KpATCC43816 Protein target profile

transcription termination/antitermination L factor

Accession: VK055_3901

Gene: AIK82449.1 nusA 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GW50

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Length 495

Pocket druggability (P2Rank · AlphaFold DB model) 0.034

Functional annotation 0 EC 9 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. Structure available AlphaFold DB model + ColabFold model

Risks to review

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: 4.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 95.758 Higher values support similarity to known essential genes.
DEG E-value: 0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT: 87.79 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) 0.034

Structure A0A0H3GW50

Pocket Pocket 1

Druggability (FPocket) 0.886

Structure A0A0H3GW50

Pocket Pocket 2

ColabFold model

P2Rank 0.064 · Pocket 1

FPocket 0.925 · Pocket 7

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 191 / 4744 genomes with a hit

Prevalence 4.0%

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.

MNKEILAVVEAVSNEKALPREKIFEALESALATATKKKYEQEIDVRVEIDRKSGDFDTFRRWLVVEEVTQPTREITLEAARFEDESMNVGDYVEDQIESVTFDRITTQTAKQVIVQKVREAERAMVVDQFREHEGEIITGVVKKVNRDNITLDLGNNAEAVILREDMLPRENFRPGDRIRGVLYAVRPEARGAQLFVTRSKPEMLIELFRIEVPEIGEEVLEIKAAARDPGSRAKIAVKTNDKRIDPVGACVGMRGARVQAVSTELGGERIDIVLWDDNPAQFVINAMAPADVASIVVDEDKHTMDIAVEAGNLAQAIGRNGQNVRLASQLSGWELNVMTVDDLQAKHQAEAHAAIDTFTKYLDIDEDFATVLVEEGFSSLEELAYVPMKELLEIDGLDEATVEALRERAKNALTTLALAQEESLGDNKPADDLLNLEGLDRALAFKLAARGVCTLEDLAEQGVDDLADIEGMTDEKAGELIMAARNICWFGDEA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

9 GO

Subcellular localization

Localization: Cytoplasmic

Gene Ontology (GO)

GO:0003676 Binding to a nucleic acid.
GO:0031554 Any process that modulates the frequency, rate, extent, or location of DNA-templated transcription termination, the process in which transcription is completed; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA.
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.
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:0000166 Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
GO:0003723 Binding to an RNA molecule or a portion thereof.
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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0003746 Functions in chain elongation during polypeptide synthesis at the ribosome.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

54 records

Show feature table

Start	End	DB	Term	Name
403	423	Coils	Coil	Coil
278	346	FunFam	G3DSA:3.30.300.20:FF:000005	Transcription termination/antitermination protein NusA
352	421	Gene3D	G3DSA:1.10.150.20	-
1	129	FunFam	G3DSA:3.30.1480.10:FF:000001	Transcription termination/antitermination protein NusA
1	126	SUPERFAMILY	SSF69705	Transcription factor NusA, N-terminal domain
1	126	InterPro	IPR036555	NusA, N-terminal domain superfamily
135	200	ProSiteProfiles	PS50126	S1 domain profile.
135	200	InterPro	IPR003029	S1 domain
429	492	SUPERFAMILY	SSF47794	Rad51 N-terminal domain-like
429	492	InterPro	IPR010995	DNA repair Rad51/transcription factor NusA, alpha-helical
132	199	CDD	cd04455	S1_NusA
278	343	Gene3D	G3DSA:3.30.300.20	-
278	343	InterPro	IPR015946	K homology domain-like, alpha/beta
201	278	SUPERFAMILY	SSF54814	Prokaryotic type KH domain (KH-domain type II)
201	278	InterPro	IPR009019	K homology domain superfamily, prokaryotic type
202	276	CDD	cd02134	KH-II_NusA_rpt1
432	486	Pfam	PF14520	Helix-hairpin-helix domain
431	490	Gene3D	G3DSA:1.10.150.20	-
355	415	SUPERFAMILY	SSF47794	Rad51 N-terminal domain-like
355	415	InterPro	IPR010995	DNA repair Rad51/transcription factor NusA, alpha-helical
279	339	CDD	cd22529	KH-II_NusA_rpt2
4	123	Pfam	PF08529	NusA N-terminal domain
4	123	InterPro	IPR013735	Transcription factor NusA, N-terminal
135	198	FunFam	G3DSA:2.40.50.140:FF:000092	Transcription termination/antitermination protein NusA
132	199	SUPERFAMILY	SSF50249	Nucleic acid-binding proteins
132	199	InterPro	IPR012340	Nucleic acid-binding, OB-fold
279	343	SUPERFAMILY	SSF54814	Prokaryotic type KH domain (KH-domain type II)
279	343	InterPro	IPR009019	K homology domain superfamily, prokaryotic type
1	129	Gene3D	G3DSA:3.30.1480.10	-
1	129	InterPro	IPR036555	NusA, N-terminal domain superfamily
134	195	Pfam	PF00575	S1 RNA binding domain
134	195	InterPro	IPR003029	S1 domain
230	297	Pfam	PF13184	NusA-like KH domain
230	297	InterPro	IPR025249	KH domain, NusA-like
1	387	PANTHER	PTHR22648	TRANSCRIPTION TERMINATION FACTOR NUSA
1	387	InterPro	IPR030842	Transcription termination/antitermination protein NusA, bacterial
2	410	Hamap	MF_00945_B	Transcription termination/antitermination protein NusA [nusA].
2	410	InterPro	IPR030842	Transcription termination/antitermination protein NusA, bacterial
365	414	NCBIfam	TIGR01954	transcription termination factor NusA, C-terminal duplication
365	414	InterPro	IPR010214	Transcription termination factor NusA, C-terminal duplication
440	489	NCBIfam	TIGR01954	transcription termination factor NusA, C-terminal duplication
440	489	InterPro	IPR010214	Transcription termination factor NusA, C-terminal duplication
199	277	Gene3D	G3DSA:3.30.300.20	-
199	277	InterPro	IPR015946	K homology domain-like, alpha/beta
135	198	Gene3D	G3DSA:2.40.50.140	-
135	198	InterPro	IPR012340	Nucleic acid-binding, OB-fold
4	342	NCBIfam	TIGR01953	transcription termination factor NusA
4	342	InterPro	IPR010213	Transcription termination factor NusA
199	277	FunFam	G3DSA:3.30.300.20:FF:000002	Transcription termination/antitermination protein NusA
352	421	FunFam	G3DSA:1.10.150.20:FF:000018	Transcription termination/antitermination protein NusA
431	490	FunFam	G3DSA:1.10.150.20:FF:000015	Transcription termination/antitermination protein NusA
302	338	ProSiteProfiles	PS50084	Type-1 KH domain profile.
133	200	SMART	SM00316	S1_6
133	200	InterPro	IPR022967	RNA-binding domain, S1

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

0.034

Likely same site as FPocket 2 2.2 Å 8 shared residues 100% of smaller site

Show in viewer

Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #2

0.886 Unusual size

Likely same site as P2Rank 1 2.2 Å 8 shared residues 100% 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_A0A0H3GW50	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_3901	ColabFold	—	—	full sequence	—	Loaded

Cross-references

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

Sequence

UniProt A0A0H3GW50