Protein profile

VK055_4413

RNA polymerase sigma factor RpoS

Genome: KpATCC43816

Gene: rpoS AIK82956.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GXG2
Amino acids 330
Annotations 6
Features 43
PDB binders 12
Druggability 0.571

Overview

Basic information about this protein and its source genome.

Accession
VK055_4413
Gene
rpoS AIK82956.1
Status
annotated
Amino acids
330
Structure source
AlphaFold + ColabFold
GO
GO:0006352 The initial step of transcription, consisting of the assembly of the RNA polymerase preinitiation complex (PIC) at a gene promoter, as well as the formation of the first few bonds of the RNA transcript. Transcription initiation includes abortive initiation events, which occur when the first few nucleotides are repeatedly synthesized and then released, and ends when promoter clearance takes place. GO:0016987 Sigma factors act as the promoter specificity subunit of eubacterial and plant plastid multisubunit RNA polymerases, whose core subunit composition is often described as alpha(2)-beta-beta-prime. Although sigma does not bind DNA on its own, when combined with the core to form the holoenzyme, the sigma factor binds specifically to promoter elements. The sigma subunit is released once elongation begins. GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. GO:0003700 A transcription regulator activity that modulates transcription of gene sets via selective and non-covalent binding to a specific double-stranded genomic DNA sequence (sometimes referred to as a motif) within a cis-regulatory region. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons. GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
45.318
DEG E-value
1.27e-73
Localization
Cytoplasmic
ColabFold pLDDT
81.4

Selected Druggability evidence

AlphaFold / UniProt model

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.571
Structure A0A0H3GXG2
Pocket Pocket 32
P2Rank 0.147
Structure A0A0H3GXG2
Pocket Pocket 1
ColabFold model
FPocket 0.453 · Pocket 2
P2Rank 0.297 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 131 / 4744 genomes with a hit
Normalized 0.028

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

6
  • GO:0006352 The initial step of transcription, consisting of the assembly of the RNA polymerase preinitiation complex (PIC) at a gene promoter, as well as the formation of the first few bonds of the RNA transcript. Transcription initiation includes abortive initiation events, which occur when the first few nucleotides are repeatedly synthesized and then released, and ends when promoter clearance takes place.
  • GO:0016987 Sigma factors act as the promoter specificity subunit of eubacterial and plant plastid multisubunit RNA polymerases, whose core subunit composition is often described as alpha(2)-beta-beta-prime. Although sigma does not bind DNA on its own, when combined with the core to form the holoenzyme, the sigma factor binds specifically to promoter elements. The sigma subunit is released once elongation begins.
  • GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
  • GO:0003700 A transcription regulator activity that modulates transcription of gene sets via selective and non-covalent binding to a specific double-stranded genomic DNA sequence (sometimes referred to as a motif) within a cis-regulatory region. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Sequence Features

Domain/signature hits from InterPro and related databases.

43 records
Show feature table
Start End DB Term Name
8 163 Gene3D G3DSA:1.10.601.10 RNA Polymerase Primary Sigma Factor
262 315 Pfam PF04545 Sigma-70, region 4
262 315 InterPro IPR007630 RNA polymerase sigma-70 region 4
245 318 FunFam G3DSA:1.10.10.10:FF:000044 RNA polymerase sigma factor RpoS
48 328 NCBIfam TIGR02394 RNA polymerase sigma factor RpoS
48 328 InterPro IPR012761 RNA polymerase sigma factor RpoS
245 317 Gene3D G3DSA:1.10.10.10 -
245 317 InterPro IPR036388 Winged helix-like DNA-binding domain superfamily
287 313 ProSitePatterns PS00716 Sigma-70 factors family signature 2.
287 313 InterPro IPR000943 RNA polymerase sigma-70
86 166 FunFam G3DSA:1.10.601.10:FF:000001 RNA polymerase sigma factor SigA
3 328 Hamap MF_00959 RNA polymerase sigma factor RpoS [rpoS].
3 328 InterPro IPR012761 RNA polymerase sigma factor RpoS
225 323 SUPERFAMILY SSF88659 Sigma3 and sigma4 domains of RNA polymerase sigma factors
225 323 InterPro IPR013324 RNA polymerase sigma factor, region 3/4-like
118 131 ProSitePatterns PS00715 Sigma-70 factors family signature 1.
118 131 InterPro IPR000943 RNA polymerase sigma-70
84 322 PANTHER PTHR30603 RNA POLYMERASE SIGMA FACTOR RPO
256 314 CDD cd06171 Sigma70_r4
90 317 NCBIfam TIGR02937 sigma-70 family RNA polymerase sigma factor
90 317 InterPro IPR014284 RNA polymerase sigma-70 like domain
56 88 Pfam PF00140 Sigma-70 factor, region 1.2
56 88 InterPro IPR009042 RNA polymerase sigma-70 region 1.2
56 164 SUPERFAMILY SSF88946 Sigma2 domain of RNA polymerase sigma factors
56 164 InterPro IPR013325 RNA polymerase sigma factor, region 2
266 278 PRINTS PR00046 Major sigma-70 factor signature
266 278 InterPro IPR000943 RNA polymerase sigma-70
287 302 PRINTS PR00046 Major sigma-70 factor signature
287 302 InterPro IPR000943 RNA polymerase sigma-70
118 131 PRINTS PR00046 Major sigma-70 factor signature
302 313 PRINTS PR00046 Major sigma-70 factor signature
302 313 InterPro IPR000943 RNA polymerase sigma-70
142 150 PRINTS PR00046 Major sigma-70 factor signature
142 150 InterPro IPR000943 RNA polymerase sigma-70
174 248 Pfam PF04539 Sigma-70 region 3
174 248 InterPro IPR007624 RNA polymerase sigma-70 region 3
167 243 FunFam G3DSA:1.10.10.10:FF:000046 RNA polymerase sigma factor RpoS
167 241 SUPERFAMILY SSF88659 Sigma3 and sigma4 domains of RNA polymerase sigma factors
167 241 InterPro IPR013324 RNA polymerase sigma factor, region 3/4-like
94 163 Pfam PF04542 Sigma-70 region 2
94 163 InterPro IPR007627 RNA polymerase sigma-70 region 2
167 243 Gene3D G3DSA:1.10.10.10 -
167 243 InterPro IPR036388 Winged helix-like DNA-binding domain superfamily

