amino acid metabolism

Amino Acid Metabolism: Analyzing KEEG Pathways

The microbiome opens the pathway to understanding how the body works more and more every day. With a Thryve Gut Test, we have the ability to analyze your DNA and look deep into many physiological functions carried out by your system on a molecular level. This is even more important when it comes to amino acid metabolism. Thanks to these advancements in technology and following KEGG pathway maps, we can determine how efficiently your body uses amino acids to burn fat, improve mood, and balance hormones. Let’s take a look at the biomarkers for amino acid metabolism and how Thryve Inside can help you feel your best!


What is Amino Acid Metabolism?

Around medical circles, amino acids are called the building blocks of life. They are necessary for everything from protein synthesis to creating the nucleotides that are responsible for our DNA. The production, use, or degradation of amino acids is known as our amino acid metabolism.
Suffice to say, we need this process to work like clockwork so we can function properly. Unfortunately, keeping your amino acid metabolism on track might be a bit tricky. That’s because there are many moving parts when it comes to amino acid metabolism.


How Many Amino Acids Do Humans Need?

Experts believe the human body needs 20 specific amino acids to run optimally [1]. We can only produce eleven of these building blocks. So, the other nine must be consumed through diet.
Typically found in animal products, these nine building blocks are called essential amino acids. Therefore, vegans must take extra precautions to ensure their amino acid metabolism is running sufficiently.
To complicate things even more, not all amino acids going through the same metabolic processes. That’s why testing your DNA with Thryve can help get you amino acid metabolism on track!


Amino Acid Metabolism: Synthesis and Degradation of Each Amino Acid

Amino acid metabolism is one of the most complex systems in KEGG pathways. There are so many roads you can take. Each protein has its own unique requirements for amino acid metabolism, just as they all serve unique functions throughout the body. Here is a quick breakdown of the amino acid metabolism of 20 amino acids.


Alanine Metabolism

This amino acid is produced when the enzyme alanine-glyoxylate transaminase reacts with a coupled interconversion of the amino acid glycine that’s gone through the glyoxylate cycle.
The enzyme alanine—tRNA ligase will bind the new L-alanine molecule to alanyl-tRNA synthetase. Together, these compounds promote protein synthesis.


Uses of Alanine

About 8% of human proteins contain this amino acid in their structure. Our body uses alanine for many things. Perhaps, one of the most important functions of this amino acid is that it serves as energy during an intermittent fasting protocol.
Much like ketosis, this form of energy production takes place in the liver. Alanine gets converted into pyruvate. As a result, it’s used to create glucose via the gluconeogenesis pathway. Otherwise, the pyruvate goes into the Citric Acid cycle to become connective tissues. 


Aspartate Metabolism

Aspartate is a byproduct of a metabolic process known as transamination. During this process, a compound will take an amino acid from a group of compounds to create other amino acids. In the case of aspartate metabolism, enzymes aspartate aminotransferase or amino acid oxidase facilitate transamination from oxaloacetate.
Just like with alanine, Aspartyl-tRNA synthetase couples aspartate to aspartyl tRNA. This interaction generates protein synthesis.


Uses of Aspartate

About 7% of human protein contains this amino acid. It’s essential for creating many molecules related to signaling within the brain. One of its main byproducts is N-acetyl-aspartate. This is the second most abundant compound in the brain [2]. It’s positioned only after the next amino acid derivative.


Glutamate Metabolism

When it comes to amino acid metabolism, biosynthesis and degradation of glutamate are one of the most complex metabolic processes. Glutamate is produced from the amino acid glutamine.
First, the enzyme glutaminase gets activated by phosphate. This new molecule comes into contact with glutamine, causing transamination. The end result is glutamate. 


Uses of Glutamate

Glutamate is an integral component in the gut-brain-axis. On its own, it’s an excitatory neurotransmitter. It helps promote focus and helps us fee; motivated.
Oddly enough, this amino acid is also the precursor to gamma-Aminobutyric acid (GABA) [3]. GABA is an essential neurotransmitter that helps promote a calming effect on the system. Seeing as glutamate is the most abundant molecule in the brain, it’s essential to have this amino acid to prevent stress.


Glycine Metabolism

Our body has many ways to synthesis glycine. Glycine production happens mostly within our liver and kidneys.
It can be created when various enzymes interact with amino acids, including:
• Serine
• Threonine
• Choline
• Hydroxyproline
Just as there many ways to create this amino acid, degradation can go down a number of paths [4]. Typically, it goes through the Glycine Cleavage System (GCS). This metabolic process happens when enzymes are triggered by excess glycine in the system.
Glycine degradation also happens in the presence of the enzyme serine hydroxymethyltransferase. The last amino acid metabolism process that results in glycine degradation is when this building block reacts with the enzyme peroxisomal D-amino acid oxidase. In the end, it creates glyoxylate that promotes carbohydrate synthesis.


