tatD Resolved · high auto-curated
H37Rv Rv1008 · MTBC0 - ·
264 aa · 1127089–1127883 (+) ·
RefSeq NP_215524.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | deoxyribonuclease TatD |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Deoxyribonuclease TatD. Pfam: TatD_DNase (PF01026.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
O08343
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized metal-dependent hydrolase TatD |
| EC (curated) |
EC 3.1.-.-
|
UniProt still lists this protein as Uncharacterized metal-dependent hydrolase TatD; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | tatD |
| eggNOG description | TatD family |
| Orthologous group | COG0084 |
| KEGG orthology |
K03424
|
| Gene Ontology (41) |
GO:0003674, GO:0003824, GO:0004518, GO:0004536, GO:0005575, GO:0005623, GO:0005886, GO:0006139, GO:0006259, GO:0006308, GO:0006725, GO:0006807 +29 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 | 0.358 · 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 |
|---|---|---|---|---|
TatD_DNase | PF01026.28 | 6.8e-76 | 2–258 | TatD related DNase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: metS (methionine--tRNA ligase), high confidence from genomic context alone (score 970 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1007c metS |
methionine--tRNA ligase | 969 | 970 ctx | neighborhood:783 fusion:723 |
Rv1010 ksgA |
rRNA small subunit methyltransferase A | 958 | 775 ctx | neighborhood:734 textmining:821 |
Rv1009 rpfB |
resuscitation-promoting factor RpfB | 913 | 736 ctx | neighborhood:734 textmining:687 |
Rv2404c lepA |
GTP-binding protein LepA | 508 | 508 ctx | cooccurence:483 |
Rv1011 ispE |
4-diphosphocytidyl-2C-methyl-D-erythritol kinase | 850 | 463 ctx | neighborhood:461 textmining:733 |
Rv2478c hyp |
hypothetical protein | 447 | 448 | coexpression:416 |
Rv0054 ssb |
single-strand DNA-binding protein | 446 | 447 | coexpression:415 |
Rv3834c serS |
serine--tRNA ligase | 440 | 440 | |
Rv3419c gcp |
O-sialoglycoprotein endopeptidase | 430 | 430 ctx | cooccurence:423 |
Rv1112 ychF |
GTP-binding protein | 427 | 425 | |
Rv2165c rsmH |
rRNA small subunit methyltransferase H | 422 | 423 ctx | cooccurence:413 |
Rv2925c rnc |
ribonuclease III | 416 | 417 | |
Rv0986 |
adhesion component ABC transporter ATP-binding protein | 413 | 414 | |
Rv2440c obg |
GTPase Obg | 427 | 392 | |
Rv2902c rnhB |
ribonuclease HII | 555 | 370 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): deoxyribonuclease TatD
- Pfam (hmmscan --cut_ga): TatD_DNase PF01026.28 (E=7e-76)
- (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_215524.1)
- Domains: Pfam-A via hmmscan --cut_ga — TatD_DNase (PF01026.28)
- 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
COG0084 - Curated reference: UniProt O08343 (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 —
32 functional partner(s); context anchor
metS - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1008|tatD MVDAHTHLDACGARDADTVRSLVERAAAAGVTAVVTVADDLESARWVTRAAEWDRRVYAAVALHPTRADALTDAARAELERLVAHPRVVAVGETGIDMYWPGRLDGCAEPHVQREAFAWHIDLAKRTGKPLMIHNRQADRDVLDVLRAEGAPDTVILHCFSSDAAMARTCVDAGWLLSLSGTVSFRTARELREAVPLMPVEQLLVETDAPYLTPHPHRGLANEPYCLPYTVRALAELVNRRPEEVALITTSNARRAYGLGWMRQ