Protein profile

VK055_3995

sigma70 factor RNA polymerase, sigma 70 (sigma D) factor

Genome: KpATCC43816

Gene: AIK82542.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3H395
Amino acids 613
Annotations 5
Features 54
PDB binders 13
Druggability 0.769

Overview

Basic information about this protein and its source genome.

Accession
VK055_3995
Gene
AIK82542.1
Status
annotated
Amino acids
613
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
96.248
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
83.12

Selected Druggability evidence

AlphaFold / UniProt 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 0.769
Structure A0A0H3H395
Pocket Pocket 4
P2Rank 0.095
Structure A0A0H3H395
Pocket Pocket 1
ColabFold model
FPocket 0.441 · Pocket 26
P2Rank 0.135 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 228 / 4744 genomes with a hit
Normalized 0.048

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5
  • GO:0006352 The initial step of transcription, consisting of the assembly of the RNA polymerase preinitiation complex (PIC) at a gene promoter, as well as the formation of the first few bonds of the RNA transcript. Transcription initiation includes abortive initiation events, which occur when the first few nucleotides are repeatedly synthesized and then released, and ends when promoter clearance takes place.
  • GO:0016987 Sigma factors act as the promoter specificity subunit of eubacterial and plant plastid multisubunit RNA polymerases, whose core subunit composition is often described as alpha(2)-beta-beta-prime. Although sigma does not bind DNA on its own, when combined with the core to form the holoenzyme, the sigma factor binds specifically to promoter elements. The sigma subunit is released once elongation begins.
  • GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
  • 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:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).

Sequence Features

Domain/signature hits from InterPro and related databases.

54 records
Show feature table
Start End DB Term Name
529 612 FunFam G3DSA:1.10.10.10:FF:000004 RNA polymerase sigma factor SigA
187 210 MobiDBLite mobidb-lite consensus disorder prediction
572 598 ProSitePatterns PS00716 Sigma-70 factors family signature 2.
572 598 InterPro IPR000943 RNA polymerase sigma-70
167 218 MobiDBLite mobidb-lite consensus disorder prediction
113 446 SUPERFAMILY SSF88946 Sigma2 domain of RNA polymerase sigma factors
113 446 InterPro IPR013325 RNA polymerase sigma factor, region 2
509 611 SUPERFAMILY SSF88659 Sigma3 and sigma4 domains of RNA polymerase sigma factors
509 611 InterPro IPR013324 RNA polymerase sigma factor, region 3/4-like
137 348 Pfam PF04546 Sigma-70, non-essential region
137 348 InterPro IPR007631 RNA polymerase sigma factor 70, non-essential domain
541 599 CDD cd06171 Sigma70_r4
111 448 FunFam G3DSA:1.10.601.10:FF:000002 RNA polymerase sigma factor RpoD
379 448 Pfam PF04542 Sigma-70 region 2
379 448 InterPro IPR007627 RNA polymerase sigma-70 region 2
4 79 Pfam PF03979 Sigma-70 factor, region 1.1
4 79 InterPro IPR007127 RNA polymerase sigma factor 70, region 1.1
375 600 NCBIfam TIGR02937 sigma-70 family RNA polymerase sigma factor
375 600 InterPro IPR014284 RNA polymerase sigma-70 like domain
403 416 ProSitePatterns PS00715 Sigma-70 factors family signature 1.
403 416 InterPro IPR000943 RNA polymerase sigma-70
458 533 Pfam PF04539 Sigma-70 region 3
458 533 InterPro IPR007624 RNA polymerase sigma-70 region 3
111 448 Gene3D G3DSA:1.10.601.10 RNA Polymerase Primary Sigma Factor
13 611 PANTHER PTHR30603 RNA POLYMERASE SIGMA FACTOR RPO
427 435 PRINTS PR00046 Major sigma-70 factor signature
427 435 InterPro IPR000943 RNA polymerase sigma-70
572 587 PRINTS PR00046 Major sigma-70 factor signature
572 587 InterPro IPR000943 RNA polymerase sigma-70
551 563 PRINTS PR00046 Major sigma-70 factor signature
551 563 InterPro IPR000943 RNA polymerase sigma-70
587 598 PRINTS PR00046 Major sigma-70 factor signature
587 598 InterPro IPR000943 RNA polymerase sigma-70
403 416 PRINTS PR00046 Major sigma-70 factor signature
529 613 Gene3D G3DSA:1.10.10.10 -
529 613 InterPro IPR036388 Winged helix-like DNA-binding domain superfamily
547 600 Pfam PF04545 Sigma-70, region 4
547 600 InterPro IPR007630 RNA polymerase sigma-70 region 4
1 64 FunFam G3DSA:1.10.220.120:FF:000001 RNA polymerase sigma factor RpoD
1 64 Gene3D G3DSA:1.10.220.120 -
1 64 InterPro IPR042189 Sigma-70 factor, region 1.1 superfamily
375 611 NCBIfam TIGR02393 RNA polymerase sigma factor RpoD
375 611 InterPro IPR012760 RNA polymerase sigma factor RpoD, C-terminal
452 525 SUPERFAMILY SSF88659 Sigma3 and sigma4 domains of RNA polymerase sigma factors
452 525 InterPro IPR013324 RNA polymerase sigma factor, region 3/4-like
573 593 Coils Coil Coil
4 612 Hamap MF_00963 RNA polymerase sigma factor RpoD [rpoD].
4 612 InterPro IPR028630 RNA polymerase sigma factor RpoD
452 528 FunFam G3DSA:1.10.10.10:FF:000002 RNA polymerase sigma factor SigA
96 126 Pfam PF00140 Sigma-70 factor, region 1.2
96 126 InterPro IPR009042 RNA polymerase sigma-70 region 1.2
330 350 Coils Coil Coil
452 528 Gene3D G3DSA:1.10.10.10 -
452 528 InterPro IPR036388 Winged helix-like DNA-binding 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.

