Proteins

Genome: KpATCC43816

Description: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome

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# Protein Description Gene Structure EC GO Metabolism Druggability (P2Rank) P2RANK ligandability score for the best pocket in the experimental structure (0–1). Higher values indicate higher predicted ligandability. Available only for genomes analyzed with the curated pipeline. Druggability (FPocket) FPocket druggability score for the preferred structure (0–1): experimental structure when available, otherwise predicted model. ≥ 0.7 highly druggable · ≥ 0.4 moderately druggable · < 0.4 low druggability. Human off-target BLASTP against the human proteome. Hit means at least one human match was detected at e-value <= 1e-5. Prefer No hit for pathogen-selective targets. Human identity (%) Best human BLAST identity percentage. Human E-value Best human BLAST E-value.
1451 VK055_0756 bacterial regulatory helix-turn-helix, lysR family protein AlphaFold DB model + ColabFold model –
GO:0003700A 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:0006355Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. GO:0043565Binding to DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. +14 total
No map 0.823 0.56 No Hit 0.0% —
1452 VK055_4977 fructose bisphosphate aldolase AlphaFold DB model + ColabFold model
4.1.2.13
GO:0016829Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring. GO:0004332Catalysis of the reaction: beta-D-fructose 1,6-bisphosphate = D-glyceraldehyde 3-phosphate + dihydroxyacetone phosphate. GO:0005737The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. +14 total
Mapped 4 0.822 0.467 No Hit 0.0% —
1453 VK055_2977 HAMP domain protein AlphaFold DB model + ColabFold model
2.7.13.3
GO:0016772Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). GO:0016020A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0000155Catalysis of the phosphorylation of a histidine residue in response to detection of an extracellular signal such as a chemical ligand or change in environment, to initiate a change in cell state or activity. The two-component sensor is a histidine kinase that autophosphorylates a histidine residue in its active site. The phosphate is then transferred to an aspartate residue in a downstream response regulator, to trigger a response. +47 total
No map 0.822 0.795 No Hit 0.0% —
1454 VK055_4307 rnfC Barrel sandwich hybrid domain protein AlphaFold DB model + ColabFold model –
GO:0016020A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0051536Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms. GO:0051539Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands. +25 total
No map 0.821 0.719 No Hit 0.0% —
1455 VK055_3384 D-serine ammonia-lyase dsdA AlphaFold DB model + ColabFold model
4.3.1.18
GO:0046416The chemical reactions and pathways involving D-amino acids, the D-enantiomers of amino acids. GO:0008721Catalysis of the reaction: D-serine = pyruvate + NH4+. GO:0006520The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups. +47 total
Mapped 2 0.821 0.608 No Hit 0.0% —
1456 VK055_2565 molybdopterin adenylyltransferase mog AlphaFold DB model + ColabFold model
2.7.7.75
GO:0006777The chemical reactions and pathways resulting in the formation of the Mo-molybdopterin cofactor, essential for the catalytic activity of some enzymes. The cofactor consists of a mononuclear molybdenum (Mo) ion coordinated by one or two molybdopterin ligands. GO:0005524Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0061598Catalysis of the reaction ATP + molybdopterin = diphosphate + adenylyl-molybdopterin.
Chokepoint 1 0.821 0.296 Hit 40.0% 7.10e-18
1457 VK055_2336 DNA polymerase III, epsilon subunit dnaQ AlphaFold DB model + ColabFold model
2.7.7.7
GO:0003887Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time. GO:0003676Binding to a nucleic acid. GO:0006260The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by the origin recognition complex, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA. +58 total
No map 0.821 0.68 No Hit 0.0% —
1458 VK055_0830 glyoxalase-like domain protein ColabFold model – – No map 0.821 0.732 No Hit 0.0% —
1459 VK055_0537 C4-dicarboxylate transporter/malic acid transport family protein tdt AlphaFold DB model + ColabFold model –
GO:0016020A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0055085The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other. GO:0005886The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. +47 total
No map 0.821 0.983 No Hit 0.0% —
1460 VK055_4630 aldose 1-epimerase family protein AlphaFold DB model + ColabFold model –
GO:0003824Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. GO:0030246Binding to a carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates. GO:0005975The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. +14 total
No map 0.820 0.767 No Hit 0.0% —
1461 VK055_3199 ATP-dependent DNA helicase Rep rep AlphaFold DB model + ColabFold model
5.6.2.4
GO:0005524Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0006268OBSOLETE. The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating unpaired template strands for DNA replication. GO:0003678Unwinding of a DNA helix, driven by ATP hydrolysis. +1013 total
No map 0.820 0.51 No Hit 0.0% —
1462 VK055_0834 NLPA lipofamily protein AlphaFold DB model + ColabFold model –
GO:0016020A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
No map 0.820 0.405 No Hit 0.0% —
1463 VK055_0361 putative ferrichrome-binding protein AlphaFold DB model + ColabFold model –
GO:0030288The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall. GO:1901678The directed movement of an iron coordination entity into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
No map 0.820 0.109 No Hit 0.0% —
1464 VK055_3994 uracil DNA glycosylase superfamily protein AlphaFold DB model + ColabFold model
