Genome KpKP13

Protein target profile

tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC

Accession: KP13_01033

Gene: mnmC AHE43439.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GWE4
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Length 662
Pocket druggability (P2Rank · AlphaFold DB model) 0.983
Functional annotation 0 EC 9 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

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

Main supporting evidence

Independent pocket support: P2Rank + FPocket Both predictors report a high-scoring binding site (P2Rank 0.98, FPocket 0.87). Use the 3D pocket comparison to verify whether they identify the same site. 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. Strong predicted binding pocket FPocket selected-pocket score 0.87. This is a computational pocket signal, not binding validation. Review the complete evidence below

Risks to review

Microbiome similarity 116 of 4744 screened genomes (2.4%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.98) — check the ligand evidence before deprioritizing on off-target risk alone.

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
2.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
0.0 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT
96.3 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.983
Structure A0A0H3GWE4
Pocket Pocket 1
Druggability (FPocket) 0.867
Structure A0A0H3GWE4
Pocket Pocket 3
ColabFold model
P2Rank 0.986 · Pocket 1
FPocket 0.664 · Pocket 22
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 116 / 4744 genomes with a hit
Prevalence 2.4%

Cross-references

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

Sequence

UniProt A0A0H3GWE4

Sequence

Primary amino-acid sequence viewer.

MKQNAIQPANLEFNAEGTPVSRDFDDVYFSNDNGLEETRYVFLGGNRLPERFPSHPRPLMIVAESGFGTGLNFLTLWQAFDVFVRDNPDVTLQRLHFISFEKYPLKAEDLRLAHQRWPELAPWAQQLQAQWPSAFGGCHRLLLDGGRVTLDLWFGDINELTRELDDSLNQQVDAWFLDGFAPAKNPDMWTQDLFSAMARLARPGGTLATFTSAGFVRRGLQEAGFTMRKSKGFGRKREMLTGEMAQTLSFPARVPWFARSSSDAREAAIIGGGIASALLSLALLRRGWQVTLYCADEAPAQGASGNRQGALYPLLSQHDPALARFFPAAFTFARRMYDALPVMFDHQWCGVTQLGWDEKSTHKIAQMLALNLPPDIACAVTAEQVAGLTGVDTGCGGITYPAGGWLCPQQLTAELLALAATRGLHVHYGYPVETLSAEGDGWLLNQQRYHQAVVLANGHRITGFAQTAQLPVYPVGGQVSHIPTTPRLAALRQVLCYDGYLTPQNPQNQQHCIGASYHRGKTDTTFSEEDQQHNRQRLIDCFPGAEWPQDVDISANDARCGVRCATRDHLPMVGNVPDYAATLTQYASLHEQPDIADSAPVCRNLFMLGALGSRGLCTAPLSAELLAAQMSAEPLPLDSDTLAALNPNRLWVRKLLKGKAVK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

9 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

9
  • GO:0016645 Catalysis of an oxidation-reduction (redox) reaction in which a CH-NH group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
  • GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule.
  • GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
  • GO:0008033 The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
  • GO:0004808 Catalysis of the reaction: 5-aminomethyl-2-thiouridine34 in tRNA + S-adenosyl-L-methionine = 5-methylaminomethyl-2-thiouridine34 in tRNA + H+ + S-adenosyl-L-homocysteine. This enzyme specifically adds the terminal methyl group of 5-[(methylamino)methyl]-2-thiouridylate.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0050660 Binding to FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
  • GO:0032259 The process in which a methyl group is covalently attached to a molecule.
  • GO:0002098 The process in which a uridine at position 34 of a tRNA is post-transcriptionally modified. The wobble nucleoside of the tRNA sequence (position 34) corresponds to the first position of the anticodon.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

22 records
Show feature table
Start End DB Term Name
9 250 Gene3D G3DSA:3.40.50.150 Vaccinia Virus protein VP39
9 250 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
348 566 Gene3D G3DSA:3.30.9.10 -
267 658 NCBIfam TIGR03197 FAD-dependent 5-carboxymethylaminomethyl-2-thiouridine(34) oxidoreductase MnmC
267 658 InterPro IPR017610 tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC, C-terminal
472 548 SUPERFAMILY SSF54373 FAD-linked reductases, C-terminal domain
267 628 Pfam PF01266 FAD dependent oxidoreductase
267 628 InterPro IPR006076 FAD dependent oxidoreductase
19 243 NCBIfam NF033855 tRNA (5-methylaminomethyl-2-thiouridine)(34)-methyltransferase MnmD
19 243 InterPro IPR047785 tRNA mnm(5)s(2)U biosynthesis bifunctional protein MnmC, N-terminal
262 658 PANTHER PTHR13847 SARCOSINE DEHYDROGENASE-RELATED
118 244 Pfam PF05430 S-adenosyl-L-methionine-dependent methyltransferase
118 244 InterPro IPR008471 MnmC-like methyltransferase
9 249 FunFam G3DSA:3.40.50.150:FF:000107 tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC
267 655 SUPERFAMILY SSF51905 FAD/NAD(P)-binding domain
267 655 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
62 239 SUPERFAMILY SSF53335 S-adenosyl-L-methionine-dependent methyltransferases
62 239 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
7 653 Hamap MF_01102 tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC [mnmC].
7 653 InterPro IPR023032 tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC
265 655 Gene3D G3DSA:3.50.50.60 -
265 655 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily

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 · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.983
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Surrounding area
Pocket 2 P2Rank #2
0.904
Likely same site as FPocket 3 2.9 Å 32 shared residues 94% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.224
Likely same site as FPocket 15 0.8 Å 14 shared residues 100% of smaller site
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Surrounding area
Pocket 4 P2Rank #4
0.173
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Surrounding area
Pocket 5 P2Rank #5
0.125
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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #3
0.867 Unusual size
Likely same site as P2Rank 2 2.9 Å 32 shared residues 94% of smaller site
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Surrounding area
Pocket 2 FPocket #15
0.725 Unusual size
Likely same site as P2Rank 3 0.8 Å 14 shared residues 100% of smaller site
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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_A0A0H3GWE4
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_01033
ColabFold — — full sequence — Loaded