KpATCC43816 Protein target profile

RNA polymerase sigma-54 factor

Accession: VK055_3865

Gene: rpoN AIK82415.1 3D evidence: Experimental + ColabFold model Metabolism Not in network UniProt A0A0H3H3L1|A0A0N9UTC1
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Length 477
Pocket druggability (P2Rank · Experimental) 0.104
Functional annotation 0 EC 4 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

Experimental structure available At least one PDB experimental structure is loaded, not just a predicted model - stronger structural coverage than AlphaFold/ColabFold alone. No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Strong predicted binding pocket FPocket selected-pocket score 0.95. This is a computational pocket signal, not binding validation. Review the complete evidence below

Risks to review

Microbiome similarity 132 of 4744 screened genomes (2.8%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.95) — check the ligand evidence before deprioritizing on off-target risk alone. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.10.

Evidence gaps

No ligand evidence No experimental PDB ligands, measured ChEMBL bioactivity, or proposed ZINC compound records are available.
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 (%)
89.937 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
81.48 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

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) 0.104
Structure 7QXI
Pocket Pocket 1
Druggability (FPocket) 0.954
Structure 7QWP
Pocket Pocket 1
ColabFold model
P2Rank 0.042 · Pocket 1
FPocket 0.607 · Pocket 3
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 132 / 4744 genomes with a hit
Prevalence 2.8%

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.

MKQGLQLRLSQQLAMTPQLQQAIRLLQLSTLELQQELQQALESNPLLEQTDLHDEVEAKEVEDRESLDTVDALEQKEMPDELPLDASWDEIYTAGTPSGNGVDYQDDELPVYQGETTQTLQDYLMWQVELTPFTDTDRAIATSIVDAVDDTGYLTIQIEDIVDSIGDDEIGLEEVEAVLKRIQRFDPVGVAAKDLRDCLLIQLSQFAKETPWLEEARLIISNHLDLLANHDFRTLMRVTRLKEEVLKEAVNLIQSLDPRPGQSIQTSEPEYVIPDVLVRKVSGRWTVELNADSIPRLKINQQYAAMGNSARNDADGQFIRSNLQEARWLIKSLESRNDTLLRVSRCIVEQQQAFFEQGEEYMKPMVLADIAQAVEMHESTISRVTTQKYLHSPRGIFELKYFFSSHVNTEGGGEASSTAIRALVKKLIAAENPAKPLSDSKLTSMLSEQGIMVARRTVAKYRESLSIPPSNQRKQLV

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

4
  • 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:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0001216 A DNA-binding transcription factor activity that activates or increases transcription of specific gene sets.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

30 records
Show feature table
Start End DB Term Name
1 476 PANTHER PTHR32248 RNA POLYMERASE SIGMA-54 FACTOR
1 476 InterPro IPR000394 RNA polymerase sigma factor 54
364 383 ProSitePatterns PS00717 Sigma-54 factors family signature 1.
364 383 InterPro IPR000394 RNA polymerase sigma factor 54
5 48 Pfam PF00309 Sigma-54 factor, Activator interacting domain (AID)
5 48 InterPro IPR000394 RNA polymerase sigma factor 54
121 193 Gene3D G3DSA:1.10.10.1330 -
121 193 InterPro IPR038709 RNA polymerase sigma-54 factor, core-binding domain superfamily
9 474 NCBIfam TIGR02395 RNA polymerase factor sigma-54
9 474 InterPro IPR000394 RNA polymerase sigma factor 54
1 477 PIRSF PIRSF000774 RpoN
1 477 InterPro IPR000394 RNA polymerase sigma factor 54
410 474 Gene3D G3DSA:1.10.10.60 -
317 475 Pfam PF04552 Sigma-54, DNA binding domain
317 475 InterPro IPR007634 RNA polymerase sigma factor 54, DNA-binding
116 303 Pfam PF04963 Sigma-54 factor, core binding domain
116 303 InterPro IPR007046 RNA polymerase sigma factor 54, core-binding domain
455 462 ProSitePatterns PS00718 Sigma-54 factors family signature 2.
455 462 InterPro IPR000394 RNA polymerase sigma factor 54
328 454 ProSiteProfiles PS50044 Sigma-54 factors family profile.
410 474 FunFam G3DSA:1.10.10.60:FF:000045 RNA polymerase sigma-54 factor
186 203 PRINTS PR00045 Sigma-54 factor signature
186 203 InterPro IPR000394 RNA polymerase sigma factor 54
376 388 PRINTS PR00045 Sigma-54 factor signature
376 388 InterPro IPR000394 RNA polymerase sigma factor 54
450 468 PRINTS PR00045 Sigma-54 factor signature
450 468 InterPro IPR000394 RNA polymerase sigma factor 54
392 403 PRINTS PR00045 Sigma-54 factor signature
392 403 InterPro IPR000394 RNA polymerase sigma factor 54
121 193 FunFam G3DSA:1.10.10.1330:FF:000001 RNA polymerase sigma-54 factor

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.

Download VMD script Full viewer

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Drag to rotate — click the view, then scroll to zoom.

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
0.954
Show in viewer
Surrounding area
Pocket 2 FPocket #24
0.407
Show in viewer
Surrounding area
All structural evidence 8 experimental · 1 predicted

Structural evidence

8 + 1

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
PDB 5UI8
X-ray — A —
PDBe RCSB PDBj File
Loaded
PDB 7QV9
X-ray — A —
PDBe RCSB PDBj File
Loaded
PDB 7QWP
X-ray — M —
PDBe RCSB PDBj File
Viewing
PDB 7QXI
X-ray — M —
PDBe RCSB PDBj File
Loaded
PDB 9Q94
X-ray — A —
PDBe RCSB PDBj File
Loaded
PDB 9Q95
X-ray — A —
PDBe RCSB PDBj File
Loaded
PDB 9Q97
X-ray — A —
PDBe RCSB PDBj File
Loaded
PDB 9Q98
X-ray — A —
PDBe RCSB PDBj File
Loaded
ColabFold VK055_3865
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3H3L1|A0A0N9UTC1

Structure

PDB 5UI8 PDB 7QV9 PDB 7QWP PDB 7QXI PDB 9Q94 PDB 9Q95 PDB 9Q97 PDB 9Q98