Protein profile

KP13_31791

RNA polymerase sigma factor RpoD

Genome: KpKP13

Gene: AHE42605.1 rpoD Structure source: AlphaFold + ColabFold UniProt A0A0H3H395
Amino acids 632
Annotations 5
Features 54
PDB binders 13
Druggability 0.769

Overview

Basic information about this protein and its source genome.

Accession
KP13_31791
Gene
AHE42605.1 rpoD
Status
annotated
Amino acids
632
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 (%)
95.652
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
81.87

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 0.421 · Pocket 26
P2Rank 0.139 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 223 / 4744 genomes with a hit
Normalized 0.047

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:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
  • 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: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).
  • 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

54 records
Show feature table
Start End DB Term Name
394 630 NCBIfam TIGR02393 RNA polymerase sigma factor RpoD
394 630 InterPro IPR012760 RNA polymerase sigma factor RpoD, C-terminal
471 547 FunFam G3DSA:1.10.10.10:FF:000002 RNA polymerase sigma factor SigA
566 619 Pfam PF04545 Sigma-70, region 4
566 619 InterPro IPR007630 RNA polymerase sigma-70 region 4
560 618 CDD cd06171 Sigma70_r4
422 435 ProSitePatterns PS00715 Sigma-70 factors family signature 1.
422 435 InterPro IPR000943 RNA polymerase sigma-70
132 465 SUPERFAMILY SSF88946 Sigma2 domain of RNA polymerase sigma factors
132 465 InterPro IPR013325 RNA polymerase sigma factor, region 2
115 145 Pfam PF00140 Sigma-70 factor, region 1.2
115 145 InterPro IPR009042 RNA polymerase sigma-70 region 1.2
548 632 Gene3D G3DSA:1.10.10.10 -
548 632 InterPro IPR036388 Winged helix-like DNA-binding domain superfamily
20 83 Gene3D G3DSA:1.10.220.120 -
20 83 InterPro IPR042189 Sigma-70 factor, region 1.1 superfamily
23 631 Hamap MF_00963 RNA polymerase sigma factor RpoD [rpoD].
23 631 InterPro IPR028630 RNA polymerase sigma factor RpoD
206 229 MobiDBLite mobidb-lite consensus disorder prediction
471 547 Gene3D G3DSA:1.10.10.10 -
471 547 InterPro IPR036388 Winged helix-like DNA-binding domain superfamily
592 612 Coils Coil Coil
20 83 FunFam G3DSA:1.10.220.120:FF:000001 RNA polymerase sigma factor RpoD
591 617 ProSitePatterns PS00716 Sigma-70 factors family signature 2.
591 617 InterPro IPR000943 RNA polymerase sigma-70
349 369 Coils Coil Coil
31 630 PANTHER PTHR30603 RNA POLYMERASE SIGMA FACTOR RPO
528 630 SUPERFAMILY SSF88659 Sigma3 and sigma4 domains of RNA polymerase sigma factors
528 630 InterPro IPR013324 RNA polymerase sigma factor, region 3/4-like
23 98 Pfam PF03979 Sigma-70 factor, region 1.1
23 98 InterPro IPR007127 RNA polymerase sigma factor 70, region 1.1
156 367 Pfam PF04546 Sigma-70, non-essential region
156 367 InterPro IPR007631 RNA polymerase sigma factor 70, non-essential domain
130 467 Gene3D G3DSA:1.10.601.10 RNA Polymerase Primary Sigma Factor
471 544 SUPERFAMILY SSF88659 Sigma3 and sigma4 domains of RNA polymerase sigma factors
471 544 InterPro IPR013324 RNA polymerase sigma factor, region 3/4-like
477 552 Pfam PF04539 Sigma-70 region 3
477 552 InterPro IPR007624 RNA polymerase sigma-70 region 3
398 467 Pfam PF04542 Sigma-70 region 2
398 467 InterPro IPR007627 RNA polymerase sigma-70 region 2
186 237 MobiDBLite mobidb-lite consensus disorder prediction
394 619 NCBIfam TIGR02937 sigma-70 family RNA polymerase sigma factor
394 619 InterPro IPR014284 RNA polymerase sigma-70 like domain
422 435 PRINTS PR00046 Major sigma-70 factor signature
606 617 PRINTS PR00046 Major sigma-70 factor signature
606 617 InterPro IPR000943 RNA polymerase sigma-70
591 606 PRINTS PR00046 Major sigma-70 factor signature
591 606 InterPro IPR000943 RNA polymerase sigma-70
446 454 PRINTS PR00046 Major sigma-70 factor signature
446 454 InterPro IPR000943 RNA polymerase sigma-70
570 582 PRINTS PR00046 Major sigma-70 factor signature
570 582 InterPro IPR000943 RNA polymerase sigma-70
548 631 FunFam G3DSA:1.10.10.10:FF:000004 RNA polymerase sigma factor SigA
130 467 FunFam G3DSA:1.10.601.10:FF:000002 RNA polymerase sigma factor RpoD

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 KP13_31791
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.