Protein profile

VK055_1352

transcription-repair coupling factor

Genome: KpATCC43816

Gene: AIK79975.1 mfd Structure source: AlphaFold + ColabFold UniProt A0A0H3GMV4
Amino acids 1148
Annotations 10
Features 57
PDB binders 1
Druggability 0.894

Overview

Basic information about this protein and its source genome.

Accession
VK055_1352
Gene
AIK79975.1 mfd
Status
annotated
Amino acids
1148
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 (%)
63.772
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
83.33

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 0.894
Structure A0A0H3GMV4
Pocket Pocket 95
P2Rank 0.901
Structure A0A0H3GMV4
Pocket Pocket 1
ColabFold model
FPocket 0.39 · Pocket 22
P2Rank 0.975 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 166 / 4744 genomes with a hit
Normalized 0.035

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0006281 The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
  • GO:0003676 Binding to a nucleic acid.
  • GO:0003684 Binding to damaged DNA.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0003678 Unwinding of a DNA helix, driven by ATP hydrolysis.
  • GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
  • GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
  • GO:0000716 The identification of lesions on the actively transcribed strand of the DNA duplex as well as a small subset of lesions not recognized by the general nucleotide-excision repair pathway.

Sequence Features

Domain/signature hits from InterPro and related databases.

57 records
Show feature table
Start End DB Term Name
1006 1097 Pfam PF03461 TRCF domain
1006 1097 InterPro IPR005118 Transcription-repair-coupling factor, C-terminal domain
475 987 Gene3D G3DSA:3.40.50.300 -
475 987 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
9 340 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
9 340 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
577 984 PANTHER PTHR47964 ATP-DEPENDENT DNA HELICASE HOMOLOG RECG, CHLOROPLASTIC
577 984 InterPro IPR047112 ATP-dependent DNA helicase RecG/Transcription-repair-coupling factor
148 1079 NCBIfam TIGR00580 transcription-repair coupling factor
148 1079 InterPro IPR004576 Transcription-repair coupling factor
128 213 FunFam G3DSA:3.30.2060.10:FF:000002 Transcription-repair-coupling factor
520 780 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
520 780 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
24 335 Gene3D G3DSA:3.40.50.11180 -
480 538 Gene3D G3DSA:2.40.10.170 -
1005 1105 SMART SM00982 TRCF_a_2_a
1005 1105 InterPro IPR005118 Transcription-repair-coupling factor, C-terminal domain
797 951 ProSiteProfiles PS51194 Superfamilies 1 and 2 helicase C-terminal domain profile.
797 951 InterPro IPR001650 Helicase, C-terminal
477 572 Pfam PF02559 CarD-like/TRCF domain
477 572 InterPro IPR003711 CarD-like/TRCF, RNAP-interacting domain
129 217 Pfam PF17757 UvrB interaction domain
129 217 InterPro IPR041471 UvrB, interaction domain
467 545 SUPERFAMILY SSF141259 CarD-like
467 545 InterPro IPR036101 CarD-like/TRCF, RNAP-interacting domain superfamily
476 573 SMART SM01058 CarD_TRCF_2
476 573 InterPro IPR003711 CarD-like/TRCF, RNAP-interacting domain
615 776 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile.
615 776 InterPro IPR014001 Helicase superfamily 1/2, ATP-binding domain
354 450 Gene3D G3DSA:3.40.50.11140 -
777 987 FunFam G3DSA:3.40.50.300:FF:000300 Transcription-repair-coupling factor
1001 1148 FunFam G3DSA:3.90.1150.50:FF:000001 Transcription-repair-coupling factor
992 1144 SUPERFAMILY SSF143517 TRCF domain-like
992 1144 InterPro IPR037235 TRCF-like, C-terminal D7 domain
597 787 SMART SM00487 ultradead3
597 787 InterPro IPR014001 Helicase superfamily 1/2, ATP-binding domain
539 776 FunFam G3DSA:3.40.50.300:FF:000546 Transcription-repair-coupling factor
586 778 CDD cd17991 DEXHc_TRCF
802 906 Pfam PF00271 Helicase conserved C-terminal domain
802 906 InterPro IPR001650 Helicase, C-terminal
779 987 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
779 987 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
602 762 Pfam PF00270 DEAD/DEAH box helicase
602 762 InterPro IPR011545 DEAD/DEAH box helicase domain
28 1127 Hamap MF_00969 Transcription-repair-coupling factor [mfd].
28 1127 InterPro IPR004576 Transcription-repair coupling factor
539 778 Gene3D G3DSA:3.40.50.300 -
539 778 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
785 935 CDD cd18810 SF2_C_TRCF
1001 1148 Gene3D G3DSA:3.90.1150.50 -
1001 1148 InterPro IPR037235 TRCF-like, C-terminal D7 domain
823 907 SMART SM00490 helicmild6
823 907 InterPro IPR001650 Helicase, C-terminal
351 463 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
351 463 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
128 213 Gene3D G3DSA:3.30.2060.10 -
480 538 FunFam G3DSA:2.40.10.170:FF:000007 Transcription-repair-coupling factor

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_A0A0H3GMV4
AlphaFold full sequence Viewing
ColabFold VK055_1352
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
95 0.894
104 0.469
59 0.257

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 14.4 0.721
2 9.0 0.482
3 7.99 0.425
4 5.68 0.274
5 4.77 0.211

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.

51 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
AGS Q72KB4 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)…

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.