# ---
# jupyter:
#   jupytext:
#     text_representation:
#       extension: .py
#       format_name: light
#       format_version: '1.5'
#       jupytext_version: 1.14.4
#   kernelspec:
#     display_name: Python 3
#     language: python
#     name: python3
# ---

# +
from Bio import Entrez

#Entrez.esearch(db,id,rettype,retmode)
#Entrez.efetch(db,id,rettype,retmode)

Entrez.email = '<EMAIL>'
handle = Entrez.esearch(db='gene',
                       term='fumarase homo sapiens',
                       sort='relevance',
                       idtype='acc')

#print(handle.read())

fastafile = ''
for i in Entrez.read(handle)['IdList']:
    h = Entrez.efetch(db='gene',id=i, rettype='fasta', retmode='text')
    seq = h.read()
    print(seq)
    fastafile = seq
#     if i == 0:
#         fastafile = seq
#         print('yea')
#         break

print(fastafile)

# +
from Bio import SeqIO

for lines in fastafile:
    print(lines)

# +
#Enzymes

#GLycolysis:(1) triosephosphate isomerase, (2) phosphoglycerate kinase, 
#(3)Phosphoenolpyruvate carboxylase, (4) Pyruvate kinase (also in pentose phosphate)

#Pentose phosphate:(1) Glucose-6-phosphate dehydrogenase (also in glycolysis),
#(2) Gluconolactonase, (3) 6-phosphogluconate dehydrogenase
#(4) transaldolase

#TCA cyle:(3)Malate dehydrogenase (also in glycolysis), (2) Fumarase ,  
# (4)Citrate synthase (1)Succinate dehydrogenase

# +
Enzyme Function

GLycolysis:(1) triosephosphate isomerase
catalyzes the reversible interconversion of the triose 
phosphate isomers dihydroxyacetone phosphate and D-glyceraldehyde 3-phosphate
EC 5.3.1.1

(2) phosphoglycerate kinase 
catalyzes the reversible transfer of a phosphate group from 1,3-bisphosphoglycerate to ADP producing 3-phosphoglycerate and ATP
EC 2.7.2.3

(3)Phosphoenolpyruvate carboxylase, 
an enzyme in the family of carboxy-lyases found in plants and some bacteria that catalyzes the addition of bicarbonate (HCO3−) to phosphoenolpyruvate (PEP) to form the four-carbon compound oxaloacetate and inorganic phosphate
EC 4.1.1.31   

(4) Pyruvate kinase (also in pentose phosphate)
It catalyzes the transfer of a phosphate group from phosphoenolpyruvate to adenosine diphosphate, yielding one molecule of pyruvate and one molecule of ATP.
EC 2.7.1.40

------------------#

Pentose phosphate:

(1) Glucose-6-phosphate dehydrogenase (also in glycolysis),
D-glucose 6-phosphate + NADP⁺ ⇌ 6-phospho-D-glucono-1,5-lactone + NADPH + H⁺
EC 1.1.1.49

(2) Gluconolactonase, 
This enzyme belongs to the family of hydrolases, specifically those acting on carboxylic ester bonds. 
EC 3.1.1.17

(3) 6-phosphogluconate dehydrogenase
It forms ribulose 5-phosphate from 6-phosphogluconate. It is an oxidative carboxylase that catalyses the decarboxylating reduction of 6-phosphogluconate into ribulose 5-phosphate in the presence of NADP
EC 1.1.1.44

(4) transaldolase
transaldolase:catalyzes the following reaction sedoheptulose 7-phosphate + glyceraldehyde 3-phosphate erythrose 4-phosphate + fructose 6-phosphate.
EC 2.2.1.2

------------------#

#TCA Cycle:

(1) Succinate dehydrogenase
This enzyme catalyzes the oxidation of succinate to fumarate with the reduction of ubiquinone to ubiquinol
EC 1.3.5.1

(2) Fumarase
It catalyzes the reversible hydration/dehydration of fumarate to malate
EC 4.2.1.2

(3) Malate dehydrogenase (also in glycolysis)
It reversibly catalyzes the oxidation of malate to oxaloacetate using the reduction of NAD+ to NADH.
EC 1.1.1.37

(4)Citrate synthase
It catalyzes the condensation reaction of the two-carbon acetate residue from acetyl coenzyme A and a molecule of four-carbon oxaloacetate to form the six-carbon citrate
EC 2.3.3.1

### TCA cycle - explanation from wikipedia


# +
# Gene description 
#Humans
#GLycolysis:(1) triosephosphate isomerase,
# This gene encodes an enzyme, consisting of two identical proteins, which catalyzes the isomerization of glyceraldehydes 3-phosphate (G3P) and dihydroxy-acetone phosphate (DHAP) in glycolysis and gluconeogenesis. Mutations in this gene are associated with triosephosphate isomerase deficiency. Pseudogenes have been identified on chromosomes 1, 4, 6 and 7

#(2) phosphoglycerate kinase 
#The protein encoded by this gene is a glycolytic enzyme that catalyzes the conversion of 1,3-diphosphoglycerate to 3-phosphoglycerate. The encoded protein may also act as a cofactor for polymerase alpha. Additionally, this protein is secreted by tumor cells where it participates in angiogenesis by functioning to reduce disulfide bonds in the serine protease, plasmin, which consequently leads to the release of the tumor blood vessel inhibitor angiostatin. The encoded protein has been identified as a moonlighting protein based on its ability to perform mechanistically distinct functions. 

