Experiment set4IT094 for Kangiella aquimarina DSM 16071

marine_broth_2216 with Sodium nitrite 20 mM

Group: stress
Media: marine_broth_2216 + Sodium nitrite (20 mM)
Culturing: Kang_ML4_MIT, Aerobic, at 30 (C)
By: Sean Kearney on 3/10/21
Media components: 5 g/L Bacto Peptone, 1 g/L Yeast Extract, 0.1 g/L Ferric citrate, 19.45 g/L Sodium Chloride, 5.9 g/L Magnesium chloride hexahydrate, 3.24 g/L Magnesium sulfate, 1.8 g/L Calcium chloride, 0.55 g/L Potassium Chloride, 0.16 g/L Sodium bicarbonate, 0.08 g/L Potassium bromide, 34 mg/L Strontium chloride, 22 mg/L Boric Acid, 4 mg/L Sodium metasilicate, 2.4 mg/L sodium fluoride, 8 mg/L Disodium phosphate

Specific Phenotypes

For 8 genes in this experiment

For stress Sodium nitrite in Kangiella aquimarina DSM 16071

For stress Sodium nitrite across organisms

SEED Subsystems

Subsystem	#Specific
Nitrosative stress	3
Catechol branch of beta-ketoadipate pathway	2
Denitrification	2
Leucine Degradation and HMG-CoA Metabolism	2
Protocatechuate branch of beta-ketoadipate pathway	2
Serine-glyoxylate cycle	2
Flavohaemoglobin	1
Na(+) H(+) antiporter	1
Oxidative stress	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
cAMP signaling in bacteria	1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

• Pyruvate metabolism
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Synthesis and degradation of ketone bodies
• Purine metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• 1- and 2-Methylnaphthalene degradation
• Butanoate metabolism
• Carbon fixation in photosynthetic organisms
• Nitrogen metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-malate degradation II	1	1	1
malate/L-aspartate shuttle pathway	2	2	1
ketolysis	3	2	1
L-carnitine degradation II	3	1	1
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	3	2
chitin deacetylation	4	2	1
gluconeogenesis I	13	11	3
nitrate reduction VII (denitrification)	5	2	1
nitrate reduction I (denitrification)	5	2	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	5	2
TCA cycle VIII (Chlamydia)	6	6	1
glyoxylate cycle	6	4	1
methylgallate degradation	6	2	1
nitrifier denitrification	6	2	1
anaerobic energy metabolism (invertebrates, cytosol)	7	4	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	6	2
incomplete reductive TCA cycle	7	3	1
pyruvate fermentation to propanoate I	7	2	1
protocatechuate degradation I (meta-cleavage pathway)	8	3	1
superpathway of anaerobic energy metabolism (invertebrates)	17	9	2
TCA cycle IV (2-oxoglutarate decarboxylase)	9	8	1
TCA cycle V (2-oxoglutarate synthase)	9	8	1
TCA cycle II (plants and fungi)	9	8	1
TCA cycle VI (Helicobacter)	9	6	1
TCA cycle I (prokaryotic)	10	9	1
TCA cycle III (animals)	10	8	1
anaerobic energy metabolism (invertebrates, mitochondrial)	10	5	1
superpathway of vanillin and vanillate degradation	10	3	1
reductive TCA cycle I	11	6	1
L-glutamate degradation VIII (to propanoate)	11	2	1
superpathway of glyoxylate bypass and TCA	12	9	1
gluconeogenesis III	12	6	1
reductive TCA cycle II	12	6	1
syringate degradation	12	3	1
formaldehyde assimilation I (serine pathway)	13	4	1
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	3	1
superpathway of glyoxylate cycle and fatty acid degradation	14	10	1
mixed acid fermentation	16	9	1
methylaspartate cycle	19	11	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	19	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	19	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	16	1