KpKP13 Protein target profile

Transcription elongation protein nusA

Accession: KP13_01101

Gene: AHE42507.1 nusA 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GW50
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Length 495
Pocket druggability (P2Rank · AlphaFold DB model) 0.034
Functional annotation 0 EC 9 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

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 0.89. This is a computational pocket signal, not binding validation. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 191 of 4744 screened genomes (4.0%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.89) — check the ligand evidence before deprioritizing on off-target risk alone. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.03.

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
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
87.67 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 0.12 · Pocket 1
FPocket 0.924 · Pocket 7
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 191 / 4744 genomes with a hit
Prevalence 4.0%

Cross-references

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

Sequence

UniProt A0A0H3GW50

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)

9
  • GO:0003676 Binding to a nucleic acid.
  • 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: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: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:0003723 Binding to an RNA molecule or a portion thereof.
  • 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: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
230 297 Pfam PF13184 NusA-like KH domain
230 297 InterPro IPR025249 KH domain, NusA-like
279 343 SUPERFAMILY SSF54814 Prokaryotic type KH domain (KH-domain type II)
279 343 InterPro IPR009019 K homology domain superfamily, prokaryotic type
278 346 FunFam G3DSA:3.30.300.20:FF:000005 Transcription termination/antitermination protein NusA
1 387 PANTHER PTHR22648 TRANSCRIPTION TERMINATION FACTOR NUSA
1 387 InterPro IPR030842 Transcription termination/antitermination protein NusA, bacterial
278 343 Gene3D G3DSA:3.30.300.20 -
278 343 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
431 490 FunFam G3DSA:1.10.150.20:FF:000015 Transcription termination/antitermination protein NusA
202 276 CDD cd02134 KH-II_NusA_rpt1
2 410 Hamap MF_00945_B Transcription termination/antitermination protein NusA [nusA].
2 410 InterPro IPR030842 Transcription termination/antitermination protein NusA, bacterial
352 421 Gene3D G3DSA:1.10.150.20 -
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
302 338 ProSiteProfiles PS50084 Type-1 KH domain profile.
1 129 FunFam G3DSA:3.30.1480.10:FF:000001 Transcription termination/antitermination protein NusA
4 342 NCBIfam TIGR01953 transcription termination factor NusA
4 342 InterPro IPR010213 Transcription termination factor NusA
432 486 Pfam PF14520 Helix-hairpin-helix domain
4 123 Pfam PF08529 NusA N-terminal domain
4 123 InterPro IPR013735 Transcription factor NusA, N-terminal
431 490 Gene3D G3DSA:1.10.150.20 -
133 200 SMART SM00316 S1_6
133 200 InterPro IPR022967 RNA-binding domain, S1
135 200 ProSiteProfiles PS50126 S1 domain profile.
135 200 InterPro IPR003029 S1 domain
135 198 FunFam G3DSA:2.40.50.140:FF:000092 Transcription termination/antitermination protein NusA
403 423 Coils Coil Coil
1 126 SUPERFAMILY SSF69705 Transcription factor NusA, N-terminal domain
1 126 InterPro IPR036555 NusA, N-terminal domain superfamily
199 277 FunFam G3DSA:3.30.300.20:FF:000002 Transcription termination/antitermination protein NusA
429 492 SUPERFAMILY SSF47794 Rad51 N-terminal domain-like
429 492 InterPro IPR010995 DNA repair Rad51/transcription factor NusA, alpha-helical
352 421 FunFam G3DSA:1.10.150.20:FF:000018 Transcription termination/antitermination protein NusA
132 199 CDD cd04455 S1_NusA
201 278 SUPERFAMILY SSF54814 Prokaryotic type KH domain (KH-domain type II)
201 278 InterPro IPR009019 K homology domain superfamily, prokaryotic type
134 195 Pfam PF00575 S1 RNA binding domain
134 195 InterPro IPR003029 S1 domain
1 129 Gene3D G3DSA:3.30.1480.10 -
1 129 InterPro IPR036555 NusA, N-terminal domain superfamily
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
132 199 SUPERFAMILY SSF50249 Nucleic acid-binding proteins
132 199 InterPro IPR012340 Nucleic acid-binding, OB-fold
199 277 Gene3D G3DSA:3.30.300.20 -
199 277 InterPro IPR015946 K homology domain-like, alpha/beta

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
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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
0.886 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 KP13_01101
ColabFold — — full sequence — Loaded