KpKP13 Protein target profile

Transcription antitermination protein nusG

Accession: KP13_01354

Gene: AHE46944.1 nusG 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GPZ5
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Length 181
Pocket druggability (P2Rank · AlphaFold DB model) 0.087
Functional annotation 0 EC 7 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

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

Main supporting evidence

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. Moderate predicted binding pocket FPocket selected-pocket score 0.41. This supports review but is not experimental validation. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 291 of 4744 screened genomes (6.1%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.41) — check the ligand evidence before deprioritizing on off-target risk alone. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.09.

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein. 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
6.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
100.0 Higher values support similarity to known essential genes.
DEG E-value
1.54e-132 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
77.77 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) 0.087
Structure A0A0H3GPZ5
Pocket Pocket 1
Druggability (FPocket) 0.408
Structure A0A0H3GPZ5
Pocket Pocket 6
ColabFold model
P2Rank 0.188 · Pocket 1
FPocket 0.397 · Pocket 9
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 291 / 4744 genomes with a hit
Prevalence 6.1%

Sequence

Primary amino-acid sequence viewer.

MSEAPKKRWYVVQAFSGFEGRVATSLREHIKLHNMEELFGEVMVPTEEVVEIRGGQRRKSERKFFPGYVLVQMVMNDASWHLVRSVPRVMGFIGGTSDRPAPISDKEVDAIMNRLQQVGDKPRPKTLFEPGEMVRVNDGPFADFNGVVEEVDYEKSRLKVSVSIFGRATPVELDFSQVEKA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

7
  • GO:0140673 A chromatin remodeling process that reestablishes the chromatin structure following the passage of RNA polymerase II during transcription elongation, thus preventing cryptic transcription initiation.
  • GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
  • GO:0032784 Any process that modulates the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides catalyzed by a DNA-dependent RNA polymerase.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0006354 The extension of an RNA molecule after transcription initiation and promoter clearance at a DNA-dependent RNA polymerase promoter by the addition of ribonucleotides catalyzed by an RNA polymerase.
  • GO:0006353 The completion of transcription: the RNA polymerase pauses, the RNA-DNA hybrid dissociates, followed by the release of the RNA polymerase from its DNA template.
  • GO:0031564 A positive regulation of gene expression mechanism that allows RNA polymerase to continue transcription beyond a termination site, thus allowing expression of downstream genes under specific conditions.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

35 records
Show feature table
Start End DB Term Name
6 115 SMART SM00738 nusgn_4
6 115 InterPro IPR006645 NusG-like, N-terminal
1 117 FunFam G3DSA:3.30.70.940:FF:000001 Transcription termination/antitermination protein NusG
1 117 Gene3D G3DSA:3.30.70.940 -
1 117 InterPro IPR036735 NusG, N-terminal domain superfamily
61 73 PRINTS PR00338 Transcription termination factor NUSG signature
61 73 InterPro IPR001062 Transcription antitermination protein, NusG
139 154 PRINTS PR00338 Transcription termination factor NUSG signature
139 154 InterPro IPR001062 Transcription antitermination protein, NusG
157 173 PRINTS PR00338 Transcription termination factor NUSG signature
157 173 InterPro IPR001062 Transcription antitermination protein, NusG
5 180 PANTHER PTHR30265 RHO-INTERACTING TRANSCRIPTION TERMINATION FACTOR NUSG
5 180 InterPro IPR043425 NusG-like
130 162 Pfam PF00467 KOW motif
130 162 InterPro IPR005824 KOW
125 180 SUPERFAMILY SSF50104 Translation proteins SH3-like domain
125 180 InterPro IPR008991 Translation protein SH3-like domain superfamily
8 115 CDD cd09891 NGN_Bact_1
8 115 InterPro IPR047050 NusG, N-terminal
6 116 SUPERFAMILY SSF82679 N-utilization substance G protein NusG, N-terminal domain
6 116 InterPro IPR036735 NusG, N-terminal domain superfamily
6 181 Hamap MF_00948 Transcription termination/antitermination protein NusG [nusG].
6 181 InterPro IPR001062 Transcription antitermination protein, NusG
127 154 SMART SM00739 kow_9
127 154 InterPro IPR005824 KOW
9 180 NCBIfam TIGR00922 transcription termination/antitermination protein NusG
9 180 InterPro IPR001062 Transcription antitermination protein, NusG
123 181 Gene3D G3DSA:2.30.30.30 -
123 181 InterPro IPR014722 Ribosomal protein L2, domain 2
121 181 FunFam G3DSA:2.30.30.30:FF:000002 Transcription termination/antitermination factor NusG
125 180 CDD cd06091 KOW_NusG
164 173 ProSitePatterns PS01014 Transcription termination factor nusG signature.
164 173 InterPro IPR015869 Transcription antitermination protein, NusG, bacteria, conserved site
7 112 Pfam PF02357 Transcription termination factor nusG
7 112 InterPro IPR006645 NusG-like, N-terminal

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
0.087
Likely same site as FPocket 6 1.1 Å 6 shared residues 100% of smaller site
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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 #6
0.408
Likely same site as P2Rank 1 1.1 Å 6 shared residues 100% of smaller site
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Surrounding area
Pocket 2 FPocket #4
0.385 Unusual size
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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_A0A0H3GPZ5
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_01354
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3GPZ5