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.
4301 VK055_1539 3-deoxy-D-manno-octulosonate cytidylyltransferase kdsB Experimental + ColabFold model
2.7.7.38
GO:0008690Catalysis of the reaction: CTP + 3-deoxy-D-manno-octulosonate = diphosphate + CMP-3-deoxy-D-manno-octulosonate. GO:0005829The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0016020A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. +25 total
Chokepoint 1 0.105 0.415 No Hit 0.0% —
4302 VK055_0183 type IV/VI secretion system, DotU family domain protein AlphaFold DB model + ColabFold model – – No map 0.105 0.83 No Hit 0.0% —
4303 VK055_4902 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:0003677Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
No map 0.104 0.358 No Hit 0.0% —
4304 VK055_4460 toxin SymE, type I toxin-antitoxin system familyprotein AlphaFold DB model + ColabFold model –
GO:0016788Catalysis of the hydrolysis of any ester bond. GO:0016070The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. GO:0003723Binding to an RNA molecule or a portion thereof. +14 total
No map N/A 0.104 No Hit 0.0% —
4305 VK055_3865 RNA polymerase sigma-54 factor rpoN Experimental + ColabFold model –
GO:0006352The 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. GO:0016987Sigma 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:0003677Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). +14 total
No map 0.104 0.954 No Hit 0.0% —
4306 VK055_3744 dsrE/DsrF-like family protein AlphaFold DB model + ColabFold model
2.8.1.-
GO:0016783Catalysis of the transfer of sulfur atoms from one compound (donor) to another (acceptor). GO:0008033The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group. GO:0005737The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. +36 total
No map 0.104 0.483 No Hit 0.0% —
4307 VK055_0349 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:0000976Binding to a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon.
No map 0.104 0.573 No Hit 0.0% —
4308 VK055_4195 urease subunit beta ureB2 AlphaFold DB model + ColabFold model
3.5.1.5
GO:0043419The chemical reactions and pathways resulting in the breakdown of urea, the water soluble compound O=C-(NH2)2. GO:0035550A multiprotein nickel-containing complex that possesses urease activity (catalysis of the hydrolysis of urea to ammonia and carbon dioxide). GO:0009039Catalysis of the reaction: urea + 2 H2O + H+ = hydrogencarbonate + 2 NH4+.
Mapped 2 N/A 0.103 No Hit 0.0% —
4309 VK055_3773 ribosomal protein L30 rpmD AlphaFold DB model + ColabFold model –
GO:0003735The action of a molecule that contributes to the structural integrity of the ribosome. GO:0006412The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome. GO:0015934The larger of the two subunits of a ribosome. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). +14 total
No map N/A 0.103 No Hit 0.0% —
4310 VK055_2154 ATP-dependent Clp endopeptidase, proteolytic subunit ClpP clpP AlphaFold DB model + ColabFold model
3.4.21.92
GO:0004252Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine). GO:0006508The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds. GO:0004176Catalysis of the hydrolysis of peptide bonds, driven by ATP hydrolysis. +47 total
No map 0.103 0.576 Hit 56.2% 5.98e-81
4311 VK055_4718 cobalamin adenosyltransferase family protein AlphaFold DB model + ColabFold model –
GO:0008817Catalysis of the reaction: 2 ATP + 2 corrinoid + reduced [electron-transfer flavoprotein] = 2 adenosylcorrinoid + 3 H+ + oxidized [electron-transfer flavoprotein] + 2 triphosphate. The corrinoid can be cob(II)yrinate a,c diamide, cob(II)inamide or cob(II)alamin. GO:0005524Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0009236The chemical reactions and pathways resulting in the formation of cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom. +14 total
No map 0.102 0.413 No Hit 0.0% —
4312 VK055_4623 regulatory protein P-II for glutamine synthetase glnB AlphaFold DB model + ColabFold model –
GO:0006808Any process that modulates the frequency, rate or extent of nitrogen utilization. GO:0030234A molecular function regulator that modulates a catalytic activity. GO:0005829The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. +14 total
No map N/A 0.102 No Hit 0.0% —
4313 VK055_4615 helix-turn-helix domain, rpiR 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:1901135The chemical reactions and pathways involving carbohydrate derivative. GO:0097367Binding to a carbohydrate derivative. +14 total
No map 0.102 0.44 No Hit 0.0% —
4314 VK055_4025 tolC outer membrane channel tolC AlphaFold DB model + ColabFold model –
GO:0019867The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites. GO:0015562Enables the transfer of a specific substance or related group of substances from the inside of the cell to the outside of the cell across a membrane. GO:0055085The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
No map 0.102 0.397 No Hit 0.0% —
4315 VK055_1793 succinyl-CoA synthetase, alpha subunit sucD AlphaFold DB model + ColabFold model
6.2.1.5
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:0009361A heterodimeric enzyme complex, composed of an alpha and beta chain, most usually found in (but not limited to) bacteria. Functions in the TCA cycle, hydrolyzing succinyl-CoA into succinate and CoA, thereby forming ATP. GO:0000166Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. +36 total
Mapped 3 0.102 0.867 Hit 68.7% 5.63e-64
4316 VK055_0721 putative gamma-glutamyltransferase ywrD Experimental + ColabFold model – – Mapped 13 0.102 0.734 Hit 30.5% 1.52e-07
4317 VK055_0357 hypothetical protein ColabFold model – – No map N/A 0.102 No Hit 0.0% —
4318 VK055_1107 type VI secretion system protein impB AlphaFold DB model + ColabFold model – – No map 0.101 0.14 No Hit 0.0% —
4319 VK055_1072 binding-protein-dependent transport system innermembrane component family 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: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. +14 total
No map 0.101 0.586 No Hit 0.0% —
4320 VK055_0451 putative inner membrane protein AlphaFold DB model + ColabFold model – – No map N/A 0.101 No Hit 0.0% —
4321 VK055_5067 hypothetical protein AlphaFold DB model + ColabFold model – – No map N/A 0.1 No Hit 0.0% —
4322 VK055_2314 crl transcriptional regulator AlphaFold DB model + ColabFold model –
GO:0045893Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription. GO:0005737The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0003677Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
No map N/A 0.1 No Hit 0.0% —
4323 VK055_2284 putative transcriptional regulator ColabFold model – – No map N/A 0.1 No Hit 0.0% —
4324 VK055_0973 methylated-DNA-[]-cysteine S-methyltransferase family protein AlphaFold DB model + ColabFold model
2.1.1.63
GO:0003908Catalysis of the reaction: DNA (containing 6-O-methylguanine) + (protein)-L-cysteine = DNA (without 6-O-methylguanine) + protein S-methyl-L-cysteine. 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: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. +36 total
Mapped 2 0.100 0.069 Hit 52.4% 1.31e-21
4325 VK055_0797 sulfite exporter TauE/SafE family 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:0005886The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
No map 0.100 0.96 No Hit 0.0% —
Page of 204 · 5081 total proteins