3.2.2.28
GO:0000700Catalysis of the removal of single bases present in mismatches by the cleavage the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar. The reaction releases a free base and leaves an apurinic/apyrimidinic (AP) site. GO:0006285The formation of an AP site, a deoxyribose sugar with a missing base, by DNA glycosylase which recognizes an altered base in DNA and catalyzes its hydrolytic removal. This sugar phosphate is the substrate recognized by the AP endonuclease, which cuts the DNA phosphodiester backbone at the 5' side of the altered site to leave a gap which is subsequently repaired. GO:0005737The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. +36 total
No map 0.819 0.868 Hit 47.5% 6.66e-07
1465 VK055_3718 nitrite reductase, large subunit nirB AlphaFold DB model + ColabFold model –
GO:0016491Catalysis 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:0050660Binding 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:0042128The nitrogen metabolic process that encompasses the uptake of nitrate from the environment and reduction to ammonia, and results in the incorporation of nitrogen derived from nitrate into cellular substances. +912 total
Mapped 2 0.819 0.967 Hit 28.6% 3.81e-23
1466 VK055_3713 ribulose-phosphate 3-epimerase rpe AlphaFold DB model + ColabFold model
5.1.3.1
GO:0016857Catalysis of a reaction that alters the configuration of one or more chiral centers in a carbohydrate molecule. GO:0004750Catalysis of the reaction: D-ribulose 5-phosphate = D-xylulose 5-phosphate. GO:0005975The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. +47 total
Mapped 2 0.819 0.267 Hit 39.5% 1.84e-39
1467 VK055_3238 bacterial regulatory helix-turn-helix, lysR family protein AlphaFold DB model + ColabFold model –
GO:0003700A 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:0006355Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. GO:0032993A macromolecular complex containing both protein and DNA molecules. +14 total
No map 0.819 0.297 No Hit 0.0% —
1468 VK055_3141 transcriptional activator RfaH rfaH ColabFold model –
GO:0140673A chromatin remodeling process that reestablishes the chromatin structure following the passage of RNA polymerase II during transcription elongation, thus preventing cryptic transcription initiation. GO:0006355Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
No map N/A 0.819 No Hit 0.0% —
1469 VK055_2788 methylmalonate-semialdehyde dehydrogenase mmsA AlphaFold DB model + ColabFold model –
GO:0016620Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP. GO:0016491Catalysis 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:0004491Catalysis of the reaction: 2-methyl-3-oxopropanoate + CoA + NAD+ = propanoyl-CoA + hydrogencarbonate + NADH + H+. Can also use malonate (3-oxopropanoate) as a substrate. The reaction occurs in two steps with the decarboxylation process preceding CoA-binding. Bicarbonate rather than CO2 is released as a final product.
Chokepoint 3 0.819 0.542 Hit 44.1% 1.30e-71
1470 VK055_2057 citrate (Si)-synthase gltA2 AlphaFold DB model + ColabFold model –
GO:0005737The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0004108OBSOLETE. Catalysis of the reaction: acetyl-CoA + H2O + oxaloacetate = citrate + CoA, where the acetyl group is added to the si-face of oxaloacetate; acetyl-CoA thus provides the two carbon atoms of the pro-S carboxymethyl group. GO:0006099A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle. +25 total
Mapped 1 0.819 0.183 Hit 22.2% 6.64e-11
1471 VK055_2034 sucrose porin scrY2 AlphaFold DB model + ColabFold model –
GO:0015288Enables the transfer of substances, sized less than 1000 Da, from one side of a membrane to the other. The transmembrane portions of porins consist exclusively of beta-strands which form a beta-barrel. They are found in the outer membranes of Gram-negative bacteria, mitochondria, plastids and possibly acid-fast Gram-positive bacteria. GO:0016020A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0034219The process in which a carbohydrate is transported across a membrane. +58 total
No map 0.819 0.912 No Hit 0.0% —
1472 VK055_1670 glycyl radical enzyme, PFL2/glycerol dehydratasefamily protein AlphaFold DB model + ColabFold model –
GO:0003824Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. GO:0005829The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0016829Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
No map 0.819 0.368 No Hit 0.0% —
1473 VK055_0591 sucrose porin scrY AlphaFold DB model + ColabFold model –
GO:0015288Enables the transfer of substances, sized less than 1000 Da, from one side of a membrane to the other. The transmembrane portions of porins consist exclusively of beta-strands which form a beta-barrel. They are found in the outer membranes of Gram-negative bacteria, mitochondria, plastids and possibly acid-fast Gram-positive bacteria. GO:0016020A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0034219The process in which a carbohydrate is transported across a membrane. +58 total
No map 0.819 0.839 No Hit 0.0% —
1474 VK055_0072 holliday junction DNA helicase RuvB ruvB AlphaFold DB model + ColabFold model
3.6.4.-
GO:0005524Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0006310Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Interchromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction. GO:0006281The 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. +69 total
No map 0.819 0.932 Hit 29.8% 2.70e-07
1475 VK055_4302 GHMP kinase N terminal domain protein AlphaFold DB model + ColabFold model
2.7.1.177
GO:0005524Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0005737The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0016301Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. +14 total
No map 0.818 0.662 No Hit 0.0% —
Page of 204 · 5081 total proteins