PathWhiz

PathWhiz ID	Pathway	Meta Data
PW002349 View Pathway	protein Operon: Nucleotide and Deoxyribonucleotide Catabolism Escherichia coli The nucleotide and deoxyribonucleotide operon is a polycistronic operon consisting of the genes DeoC, DeoA, DeoB and DeoD. This operon's transcription is activated by Fis DNA-binding transcriptional dual regulator binding to a -102 bp site off the promoter. This operon can also be activated by having CRP-cAMP DNA-binding transcriptional dual regulator binding either to -93.5 or -40.5. The repression of the operon's transcription can be controlled by multiple sites upsteam the promoter: - DeoR (DeoR DNA-binding transcriptional repressor) -887, -309, -8 for promoter deop2 and -609, -8, and 269 for promoter deop1 - CRP-cAMP DNA-binding transcriptional dual regulator binding at -93.5 for promoter deop2 - CytR (CytR DNA-binding transcriptional repressor) -87.5, -70.5, -61 for promoter deop2 -ModE-MoO42- DNA-binding transcriptional dual regulator -35 for promoter deop2 BioPAX SVG SBGN SBML PWML All files (.zip)	Creator: miguel ramirez Created On: November 12, 2015 at 11:28 Last Updated: November 12, 2015 at 11:28
PW002350 View Pathway	protein Operon: Nucleotide and Deoxyribonucleotide Catabolism II Escherichia coli The nucleotide and deoxyribonucleotide operon is a polycistronic operon consisting of the genes DeoC, DeoA, DeoB and DeoD. This operon's transcription is activated by Fis DNA-binding transcriptional dual regulator binding to a -102 bp site off the promoter. This operon can also be activated by having CRP-cAMP DNA-binding transcriptional dual regulator binding either to -93.5 or -40.5. The repression of the operon's transcription can be controlled by multiple sites upsteam the promoter: - DeoR (DeoR DNA-binding transcriptional repressor) -887, -309, -8 for promoter deop2 and -609, -8, and 269 for promoter deop1 - CRP-cAMP DNA-binding transcriptional dual regulator binding at -93.5 for promoter deop2 - CytR (CytR DNA-binding transcriptional repressor) -87.5, -70.5, -61 for promoter deop2 -ModE-MoO42- DNA-binding transcriptional dual regulator -35 for promoter deop2 BioPAX SVG SBGN SBML PWML All files (.zip)	Creator: miguel ramirez Created On: November 12, 2015 at 14:34 Last Updated: November 12, 2015 at 14:34
PW002351 View Pathway	protein Operon: Nucleotide and Deoxyribonucleotide Catabolism III Escherichia coli The nucleotide and deoxyribonucleotide operon is a polycistronic operon consisting of the genes DeoC, DeoA, DeoB and DeoD. This operon's transcription is activated by Fis DNA-binding transcriptional dual regulator binding to a -102 bp site off the promoter. This operon can also be activated by having CRP-cAMP DNA-binding transcriptional dual regulator binding either to -93.5 or -40.5. The repression of the operon's transcription can be controlled by multiple sites upsteam the promoter: - DeoR (DeoR DNA-binding transcriptional repressor) -887, -309, -8 for promoter deop2 and -609, -8, and 269 for promoter deop1 - CRP-cAMP DNA-binding transcriptional dual regulator binding at -93.5 for promoter deop2 - CytR (CytR DNA-binding transcriptional repressor) -87.5, -70.5, -61 for promoter deop2 -ModE-MoO42- DNA-binding transcriptional dual regulator -35 for promoter deop2 BioPAX SVG SBGN SBML PWML All files (.zip)	Creator: miguel ramirez Created On: November 12, 2015 at 14:51 Last Updated: November 12, 2015 at 14:51