Uses of Glycine

As complex as the amino acid metabolism of glycine is, so is its various uses. Glycine plays a monumental role in digestive health. It’s essential for the production of bile acids that make for smoother bowel movements.
It also has potent antioxidant abilities. This amino acid plays a large role in our gut-immunity-axis. Lastly, glycine may help with creating proteins that help with wounds.


Serine Metabolism

Amino acid metabolism is very dependent on other amino acids. Such is the case with serine and glycine metabolism. In fact, as we mentioned, serine derivatives are essential for the degradation of glycine.
Serine is synthesized by a long chain of reactions. The molecule glycerate interacts with the enzyme glycerate kinase. This process yields glycerate 3-phosphate.
When glycerate 3-phosphate comes into contact with phosphoglycerate dehydrogenase, it becomes phosphohydroxypyruvate. Lastly, phosphohydroxypyruvate gets converted into serine when it interacts with phosphoserine transaminase.


Uses of Serine

It takes a lot of work to make serine. However, it’s necessary for so many metabolic functions. This nonessential amino acid is essential for the production of purines and pyrimidines during nucleotide metabolism.
As we discussed, serine is necessary for glycine synthesis. However, you also need serine to create cysteine.


Threonine Metabolism

This amino acid is essential, so you must consume it through diet. Plants and microbes produce this amino acid when the amino acid homoserine interacts with the enzyme α-aspartyl-semialdehyde. This new compound reacts with aspartic acid to create the amino acid. We can consume this amino acid from plant products or animals that eat a lot of it.
Threonine degradation happens when the enzyme threonine dehydrogenase turns the amino acid into pyruvate. Along this metabolic pathway, the new compound undergoes a process known as thiolysis.
In thiolysis, a compound interacts with an alcohol known as thiol. In threonine production, thiolysis is accelerated by coenzyme-A (CoA). The end result is either glycine or acetyl-CoA. Acetyl-CoA is essential for many functions, including fat metabolism. 


Uses of Threonine

This amino acid plays a significant part in our central nervous system. It is tied to many spine-related functions. It has been used to treat incurable conditions, such as multiple sclerosis (MS) and amyotrophic lateral sclerosis (ALS/Lou Gehrig’s Disease).


Cysteine Metabolism

This amino acid is considered semiessential. That means our metabolism can synthesize cysteine, but not enough to support the human body’s needs. There are many metabolic functions that result in cysteine production, including serine, glycine, and threonine metabolism.
Many enzymes play a role in the degradation of cysteine, including:
• Cysteine Dioxygenase
• Amino-Acid Racemase
• Cysteine Lyase
• Cystathionine γ-lyase
• Cysteine—tRNA ligase
• Cysteine Reductase
• Cysteine Transaminase
The end result is a number of molecules essential to several functions, including energy metabolism.


Uses of Cysteine

This amino acid is crucial for protein synthesis. It’s also essential for the production of glutathione. Glutathione is a potent antioxidant that helps boost your immune system and improve your skin health [5].


Methionine Metabolism

Methionine is a sulfur-based essential amino acid that gets metabolized along two pathways. The most well-known is the Methionine Cycle [6]. Here, ATP (our energetic currency) offers up adenosine. Adenosine interacts with sulfur in methionine.
This reaction activates the amino acid’s methyl group, forming S−Adenosyl Methionine (SAMe). From there, the methyl group can become removed from SAMe to create S−Adenosyl Homocysteine (SAH). The body then can covert SAH to create the amino acid homocysteine.
From there, homocysteine goes through a new pathway, called a transsulfuration sequence. Vitamin B6 catalyzes this process, predominantly in the liver. Here the amino acid is metabolized for its benefits.
When cysteine enters the cycle, it can then create the super antioxidant, glutathione. If it does become oxidized, it will instead transform into taurine.
If methionine doesn’t go through these processes, it can be metabolized back into methionine. The most common way for this to happens is when the enzyme methionine synthase commandeers a methyl group from the compound methylated folic acid (MTHF).
With the assistance of Vitamin B12, this new compound then interacts with homocysteine, which diverts back to methionine.
Otherwise, a similar process will take place in the liver. Instead, this time it’s betaine (TMG) that changes homocysteine into methionine instead of MTHF.


