KpATCC43816 Protein target profile

RNA polymerase sigma factor RpoE

Accession: VK055_4603

Gene: rpoE AIK83137.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GTU4

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Length 191

Pocket druggability (FPocket · AlphaFold DB model) 0.939

Direct ligand evidence 0 51 total records

Functional annotation 0 EC 7 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.

Main supporting evidence

Risks to review

Evidence coverage

Core evidence streams are available for this target.

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: 3.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 96.859 Higher values support similarity to known essential genes.
DEG E-value: 2.02e-136 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT: 82.25 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)

Structure A0A0H3GTU4

Pocket No pockets

Druggability (FPocket) 0.939

Structure A0A0H3GTU4

Pocket Pocket 1

ColabFold model

P2Rank 0.005 · Pocket 1

FPocket 0.794 · Pocket 2

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 184 / 4744 genomes with a hit

Prevalence 3.9%

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MSEQLTDQVLVERVQKGDQKAFNLLVVRYQHKVASLVSRYVPPGDIADVVQESFVKAWRALDSFRGDSAFYTWLYRIAVNTAKNYLVAQGRRPPSSDVDANEAENFESGGALKEISNPENLMLSEELRQIVFRTIESLPEDLRMAITLRELDGLSYEEIAAIMDCPVGTVRSRIFRAREAIDNKVQPLIRR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Subcellular localization

Localization: Cytoplasmic

Gene Ontology (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:0006950 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
GO:0009266 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a temperature stimulus.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

20 records

Show feature table

Start	End	DB	Term	Name
121	191	FunFam	G3DSA:1.10.10.10:FF:000043	RNA polymerase sigma factor
1	120	Gene3D	G3DSA:1.10.1740.10	-
25	91	Pfam	PF04542	Sigma-70 region 2
25	91	InterPro	IPR007627	RNA polymerase sigma-70 region 2
122	183	SUPERFAMILY	SSF88659	Sigma3 and sigma4 domains of RNA polymerase sigma factors
122	183	InterPro	IPR013324	RNA polymerase sigma factor, region 3/4-like
2	185	PANTHER	PTHR43133	RNA POLYMERASE ECF-TYPE SIGMA FACTO
2	185	InterPro	IPR039425	RNA polymerase sigma-70 like
2	104	SUPERFAMILY	SSF88946	Sigma2 domain of RNA polymerase sigma factors
2	104	InterPro	IPR013325	RNA polymerase sigma factor, region 2
21	183	NCBIfam	TIGR02937	sigma-70 family RNA polymerase sigma factor
21	183	InterPro	IPR014284	RNA polymerase sigma-70 like domain
128	181	CDD	cd06171	Sigma70_r4
1	189	NCBIfam	TIGR02939	RNA polymerase sigma factor RpoE
1	189	InterPro	IPR014286	RNA polymerase sigma-70 RpoE type
129	180	Pfam	PF08281	Sigma-70, region 4
129	180	InterPro	IPR013249	RNA polymerase sigma factor 70, region 4 type 2
1	120	FunFam	G3DSA:1.10.1740.10:FF:000001	RNA polymerase sigma factor
121	191	Gene3D	G3DSA:1.10.10.10	-
121	191	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 · FPocket

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

Pocket 1 FPocket #1

0.939 Unusual size

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Surrounding area

Pocket 2 FPocket #4

0.717

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Surrounding area

Pocket 3 FPocket #3

0.516

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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #2

0.794

Likely same site as P2Rank 1 8.0 Å 5 shared residues 71% of smaller site

Show in viewer

Surrounding area

Pocket 2 FPocket #4

0.491

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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_A0A0H3GTU4	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_4603	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.

51 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 1 records from similar proteins

Structural ligands 1 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

NCA PDB via homolog 122.1 Da · LogP 0.18 · TPSA 56.0 Open detail RCSB PDB

ZINC1592410 ZINC proposed compound · Tanimoto 0.708 Detail ZINC

ZINC116431 ZINC proposed compound · Tanimoto 0.636 Detail ZINC

ZINC10030294 ZINC proposed compound · Tanimoto 0.618 Detail ZINC

ZINC8379324 ZINC proposed compound · Tanimoto 0.618 Detail ZINC

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, use Open crystal to inspect it in the structure viewer.

