Rv1358 Family assigned · medium auto-curated
H37Rv Rv1358 · MTBC0 mtbc0_001459 ·
1159 aa · 1537314–1540793 (+) ·
RefSeq NP_215874.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | LuxR C-terminal-related transcriptional regulator |
| Revised (this work) | LuxR C-terminal-related transcriptional regulator. Pfam: HTH_77 (PF25872.1), GerE (PF00196.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
Q11028
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable transcriptional regulatory protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | involved in signal transduction (via phosphorylation) involved in transcriptional regulatory mechanism and in the regulation of secondary metabolites catalytic activity ATP a protein ADP a phosphoprotein |
| Orthologous group | COG2114 |
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) pseudogene candidate
| pN/pS | 0.619 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 10 synonymous, 18 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 10.06% of strains (14615) · clonal |
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 |
|---|---|---|---|---|
HTH_77 | PF25872.1 | 4.9e-09 | 510–587 | Winged helix-turn-helix domain |
GerE | PF00196.26 | 9.6e-16 | 1099–1153 | Bacterial regulatory proteins, luxR family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1359 (transcriptional regulator), high confidence from genomic context alone (score 904 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1354c hyp |
hypothetical protein | 968 | 925 ctx | neighborhood:544 coexpression:842 textmining:593 |
Rv1359 |
transcriptional regulator | 920 | 904 ctx | neighborhood:551 coexpression:731 |
Rv1355c moeY |
molybdopterin biosynthesis protein MoeY | 870 | 871 | coexpression:852 |
Rv1357c hyp |
hypothetical protein | 871 | 863 | coexpression:804 |
Rv1356c hyp |
hypothetical protein | 846 | 846 | coexpression:846 |
Rv0895 |
diacyglycerol O-acyltransferase | 806 | 804 | coexpression:803 |
Rv0894 |
transcriptional regulator | 795 | 787 | coexpression:772 |
Rv1353c |
HTH-type transcriptional regulator | 785 | 775 | coexpression:774 |
Rv3113 |
phosphatase | 772 | 772 | coexpression:736 |
Rv3114 hyp |
hypothetical protein | 765 | 765 | coexpression:765 |
Rv0104 hyp |
hypothetical protein | 711 | 656 | experimental:440 |
Rv3728 |
membrane protein | 722 | 655 | experimental:440 |
Rv2434c |
transmembrane protein | 687 | 654 | experimental:440 |
Rv3239c |
transmembrane transport protein | 718 | 650 | experimental:440 |
Rv1675c cmr |
HTH-type transcriptional regulator Cmr | 678 | 650 | experimental:440 |
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: transcriptional regulator
- MTBC0 PGAP product: LuxR C-terminal-related transcriptional regulator
- Pfam (hmmscan --cut_ga): HTH_77 PF25872.1 (E=5e-09), GerE PF00196.26 (E=1e-15)
- (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_215874.1)
- Domains: Pfam-A via hmmscan --cut_ga — HTH_77 (PF25872.1), GerE (PF00196.26)
- 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 Q11028 (TrEMBL, unreviewed; 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 —
67 functional partner(s); context anchor
Rv1359 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001459|Rv1358| MFLSAPAFRVEPTRSRHSALRWARHRRFADGPRWQMLRSLQIADQIARTGHMPVRRLDLIWISARNAARRELDLGVAALVEAVTLLTADVEGSTRLSQTRLNELAADYPTLDQNISEAVAAHGGVTRPVDQEVGSGLVVAFLRAGDAIACALELQLSTLAPMRPRVGVHTGDVRLRGDGTITGSAINESACLRDLAHEGQTLLSAATGDLVIDQLPANTWLTDVGKYPLRGLHRQERVIQLCHRDLRNEFPPLRMSVGNRSSLPAQFTTFVGRDAQINEVQEVLTNYRLVTLRGEGGVGKTRLAIQIAAASEFRDGLCFVDLAPIADPGMVSTTAAHALGLIDRPGSSTFDTLSHAIGNCHMLMVLDNCEHVLDACAELVVELLGACPELSILATSRESIGVTGEVTWVVPSLSPANEAIQLFTERARLVQPNFEIVADNFDAVSEICRRLDGMPLAIELAAARLRSLSPNEIANSLDDRFRLLTGGARSTVQRQQTLRASMDWSYALLTDTERILFRRLAVFVGGFDLTAASEVAAAGGDDFVERYSVLDQLTLLVDKSLVVAEESRGSTRYRLLETVRQYALEKLNESEEIDGVRARHRTHYATMAAGLNVPASTDYEQRLLQAEAEIDNLRAAFTWSRGNGDIAAALQLASALQPLWSQGRMREGLAWLESILEREGDNHLVPAGVWARALAEKVILKAWPATSPMGAPDIVAQAHHALALARDAGDCAVLARALVACGCGSGCDTEAAQPYFAEAIELARAINDEWTLSQIDYWQVVGIFISGQPIPLRAAAEQARELADSIGNRFVSRQCRLFACLAQIWEGDANGALALSRDVTAEAEVANDVVTKVLGLYVEAMALSYIGDSAARTIAGAALEAATELGGIYQDLGYGAITRAALAAGDVAAIEASEASWDLRNQHNVVTAHHELMAQAALVRGDVTTARRFADEAVLASTGWHLMMALIARARVAIAQDELGKARDDAHAAVACGVGVQTYLAMPDALELLAGLAGEAGNHGQAVRLFGAAAAQRQRTGEVRHKIWDAGYEAATAALRDAMGDEDFTAAWAEGAAAPLDEAIAYAQRGRGERKRPSNGWDALTPAEHKIVKLVTEGLVTKDIAARLFVSPRTVQTHLTHIYTKLDVTSRVQLVQEAAQHST