Protein profile

VK055_4881

response regulator

Genome: KpATCC43816

Gene: AIK83408.1 Structure source: ColabFold
Amino acids 966
Annotations 10
Features 84
PDB binders 7
Druggability 0.777

Overview

Basic information about this protein and its source genome.

Accession
VK055_4881
Gene
AIK83408.1
Status
annotated
Amino acids
966
Structure source
ColabFold
GO
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.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
No hit
Essential (DEG)
N
DEG identity (%)
47.414
Localization
CytoplasmicMembrane
ColabFold pLDDT
82.12

Selected Druggability evidence

ColabFold / curated model

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.777
Structure CB_VK055_4881
Pocket Pocket 78
P2Rank 0.714
Structure CB_VK055_4881
Pocket Pocket 1
ColabFold model
FPocket 0.777 · Pocket 78
P2Rank 0.714 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 0 / 4744 genomes with a hit
Normalized 0

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

10 GO

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 Features

Domain/signature hits 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; predicted models typically cover the full protein.

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Structural evidence

0 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
ColabFold VK055_4881
ColabFold full sequence Viewing
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET Sticks Spheres Surfaces Druggability Labels Zoom Positions
78 0.777

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 7.57 0.399
2 4.57 0.196
3 4.29 0.177
4 3.18 0.109
5 2.8 0.086

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

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 O67198 [Be](OP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@…
5QT Q1ZS18 272.3 Da LogP 0.83 TPSA 99.9 ✓ Ro5 ✓ Clean CC(C)(C)COC(=O)CNC1=NNC(=O)NC1=S
AGS 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 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 Q1ZS18 273.3 Da LogP 0.14 TPSA 104.9 ✓ Ro5 ✓ Clean CC(C)(C)COC(=O)CSC1=NNC(=O)NC1=O
BEF P41789 66.0 Da LogP 0.88 TPSA 0.0 ✓ Ro5 ✓ Clean [Be-](F)(F)F
C2E 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.