No PDB structure with a co-crystallized ligand found for this exact protein.

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.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
NCA RCSB PDB	6IN7	Q06198	122.1 Da LogP 0.18 TPSA 56.0	✓ Ro5	✓ Clean	`c1cc(cnc1)C(=O)N`

Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL bioactivity data found for this exact protein.

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL hits found through similar proteins.

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

Ligand	Tanimoto	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ZINC1592410 ZINC	0.708	212.2 Da LogP 1.54 TPSA 59.9	✓ Ro5	Alert	`O=C(C(=O)c1cccnc1)c1cccnc1`
ZINC116431 ZINC	0.636	241.2 Da LogP 1.43 TPSA 85.1	✓ Ro5	✓ Clean	`NC(=O)c1ccc(NC(=O)c2cccnc2)cc1`
ZINC10030294 ZINC	0.618	241.2 Da LogP 1.43 TPSA 85.1	✓ Ro5	✓ Clean	`NC(=O)c1cccc(NC(=O)c2cccnc2)c1`
ZINC8379324 ZINC	0.618	284.3 Da LogP 0.53 TPSA 128.2	✓ Ro5	✓ Clean	`NC(=O)c1cc(NC(=O)c2cccnc2)cc(C(N)=O)c1`
ZINC100083979 ZINC	0.607	226.2 Da LogP 1.93 TPSA 59.9	✓ Ro5	✓ Clean	`O=C(CC(=O)c1cccnc1)c1cccnc1`
ZINC95951757 ZINC	0.607	240.3 Da LogP 0.50 TPSA 102.5	✓ Ro5	✓ Clean	`N/C(=N\N=C(/N)c1cccnc1)c1cccnc1`
ZINC1698713 ZINC	0.600	272.3 Da LogP 1.49 TPSA 78.4	✓ Ro5	✓ Clean	`O=C(OCCOC(=O)c1cccnc1)c1cccnc1`
ZINC100077468 ZINC	0.567	225.2 Da LogP 2.54 TPSA 47.0	✓ Ro5	✓ Clean	`O=C(CC(=O)c1cccnc1)c1ccccc1`
ZINC101814612 ZINC	0.563	225.2 Da LogP 2.86 TPSA 50.2	✓ Ro5	✓ Clean	`O=C(/C=C(\O)c1cccnc1)c1ccccc1`
ZINC1997173 ZINC	0.563	286.3 Da LogP 1.88 TPSA 78.4	✓ Ro5	✓ Clean	`O=C(OCCCOC(=O)c1cccnc1)c1cccnc1`
ZINC127526 ZINC	0.556	241.2 Da LogP 1.43 TPSA 85.1	✓ Ro5	✓ Clean	`NC(=O)c1ccccc1NC(=O)c1cccnc1`
ZINC1582115 ZINC	0.548	270.3 Da LogP 0.64 TPSA 84.0	✓ Ro5	✓ Clean	`O=C(NCCNC(=O)c1cccnc1)c1cccnc1`
ZINC241589 ZINC	0.548	200.2 Da LogP 1.70 TPSA 52.1	✓ Ro5	✓ Clean	`O=C(Oc1cccnc1)c1cccnc1`
ZINC3077252 ZINC	0.548	318.3 Da LogP 2.98 TPSA 84.0	✓ Ro5	✓ Clean	`O=C(Nc1ccc(NC(=O)c2cccnc2)cc1)c1cccnc1`
ZINC3150114 ZINC	0.548	296.3 Da LogP 1.07 TPSA 66.4	✓ Ro5	✓ Clean	`O=C(c1cccnc1)N1CCN(C(=O)c2cccnc2)CC1`
