KpKP13 Protein target profile

RNA polymerase sigma factor rpoS

Accession: KP13_02521

Gene: rpoS AHE42985.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GXG2
Length 330
Pocket druggability (P2Rank · AlphaFold DB model) 0.147
Direct ligand evidence 0 62 total records
Functional annotation 0 EC 6 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target
No hit
Gut microbiome similarity
2.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
42.857 Higher values support similarity to known essential genes.
DEG E-value
2.44e-79 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
81.32 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.147
Structure A0A0H3GXG2
Pocket Pocket 1
Druggability (FPocket) 0.571
Structure A0A0H3GXG2
Pocket Pocket 32
ColabFold model
P2Rank 0.311 · Pocket 1
FPocket 0.04 · Pocket 32
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 131 / 4744 genomes with a hit
Prevalence 2.8%

Sequence

Primary amino-acid sequence viewer.

MSQNTLKVHDLNEDAEFDENGIEVFDEKALVEEEPSDSDLAEEELLSQGATQRVLDATQLYLGEIGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQGQGLNIEALFRE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

6
  • GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
  • 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: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: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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

43 records
Show feature table
Start End DB Term Name
118 131 ProSitePatterns PS00715 Sigma-70 factors family signature 1.
118 131 InterPro IPR000943 RNA polymerase sigma-70
287 313 ProSitePatterns PS00716 Sigma-70 factors family signature 2.
287 313 InterPro IPR000943 RNA polymerase sigma-70
56 88 Pfam PF00140 Sigma-70 factor, region 1.2
56 88 InterPro IPR009042 RNA polymerase sigma-70 region 1.2
245 318 FunFam G3DSA:1.10.10.10:FF:000044 RNA polymerase sigma factor RpoS
94 163 Pfam PF04542 Sigma-70 region 2
94 163 InterPro IPR007627 RNA polymerase sigma-70 region 2
84 322 PANTHER PTHR30603 RNA POLYMERASE SIGMA FACTOR RPO
8 163 Gene3D G3DSA:1.10.601.10 RNA Polymerase Primary Sigma Factor
174 248 Pfam PF04539 Sigma-70 region 3
174 248 InterPro IPR007624 RNA polymerase sigma-70 region 3
90 317 NCBIfam TIGR02937 sigma-70 family RNA polymerase sigma factor
90 317 InterPro IPR014284 RNA polymerase sigma-70 like domain
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
245 317 Gene3D G3DSA:1.10.10.10 -
245 317 InterPro IPR036388 Winged helix-like DNA-binding domain superfamily
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
256 314 CDD cd06171 Sigma70_r4
3 328 Hamap MF_00959 RNA polymerase sigma factor RpoS [rpoS].
3 328 InterPro IPR012761 RNA polymerase sigma factor RpoS
167 243 FunFam G3DSA:1.10.10.10:FF:000046 RNA polymerase sigma factor RpoS
56 164 SUPERFAMILY SSF88946 Sigma2 domain of RNA polymerase sigma factors
56 164 InterPro IPR013325 RNA polymerase sigma factor, region 2
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
262 315 Pfam PF04545 Sigma-70, region 4
262 315 InterPro IPR007630 RNA polymerase sigma-70 region 4
48 328 NCBIfam TIGR02394 RNA polymerase sigma factor RpoS
48 328 InterPro IPR012761 RNA polymerase sigma factor RpoS
86 166 FunFam G3DSA:1.10.601.10:FF:000001 RNA polymerase sigma factor SigA
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; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

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Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.147
Likely same site as FPocket 32 6.4 Å 8 shared residues 67% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.102
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.016
Show in viewer
Surrounding area

Binding pockets · FPocket

Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #32
0.571 Unusual size
Likely same site as P2Rank 1 6.4 Å 8 shared residues 67% of smaller site
Show in viewer
Surrounding area
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold DB AF_A0A0H3GXG2
AlphaFold DB full sequence Viewing
ColabFold KP13_02521
ColabFold full sequence Loaded

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
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 12 records from similar proteins
Structural ligands 12 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
118 PDB via homolog 430.2 Da · LogP 3.06 · TPSA 0.0 Open detail RCSB PDB
1N7 PDB via homolog Detail RCSB PDB
1RL PDB via homolog Detail RCSB PDB
1RM PDB via homolog Detail RCSB PDB
88G PDB via homolog Detail RCSB PDB

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 RCSB PDB P00579 430.2 Da LogP 3.06 TPSA 0.0 ✓ Ro5 ✓ Clean c1ccc(cc1)[Sb+](c2ccccc2)(c3ccccc3)c4ccccc4
1N7 RCSB PDB 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 RCSB PDB P00579 900.0 Da LogP 6.67 TPSA 216.4 3 viol. ✓ Clean CCN(CC)CCOc1cccc2c1N=C3c4c5c(c(c6c4C(=O)[C@](O6…
1RM RCSB PDB 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 RCSB PDB P9WGI1 358.4 Da LogP 3.97 TPSA 58.2 ✓ Ro5 ✓ Clean Cc1ccccc1NC(=O)[C@@H](Cc2ccccc2)NC(=O)c3ccccc3
BU3 RCSB PDB A0A0H3CAV3 90.1 Da LogP -0.25 TPSA 40.5 ✓ Ro5 ✓ Clean C[C@H]([C@@H](C)O)O
FI8 RCSB PDB 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 RCSB PDB 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 RCSB PDB 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 RCSB PDB 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 RCSB PDB 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 RCSB PDB 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.

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.