#(3)Phosphoenolpyruvate carboxylase 
#This gene is a main control point for the regulation of gluconeogenesis. The cytosolic enzyme encoded by this gene, along with GTP, catalyzes the formation of phosphoenolpyruvate from oxaloacetate, with the release of carbon dioxide and GDP. The expression of this gene can be regulated by insulin, glucocorticoids, glucagon, cAMP, and diet. 

#(4) Pyruvate kinase (also in pentose phosphate)
# This gene encodes a protein involved in glycolysis. The encoded protein is a pyruvate kinase that catalyzes the transfer of a phosphoryl group from phosphoenolpyruvate to ADP, generating ATP and pyruvate. This protein has been shown to interact with thyroid hormone and may mediate cellular metabolic effects induced by thyroid hormones. This protein has been found to bind Opa protein, a bacterial outer membrane protein involved in gonococcal adherence to and invasion of human cells, suggesting a role of this protein in bacterial pathogenesis. 



#Pentose phosphate:
#(1) Glucose-6-phosphate dehydrogenase (also in glycolysis)
# This gene encodes glucose-6-phosphate dehydrogenase. This protein is a cytosolic enzyme encoded by a housekeeping X-linked gene whose main function is to produce NADPH, a key electron donor in the defense against oxidizing agents and in reductive biosynthetic reactions. G6PD is remarkable for its genetic diversity. Many variants of G6PD, mostly produced from missense mutations, have been described with wide ranging levels of enzyme activity and associated clinical symptoms.

#(2) Gluconolactonase
#protein encoded by this gene is a highly conserved, calcium-binding protein, that is preferentially expressed in the liver and kidney. It may have an important role in calcium homeostasis. Studies in rat indicate that this protein may also play a role in aging, as it shows age-associated down-regulation. This gene is part of a gene cluster on chromosome Xp11.3-Xp11.23.

#(3) 6-phosphogluconate dehydrogenase
# This gene, which encodes a member of the serine/threonine kinase family, regulates cell polarity and functions as a tumor suppressor. Mutations in this gene have been associated with Peutz-Jeghers syndrome, an autosomal dominant disorder characterized by the growth of polyps in the gastrointestinal tract, pigmented macules on the skin and mouth, and other neoplasms

#(4) transaldolase
# Transaldolase 1 is a key enzyme of the nonoxidative pentose phosphate pathway providing ribose-5-phosphate for nucleic acid synthesis and NADPH for lipid biosynthesis. This pathway can also maintain glutathione at a reduced state and thus protect sulfhydryl groups and cellular integrity from oxygen radicals. The functional gene of transaldolase 1 is located on chromosome 11 and a pseudogene is identified on chromosome 1 but there are conflicting map locations. The second and third exon of this gene were developed by insertion of a retrotransposable element. This gene is thought to be involved in multiple sclerosis


#TCA Cycle:
(1) Succinate dehydrogenase
des1

(2) Fumarase

(3) Malate dehydrogenase (also in glycolysis)

(4)Citrate synthase

#------------------#

#E coli
# GLycolysis:
# (1)triosephosphate isomerase
#Binds TrxA 

#(2) phosphoglycerate kinase 
#Phosphoglycerate kinase is one of the proteins induced by anaerobiosis. 


#(3)Phosphoenolpyruvate carboxylase 
#Mutant has reduced growth rate with little acetate excreation, decrease glucose consumption and a decreased carbon dioxide evolution rate.


#(4) Pyruvate kinase (also in pentose phosphate)
#Pyruvate kinase I and pyruvate kinase II differ in physical and chemical properties as well as in their kinetic behavior


#Pentose phosphate:
#(1) Glucose-6-phosphate dehydrogenase (also in glycolysis),
# ATP-regulated binding and release of polypeptide substrates. [More information is available at EcoGene: EG10241]. Hsc56 exhibits specificity toward Hsc62, as Hsc56 does not activate DnaK or Hsc66 ATPase activity


#(2) Gluconolactonase  may be an issue did no show in database
#


#(3) 6-phosphogluconate dehydrogenase
# A null mutation in the gnd gene encoding 6-phosphogluconate dehydrogenase does not affect the growth rate significantly. [More information is available at EcoCyc: EG10411].


#(4) transaldolase
#Transaldolase is an enzyme of the pentose phosphate pathway, where it catalyzes the reversible interconversion of glyceraldehyde-3-phosphate and sedoheptulose-7-phosphate to fructose-6-phosphate and erythrose-4-phosphate


#TCA Cycle:
(1) Succinate dehydrogenase

(2) Fumarase

(3) Malate dehydrogenase (also in glycolysis)

(4)Citrate synthase


#------------------#

Drosphilia

GLycolysis:
(1)triosephosphate isomerase

(2) phosphoglycerate kinase 

(3)Phosphoenolpyruvate carboxylase 

(4) Pyruvate kinase (also in pentose phosphate)



Pentose phosphate:
(1) Glucose-6-phosphate dehydrogenase (also in glycolysis),

(2) Gluconolactonase  may be an issue did no show in database

(3) 6-phosphogluconate dehydrogenase

(4) transaldolase



TCA Cycle:
(1) Succinate dehydrogenase

(2) Fumarase

(3) Malate dehydrogenase (also in glycolysis)

(4)Citrate synthase






StarcoderdataJupyterScriptsDedupFiltered