ZINC65751 ZINC	0.545	318.3 Da LogP 2.98 TPSA 84.0	✓ Ro5	✓ Clean	`O=C(Nc1cccc(NC(=O)c2cccnc2)c1)c1cccnc1`
ZINC8288513 ZINC	0.545	348.4 Da LogP 3.19 TPSA 78.4	✓ Ro5	✓ Clean	`O=C(OCc1ccc(COC(=O)c2cccnc2)cc1)c1cccnc1`
ZINC18161669 ZINC	0.543	241.3 Da LogP 1.56 TPSA 77.6	✓ Ro5	✓ Clean	`N/C(=N\OC(=O)c1ccccc1)c1cccnc1`
ZINC82205 ZINC	0.543	204.3 Da LogP 2.00 TPSA 56.0	✓ Ro5	✓ Clean	`CC(C)(C)C(=O)/C=C(\N)c1cccnc1`
ZINC152815394 ZINC	0.541	242.2 Da LogP 0.83 TPSA 98.0	✓ Ro5	✓ Clean	`NC(=O)c1cccc(NC(=O)c2cccnc2)n1`
ZINC1722453 ZINC	0.531	225.2 Da LogP 2.52 TPSA 47.0	✓ Ro5	✓ Clean	`CC(=O)c1ccc(C(=O)c2cccnc2)cc1`
ZINC235763 ZINC	0.531	201.2 Da LogP 2.45 TPSA 30.0	✓ Ro5	✓ Clean	`O=C(c1ccc(F)cc1)c1cccnc1`
ZINC2584594 ZINC	0.531	262.1 Da LogP 3.08 TPSA 30.0	✓ Ro5	✓ Clean	`O=C(c1ccc(Br)cc1)c1cccnc1`
ZINC2748110 ZINC	0.531	318.3 Da LogP 2.98 TPSA 84.0	✓ Ro5	✓ Clean	`O=C(Nc1ccccc1NC(=O)c1cccnc1)c1cccnc1`
ZINC394834 ZINC	0.531	217.7 Da LogP 2.97 TPSA 30.0	✓ Ro5	✓ Clean	`O=C(c1ccc(Cl)cc1)c1cccnc1`
ZINC45028795 ZINC	0.531	252.1 Da LogP 3.62 TPSA 30.0	✓ Ro5	✓ Clean	`O=C(c1cccnc1)c1c(Cl)cccc1Cl`
ZINC45028802 ZINC	0.531	211.3 Da LogP 2.93 TPSA 30.0	✓ Ro5	✓ Clean	`Cc1cccc(C)c1C(=O)c1cccnc1`
ZINC103568534 ZINC	0.529	226.2 Da LogP 2.26 TPSA 63.1	✓ Ro5	✓ Clean	`O=C(/C=C(\O)c1cccnc1)c1ccncc1`
ZINC13208874 ZINC	0.529	214.2 Da LogP 1.83 TPSA 52.1	✓ Ro5	✓ Clean	`O=C(OCc1cccnc1)c1cccnc1`
ZINC1714962 ZINC	0.529	302.3 Da LogP 0.85 TPSA 98.6	✓ Ro5	✓ Clean	`O=C(OCC(O)COC(=O)c1cccnc1)c1cccnc1`
ZINC5013042 ZINC	0.528	242.2 Da LogP 0.95 TPSA 90.5	✓ Ro5	✓ Clean	`N/C(=N\OC(=O)c1ccncc1)c1cccnc1`
ZINC47360984 ZINC	0.526	228.3 Da LogP 1.76 TPSA 65.2	✓ Ro5	✓ Clean	`NC(=O)c1cccc(OCc2cccnc2)c1`
ZINC1541026 ZINC	0.515	284.3 Da LogP 1.03 TPSA 84.0	✓ Ro5	✓ Clean	`O=C(NCCCNC(=O)c1cccnc1)c1cccnc1`
ZINC1541027 ZINC	0.515	298.3 Da LogP 1.42 TPSA 84.0	✓ Ro5	✓ Clean	`O=C(NCCCCNC(=O)c1cccnc1)c1cccnc1`
ZINC2382313354 ZINC	0.515	340.4 Da LogP 4.27 TPSA 59.9	✓ Ro5	✓ Clean	`O=C(C=Cc1ccc(C=CC(=O)c2cccnc2)cc1)c1cccnc1`
ZINC25692080 ZINC	0.515	340.4 Da LogP 4.27 TPSA 59.9	✓ Ro5	✓ Clean	`O=C(/C=C\c1ccc(/C=C/C(=O)c2cccnc2)cc1)c1cccnc1`
