sigD Resolved · high auto-curated
H37Rv Rv3414c · MTBC0 - ·
212 aa · 3833038–3833676 (-) ·
RefSeq NP_217931.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ECF RNA polymerase sigma factor SigD |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | ECF RNA polymerase sigma factor SigD. Pfam: Sigma70_r2 (PF04542.21), Sigma70_r4_2 (PF08281.19), Sigma70_r4 (PF04545.23). |
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 |
P9WGG9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ECF RNA polymerase sigma factor SigD |
| 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 by regulated intramembrane proteolysis. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | sigD |
| eggNOG description | Belongs to the sigma-70 factor family. ECF subfamily |
| Orthologous group | COG1595 |
| KEGG orthology |
K03088
|
| Gene Ontology (50) |
GO:0000988, GO:0000990, GO:0002791, GO:0003674, GO:0006355, GO:0006950, GO:0008150, GO:0009266, GO:0009405, GO:0009408, GO:0009628, GO:0009889 +38 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 | 0.364 · 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
Sigma70_r2 | PF04542.21 | 1.2e-12 | 50–119 | Sigma-70 region 2 |
Sigma70_r4_2 | PF08281.19 | 2.5e-10 | 152–201 | Sigma-70, region 4 |
Sigma70_r4 | PF04545.23 | 2.5e-09 | 154–202 | Sigma-70, region 4 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rsdA (anti-sigma-D factor RsdA), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3413c rsdA |
anti-sigma-D factor RsdA | 999 | 1000 ctx | neighborhood:882 cooccurence:488 experimental:999 |
Rv2721c hyp |
hypothetical protein | 785 | 785 | coexpression:785 |
Rv3415c hyp |
hypothetical protein | 783 | 784 ctx | neighborhood:783 |
Rv1477 ripA |
peptidoglycan endopeptidase RipA | 774 | 774 | coexpression:770 |
Rv3810 pirG |
cell surface protein | 778 | 747 | coexpression:746 |
Rv3717 hyp |
hypothetical protein | 742 | 742 | coexpression:734 |
Rv0063 |
oxidoreductase | 734 | 734 | coexpression:734 |
Rv0179c lprO |
lipoprotein LprO | 730 | 730 | coexpression:730 |
Rv0312 hyp |
hypothetical protein | 714 | 703 | coexpression:703 |
Rv1987 |
chitinase | 651 | 652 | coexpression:651 |
Rv2145c wag31 |
cell wall synthesis protein Wag31 | 642 | 643 | coexpression:586 |
Rv3221A rshA |
anti-sigma factor RshA | 686 | 557 | |
Rv1221 sigE |
ECF RNA polymerase sigma factor SigE | 551 | 552 ctx | cooccurence:549 |
Rv3911 sigM |
ECF RNA polymerase sigma factor SigM | 894 | 513 ctx | cooccurence:510 textmining:792 |
Rv0736 rslA |
anti-sigma-L factor RslA | 539 | 486 |
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): ECF RNA polymerase sigma factor SigD
- Pfam (hmmscan --cut_ga): Sigma70_r2 PF04542.21 (E=1e-12), Sigma70_r4_2 PF08281.19 (E=3e-10), Sigma70_r4 PF04545.23 (E=3e-09)
- (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_217931.1)
- Domains: Pfam-A via hmmscan --cut_ga — Sigma70_r2 (PF04542.21), Sigma70_r4_2 (PF08281.19), Sigma70_r4 (PF04545.23)
- 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 P9WGG9 (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 —
42 functional partner(s); context anchor
rsdA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3414c|sigD MVDPGVSPGCVRFVTLEISPSMTMQGERLDAVVAEAVAGDRNALREVLETIRPIVVRYCRARVGTVERSGLSADDVAQEVCLATITALPRYRDRGRPFLAFLYGIAAHKVADAHRAAGRDRAYPAETLPERWSADAGPEQMAIEADSVTRMNELLEILPAKQREILILRVVVGLSAEETAAAVGSTTGAVRVAQHRALQRLKDEIVAAGDYA