msrB Resolved · high auto-curated
H37Rv Rv2674 · MTBC0 mtbc0_002848 ·
136 aa · 3013019–3013429 (+) ·
RefSeq NP_217190.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | peptide methionine sulfoxide reductase MsrB |
|---|---|
| MTBC0 PGAP re-annotation | peptide-methionine (R)-S-oxide reductase MsrB |
| Revised (this work) | Peptide-methionine (R)-S-oxide reductase MsrB. Pfam: SelR (PF01641.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6YA00
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | peptide-methionine |
| EC (curated) |
EC 1.8.4.12
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
O Post-translational modification, protein turnover, chaperones
|
|---|---|
| Preferred name | msrB |
| eggNOG description | Peptide-methionine (R)-S-oxide reductase |
| Orthologous group | COG0229 |
| EC number |
EC 1.8.4.12
|
| KEGG orthology |
K07305
|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 4 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 |
|---|---|---|---|---|
SelR | PF01641.27 | 2.2e-50 | 17–132 | SelR domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: msrA (peptide methionine sulfoxide reductase MsrA), high confidence from genomic context alone (score 993 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0137c msrA |
peptide methionine sulfoxide reductase MsrA | 999 | 993 ctx | fusion:900 cooccurence:749 coexpression:656 textmining:885 |
Rv2673 aftC |
alpha-(1->3)-arabinofuranosyltransferase | 768 | 768 ctx | neighborhood:765 |
Rv2672 |
protease | 748 | 749 ctx | neighborhood:747 |
Rv2874 dipZ |
integral membrane C-type cytochrome biogenesis protein DipZ | 775 | 694 | database:594 |
Rv3673c |
membrane-anchored thioredoxin-like protein | 678 | 657 | database:594 |
Rv1677 dsbF |
lipoprotein DsbF | 677 | 656 | database:594 |
Rv2878c mpt53 |
soluble secreted antigen Mpt53 | 674 | 654 | database:594 |
Rv0526 |
thioredoxin | 674 | 654 | database:594 |
Rv0816c thiX |
thioredoxin ThiX | 674 | 654 | database:594 |
Rv2671 ribD |
bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase | 525 | 526 ctx | neighborhood:523 |
Rv1643 rplT |
50S ribosomal protein L20 | 561 | 506 | experimental:474 |
Rv3316 sdhC |
succinate dehydrogenase cytochrome B-556 subunit | 514 | 491 | coexpression:489 |
Rv3442c rpsI |
30S ribosomal protein S9 | 489 | 489 | experimental:474 |
Rv3317 sdhD |
succinate dehydrogenase hydrophobic membrane anchor subunit | 484 | 485 | coexpression:483 |
Rv0640 rplK |
50S ribosomal protein L11 | 635 | 482 | experimental:474 |
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: peptide methionine sulfoxide reductase MsrB
- MTBC0 PGAP product: peptide-methionine (R)-S-oxide reductase MsrB
- Pfam (hmmscan --cut_ga): SelR PF01641.27 (E=2e-50)
- (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_217190.1)
- Domains: Pfam-A via hmmscan --cut_ga — SelR (PF01641.27)
- 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
COG0229 - Curated reference: UniProt I6YA00 (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 —
59 functional partner(s); context anchor
msrA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002848|Rv2674|msrB MTRPKLELSDDEWRQKLTPQEFHVLRRAGTERPFTGEYTDTTTAGIYQCRACGAELFRSTEKFESHCGWPSFFDPKSSDAVTLRPDHSLGMTRTEVLCANCDSHLGHVFAGEGYPTPTDKRYCINSISLRLVPGSV