dsbF Resolved · high auto-curated
H37Rv Rv1677 · MTBC0 mtbc0_001785 ·
182 aa · 1913763–1914311 (+) ·
RefSeq NP_216193.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein DsbF |
|---|---|
| MTBC0 PGAP re-annotation | protein disulfide oxidoreductase |
| Revised (this work) | Protein disulfide oxidoreductase. Pfam: Redoxin (PF08534.17), AhpC-TSA (PF00578.28), Thioredoxin_2 (PF13098.14), Thioredoxin (PF00085.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6XYM2
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Soluble secreted antigen MPT53 |
| Curated function | Disulfide oxidoreductase that catalyzes the oxidation of reduced, unfolded secreted proteins to form disulfide bonds. Despite a weak homology to thioredoxin this cannot serve as a substrate for thioredoxin reductase. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversionO Post-translational modification, protein turnover, chaperones
|
|---|---|
| Preferred name | dsbF |
| eggNOG description | possibly involved in thiol disulfide interchange. contains PS00013 prokaryotic membrane lipoprotein lipid attachment site, N-term signal pepitde sequence and PS00194 thioredoxin family active site |
| Orthologous group | COG0526 |
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 | 0.342 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 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 |
|---|---|---|---|---|
Redoxin | PF08534.17 | 4.6e-12 | 44–160 | Redoxin |
AhpC-TSA | PF00578.28 | 1.1e-14 | 53–161 | AhpC/TSA family |
Thioredoxin_2 | PF13098.14 | 3.1e-07 | 71–175 | Thioredoxin-like domain |
Thioredoxin | PF00085.27 | 9.4e-06 | 72–127 | Thioredoxin |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2877c (integral membrane protein), high confidence from genomic context alone (score 783 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2428 ahpC |
alkyl hydroperoxide reductase subunit AhpC | 882 | 831 | experimental:468 database:611 |
Rv0137c msrA |
peptide methionine sulfoxide reductase MsrA | 832 | 821 | experimental:562 database:596 |
Rv1676 hyp |
hypothetical protein | 974 | 810 ctx | neighborhood:781 textmining:870 |
Rv2877c |
integral membrane protein | 972 | 783 ctx | cooccurence:699 textmining:876 |
Rv0462 lpdC |
dihydrolipoamide dehydrogenase | 763 | 753 | experimental:410 database:550 |
Rv3303c lpdA |
NAD(P)H quinone reductase LpdA | 755 | 745 | experimental:410 database:550 |
Rv0794c |
oxidoreductase | 754 | 743 | experimental:410 database:550 |
Rv2855 mtr |
mycothione reductase | 754 | 743 | experimental:410 database:550 |
Rv2713 sthA |
pyridine nucleotide transhydrogenase | 753 | 742 | experimental:410 database:550 |
Rv3672c hyp |
hypothetical protein | 734 | 724 | coexpression:649 |
Rv3051c nrdE |
ribonucleoside-diphosphate reductase subunit alpha | 712 | 697 | database:578 |
Rv0570 nrdZ |
vitamin B12-dependent ribonucleoside-diphosphate reductase | 709 | 695 | database:578 |
Rv2674 msrB |
peptide methionine sulfoxide reductase MsrB | 677 | 656 | database:594 |
Rv0432 sodC |
superoxide dismutase | 677 | 656 | database:595 |
Rv0038 hyp |
hypothetical protein | 632 | 619 | database:602 |
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: lipoprotein DsbF
- MTBC0 PGAP product: protein disulfide oxidoreductase
- Pfam (hmmscan --cut_ga): Redoxin PF08534.17 (E=5e-12), AhpC-TSA PF00578.28 (E=1e-14), Thioredoxin_2 PF13098.14 (E=3e-07), Thioredoxin PF00085.27 (E=9e-06)
- (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_216193.1)
- Domains: Pfam-A via hmmscan --cut_ga — Redoxin (PF08534.17), AhpC-TSA (PF00578.28), Thioredoxin_2 (PF13098.14), Thioredoxin (PF00085.27)
- 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 I6XYM2 (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 —
106 functional partner(s); context anchor
Rv2877c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001785|Rv1677|dsbF MTHSRLIGALTVVAIIVTACGSQPKSQPAVAPTGDAAAATQVPAGQTVPAQLQFSAKTLDGHDFHGESLLGKPAVLWFWAPWCPTCQGEAPVVGQVAASHPEVTFVGVAGLDQVPAMQEFVNKYPVKTFTQLADTDGSVWANFGVTQQPAYAFVDPHGNVDVVRGRMSQDELTRRVTALTSR