Rv1359 Family assigned · low auto-curated
H37Rv Rv1359 · MTBC0 - ·
250 aa · 1530173–1530925 (+) ·
RefSeq NP_215875.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Transcriptional regulator. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WM05
SwissProt · reviewed
· Predicted
|
|---|---|
| UniProt name | Uncharacterized protein Rv1359 |
UniProt still lists this protein as Uncharacterized protein Rv1359; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | regulation of cellular process |
| Orthologous group | COG2114 |
| Gene Ontology (13) |
GO:0008150, GO:0010468, GO:0010565, GO:0019216, GO:0019217, GO:0019222, GO:0031323, GO:0050789, GO:0050794, GO:0060255, GO:0062012, GO:0065007 +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 | 0.339 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1358 (transcriptional regulator), high confidence from genomic context alone (score 904 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1358 |
transcriptional regulator | 920 | 904 ctx | neighborhood:551 coexpression:731 |
Rv1675c cmr |
HTH-type transcriptional regulator Cmr | 898 | 895 | coexpression:833 |
Rv0894 |
transcriptional regulator | 893 | 894 | coexpression:860 |
Rv3830c |
TetR family transcriptional regulator | 890 | 891 | coexpression:827 |
Rv3263 |
DNA methylase | 876 | 877 | coexpression:860 |
Rv3840 |
transcriptional regulator | 860 | 860 | coexpression:860 |
Rv3167c |
TetR family transcriptional regulator | 860 | 860 | coexpression:860 |
Rv0691c mftR |
mycofactocin biosynthesis transcriptional regulator MftR | 860 | 860 | coexpression:860 |
Rv0602c tcrA |
two component DNA binding transcriptional regulator TcrA | 858 | 858 | coexpression:839 |
Rv0212c nadR |
transcriptional regulator NadR | 857 | 857 | coexpression:857 |
Rv1931c |
transcriptional regulator | 855 | 855 | coexpression:855 |
Rv1674c |
transcriptional regulator | 850 | 850 | coexpression:850 |
Rv1776c |
transcriptional regulator | 848 | 848 | coexpression:815 |
Rv2488c |
LuxR family transcriptional regulator | 846 | 847 | coexpression:805 |
Rv3736 |
AraC/XylS family transcriptional regulator | 846 | 846 | coexpression:846 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): transcriptional regulator
- (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_215875.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
COG2114 - Curated reference: UniProt P9WM05 (SwissProt, reviewed; Predicted)
- 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 —
149 functional partner(s); context anchor
Rv1358 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1359| MFMALRAPMLERMNGLHTDDAPVNWLERRGGRLTSRRRVTLLHAGVEHPMRLWGVQSEAITAAMVLSRKVSAIIAGHCGVRLVDQGVGDGFVAAFAHASDAVACALELHQAPLSPIVLRIGIHTGEAQLVDERIYAGATMNLAAELRDLAHGGQTVMSGATEDAVLGRLPMRAWLIGLRPMEGSPEGHNFPQSQRIAQLCHPNLRNTFPPLRMRIADASGIPYVGRILVNVQVVPHWEGGCAAAGMVLAG