Rv1676 Family assigned · medium auto-curated
H37Rv Rv1676 · MTBC0 mtbc0_001784 ·
234 aa · 1913062–1913766 (+) ·
RefSeq NP_216192.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | peroxiredoxin-like family protein |
| Revised (this work) | Peroxiredoxin-like family protein. Pfam: AhpC-TSA (PF00578.28), AhpC-TSA_2 (PF13911.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53923
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein |
UniProt still lists this protein as Uncharacterized protein; 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
|
|---|---|
| eggNOG description | AhpC/TSA family |
| Orthologous group | COG1225 |
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 | 0.205 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 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 |
|---|---|---|---|---|
AhpC-TSA | PF00578.28 | 1.6e-06 | 51–205 | AhpC/TSA family |
AhpC-TSA_2 | PF13911.13 | 1.0e-07 | 97–211 | AhpC/TSA antioxidant enzyme |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: dsbF (lipoprotein DsbF), high confidence from genomic context alone (score 810 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1677 dsbF |
lipoprotein DsbF | 974 | 810 ctx | neighborhood:781 textmining:870 |
Rv1680 hyp |
hypothetical protein | 637 | 637 ctx | neighborhood:566 |
Rv1675c cmr |
HTH-type transcriptional regulator Cmr | 686 | 636 ctx | neighborhood:558 |
Rv1681 moeX |
molybdopterin biosynthesis protein MoeX | 635 | 624 ctx | neighborhood:537 |
Rv1679 fadE16 |
acyl-CoA dehydrogenase FadE16 | 591 | 590 ctx | neighborhood:571 |
Rv1678 |
integral membrane protein | 564 | 563 ctx | neighborhood:540 |
Rv1682 hyp |
hypothetical protein | 451 | 451 | |
Rv1004c |
membrane protein | 447 | 447 | |
Rv3081 hyp |
hypothetical protein | 443 | 443 ctx | cooccurence:443 |
Rv2735c hyp |
hypothetical protein | 426 | 426 ctx | cooccurence:423 |
Rv1674c |
transcriptional regulator | 491 | 360 | |
Rv3673c |
membrane-anchored thioredoxin-like protein | 626 | 231 | textmining:534 |
Rv2428 ahpC |
alkyl hydroperoxide reductase subunit AhpC | 447 | 203 | |
Rv2874 dipZ |
integral membrane C-type cytochrome biogenesis protein DipZ | 849 | 166 | textmining:827 |
Rv2877c |
integral membrane protein | 881 | 136 | textmining:868 |
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: hypothetical protein
- MTBC0 PGAP product: peroxiredoxin-like family protein
- Pfam (hmmscan --cut_ga): AhpC-TSA PF00578.28 (E=2e-06), AhpC-TSA_2 PF13911.13 (E=1e-07)
- (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_216192.1)
- Domains: Pfam-A via hmmscan --cut_ga — AhpC-TSA (PF00578.28), AhpC-TSA_2 (PF13911.13)
- 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
COG1225 - Curated reference: UniProt O53923 (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 —
20 functional partner(s); context anchor
dsbF - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001784|Rv1676| MACPEWEISRSKRTRKPVLRPRHSVSTLTNRFLAEFCHRYGIGVPTRLARGATVPTRRLQDINDQPVDVPAATGRTHLQFRRFAACPICHLHLRSFANRHQEVADSGITEVVFFHSAADALRGYQSLLPFAVIADPDRVQYREFGVEKSLGAITHPRALWAAVRGSAAMLHRNDPERAGVGFGDGTTHLGLPADFLLDADGTVAAVHYGRHADDQWSVDQLIDINRSLGGKGTQ