tsaB Family assigned · medium auto-curated
H37Rv Rv3421c · MTBC0 mtbc0_003635 ·
211 aa · 3864498–3865133 (-) ·
RefSeq NP_217938.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | tRNA (adenosine(37)-N6)-threonylcarbamoyltransferase complex dimerization subunit type 1 TsaB |
| Revised (this work) | TRNA (adenosine(37)-N6)-threonylcarbamoyltransferase complex dimerization subunit type 1 TsaB. Pfam: TsaD (PF00814.32). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WKY7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv3421c |
UniProt still lists this protein as Uncharacterized protein Rv3421c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
O Post-translational modification, protein turnover, chaperones
|
|---|---|
| Preferred name | yeaZ |
| eggNOG description | Peptidase M22, glycoprotease |
| Orthologous group | COG1214 |
| KEGG orthology |
K14742
|
| Gene Ontology (32) |
GO:0002949, GO:0005575, GO:0005618, GO:0005623, GO:0006139, GO:0006396, GO:0006399, GO:0006400, GO:0006725, GO:0006807, GO:0008033, GO:0008150 +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 | 0.389 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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 | 3.2e-26 | 40–147 | tRNA N6-adenosine threonylcarbamoyltransferase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: tsaE (tRNA threonylcarbamoyladenosine biosynthesis protein), high confidence from genomic context alone (score 996 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) |
|---|---|---|---|---|
Rv3422c tsaE |
tRNA threonylcarbamoyladenosine biosynthesis protein | 999 | 996 ctx | neighborhood:881 coexpression:777 experimental:803 textmining:895 |
Rv3419c gcp |
O-sialoglycoprotein endopeptidase | 999 | 996 ctx | neighborhood:882 coexpression:546 experimental:922 textmining:895 |
Rv3420c rimI |
ribosomal-protein-alanine acetyltransferase RimI | 996 | 974 ctx | neighborhood:882 fusion:634 textmining:878 |
Rv3423c alr |
alanine racemase | 955 | 906 ctx | neighborhood:881 textmining:548 |
Rv3279c birA |
bifunctional biotin operon repressor/biotin--[acetyl-CoA-carboxylase | 617 | 618 | coexpression:503 |
Rv3433c nnr |
bifunctional ADP-dependent (S)-NAD(P)H-hydrate dehydratase/NAD(P)H-hydrate epimerase | 550 | 551 ctx | neighborhood:544 |
Rv3432c gadB |
glutamate decarboxylase GadB | 544 | 544 ctx | neighborhood:544 |
Rv1259 udgB |
uracil DNA glycosylase | 540 | 541 | coexpression:503 |
Rv3418c groES |
chaperonin GroES | 761 | 533 ctx | neighborhood:531 textmining:511 |
Rv0949 uvrD1 |
ATP-dependent DNA helicase UvrD | 490 | 491 | coexpression:403 |
Rv2977c thiL |
thiamine-monophosphate kinase | 465 | 465 | coexpression:421 |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 463 | 463 | |
Rv0819 mshD |
mycothiol acetyltransferase | 486 | 453 | |
Rv2170 |
GCN5-like N-acetyltransferase | 481 | 449 | |
Rv0428c |
GCN5-like N-acetyltransferase | 481 | 449 |
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: hypothetical protein
- MTBC0 PGAP product: tRNA (adenosine(37)-N6)-threonylcarbamoyltransferase complex dimerization subunit type 1 TsaB
- Pfam (hmmscan --cut_ga): TsaD PF00814.32 (E=3e-26)
- (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_217938.1)
- Domains: Pfam-A via hmmscan --cut_ga — TsaD (PF00814.32)
- 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
COG1214 - Curated reference: UniProt P9WKY7 (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 —
39 functional partner(s); context anchor
tsaE - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003635|Rv3421c|tsaB MSRVQISTVLAIDTATPAVTAGIVRRHDLVVLGERVTVDARAHAERLTPNVLAALADAALTMADLDAVVVGCGPGPFTGLRAGMASAAAYGHALGIPVYGVCSLDAIGGQTIGDTLVVTDARRREVYWARYCDGIRTVGPAVNAAADVDPGPALAVAGAPEHAALFALPCVEPSRPSPAGLVAAVNWADKPAPLVPLYLRRPDAKPLAVCT