sigG Family assigned · medium auto-curated
H37Rv Rv0182c · MTBC0 mtbc0_000195 ·
370 aa · 213376–214488 (-) ·
RefSeq NP_214696.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ECF RNA polymerase sigma factor SigG |
|---|---|
| MTBC0 PGAP re-annotation | sigma-70 family RNA polymerase sigma factor SigG |
| Revised (this work) | Sigma-70 family RNA polymerase sigma factor SigG. Pfam: Sigma70_r2 (PF04542.21), Sigma70_r4_2 (PF08281.19), Sigma70_r4 (PF04545.23), SnoaL_4 (PF13577.13), 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 |
P9WGG5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ECF RNA polymerase sigma factor SigG |
| 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 a cognate anti-sigma factor until released, although no anti-sigma factor is known for this protein. May be involved in host intracellular survival after infection (strains H37Rv and CDC 1551). A role in the SOS response is controversial; it has been seen in strain CDC 1551 but not in H37Rv. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | sigG |
| eggNOG description | Belongs to the sigma-70 factor family. ECF subfamily |
| Orthologous group | COG1595 |
| KEGG orthology |
K03088
|
| Gene Ontology (12) |
GO:0001101, GO:0001666, GO:0006950, GO:0008150, GO:0009415, GO:0009628, GO:0010035, GO:0036293, GO:0042221, GO:0050896, GO:0070482, GO:1901700
|
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 | 0.953 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 8 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 | 2.5e-20 | 64–129 | Sigma-70 region 2 |
Sigma70_r4_2 | PF08281.19 | 7.0e-14 | 180–232 | Sigma-70, region 4 |
Sigma70_r4 | PF04545.23 | 2.2e-06 | 185–233 | Sigma-70, region 4 |
SnoaL_4 | PF13577.13 | 2.0e-05 | 249–307 | SnoaL-like domain |
SnoaL_2 | PF12680.14 | 1.5e-08 | 256–331 | SnoaL-like domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0180c (transmembrane protein), medium confidence from genomic context alone (score 674 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0181c hyp |
hypothetical protein | 836 | 767 ctx | neighborhood:745 |
Rv0180c |
transmembrane protein | 740 | 674 ctx | neighborhood:662 |
Rv0183 |
lysophospholipase | 657 | 585 ctx | neighborhood:580 |
Rv0185 hyp |
hypothetical protein | 505 | 505 ctx | neighborhood:481 |
Rv0184 hyp |
hypothetical protein | 504 | 504 ctx | neighborhood:481 |
Rv3911 sigM |
ECF RNA polymerase sigma factor SigM | 748 | 503 ctx | cooccurence:492 textmining:515 |
Rv0736 rslA |
anti-sigma-L factor RslA | 513 | 490 | |
Rv3221A rshA |
anti-sigma factor RshA | 511 | 489 | |
Rv0179c lprO |
lipoprotein LprO | 573 | 487 ctx | neighborhood:484 |
Rv1222 rseA |
anti-sigma E factor RseA | 495 | 473 | |
Rv0668 rpoC |
DNA-directed RNA polymerase subunit beta' | 490 | 462 | experimental:456 |
Rv0667 rpoB |
DNA-directed RNA polymerase subunit beta | 485 | 456 | experimental:451 |
Rv0186 bglS |
beta-glucosidase BglS | 437 | 437 ctx | neighborhood:419 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 466 | 435 | experimental:431 |
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha | 464 | 435 | experimental:431 |
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 SigG
- MTBC0 PGAP product: sigma-70 family RNA polymerase sigma factor SigG
- Pfam (hmmscan --cut_ga): Sigma70_r2 PF04542.21 (E=2e-20), Sigma70_r4_2 PF08281.19 (E=7e-14), Sigma70_r4 PF04545.23 (E=2e-06), SnoaL_4 PF13577.13 (E=2e-05), SnoaL_2 PF12680.14 (E=1e-08)
- (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_214696.1)
- Domains: Pfam-A via hmmscan --cut_ga — Sigma70_r2 (PF04542.21), Sigma70_r4_2 (PF08281.19), Sigma70_r4 (PF04545.23), SnoaL_4 (PF13577.13), 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 P9WGG5 (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 —
37 functional partner(s); context anchor
Rv0180c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000195|Rv0182c|sigG MRTSPMPAKFRSVRVVVITGSVTAAPVRVSETLRRLIDVSVLAENSGREPADERRGDFSAHTEPYRRELLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIATNTCLTALEGRRRRPLPTGLGRPSADPSGELVERREVSWLEPLPDVTDDPADPSTIVGNRESVRLAFVAALQHLSPRQRAVLLLRDVLQWKSAEVADAIGTSTVAVNSLLQRARSQLQTVRPSAADRLSAPDSPEAQDLLARYIAAFEAYDIDRLVELFTAEAIWEMPPYTGWYQGAQAIVTLIHQQCPAYSPGDMRLISLIANGQPAAAMYMRAGDVHLPFQLHVLDMAADRVSHVVAFLDTTLFPKFGLPDSL