PW002352 View Pathway	protein Operon: Nucleotide and Deoxyribonucleotide Catabolism Inactivation Escherichia coli The nucleotide and deoxyribonucleotide operon is a polycistronic operon consisting of the genes DeoC, DeoA, DeoB and DeoD. DeoC encodes for a ribose-1,5-bisphosphate isomerase, DeoA encodes for a deoxyribose-5-phosphate aldolase, DeoB encodes for a ribose-5-phosphate isomerase and DeoD encodes for a deoxyribose-5-phosphate isomerase. This operon's transcription is activated by Fis DNA-binding transcriptional dual regulator binding to a -102 bp site off the promoter, thus enhancing RNA polymerase binding. This operon can also be activated by having CRP-cAMP DNA-binding transcriptional dual regulator binding either to -93.5 or -40.5. The repression of the operon's transcription can be controlled by multiple sites upsteam the promoter. DeoR (DeoR DNA-binding transcriptional repressor) which binds to -887, -309, -8 sites of the promoter deoP2, preventing RNA polymerase from initiating transcription. For promoter deoP1, DeoR binds at -609, -8, 269 sites, repressing transcription by blocking access to the promoter. CRP-cAMP DNA-binding transcriptional dual regulator binds at -93.5 for promoter deop2, CytR (CytR DNA-binding transcriptional repressor) binds to -87.5, -70.5, -61 for promoter deop2 and ModE-MoO42- DNA-binding transcriptional dual regulator binds to -35 for promoter deop2 BioPAX SVG SBGN SBML PWML All files (.zip)	Creator: miguel ramirez Created On: November 12, 2015 at 15:26 Last Updated: November 12, 2015 at 15:26
PW002266 View Pathway	protein Operon: Periplasmic Binding Protein Inner Membrane Protein Controlled by araC Escherichia coli The araFGH operon in E. coli contains three genes that encode the proteins that make up an ABC transporter complex involved in the transport of arabinose into the cell. The operon can be activated by the cAMP-activated global transcriptional regulator CRP (CAP), which in turn is activated by the binding of cAMP to the protein. Activated CRP can bind to DNA upstream of the promoter, and can interacrt with RNA polymerase, activating transcription of the operon. The binding of cAMP occurs when the levels are high, typically in instances where glucose is lacking in the cell. The operon can also be activated by the binding of the AraC family transcriptional regulator. AraC is activated in the presence of alpha-L-arabinopyranose, which binds to the protein and allows it to bind more strongly to its binding sites upstream of the CRP binding site. In this operon, AraC can bind in four different locations, and allow the operon to be transcribed. The first gene in the operon, araF, encodes an L-arabinose-binding periplasmic protein, which is one of the five subunits making up the arabinose transporter complex. The second gene, araG, encodes the arabinose import ATP-binding protein AraG, which is likely responsible for the ATP coupling involved in the transport of arabinose. Two AraG subunits are involved in the transporter complex. The final gene, araH, encodes the L-arabinose transport system permease protein AraH, which is likely involved in the translocation of arabinose across the cell membrane. Two AraH subunits are involved in the transporter complex. BioPAX SVG SBGN SBML PWML All files (.zip)	Creator: miguel ramirez Created On: October 29, 2015 at 14:54 Last Updated: October 29, 2015 at 14:54
PW002328 View Pathway	protein Operon: Phosphonate Utilization Escherichia coli The phosphonate utilization operon is a polycistronic operon consist of the genes: phnC, phnD, phnE, phnF, phnG, phnH, phnI, phnJ, phnK, phnL, phnM, phnN,phnO and phnQ. This operon's transcription is activated by a PhoB-Phosphorylated DNA-binding transcriptional dual regulator binding on an unspecified binding site. BioPAX SVG SBGN SBML PWML All files (.zip)	Creator: miguel ramirez Created On: November 09, 2015 at 11:47 Last Updated: November 09, 2015 at 11:47
