dipZ Resolved · high auto-curated
H37Rv Rv2874 · MTBC0 - ·
695 aa · 3184847–3186934 (+) ·
RefSeq NP_217390.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | integral membrane C-type cytochrome biogenesis protein DipZ |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Integral membrane C-type cytochrome biogenesis protein DipZ. Pfam: DsbD_TM (PF02683.23), Redoxin (PF08534.17), AhpC-TSA (PF00578.28), Thioredoxin_10 (PF17991.8). |
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 |
P9WG63
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Protein DipZ |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversionO Post-translational modification, protein turnover, chaperones
|
|---|---|
| Preferred name | dipZ |
| eggNOG description | biogenesis protein |
| Orthologous group | COG0526 |
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, GO:0044464, GO:0071944
|
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 | 0.649 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 8 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.12% of strains (169) · clonal |
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 |
|---|---|---|---|---|
DsbD_TM | PF02683.23 | 1.2e-27 | 116–334 | Cytochrome C biogenesis protein transmembrane domain |
Redoxin | PF08534.17 | 3.1e-09 | 400–529 | Redoxin |
AhpC-TSA | PF00578.28 | 1.1e-12 | 413–523 | AhpC/TSA family |
Thioredoxin_10 | PF17991.8 | 2.6e-32 | 568–695 | Thioredoxin like C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mpt70 (major secreted immunogenic protein Mpt70), high confidence from genomic context alone (score 853 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2875 mpt70 |
major secreted immunogenic protein Mpt70 | 949 | 853 ctx | neighborhood:775 textmining:668 |
Rv0137c msrA |
peptide methionine sulfoxide reductase MsrA | 884 | 839 | experimental:562 database:596 |
Rv2428 ahpC |
alkyl hydroperoxide reductase subunit AhpC | 873 | 834 | experimental:468 database:611 |
Rv0794c |
oxidoreductase | 766 | 755 | experimental:410 database:550 |
Rv2713 sthA |
pyridine nucleotide transhydrogenase | 765 | 754 | experimental:410 database:550 |
Rv0462 lpdC |
dihydrolipoamide dehydrogenase | 804 | 753 | experimental:410 database:550 |
Rv2855 mtr |
mycothione reductase | 765 | 753 | experimental:410 database:550 |
Rv3303c lpdA |
NAD(P)H quinone reductase LpdA | 765 | 753 | experimental:410 database:550 |
Rv0570 nrdZ |
vitamin B12-dependent ribonucleoside-diphosphate reductase | 711 | 697 | database:578 |
Rv3051c nrdE |
ribonucleoside-diphosphate reductase subunit alpha | 711 | 697 | database:578 |
Rv2674 msrB |
peptide methionine sulfoxide reductase MsrB | 775 | 694 | database:594 |
Rv3446c hyp |
hypothetical protein | 707 | 675 | database:444 |
Rv1937 |
oxygenase | 717 | 674 | database:506 |
Rv0529 ccsA |
cytochrome C-type biogenesis protein CcsA | 914 | 666 | coexpression:619 textmining:754 |
Rv2873 mpt83 |
cell surface lipoprotein | 821 | 660 ctx | neighborhood:485 textmining:496 |
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): integral membrane C-type cytochrome biogenesis protein DipZ
- Pfam (hmmscan --cut_ga): DsbD_TM PF02683.23 (E=1e-27), Redoxin PF08534.17 (E=3e-09), AhpC-TSA PF00578.28 (E=1e-12), Thioredoxin_10 PF17991.8 (E=3e-32)
- (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_217390.1)
- Domains: Pfam-A via hmmscan --cut_ga — DsbD_TM (PF02683.23), Redoxin (PF08534.17), AhpC-TSA (PF00578.28), Thioredoxin_10 (PF17991.8)
- 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
COG0526 - Curated reference: UniProt P9WG63 (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 —
122 functional partner(s); context anchor
mpt70 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2874|dipZ MVESRRAAAAASAYASRCGIAPATSQRSLATPPTISVPSGEGRCRCHVARGAGRDPRRRLRRRRWCGRCGYHSHLTGGEFDVNRLCQQRSRERSCQLVAVPADPRPKRQRITDVLTLALVGFLGGLITGISPCILPVLPVIFFSGAQSVDAAQVAKPEGAVAVRRKRALSATLRPYRVIGGLVLSFGMVTLLGSALLSVLHLPQDAIRWAALVALVAIGAGLIFPRFEQLLEKPFSRIPQKQIVTRSNGFGLGLALGVLYVPCAGPILAAIVVAGATATIGLGTVVLTATFALGAALPLLFFALAGQRIAERVGAFRRRQREIRIATGSVTILLAVALVFDLPAALQRAIPDYTASLQQQISTGTEIREQLNLGGIVNAQNAQLSNCSDGAAQLESCGTAPDLKGITGWLNTPGNKPIDLKSLRGKVVLIDFWAYSCINCQRAIPHVVGWYQAYKDSGLAVIGVHTPEYAFEKVPGNVAKGAANLGISYPIALDNNYATWTNYRNRYWPAEYLIDATGTVRHIKFGEGDYNVTETLVRQLLNDAKPGVKLPQPSSTTTPDLTPRAALTPETYFGVGKVVNYGGGGAYDEGSAVFDYPPSLAANSFALRGRWALDYQGATSDGNDAAIKLNYHAKDVYIVVGGTGTLTVVRDGKPATLPISGPPTTHQVVAGYRLASETLEVRPSKGLQVFSFTYG