Rv1825 Still unknown · low auto-curated
H37Rv Rv1825 · MTBC0 mtbc0_001939 ·
292 aa · 2089124–2090002 (+) ·
RefSeq NP_216341.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF881 domain-containing protein |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF881. Function unknown. Foldseek best (non-significant) hit: 3gmg-assembly1_B Crystal structure of an uncharacterized conserved pro (prob 1.00, TM 0.93). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFG3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | UPF0749 protein Rv1825 |
UniProt still lists this protein as UPF0749 protein Rv1825; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Bacterial protein of unknown function (DUF881) |
| Orthologous group | COG3879 |
| Gene Ontology (13) |
GO:0005575, GO:0005576, GO:0005623, GO:0005886, GO:0005887, GO:0016020, GO:0016021, GO:0031224, GO:0031226, GO:0044425, GO:0044459, GO:0044464 +1 more
|
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 | 1.471 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
DUF881 | PF05949.18 | 1.5e-34 | 151–289 | Bacterial protein of unknown function (DUF881) |
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 86.4 (confident). A confident model makes the fold comparison meaningful.
Best matches against the PDB, ranked by Foldseek homology probability. A high probability / TM-score suggests a shared fold; unless flagged sig (E < 0.01) these are fold hypotheses, not assignments.
| Target | Prob | TM | E-value | Description |
|---|---|---|---|---|
3gmg-assembly1_B |
1.00 | 0.93 | 1.7e-28 sig | 3gmg-assembly1_B Crystal structure of an uncharacterized conserved protein from Mycobacterium tuberculosis |
7jts-assembly1_s |
0.07 | 0.24 | 5.4e+00 | 7jts-assembly1_s Stalk of radial spoke 1 attached with doublet microtubule from Chlamydomonas reinhardtii |
3jcm-assembly1_K |
0.06 | 0.20 | 1.8e+00 | 3jcm-assembly1_K Cryo-EM structure of the spliceosomal U4/U6.U5 tri-snRNP |
7ju4-assembly1_F |
0.04 | 0.22 | 8.4e+00 | 7ju4-assembly1_F Radial spoke 2 stalk, IDAc, and N-DRC attached with doublet microtubule |
8h6l-assembly1_4B |
0.04 | 0.20 | 2.4e+00 | 8h6l-assembly1_4B Cryo-EM structure of human exon-defined spliceosome in the early B state. |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: gcvH (glycine cleavage system protein H), high confidence from genomic context alone (score 835 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) |
|---|---|---|---|---|
Rv1824 hyp |
hypothetical protein | 979 | 978 ctx | neighborhood:861 cooccurence:774 |
Rv1823 hyp |
hypothetical protein | 921 | 882 ctx | neighborhood:822 |
Rv1826 gcvH |
glycine cleavage system protein H | 835 | 835 ctx | neighborhood:826 |
Rv1822 pgsA2 |
CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase | 824 | 825 ctx | neighborhood:822 |
Rv0012 |
membrane protein | 774 | 775 ctx | cooccurence:774 |
Rv1821 secA2 |
accessory Sec system translocase SecA2 | 708 | 708 ctx | neighborhood:705 |
Rv1820 ilvG |
acetolactate synthase large subunit IlvG | 698 | 699 ctx | neighborhood:699 |
Rv1827 garA |
glycogen accumulation regulator GarA | 658 | 658 ctx | neighborhood:653 |
Rv1819c bacA |
vitamin B12 transport ATP-binding protein BacA | 601 | 602 ctx | neighborhood:599 |
Rv1828 |
HTH-type transcriptional regulator | 556 | 556 ctx | neighborhood:536 |
Rv1829 hyp |
hypothetical protein | 925 | 451 ctx | neighborhood:442 textmining:870 |
Rv1009 rpfB |
resuscitation-promoting factor RpfB | 408 | 409 | |
Rv3586 disA |
DNA integrity scanning protein DisA | 405 | 406 ctx | cooccurence:404 |
Rv2612c pgsA1 |
CDP-diacylglycerol--inositol 3-phosphatidyltransferase | 831 | 178 | textmining:803 |
Rv2746c pgsA3 |
CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase | 874 | 77 | textmining:870 |
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: DUF881 domain-containing protein
- Pfam (hmmscan --cut_ga): DUF881 PF05949.18 (E=1e-34)
- Foldseek best: 3gmg-assembly1_B Crystal structure of an uncharacterized conserved protein from (prob 1.00, E=2e-28, TM=0.93)
- (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_216341.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF881 (PF05949.18)
- 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
COG3879 - Curated reference: UniProt P9WFG3 (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)
- Model confidence: ESMFold per-residue pLDDT (mean 86.4, confident)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
17 functional partner(s); context anchor
gcvH - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001939|Rv1825| MSENRPEPVAAETSAATTARHSQADAGAHDAVRRGRHELPADHPRSKVGPLRRTRLTEILRGGRSRLVFGTLAILLCLVLGVAIVTQVRQTDSGDSLETARPADLLVLLDSLRQREATLNAEVIDLQNTLNALQASGNTDQAALESAQARLAALSILVGAVGATGPGVMITIDDPGPGVAPEVMIDVINELRAAGAEAIQINDAHRSVRVGVDTWVVGVPGSLTVDTKVLSPPYSILAIGDPPTLAAAMNIPGGAQDGVKRVGGRMVVQQADRVDVTALRQPKQHQYAQPVK