3D visualization script Full viewer

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Structural evidence

0 + 2

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

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3H395
AlphaFold full sequence Viewing
ColabFold VK055_3995
ColabFold full sequence Loaded
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
4 0.769
44 0.351

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 2.37 0.062
2 2.34 0.061
3 2.18 0.052
4 2.12 0.049
5 1.37 0.016

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.

63 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
118 P00579 430.2 Da LogP 3.06 TPSA 0.0 ✓ Ro5 ✓ Clean c1ccc(cc1)[Sb+](c2ccccc2)(c3ccccc3)c4ccccc4
1N7 P00579 631.9 Da LogP 2.20 TPSA 164.4 2 viol. ✓ Clean C[C@H](CCC(=O)NCCC[N+](C)(C)CC(CS(=O)(=O)O)O)[C…
1RL P00579 900.0 Da LogP 6.67 TPSA 216.4 3 viol. ✓ Clean CCN(CC)CCOc1cccc2c1N=C3c4c5c(c(c6c4C(=O)[C@](O6…
1RM P00579 1035.2 Da LogP 6.62 TPSA 237.5 3 viol. ✓ Clean Cc1c(c2c3c4c1O[C@@](C4=O)(O/C=C/[C@@H]([C@H]([C…
88G P9WGI1 358.4 Da LogP 3.97 TPSA 58.2 ✓ Ro5 ✓ Clean Cc1ccccc1NC(=O)[C@@H](Cc2ccccc2)NC(=O)c3ccccc3
BU3 A0A0H3CAV3 90.1 Da LogP -0.25 TPSA 40.5 ✓ Ro5 ✓ Clean C[C@H]([C@@H](C)O)O
C2E A0A023X3C8 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…
FI8 P9WGI1 1058.1 Da LogP 6.23 TPSA 266.7 4 viol. ✓ Clean CCc1c(c(c(c(c1Cl)O)Cl)O)C(=O)O[C@@H]2[C@H](O[C@…
KNG P00579 986.1 Da LogP 5.64 TPSA 292.6 4 viol. Alert Cc1c(c2c3c(cc(c2O)NC(=O)/C(=C\CC[C@@H]([C@@H]([…
RBT Q5SKW1 847.0 Da LogP 4.62 TPSA 205.5 2 viol. Alert Cc1c(c2c3c4c1O[C@@](C4=O)(O\C=C\[C@@H]([C@H]([C…
RFP P9WGI1 823.0 Da LogP 4.34 TPSA 220.1 3 viol. Alert Cc1c(c2c3c4c1O[C@@](C4=O)(O\C=C\[C@@H]([C@H]([C…
RFV Q5SKW1 699.8 Da LogP 4.60 TPSA 204.5 3 viol. ✓ Clean Cc1c(c2c3c(cc(c2O)NC(=O)C(=C/C=C/[C@@H]([C@@H](…
SRN P9WGI1 807.0 Da LogP 6.80 TPSA 161.2 2 viol. ✓ Clean C[C@H]1[C@H]2C\C=C\[C@H]3[C@@H]([C@H]4C[C@@H](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.