KpATCC43816 Protein target profile

response regulator

Accession: VK055_4881

Gene: AIK83408.1 3D evidence: ColabFold model Metabolism Not in network
Length 966
Pocket druggability (P2Rank · ColabFold model) 0.714
Direct ligand evidence 0 57 total records
Functional annotation 0 EC 10 GO
Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

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
0.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
47.414 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT
82.12 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

ColabFold / curated 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) 0.714
Structure CB_VK055_4881
Pocket Pocket 1
Druggability (FPocket) 0.777
Structure CB_VK055_4881
Pocket Pocket 78
ColabFold model
P2Rank 0.714 · Pocket 1
FPocket 0.777 · Pocket 78
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 0 / 4744 genomes with a hit
Prevalence 0.0%

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.

MHWLKRIYPRRLRNQMILMAILMVIVPTLSIGYIVETEGRSAVLSEKEKKLSAVVHLLDEALGERFSQHSQLSRAERIRMLNAELSPVTERITHAFPGIGAGYYNKALDAIITYAPSALYQNNVGVTIAADHPGREVMRANAPRVFSGRQVRGDILNSMIPIARHGEVLGYIWANELTEDIRQQAWKMDVRIIAVLAAGLISSLLLIVLFSRRLSANIDIITDGLPTLAQKIPAQLPDLPGELGQISRSVNALAQTLRETKTLNDLIIDNAADGVIAIDREGNVTTMNPAAEVITGYKLDELVGQPYATLFANTHFYSPVLDTLAHGTEHLAQEVSFPGRDRTIEISVTTSRIHNANGELIGALVIFSDLTARKEAQRRLAQTERLATLGELMAGVAHEVRNPLTAIRGYVQIIRQQTTLPVHQEYLSVVLNEIDSINKVIQQLLDFSRPRQSQWQQVQLKALIEEALILVQTSGVQARIDFSTQFDAELPAIVADRELLKQVLLNLLINAVQAIGARGEIRIRTWRDTSTHLALTIEDNGCGIDSDVQKKIFDPFFTTKASGTGLGLALSQRIINAQQPRIPIILMTAYAEVETAVEALRSGAFDYVIKPFDLDELNLLIQRALQLQAMKQEIRSLHQALSTSWQWGHILTNSPRMMDICKDTAKIALSQASVLICGESGTGKELIARAIHYNSRRANGPFIKINCAALPESLLESELFGHEKGAFTGAQTQRQGLFERAHQGTLLLDEIGEMPLVLQAKLLRILQEREFERIGGQQTIQVDIRIVAATNRDLAAMVKEGTFREDLFYRLNVIHLLLPPLRERREDIALLANHFLQKFSAENQRDMIEIDPAAMSRLTAWPWPGNIRELSNVIERAVVMSTGAVIFAEDLPAPFRQPVSKGGEVKAAQPGERNLKEEIKREERRIIMEVLEQQEGNRTRSALMLGISRRALMYKLQEYGIDPAGL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

10 GO

Subcellular localization

Localization
CytoplasmicMembrane

Gene Ontology (GO)

10
  • GO:0043565 Binding to DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0016772 Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
  • GO:0008134 Binding to a transcription factor, a protein required to initiate or regulate transcription.
  • GO:0000155 Catalysis of the phosphorylation of a histidine residue in response to detection of an extracellular signal such as a chemical ligand or change in environment, to initiate a change in cell state or activity. The two-component sensor is a histidine kinase that autophosphorylates a histidine residue in its active site. The phosphate is then transferred to an aspartate residue in a downstream response regulator, to trigger a response.
  • GO:0007165 The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
  • GO:0000160 A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
  • GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
  • GO:0016310 The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
  • 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.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

