hadA Family assigned · medium auto-curated
H37Rv Rv0635 · MTBC0 mtbc0_000672 ·
158 aa · 735483–735959 (+) ·
RefSeq NP_215149.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | (3R)-hydroxyacyl-ACP dehydratase subunit HadA |
|---|---|
| MTBC0 PGAP re-annotation | (3R)-hydroxyacyl-ACP dehydratase subunit HadA |
| Revised (this work) | (3R)-hydroxyacyl-ACP dehydratase subunit HadA. Pfam: FAS1_DH_region (PF13452.12). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFK1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | UPF0336 protein Rv0635 |
UniProt still lists this protein as UPF0336 protein Rv0635; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | hadA |
| eggNOG description | Belongs to the UPF0336 family |
| Orthologous group | COG2030 |
| Gene Ontology (41) |
GO:0001676, GO:0003674, GO:0003824, GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0006082, GO:0006629, GO:0006631, GO:0006633, GO:0008150 +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 | 0.073 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 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 |
|---|---|---|---|---|
FAS1_DH_region | PF13452.12 | 2.6e-27 | 8–137 | FAS1-like, dehydratase domain region |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: hadB ((3R)-hydroxyacyl-ACP dehydratase subunit HadB), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0636 hadB |
(3R)-hydroxyacyl-ACP dehydratase subunit HadB | 999 | 1000 ctx | neighborhood:882 fusion:760 cooccurence:734 coexpression:800 experimental:999 textmining:484 |
Rv0637 hadC |
(3R)-hydroxyacyl-ACP dehydratase subunit HadC | 934 | 934 ctx | neighborhood:882 coexpression:431 |
Rv0634B rpmG2 |
50S ribosomal protein L33 | 816 | 817 ctx | neighborhood:811 |
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha | 735 | 736 | coexpression:736 |
Rv3339c icd1 |
isocitrate dehydrogenase | 634 | 634 | database:476 |
Rv0632c echA3 |
enoyl-CoA hydratase EchA3 | 627 | 626 | |
Rv2242 hyp |
hypothetical protein | 608 | 608 ctx | cooccurence:605 |
Rv1483 fabG1 |
3-oxoacyl-ACP reductase FabG | 648 | 590 | |
Rv0640 rplK |
50S ribosomal protein L11 | 575 | 576 ctx | neighborhood:544 |
Rv0860 fadB |
fatty oxidation protein FadB | 589 | 563 | |
Rv0125 pepA |
serine protease PepA | 560 | 560 | database:498 |
Rv3671c marP |
serine protease | 559 | 560 | database:498 |
Rv0952 sucD |
succinyl-CoA ligase subunit alpha | 572 | 559 | coexpression:557 |
Rv0639 nusG |
transcription termination/antitermination protein NusG | 555 | 556 ctx | neighborhood:529 |
Rv2243 fabD |
malonyl CoA-acyl carrier protein transacylase | 570 | 553 ctx | cooccurence:550 |
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: (3R)-hydroxyacyl-ACP dehydratase subunit HadA
- MTBC0 PGAP product: (3R)-hydroxyacyl-ACP dehydratase subunit HadA
- Pfam (hmmscan --cut_ga): FAS1_DH_region PF13452.12 (E=3e-27)
- (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_215149.1)
- Domains: Pfam-A via hmmscan --cut_ga — FAS1_DH_region (PF13452.12)
- 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
COG2030 - Curated reference: UniProt P9WFK1 (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 —
149 functional partner(s); context anchor
hadB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000672|Rv0635|hadA MALSADIVGMHYRYPDHYEVEREKIREYAVAVQNDDAWYFEEDGAAELGYKGLLAPLTFICVFGYKAQAAFFKHANIATAEAQIVQVDQVLKFEKPIVAGDKLYCDVYVDSVREAHGTQIIVTKNIVTNEEGDLVQETYTTLAGRAGEDGEGFSDGAA