Uses of Methionine

Methionine is essential angiogenesis. This process is what promotes the growth of healthy blood cells. However, levels of methionine can’t get too high. An overabundance can be a prelude to cancer. Levels need to remain balanced between methionine and cysteine. That’s why it’s important to analyze your KEGG pathways with Thryve.


Valine, Leucine, and Isoleucine Metabolism 

These are the three essential branch-chained amino acids. These amino acid are synthesized in plants through a series of events that produces pyruvic acid. The process creates an intermediate known as α-ketoisovalerate.
From there, α-ketoisovalerate interacts with one of the following enzymes:
• Acetolactate Synthase
• Acetohydroxy Acid Isomeroreductase
• Dihydroxyacid Dehydratase
• Valine Aminotransferase
Catabolizing these branch-chained amino acids is different than the other 20. Much of this process transpires within muscles. The two main enzymes to kickstart the process for all three are aminotransferase and dehydrogenase. These findings are interesting because valine is glucogenic, leucine is ketogenic, and isoleucine is both.


Uses of Branch-Chained Amino Acids

Branched-chained amino acids are crucial for hematopoietic stem cell self-renewal. This autonomous process sees news cells push healthy ones out into the bloodstream so they can do their work while the next batch grows. Unfortunately, too much valine can lead to insulin resistance [7]. So, it’s imperative you know how your valine levels look.


Lysine Metabolism

Plants, bacteria, and algae synthesize this essential amino acid in two different ways. The first is the diaminopimelate pathway. This process includes aspartate, much like the production of threonine.
Otherwise, it heads down the α-aminoadipate (AAA) pathway. This process is catalyzed by members of the glutamate family. It also is a common metabolic pathway for yeast species. Both pathways have their own array of enzymes to carry out these complex processes.
The most common way to catabolize lysine is through the saccharopine pathway. This process usually transpires within mitochondria inside the liver. First, the enzyme α-aminoadipic semialdehyde synthase (AASS) releases lysine-ketoglutarate reductase (LKR) to break down the lysine.
When α-ketoglutarate enters the scene, it produces saccharopine, thanks to NADPH donating a proton. Next, saccharopine dehydrogenase (SDH) dehydrates the compound. In the end, you get either AASS or glutamate.
These molecules then get broken down further into α-ketoadipate. Eventually, it continues to degrade until it reaches glutaryl-CoA. Inevitably, glutaryl-CoA gets oxidated and decarboxylated to become acetyl-CoA. This metabolite is essential for carbohydrate metabolism.


Uses of Lysine

Lysine is used for so many vital functions. It plays a pivotal role in the production of protein. However, it also cross-links collagen peptides. Therefore, lysine is a must for all-natural skincare.
This essential amino acid is also required for the uptake of nutrients. Low level of lysine can leave you susceptible to anemia. However, too much may lead to mental health issues.


Analyze Your Amino Acid Metabolism

Want to make sure your body is getting the protein it needs? The best way to find out if this is happening is to get your gut tested. Using KEGG pathways, we can map out where the deficiencies are. That way, we can get your gut health on the right track. From there, you will metabolize amino acids efficiently to create healthy blood cells, hair follicles, and muscle!


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[1] National Research Council (US) Subcommittee on the Tenth Edition of the Recommended Dietary Allowances. Recommended Dietary Allowances: 10th Edition. Washington (DC): National Academies Press (US); 1989. 6, Protein and Amino Acids. Available from:
[2] Tsai, G, and J T Coyle. “N-Acetylaspartate in Neuropsychiatric Disorders.” Progress in Neurobiology, U.S. National Library of Medicine, Aug. 1995,
[3] Petroff, Ognen A C. “GABA and Glutamate in the Human Brain.” The Neuroscientist : a Review Journal Bringing Neurobiology, Neurology and Psychiatry, U.S. National Library of Medicine, Dec. 2002,
[4] Wang, Weiwei, et al. “Glycine Metabolism in Animals and Humans: Implications for Nutrition and Health.” Amino Acids, U.S. National Library of Medicine, Sept. 2013,
[5] Kerksick, C., & Willoughby, D. (2005). The antioxidant role of glutathione and N-acetyl-cysteine supplements and exercise-induced oxidative stress. Journal of the International Society of Sports Nutrition, 2(2), 38–44.
[6] Creative Proteomics. “Methionine Cycle Analysis Service.” Creative Proteomics, 1 May 2020,
[7] Liao, Xiaoyu, et al. “A High Level of Circulating Valine Is a Biomarker for Type 2 Diabetes and Associated with the Hypoglycemic Effect of Sitagliptin.” Mediators of Inflammation, Hindawi, 11 Nov. 2019,

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