84 records
Show feature table
Start End DB Term Name
379 452 SUPERFAMILY SSF47384 Homodimeric domain of signal transducing histidine kinase
379 452 InterPro IPR036097 Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily
389 450 Pfam PF00512 His Kinase A (phospho-acceptor) domain
389 450 InterPro IPR003661 Signal transduction histidine kinase, dimerisation/phosphoacceptor domain
265 369 Pfam PF00989 PAS fold
265 369 InterPro IPR013767 PAS fold
388 453 SMART SM00388 HisKA_10
388 453 InterPro IPR003661 Signal transduction histidine kinase, dimerisation/phosphoacceptor domain
567 619 Pfam PF00072 Response regulator receiver domain
567 619 InterPro IPR001789 Signal transduction response regulator, receiver domain
260 305 ProSiteProfiles PS50112 PAS repeat profile.
260 305 InterPro IPR000014 PAS domain
638 820 Gene3D G3DSA:3.40.50.300 -
638 820 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
211 966 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
653 892 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
653 892 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
395 584 ProSiteProfiles PS50109 Histidine kinase domain profile.
395 584 InterPro IPR005467 Histidine kinase domain
491 625 ProSiteProfiles PS50110 Response regulatory domain profile.
491 625 InterPro IPR001789 Signal transduction response regulator, receiver domain
821 893 FunFam G3DSA:1.10.8.60:FF:000014 DNA-binding transcriptional regulator NtrC
821 887 Gene3D G3DSA:1.10.8.60 -
496 576 Pfam PF02518 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
496 576 InterPro IPR003594 Histidine kinase/HSP90-like ATPase
271 370 CDD cd00130 PAS
271 370 InterPro IPR000014 PAS domain
454 585 Gene3D G3DSA:3.30.565.10 -
454 585 InterPro IPR036890 Histidine kinase/HSP90-like ATPase superfamily
373 453 Gene3D G3DSA:1.10.287.130 -
192 210 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
15 37 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
326 382 ProSiteProfiles PS50113 PAC domain profile.
326 382 InterPro IPR000700 PAS-associated, C-terminal
490 621 SMART SM00448 REC_2
490 621 InterPro IPR001789 Signal transduction response regulator, receiver domain
386 449 CDD cd00082 HisKA
386 449 InterPro IPR003661 Signal transduction histidine kinase, dimerisation/phosphoacceptor domain
670 820 CDD cd00009 AAA
192 211 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
36 191 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
651 816 Pfam PF00158 Sigma-54 interaction domain
651 816 InterPro IPR002078 RNA polymerase sigma factor 54 interaction domain
250 371 Gene3D G3DSA:3.30.450.20 PAS domain
253 367 SUPERFAMILY SSF55785 PYP-like sensor domain (PAS domain)
253 367 InterPro IPR035965 PAS domain superfamily
572 641 SUPERFAMILY SSF52172 CheY-like
572 641 InterPro IPR011006 CheY-like superfamily
888 963 Gene3D G3DSA:1.10.10.60 -
262 329 SMART SM00091 pas_2
262 329 InterPro IPR000014 PAS domain
265 380 NCBIfam TIGR00229 PAS domain S-box protein
265 380 InterPro IPR000014 PAS domain
925 942 PRINTS PR01590 FIS bacterial regulatory protein HTH signature
925 942 InterPro IPR002197 DNA binding HTH domain, Fis-type
942 962 PRINTS PR01590 FIS bacterial regulatory protein HTH signature
942 962 InterPro IPR002197 DNA binding HTH domain, Fis-type
443 582 SUPERFAMILY SSF55874 ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
443 582 InterPro IPR036890 Histidine kinase/HSP90-like ATPase superfamily
591 626 Gene3D G3DSA:6.10.250.690 -
1 15 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
16 35 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
923 959 Pfam PF02954 Bacterial regulatory protein, Fis family
923 959 InterPro IPR002197 DNA binding HTH domain, Fis-type
674 687 ProSitePatterns PS00675 Sigma-54 interaction domain ATP-binding region A signature.
674 687 InterPro IPR025662 Sigma-54 interaction domain, ATP-binding site 1
863 872 ProSitePatterns PS00688 Sigma-54 interaction domain C-terminal part signature.
863 872 InterPro IPR025944 Sigma-54 interaction domain, conserved site
495 601 SMART SM00387 HKATPase_4
495 601 InterPro IPR003594 Histidine kinase/HSP90-like ATPase
650 879 ProSiteProfiles PS50045 Sigma-54 interaction domain profile.
650 879 InterPro IPR002078 RNA polymerase sigma factor 54 interaction domain
643 820 FunFam G3DSA:3.40.50.300:FF:000006 DNA-binding transcriptional regulator NtrC
670 813 SMART SM00382 AAA_5
670 813 InterPro IPR003593 AAA+ ATPase domain
533 547 PRINTS PR00344 Bacterial sensor protein C-terminal signature
533 547 InterPro IPR004358 Signal transduction histidine kinase-related protein, C-terminal
551 561 PRINTS PR00344 Bacterial sensor protein C-terminal signature
551 561 InterPro IPR004358 Signal transduction histidine kinase-related protein, C-terminal
562 580 PRINTS PR00344 Bacterial sensor protein C-terminal signature
562 580 InterPro IPR004358 Signal transduction histidine kinase-related protein, C-terminal
512 962 PANTHER PTHR32071 TRANSCRIPTIONAL REGULATORY PROTEIN
863 962 SUPERFAMILY SSF46689 Homeodomain-like
863 962 InterPro IPR009057 Homeobox-like domain superfamily

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
0.714
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Surrounding area
Pocket 2 P2Rank #2
0.505
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Surrounding area
Pocket 3 P2Rank #3
0.278
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Surrounding area
Pocket 4 P2Rank #4
0.231
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Surrounding area
Pocket 5 P2Rank #5
0.07
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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 #78
0.777
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Surrounding area
All structural evidence 0 experimental · 1 predicted

Structural evidence

0 + 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
ColabFold VK055_4881
ColabFold full sequence Viewing

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.

57 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 7 records from similar proteins
Structural ligands 7 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
08T PDB via homolog Open detail RCSB PDB
5QT PDB via homolog Detail RCSB PDB
AGS PDB via homolog Detail RCSB PDB
ANP PDB via homolog Detail RCSB PDB
AZU 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
08T RCSB PDB O67198 [Be](OP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@…
5QT RCSB PDB Q1ZS18 272.3 Da LogP 0.83 TPSA 99.9 ✓ Ro5 ✓ Clean CC(C)(C)COC(=O)CNC1=NNC(=O)NC1=S
AGS RCSB PDB G3XCV0 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 A0A0H3AHP1 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)…
AZU RCSB PDB Q1ZS18 273.3 Da LogP 0.14 TPSA 104.9 ✓ Ro5 ✓ Clean CC(C)(C)COC(=O)CSC1=NNC(=O)NC1=O
BEF RCSB PDB P41789 66.0 Da LogP 0.88 TPSA 0.0 ✓ Ro5 ✓ Clean [Be-](F)(F)F
C2E RCSB PDB G3XCV0 690.4 Da LogP -3.05 TPSA 349.6 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@H]4[C@H](O3)CO[P@@](=O…

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.