KpATCC43816 Protein target profile

transcription termination factor Rho

Accession: VK055_3192

Gene: AIK81760.1 rho 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GH32
Length 419
Pocket druggability (P2Rank · AlphaFold DB model) 0.093
Direct ligand evidence 0 61 total records
Functional annotation 1 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.

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
55.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
94.93 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) 0.093
Structure A0A0H3GH32
Pocket Pocket 1
Druggability (FPocket) 0.332
Structure A0A0H3GH32
Pocket Pocket 5
ColabFold model
P2Rank 0.312 · Pocket 1
FPocket 0.586 · Pocket 4
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 2651 / 4744 genomes with a hit
Prevalence 55.9%

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.

MNLTELKNTPVSELITLGENMGLENLARMRKQDIIFAILKQHSKSGEDIFGDGVLEILQDGFGFLRSADSSYLAGPDDIYVSPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVNEVNYDKPENARNKILFENLTPLHANSRLRMERGNGSTEDLTARVLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQSIAYNHPDCVLMVLLIDERPEEVTEMQRLVKGEVVASTFDEPASRHVQVAEMVIEKAKRLVEHKKDVIILLDSITRLARAYNTVVPASGKVLTGGVDANALHRPKRFFGAARNVEEGGSLTIIATALIDTGSKMDEVIYEEFKGTGNMELHLSRKIAEKRVFPAIDYNRSGTRKEELLTTQEELQKMWILRKIIHPMGEIDAMEFLINKLAMTKTNDDFFDMMKRS

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0008186 Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of RNA, and it drives another reaction.
  • GO:0003676 Binding to a nucleic acid.
  • GO:0003723 Binding to an RNA molecule or a portion thereof.
  • GO:0016887 Catalysis of the reaction: ATP + H2O = ADP + H+ phosphate. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient.
  • 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:0004386 Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix.
  • GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

37 records
Show feature table
Start End DB Term Name
1 47 FunFam G3DSA:1.10.720.10:FF:000001 Transcription termination factor Rho
48 122 FunFam G3DSA:2.40.50.140:FF:000010 Transcription termination factor Rho
1 418 PANTHER PTHR46425 TRANSCRIPTION TERMINATION FACTOR RHO
1 418 InterPro IPR004665 Transcription termination factor Rho
1 47 Gene3D G3DSA:1.10.720.10 -
52 125 Pfam PF07497 Rho termination factor, RNA-binding domain
52 125 InterPro IPR011113 Rho termination factor, RNA-binding domain
52 118 SMART SM00357 csp_8
52 118 InterPro IPR011129 Cold shock domain
1 46 SUPERFAMILY SSF68912 Rho N-terminal domain-like
1 46 InterPro IPR036269 Rho termination factor, N-terminal domain superfamily
48 123 ProSiteProfiles PS51856 Rho RNA-binding domain profile.
48 123 InterPro IPR011113 Rho termination factor, RNA-binding domain
1 419 Hamap MF_01884 Transcription termination factor Rho [rho].
1 419 InterPro IPR004665 Transcription termination factor Rho
130 419 Gene3D G3DSA:3.40.50.300 -
130 419 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
48 125 SUPERFAMILY SSF50249 Nucleic acid-binding proteins
48 125 InterPro IPR012340 Nucleic acid-binding, OB-fold
156 404 CDD cd01128 rho_factor_C
156 404 InterPro IPR041703 Transcription termination factor Rho, ATP binding domain
160 363 Pfam PF00006 ATP synthase alpha/beta family, nucleotide-binding domain
160 363 InterPro IPR000194 ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain
48 122 Gene3D G3DSA:2.40.50.140 -
48 122 InterPro IPR012340 Nucleic acid-binding, OB-fold
5 47 SMART SM00959 Rho_N_2_a
5 47 InterPro IPR011112 Rho termination factor, N-terminal
2 417 NCBIfam TIGR00767 transcription termination factor Rho
2 417 InterPro IPR004665 Transcription termination factor Rho
90 371 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
90 371 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
51 118 CDD cd04459 Rho_CSD
51 118 InterPro IPR011113 Rho termination factor, RNA-binding domain
170 355 SMART SM00382 AAA_5
170 355 InterPro IPR003593 AAA+ ATPase domain
5 47 Pfam PF07498 Rho termination factor, N-terminal domain
130 419 FunFam G3DSA:3.40.50.300:FF:000072 Transcription termination factor Rho

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
0.093
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Surrounding area
Pocket 2 P2Rank #2
0.049
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Surrounding area
Pocket 3 P2Rank #3
0.04
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Surrounding area
Pocket 4 P2Rank #4
0.031
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Surrounding area
Pocket 5 P2Rank #5
0.018
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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 #5
0.332
Show in viewer
Surrounding area
Pocket 2 FPocket #10
0.275
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Surrounding area
Residue sets
UniProt: Binding site:169-174
UniProt: Binding site:181-186
UniProt: Binding site:212-212
UniProt: Site:326-326 RNA-binding 2
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_A0A0H3GH32
AlphaFold DB full sequence Viewing
ColabFold VK055_3192
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.

61 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 11 records from similar proteins
Structural ligands 11 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
AF3 PDB via homolog 84.0 Da · LogP 0.88 · TPSA 0.0 Open detail RCSB PDB
AGS PDB via homolog Detail RCSB PDB
ANP PDB via homolog Detail RCSB PDB
BCM PDB via homolog Detail RCSB PDB
BEF PDB via homolog Detail RCSB PDB

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.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
AF3 RCSB PDB B7UMA6 84.0 Da LogP 0.88 TPSA 0.0 ✓ Ro5 ✓ Clean F[Al](F)F
AGS RCSB PDB P0AG30 523.2 Da LogP -1.51 TPSA 262.1 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
ANP RCSB PDB P0AG30 506.2 Da LogP -2.06 TPSA 281.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
BCM RCSB PDB P0AG30 302.3 Da LogP -3.30 TPSA 148.3 1 viol. ✓ Clean C[C@](CO)([C@@H]([C@@]12C(=O)N[C@@](C(=C)CCO1)(…
BEF RCSB PDB P0AG30 66.0 Da LogP 0.88 TPSA 0.0 ✓ Ro5 ✓ Clean [Be-](F)(F)F
DG RCSB PDB P0AG30 347.2 Da LogP -1.54 TPSA 185.8 ✓ Ro5 ✓ Clean c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N…
DT RCSB PDB P0AG30 322.2 Da LogP -1.40 TPSA 151.1 ✓ Ro5 ✓ Clean CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O…
FB RCSB PDB P0AG30 330.3 Da LogP -3.73 TPSA 165.4 1 viol. ✓ Clean C[C@](CO)([C@@H]([C@@]12C(=O)N[C@@](C(=CC=O)CCO…
FPD RCSB PDB P0AG30 440.5 Da LogP -1.64 TPSA 165.4 1 viol. ✓ Clean C[C@](CO)([C@@H]([C@@]12C(=O)N[C@@]([C@@H](CCO1…
IUM RCSB PDB P38527 270.0 Da LogP -2.38 TPSA 46.1 ✓ Ro5 ✓ Clean [O-][U+4][O-]
SPD RCSB PDB P0AG30 145.2 Da LogP -0.34 TPSA 64.1 ✓ Ro5 ✓ Clean C(CCNCCCN)CN

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.