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

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Structural evidence

0 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3GXG2
AlphaFold full sequence Viewing
ColabFold VK055_4413
ColabFold full sequence Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET Sticks Spheres Surfaces Druggability Labels Zoom Positions
32 0.571
30 0.001
25 0.0
31 0.0

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 4.3 0.147
2 3.49 0.102
3 1.44 0.016

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

62 records

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
118 P00579 430.2 Da LogP 3.06 TPSA 0.0 ✓ Ro5 ✓ Clean c1ccc(cc1)[Sb+](c2ccccc2)(c3ccccc3)c4ccccc4
1N7 P00579 631.9 Da LogP 2.20 TPSA 164.4 2 viol. ✓ Clean C[C@H](CCC(=O)NCCC[N+](C)(C)CC(CS(=O)(=O)O)O)[C…
1RL P00579 900.0 Da LogP 6.67 TPSA 216.4 3 viol. ✓ Clean CCN(CC)CCOc1cccc2c1N=C3c4c5c(c(c6c4C(=O)[C@](O6…
1RM P00579 1035.2 Da LogP 6.62 TPSA 237.5 3 viol. ✓ Clean Cc1c(c2c3c4c1O[C@@](C4=O)(O/C=C/[C@@H]([C@H]([C…
88G P9WGI1 358.4 Da LogP 3.97 TPSA 58.2 ✓ Ro5 ✓ Clean Cc1ccccc1NC(=O)[C@@H](Cc2ccccc2)NC(=O)c3ccccc3
BU3 A0A0H3CAV3 90.1 Da LogP -0.25 TPSA 40.5 ✓ Ro5 ✓ Clean C[C@H]([C@@H](C)O)O
FI8 P9WGI1 1058.1 Da LogP 6.23 TPSA 266.7 4 viol. ✓ Clean CCc1c(c(c(c(c1Cl)O)Cl)O)C(=O)O[C@@H]2[C@H](O[C@…
KNG A0QW02 986.1 Da LogP 5.64 TPSA 292.6 4 viol. Alert Cc1c(c2c3c(cc(c2O)NC(=O)/C(=C\CC[C@@H]([C@@H]([…
RBT Q5SKW1 847.0 Da LogP 4.62 TPSA 205.5 2 viol. Alert Cc1c(c2c3c4c1O[C@@](C4=O)(O\C=C\[C@@H]([C@H]([C…
RFP A0QW02 823.0 Da LogP 4.34 TPSA 220.1 3 viol. Alert Cc1c(c2c3c4c1O[C@@](C4=O)(O\C=C\[C@@H]([C@H]([C…
RFV Q5SKW1 699.8 Da LogP 4.60 TPSA 204.5 3 viol. ✓ Clean Cc1c(c2c3c(cc(c2O)NC(=O)C(=C/C=C/[C@@H]([C@@H](…
SRN A0QW02 807.0 Da LogP 6.80 TPSA 161.2 2 viol. ✓ Clean C[C@H]1[C@H]2C\C=C\[C@H]3[C@@H]([C@H]4C[C@@H](O…

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.