Rv1324 Resolved · high auto-curated
H37Rv Rv1324 · MTBC0 mtbc0_001421 ·
304 aa · 1497863–1498777 (+) ·
RefSeq NP_215840.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | thioredoxin |
|---|---|
| MTBC0 PGAP re-annotation | co-chaperone YbbN |
| Revised (this work) | Co-chaperone YbbN. Pfam: Thioredoxin (PF00085.27), TPR_20 (PF14561.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WG61
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv1324 |
UniProt still lists this protein as Uncharacterized protein Rv1324; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
O Post-translational modification, protein turnover, chaperones
|
|---|---|
| Preferred name | ybbN |
| eggNOG description | Thioredoxin |
| Orthologous group | COG3118 |
| KEGG orthology |
K05838
|
| Gene Ontology (8) |
GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0016020, GO:0030312, 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 | 0.881 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 5 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 |
|---|---|---|---|---|
Thioredoxin | PF00085.27 | 1.3e-10 | 45–147 | Thioredoxin |
TPR_20 | PF14561.13 | 4.0e-17 | 232–304 | Tetratricopeptide repeat |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadA4 (acetyl-CoA acetyltransferase), high confidence from genomic context alone (score 769 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3913 trxB2 |
thioredoxin reductase | 911 | 795 | experimental:770 textmining:589 |
Rv1836c hyp |
hypothetical protein | 779 | 779 | coexpression:778 |
Rv0511 hemD |
uroporphyrin-III C-methyltransferase | 773 | 773 | coexpression:761 |
Rv1323 fadA4 |
acetyl-CoA acetyltransferase | 769 | 769 ctx | neighborhood:758 |
Rv1436 gap |
glyceraldehyde 3-phosphate dehydrogenase | 628 | 593 | experimental:441 |
Rv1322A hyp |
hypothetical protein | 571 | 550 ctx | neighborhood:537 |
Rv2299c htpG |
chaperone protein HtpG | 563 | 529 | |
Rv0440 groEL2 |
molecular chaperone GroEL | 553 | 525 | |
Rv3417c groEL1 |
chaperonin GroEL | 553 | 525 | |
Rv2643 arsC |
arsenic-transport integral membrane protein ArsC | 643 | 523 | experimental:438 |
Rv1310 atpD |
ATP synthase subunit beta | 507 | 507 | |
Rv1308 atpA |
ATP synthase subunit alpha | 525 | 500 | |
Rv0462 lpdC |
dihydrolipoamide dehydrogenase | 502 | 478 | |
Rv2234 ptpA |
protein-tyrosine-phosphatase | 508 | 477 | experimental:438 |
Rv3610c ftsH |
zinc metalloprotease FtsH | 518 | 475 |
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: thioredoxin
- MTBC0 PGAP product: co-chaperone YbbN
- Pfam (hmmscan --cut_ga): Thioredoxin PF00085.27 (E=1e-10), TPR_20 PF14561.13 (E=4e-17)
- (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_215840.1)
- Domains: Pfam-A via hmmscan --cut_ga — Thioredoxin (PF00085.27), TPR_20 (PF14561.13)
- 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
COG3118 - Curated reference: UniProt P9WG61 (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 —
46 functional partner(s); context anchor
fadA4 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001421|Rv1324| MTRPRPPLGPAMAGAVDLSGIKQRAQQNAAASTDADRALSTPSGVTEITEANFEDEVIVRSDEVPVVVLLWSPRSEVCVDLLDTLSGLAAAAKGKWSLASVNVDVAPRVAQIFGVQAVPTVVALAAGQPISSFQGLQPADQLSRWVDSLLSATAGKLKGAASSEESTEVDPAVAQARQQLEDGDFVAARKSYQAILDANPGSVEAKAAIRQIEFLIRATAQRPDAVSVADSLSDDIDAAFAAADVQVLNQDVSAAFERLIALVRRTSGEERTRVRTRLIELFELFDPADPEVVAGRRNLANALY