sigJ Family assigned · medium auto-curated
H37Rv Rv3328c · MTBC0 mtbc0_003541 ·
312 aa · 3739379–3740317 (-) ·
RefSeq NP_217845.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ECF RNA polymerase sigma factor SigJ |
|---|---|
| MTBC0 PGAP re-annotation | sigma-70 family RNA polymerase sigma factor SigJ |
| Revised (this work) | Sigma-70 family RNA polymerase sigma factor SigJ. Pfam: Sigma70_r2 (PF04542.21), Sigma70_r4_2 (PF08281.19), SnoaL_2 (PF12680.14). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
L0TCG5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ECF RNA polymerase sigma factor SigJ |
| Curated function | Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. Extracytoplasmic function (ECF) sigma factors are held in an inactive form by an anti-sigma factor until released, although no anti-sigma factor is known for this protein (By similarity). Regulates the promoter of SigI, may not be autoregulated. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | sigJ |
| eggNOG description | Belongs to the sigma-70 factor family. ECF subfamily |
| Orthologous group | COG1595 |
| KEGG orthology |
K03088
|
| Gene Ontology (28) |
GO:0000988, GO:0000990, GO:0003674, GO:0006355, GO:0008150, GO:0009889, GO:0010468, GO:0010556, GO:0016987, GO:0019219, GO:0019222, GO:0031323 +16 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 | 0.309 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 5 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 |
|---|---|---|---|---|
Sigma70_r2 | PF04542.21 | 3.2e-12 | 6–68 | Sigma-70 region 2 |
Sigma70_r4_2 | PF08281.19 | 6.2e-12 | 107–155 | Sigma-70, region 4 |
SnoaL_2 | PF12680.14 | 5.3e-07 | 176–280 | SnoaL-like domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1931c (transcriptional regulator), high confidence from genomic context alone (score 876 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1931c |
transcriptional regulator | 880 | 876 ctx | cooccurence:524 coexpression:751 |
Rv1725c hyp |
hypothetical protein | 858 | 859 | coexpression:822 |
Rv2488c |
LuxR family transcriptional regulator | 846 | 837 | coexpression:804 |
Rv2788 sirR |
transcriptional repressor SirR | 827 | 826 | coexpression:822 |
Rv3736 |
AraC/XylS family transcriptional regulator | 815 | 808 | coexpression:808 |
Rv0377 |
HTH-type transcriptional regulator | 815 | 808 | coexpression:808 |
Rv3167c |
TetR family transcriptional regulator | 801 | 802 | coexpression:731 |
Rv3263 |
DNA methylase | 799 | 799 | coexpression:799 |
Rv2760c vapB42 |
antitoxin VapB42 | 799 | 799 | coexpression:799 |
Rv1773c |
transcriptional regulator | 804 | 797 | coexpression:797 |
Rv1359 |
transcriptional regulator | 796 | 796 | coexpression:796 |
Rv3164c moxR3 |
methanol dehydrogenase transcriptional regulator MoxR | 796 | 796 | coexpression:796 |
Rv1189 sigI |
ECF RNA polymerase sigma factor SigI | 833 | 793 | coexpression:730 |
Rv0653c |
transcriptional regulator | 791 | 792 | coexpression:732 |
Rv0691c mftR |
mycofactocin biosynthesis transcriptional regulator MftR | 793 | 788 | coexpression:788 |
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: ECF RNA polymerase sigma factor SigJ
- MTBC0 PGAP product: sigma-70 family RNA polymerase sigma factor SigJ
- Pfam (hmmscan --cut_ga): Sigma70_r2 PF04542.21 (E=3e-12), Sigma70_r4_2 PF08281.19 (E=6e-12), SnoaL_2 PF12680.14 (E=5e-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_217845.1)
- Domains: Pfam-A via hmmscan --cut_ga — Sigma70_r2 (PF04542.21), Sigma70_r4_2 (PF08281.19), SnoaL_2 (PF12680.14)
- 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
COG1595 - Curated reference: UniProt L0TCG5 (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)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
84 functional partner(s); context anchor
Rv1931c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003541|Rv3328c|sigJ MEVSEFEALRQHLMSVAYRLTGTVADAEDIVQEAWLRWDSQDTVIADPRAWLTTVVSRLGLDKLRSAAHRRETYTGTWLPEPVVTGLDATDPLAAVVAAEDARFAAMVVLERLRPDQRVAFVLHDGFAVPFAEVAEVLGTSEAAARQLASRARKAVTAQPALISGDPDPAHNEVVGRLMAAMAAGDLDTVVSLLHPDVTFTGDSNGKAPTAVRAVRGSDKVVRFILGLVQRYGPGLFGANQLALVNGELGAYTAGLPGVDGYRAMAPRITAITVRDGKVCALWDIANPDKFTGSPLKERRAQPTGRGRHHRN