hadB Family assigned · medium auto-curated
H37Rv Rv0636 · MTBC0 mtbc0_000673 ·
142 aa · 735946–736374 (+) ·
RefSeq NP_215150.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | (3R)-hydroxyacyl-ACP dehydratase subunit HadB |
|---|---|
| MTBC0 PGAP re-annotation | (3R)-hydroxyacyl-ACP dehydratase subunit HadB |
| Revised (this work) | (3R)-hydroxyacyl-ACP dehydratase subunit HadB. Pfam: MaoC_dehydratas (PF01575.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6WYY7
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | (3R)-hydroxyacyl-ACP dehydratase subunit HadB |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | hadB |
| eggNOG description | Functions as a heterodimer along with HadA or HadC in fatty acid biosynthesis |
| Orthologous group | COG2030 |
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 | 0.336 · 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 |
|---|---|---|---|---|
MaoC_dehydratas | PF01575.26 | 2.0e-29 | 15–126 | MaoC like domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: hadA ((3R)-hydroxyacyl-ACP dehydratase subunit HadA), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0635 hadA |
(3R)-hydroxyacyl-ACP dehydratase subunit HadA | 999 | 1000 ctx | neighborhood:882 fusion:760 cooccurence:734 coexpression:800 experimental:999 textmining:484 |
Rv0637 hadC |
(3R)-hydroxyacyl-ACP dehydratase subunit HadC | 999 | 1000 ctx | neighborhood:882 cooccurence:756 coexpression:855 experimental:999 textmining:934 |
Rv0504c hyp |
hypothetical protein | 999 | 997 ctx | cooccurence:756 experimental:987 textmining:860 |
Rv0733 adk |
adenylate kinase | 837 | 831 | coexpression:830 |
Rv0634B rpmG2 |
50S ribosomal protein L33 | 881 | 820 ctx | neighborhood:811 |
Rv0719 rplF |
50S ribosomal protein L6 | 761 | 761 | coexpression:761 |
Rv0718 rpsH |
30S ribosomal protein S8 | 760 | 759 | coexpression:759 |
Rv1630 rpsA |
30S ribosomal protein S1 | 733 | 734 | coexpression:733 |
Rv1078 pra hyp |
hypothetical protein | 732 | 732 | coexpression:732 |
Rv0715 rplX |
50S ribosomal protein L24 | 730 | 730 | coexpression:730 |
Rv0716 rplE |
50S ribosomal protein L5 | 703 | 703 | coexpression:703 |
Rv3339c icd1 |
isocitrate dehydrogenase | 633 | 633 | database:476 |
Rv0632c echA3 |
enoyl-CoA hydratase EchA3 | 638 | 625 | |
Rv3274c fadE25 |
acyl-CoA dehydrogenase | 629 | 612 | |
Rv0640 rplK |
50S ribosomal protein L11 | 566 | 567 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: (3R)-hydroxyacyl-ACP dehydratase subunit HadB
- MTBC0 PGAP product: (3R)-hydroxyacyl-ACP dehydratase subunit HadB
- Pfam (hmmscan --cut_ga): MaoC_dehydratas PF01575.26 (E=2e-29)
- (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_215150.1)
- Domains: Pfam-A via hmmscan --cut_ga — MaoC_dehydratas (PF01575.26)
- 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 I6WYY7 (TrEMBL, unreviewed; 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 —
165 functional partner(s); context anchor
hadA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000673|Rv0636|hadB MALREFSSVKVGDQLPEKTYPLTRQDLVNYAGVSGDLNPIHWDDEIAKVVGLDTAIAHGMLTMGIGGGYVTSWVGDPGAVTEYNVRFTAVVPVPNDGKGAELVFNGRVKSVDPESKSVTIALTATTGGKKIFGRAIASAKLA