PW002279 View Pathway	signaling Operon: Pyridoxal 5'-Phosphate Biosynthesis Escherichia coli The rnc-era-recO-pdxJ-acpS operon in E. coli contains five genes which encode various proteins. The operon can be transcribed in its entirety, or it can be transcribed from a second promoter before pdxJ, in which case only pdxJ and acpS are transcribed. There are no currently known activators or inhibitors of this operon. The first gene in the operon, rnc, encodes ribonuclease 3, an enzyme that digests dsRNA, and is involved in the formation of 16S rRNA and 23S rRNA. The second gene, era, encodes a GTPase that is involved in many cellular processes such as the regulation of the cell cycle and metabolism, and binds GDP and GTP. It is also used as a chapeone for formation of 16S rRNA and ribosomal subunit formation. The third gene, recO, encodes the DNA repair protein RecO, which is involved in DNA repair. It is also present in the RecFOR pathway that repairs bacterial DNA via homologous recombination. In this pathway, along with the RecF DNA replication and repair protein, and RecR recombination protein. The fourth gene, pdxJ, encodes pyridoxine 5'-synthase, which catalyzes formation of the ring of pyridoxine 5'-phosphate (PNP) from 1-deoxy-D-xylulose 5-phosphate (DXP) and 3-amino-2-oxopropyl phosphate. PNP is then used in cofactor biosynthesis. The final gene, acpS, encodes holo-[acyl-carrier-protein] synthase, an enzyme that transfers a 4'-phosphopanthethine from CoA to an acyl-carrier protein BioPAX SVG SBGN SBML PWML All files (.zip)	Creator: miguel ramirez Created On: November 03, 2015 at 10:28 Last Updated: November 03, 2015 at 10:28
PW002340 View Pathway	signaling Operon: Pyrimidine Biosynthesis Escherichia coli The pyrimidine biosynthesis operon consists of the genes pyrB and pyrI. This is a bicistronic operon. The operon transcription is negatively regulated by the intracellullar levels of UTP. The higher the UTP levels, the less expressiong of the operon BioPAX SVG SBGN SBML PWML All files (.zip)	Creator: miguel ramirez Created On: November 10, 2015 at 14:12 Last Updated: November 10, 2015 at 14:12
PW002341 View Pathway	signaling Operon: Pyrimidine Biosynthesis Inactivation Escherichia coli The pyrimidine biosynthesis operon consists of the genes pyrB and pyrI. This is a bicistronic operon. The operon transcription is negatively regulated by the intracellular levels of UTP. The higher the UTP levels, the less expression of the operon. High concentrations of UTP indicate sufficient pyrimidine levels hence UTP binds to the regulatory subunit of ATCase ( catalyzes the first committed step in pyrimidine biosynthesis), resulting in a conformational change and reduced activity. High UTP levels also repress the transcription of this operon through the pyrl regulatory protein, which binds to the promoter region of the pyr operon, preventing RNA polymerase from binding and initiating transcription. BioPAX SVG SBGN SBML PWML All files (.zip)	Creator: miguel ramirez Created On: November 10, 2015 at 14:38 Last Updated: November 10, 2015 at 14:38
PW001876 View Pathway	signaling Operon: Redox Process Escherichia coli The fixABCX operon in E. coli contains four genes which encode for proteins that are potentially used in the anaerobic metabolism of carnitine, similar to those in the caiTABCDE operon. This operon can be activated by the cAMP-activated global transcriptional regulator CRP. Both the fix and cai operons are expressed in anaerobic conditions to metabolize carnitine, and they are found very close to one another in the genome, in opposite directions. The first gene, fixA, encodes for a protein which, with the protein produced by fixB, form a heterodimer protein. This protein may work as an electron transfer proteins, due to their similarity to electron transport flavoproteins in mammals. The third gene, fixC, encodes a protein that may be part of an electron transfer system in the anaerobic metabolism of carnitine. The final gene, fixX, encodes a ferredoxin-like protein involved in carnitine reduction. BioPAX SVG SBGN SBML PWML All files (.zip)	Creator: miguel ramirez Created On: September 08, 2015 at 17:24 Last Updated: September 08, 2015 at 17:24