Rv1824 Family assigned · low auto-curated
H37Rv Rv1824 · MTBC0 mtbc0_001938 ·
121 aa · 2088742–2089107 (+) ·
RefSeq NP_216340.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | small basic family protein |
| Revised (this work) | Small basic family protein. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WLR7
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Uncharacterized protein Rv1824 |
UniProt still lists this protein as Uncharacterized protein Rv1824; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | sbp |
| eggNOG description | Protein of unknown function (DUF1290) |
| Orthologous group | COG3856 |
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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 0 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 |
|---|---|---|---|---|
DUF1290 | PF06947.18 | 6.3e-34 | 32–119 | Protein of unknown function (DUF1290) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pgsA2 (CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase), high confidence from genomic context alone (score 841 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) |
|---|---|---|---|---|
Rv1823 hyp |
hypothetical protein | 992 | 992 ctx | neighborhood:839 cooccurence:774 coexpression:797 |
Rv1825 hyp |
hypothetical protein | 979 | 978 ctx | neighborhood:861 cooccurence:774 |
Rv1822 pgsA2 |
CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase | 841 | 841 ctx | neighborhood:839 |
Rv0012 |
membrane protein | 840 | 834 ctx | cooccurence:774 |
Rv1826 gcvH |
glycine cleavage system protein H | 819 | 820 ctx | neighborhood:810 |
Rv1821 secA2 |
accessory Sec system translocase SecA2 | 724 | 724 ctx | neighborhood:714 |
Rv1820 ilvG |
acetolactate synthase large subunit IlvG | 708 | 708 ctx | neighborhood:707 |
Rv1828 |
HTH-type transcriptional regulator | 696 | 696 ctx | neighborhood:692 |
Rv1827 garA |
glycogen accumulation regulator GarA | 696 | 696 ctx | neighborhood:692 |
Rv1829 hyp |
hypothetical protein | 640 | 641 ctx | neighborhood:632 |
Rv1819c bacA |
vitamin B12 transport ATP-binding protein BacA | 551 | 552 ctx | neighborhood:548 |
Rv1629 polA |
DNA polymerase I | 478 | 479 | coexpression:403 |
Rv3261 fbiA |
2-phospho-L-lactate transferase | 441 | 441 | coexpression:441 |
Rv2375 hyp |
hypothetical protein | 436 | 436 ctx | cooccurence:434 |
Rv1009 rpfB |
resuscitation-promoting factor RpfB | 421 | 421 ctx | cooccurence:409 |
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: small basic family protein
- Pfam (hmmscan --cut_ga): DUF1290 PF06947.18 (E=6e-34)
- (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_216340.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF1290 (PF06947.18)
- 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
COG3856 - Curated reference: UniProt P9WLR7 (SwissProt, reviewed; Inferred from homology)
- 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 —
24 functional partner(s); context anchor
pgsA2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001938|Rv1824| MGSDTAWSPARMIGIAALAVGIVLGLVFHPGVPEVIQPYLPIAVVAALDAVFGGLRAYLERIFDPKVFVVSFVFNVLVAALIVYVGDQLGVGTQLSTAIIVVLGIRIFGNTAALRRRLFGA