ZINC3153101 ZINC	0.515	274.3 Da LogP 4.06 TPSA 33.2	✓ Ro5	✓ Clean	`O=C(c1cccnc1)N(c1ccccc1)c1ccccc1`
ZINC34403957 ZINC	0.515	259.3 Da LogP 3.98 TPSA 30.0	✓ Ro5	✓ Clean	`O=C(c1ccc(-c2ccccc2)cc1)c1cccnc1`
ZINC3654376 ZINC	0.515	200.2 Da LogP 1.12 TPSA 67.8	✓ Ro5	✓ Clean	`O=C(Nc1ncccn1)c1cccnc1`
ZINC37745990 ZINC	0.515	211.3 Da LogP 2.93 TPSA 30.0	✓ Ro5	✓ Clean	`Cc1cc(C)cc(C(=O)c2cccnc2)c1`
ZINC394119 ZINC	0.515	206.3 Da LogP 2.34 TPSA 33.2	✓ Ro5	✓ Clean	`CC(C)N(C(=O)c1cccnc1)C(C)C`
ZINC45028796 ZINC	0.515	252.1 Da LogP 3.62 TPSA 30.0	✓ Ro5	✓ Clean	`O=C(c1cccnc1)c1cc(Cl)cc(Cl)c1`
ZINC4566998 ZINC	0.515	340.4 Da LogP 4.27 TPSA 59.9	✓ Ro5	✓ Clean	`O=C(/C=C\c1ccc(/C=C\C(=O)c2cccnc2)cc1)c1cccnc1`
ZINC4771102 ZINC	0.515	217.7 Da LogP 2.97 TPSA 30.0	✓ Ro5	✓ Clean	`O=C(c1cccnc1)c1ccccc1Cl`
ZINC5224194 ZINC	0.515	340.4 Da LogP 4.27 TPSA 59.9	✓ Ro5	✓ Clean	`O=C(/C=C/c1ccc(/C=C/C(=O)c2cccnc2)cc1)c1cccnc1`
ZINC670700 ZINC	0.515	437.5 Da LogP 4.23 TPSA 113.1	✓ Ro5	✓ Clean	`O=C(Nc1ccc(NC(=O)c2cccnc2)cc1)c1ccc(NC(=O)c2ccc…`
ZINC2145862 ZINC	0.514	320.3 Da LogP 1.50 TPSA 78.4	✓ Ro5	✓ Clean	`O=C(OCC#CC#CCOC(=O)c1cccnc1)c1cccnc1`
ZINC24912456 ZINC	0.514	318.3 Da LogP 2.98 TPSA 84.0	✓ Ro5	✓ Clean	`O=C(Nc1cccnc1)c1ccc(NC(=O)c2cccnc2)cc1`
ZINC75491439 ZINC	0.514	204.3 Da LogP 1.96 TPSA 56.0	✓ Ro5	✓ Clean	`Nc1sccc1C(=O)c1cccnc1`
ZINC91366305 ZINC	0.514	200.2 Da LogP 0.64 TPSA 81.8	✓ Ro5	✓ Clean	`NC(=O)c1cncc(-c2cccnn2)c1`

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.

Sequence

UniProt A0A0H3GTU4

RNA polymerase sigma factor RpoE

Promising target candidate with multiple supporting evidence streams.

Main supporting evidence

Risks to review

Evidence coverage

Prioritization evidence

Off-target risk

Essentiality

Structure confidence

Binding-site evidence

Metabolic context

Sequence

Functional annotations

Subcellular localization

Gene Ontology (GO)

Sequence domains and features

3D structure

Binding pockets · FPocket

Binding pockets · P2Rank

Binding pockets · FPocket

Structural evidence

Ligand evidence

Cross-references

Sequence