Protein target profile

KP13_32211

transcription elongation factor GreB

Genome: KpKP13 Gene: AHE42307.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GZG0
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Length 157
Pocket druggability 0.419
Functional annotation 0 EC 5 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Main supporting evidence

No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Moderate predicted binding pocket FPocket selected-pocket score 0.42. This supports review but is not experimental validation. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 192 of 4744 screened genomes (4.0%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.42) — check the ligand evidence before deprioritizing on off-target risk alone. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.01.

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein. No ligand evidence No experimental PDB ligands, measured ChEMBL bioactivity, or proposed ZINC compound records are available.
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
4.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
61.538 Higher values support similarity to known essential genes.
DEG E-value
1.44e-63 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
91.15 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.419
Structure A0A0H3GZG0
Pocket Pocket 4
P2Rank 0.011
Structure A0A0H3GZG0
Pocket Pocket 1
ColabFold model
FPocket 0.268 · Pocket 11
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 192 / 4744 genomes with a hit
Prevalence 4.0%

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Sequence

UniProt A0A0H3GZG0

Sequence

Primary amino-acid sequence viewer.

MKTPLITREGYEKLKQEMDYLWRQERPEVTKKVTWAASLGDRSENADYQYNKKRLREIDRRVRYLTKCLEQLKIVDYSPQQEGKVFFGAWVEIENDEGDIKRFRIVGYDEIFGRKDYISIDSPMARALLKKEVGDLAIVNTPAGEASWYVNEIEYVK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5
  • GO:0032784 Any process that modulates the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides catalyzed by a DNA-dependent RNA polymerase.
  • GO:0070063 Binding to an RNA polymerase molecule or complex.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0003746 Functions in chain elongation during polypeptide synthesis at the ribosome.
  • GO:0006354 The extension of an RNA molecule after transcription initiation and promoter clearance at a DNA-dependent RNA polymerase promoter by the addition of ribonucleotides catalyzed by an RNA polymerase.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

25 records
Show feature table
Start End DB Term Name
80 155 SUPERFAMILY SSF54534 FKBP-like
2 157 NCBIfam TIGR01461 transcription elongation factor GreB
2 157 InterPro IPR006358 Transcription elongation factor GreB
2 154 Hamap MF_00105 Transcription elongation factor GreA [greA].
2 154 InterPro IPR028624 Transcription elongation factor GreA/GreB
77 157 Gene3D G3DSA:3.10.50.30 -
77 157 InterPro IPR036953 Transcription elongation factor GreA/GreB, C-terminal domain superfamily
81 155 Pfam PF01272 Transcription elongation factor, GreA/GreB, C-term
81 155 InterPro IPR001437 Transcription elongation factor, GreA/GreB, C-terminal
3 78 SUPERFAMILY SSF46557 GreA transcript cleavage protein, N-terminal domain
3 78 InterPro IPR036805 Transcription elongation factor, GreA/GreB, N-terminal domain superfamily
1 157 PIRSF PIRSF006092 GreA_GreB
1 157 InterPro IPR023459 Transcription elongation factor GreA/GreB family
1 76 FunFam G3DSA:1.10.287.180:FF:000001 Transcription elongation factor GreA
3 156 PANTHER PTHR30437 TRANSCRIPTION ELONGATION FACTOR GREA
3 156 InterPro IPR023459 Transcription elongation factor GreA/GreB family
80 156 FunFam G3DSA:3.10.50.30:FF:000001 Transcription elongation factor GreA
1 156 Hamap MF_00930 Transcription elongation factor GreB [greB].
1 156 InterPro IPR006358 Transcription elongation factor GreB
119 135 ProSitePatterns PS00830 Prokaryotic transcription elongation factors signature 2.
119 135 InterPro IPR018151 Transcription elongation factor, GreA/GreB, conserved site
1 76 Gene3D G3DSA:1.10.287.180 -
1 76 InterPro IPR036805 Transcription elongation factor, GreA/GreB, N-terminal domain superfamily
5 74 Pfam PF03449 Transcription elongation factor, N-terminal
5 74 InterPro IPR022691 Transcription elongation factor, GreA/GreB, N-terminal

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 · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #4
0.419
Show in viewer
Surrounding area
Site 2 FPocket #3
0.241
Show in viewer
Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.011
Show in viewer
Surrounding area
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

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
AlphaFold DB AF_A0A0H3GZG0
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_32211
ColabFold — — full sequence — Loaded