF22521.3). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHT7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | tRNA N6-adenosine threonylcarbamoyltransferase |
| EC (curated) |
EC 2.3.1.234
|
| 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 TsaE and TsaB. TsaD likely plays a direct catalytic role in this reaction. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | tsaD |
| eggNOG description | 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 TsaE and TsaB. TsaD likely plays a direct catalytic role in this reaction |
| Orthologous group | COG0533 |
| EC number |
EC 2.3.1.234
|
| KEGG orthology |
K01409
|
| Gene Ontology (33) |
GO:0000408, GO:0002949, GO:0005575, GO:0005622, GO:0005623, GO:0006139, GO:0006396, GO:0006399, GO:0006400, GO:0006725, GO:0006807, GO:0008033 +21 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 | 1.12 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 3 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 |
|---|---|---|---|---|
TsaD | PF00814.32 | 3.9e-82 | 29–312 | tRNA N6-adenosine threonylcarbamoyltransferase |
HypF_C_2 | PF22521.3 | 1.0e-06 | 210–308 | Carbamoyltransferase, Kae1-like Domain, second subdomain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: tsaE (tRNA threonylcarbamoyladenosine biosynthesis protein), high confidence from genomic context alone (score 990 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3421c tsaB hyp |
hypothetical protein | 999 | 996 ctx | neighborhood:882 coexpression:546 experimental:922 textmining:895 |
Rv3422c tsaE |
tRNA threonylcarbamoyladenosine biosynthesis protein | 999 | 990 ctx | neighborhood:881 coexpression:553 experimental:790 textmining:922 |
Rv3420c rimI |
ribosomal-protein-alanine acetyltransferase RimI | 980 | 902 ctx | neighborhood:882 textmining:810 |
Rv3423c alr |
alanine racemase | 916 | 887 ctx | neighborhood:881 |
Rv3418c groES |
chaperonin GroES | 758 | 627 ctx | neighborhood:576 |
Rv1649 pheS |
phenylalanine--tRNA ligase subunit alpha | 713 | 623 ctx | cooccurence:590 |
Rv0986 |
adhesion component ABC transporter ATP-binding protein | 617 | 617 ctx | cooccurence:592 |
Rv0073 |
glutamine ABC transporter ATP-binding protein | 617 | 617 ctx | cooccurence:570 |
Rv1010 ksgA |
rRNA small subunit methyltransferase A | 798 | 615 ctx | cooccurence:507 textmining:497 |
Rv2564 glnQ |
glutamine ABC transporter ATP-binding protein | 610 | 610 ctx | cooccurence:567 |
Rv3433c nnr |
bifunctional ADP-dependent (S)-NAD(P)H-hydrate dehydratase/NAD(P)H-hydrate epimerase | 604 | 599 ctx | neighborhood:544 |
Rv2538c aroB |
3-dehydroquinate synthase | 597 | 597 ctx | fusion:567 |
Rv0350 dnaK |
chaperone protein DnaK | 582 | 556 ctx | cooccurence:483 |
Rv3580c cysS1 |
cysteine--tRNA ligase | 602 | 554 ctx | cooccurence:527 |
Rv3432c gadB |
glutamate decarboxylase GadB | 545 | 545 ctx | neighborhood:544 |
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: O-sialoglycoprotein endopeptidase
- MTBC0 PGAP product: tRNA (adenosine(37)-N6)-threonylcarbamoyltransferase complex transferase subunit TsaD
- Pfam (hmmscan --cut_ga): TsaD PF00814.32 (E=4e-82), HypF_C_2 PF22521.3 (E=1e-06)
- (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_217936.1)
- Domains: Pfam-A via hmmscan --cut_ga — TsaD (PF00814.32), HypF_C_2 (PF22521.3)
- 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
COG0533 - Curated reference: UniProt P9WHT7 (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 —
93 functional partner(s); context anchor
tsaE - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003633|Rv3419c|gcp MTTVLGIETSCDETGVGIARLDPDGTVTLLADEVASSVDEHVRFGGVVPEIASRAHLEALGPAMRRALAAAGLKQPDIVAATIGPGLAGALLVGVAAAKAYSAAWGVPFYAVNHLGGHLAADVYEHGPLPECVALLVSGGHTHLLHVRSLGEPIIELGSTVDDAAGEAYDKVARLLGLGYPGGKALDDLARTGDRDAIVFPRGMSGPADDRYAFSFSGLKTAVARYVESHAADPGFRTADIAAGFQEAVADVLTMKAVRAATALGVSTLLIAGGVAANSRLRELATQRCGEAGRTLRIPSPRLCTDNGAMIAAFAAQLVAAGAPPSPLDVPSDPGLPVMQGQVR