superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation

Thorpe C, Kim JP. Structure and mechanism of action of the Acyl-CoA dehydrogenases 1. The FASEB Journal. 1995 Jun;9(9):718–25. doi: 10.1096/fasebj.9.9.7601336.; Hauge JG, Crane FL, Beinert H. ON THE MECHANISM OF DEHYDROGENATION OF FATTY ACYL DERIVATIVES OF COENZYME A. Journal of Biological Chemistry. 1956 Apr;219(2):727–33. doi: 10.1016/s0021-9258(18)65732-1.; Green DE, Mii S, Mahler HR, Bock RM. STUDIES ON THE FATTY ACID OXIDIZING SYSTEM OF ANIMAL TISSUES. Journal of Biological Chemistry. 1954 Jan;206(1):1–12. doi: 10.1016/s0021-9258(18)71290-8.; MAHLER HR. Studies on the fatty acid oxidizing system of animal tissues. IV. The prosthetic group of butyryl coenzyme A dehydrogenase. J Biol Chem. 1954 Jan;206(1):13–26. PMID: 13130522.

Metabolites

1-Butanol

Formula: C4H10O (74.073161)

CAS ID: 71-36-3

1,10-Phenanthroline

Formula: C12H8N2 (180.0687448)

CAS ID: 66-71-7

Acetaldehyde

Formula: C2H4O (44.0262134)

CAS ID: 75-07-0

Acetone

Formula: C3H6O (58.041862599999995)

CAS ID: 67-64-1

Butanal

Formula: C4H8O (72.0575118)

CAS ID: 123-72-8

CO2

Formula: CO2 (43.98983)

CAS ID: 124-38-9

Ethanol

Formula: C2H6O (46.0418626)

CAS ID: 64-17-5

H+

Formula: H (1.0078246)

CAS ID: 12408-02-5

H2O

Formula: H2O (18.0105642)

CAS ID: 7732-18-5

Hydrogen cyanide

Formula: CHN (27.010898599999997)

CAS ID: 74-90-8

Manganese(2+)

Formula: Mn (54.938046)

CAS ID: 7439-96-5

Mercury(2+)

Formula: Hg (201.970632)

CAS ID: 14302-87-5

Methyl ethyl ketone

Formula: C4H8O (72.0575118)

CAS ID: 78-93-3

Pentane-2,4-dione

Formula: C5H8O2 (100.05242679999999)

CAS ID: 123-54-6

Potassium cation

Formula: K (38.963708)

CAS ID: 24203-36-9

Propane-1-ol

Formula: C3H8O (60.0575118)

CAS ID: 71-23-8

Sodium cation

Formula: Na (22.98977)

CAS ID: 17341-25-2

Zinc cation

Formula: Zn (63.929145)

CAS ID: 23713-49-7

iodoacetamide

Formula: C2H4INO (184.9337644)

CAS ID: 144-48-9

acetoacetate

Formula: C4H5O3 (101.02386800000001)

CAS ID: 141-81-1

4,7-Phenanthroline

Formula: C12H8N2 (180.0687448)

CAS ID: 230-07-9

acetate (ion)

Formula: C2H3O2 (59.0133038)

CAS ID: 71-50-1

pyruvate

Formula: C3H3O3 (87.00821880000001)

CAS ID: 57-60-3

acetylpyruvate

Formula: C5H5O4 (129.018783)

CAS ID: 5699-58-1

butyrate

Formula: C4H7O2 (87.0446022)

CAS ID: 461-55-2

dodecyl sulfate

Formula: C12H25O4S (265.147347)

CAS ID:

p-chloromercuribenzenesulfonate

Formula: C6H4ClHgO3S (392.92760039999996)

CAS ID: 368-93-4

adenosine 5'-monophosphate(2-)

Formula: C10H12N5O7P (345.0474332)

CAS ID:

NADPH(4-)

Formula: C21H26N7O17P3 (741.0598016)

CAS ID: 53-57-6

ATP(4-)

Formula: C10H12N5O13P3 (502.9644492)

CAS ID:

thiamine(1+) diphosphate(3-)

Formula: C12H16N4O7P2S (422.0214926)

CAS ID:

NADH(2-)

Formula: C21H27N7O14P2 (663.1091182000001)

CAS ID:

NAD(1-)

Formula: C21H26N7O14P2 (662.1012936000001)

CAS ID: 53-84-9

ADP(3-)

Formula: C10H12N5O10P2 (424.0059412)

CAS ID:

NADP(3-)

Formula: C21H25N7O17P3 (740.051977)

CAS ID: 53-59-8

borohydride

Formula: BH4 (15.040603399999998)

CAS ID: 16971-29-2

p-hydroxymercuribenzoic acid

Formula: C7H6HgO3 (340.00232459999995)

CAS ID: 1126-48-3

Dithionitrobenzoic acid

Formula: C14H6N2O8S2-2 (393.9565596)

CAS ID:

Benzoylacetone

Formula: C10H10O2 (162.06807600000002)

CAS ID: 93-91-4



Enzyme

EC Number name full name note
1.1.1.-
1.1.1.1 alcohol dehydrogenase alcohol:NAD+ oxidoreductase
1.1.1.157 3-hydroxybutyryl-CoA dehydrogenase (S)-3-hydroxybutanoyl-CoA:NADP+ oxidoreductase
1.2.1.3 aldehyde dehydrogenase (NAD+) aldehyde:NAD+ oxidoreductase
1.3.8.1 short-chain acyl-CoA dehydrogenase short-chain acyl-CoA:electron-transfer flavoprotein 2,3-oxidoreductase
2.3.1.19 phosphate butyryltransferase butanoyl-CoA:phosphate butanoyltransferase
2.3.1.8 phosphate acetyltransferase acetyl-CoA:phosphate acetyltransferase
2.3.1.9 acetyl-CoA C-acetyltransferase acetyl-CoA:acetyl-CoA C-acetyltransferase
2.7.2.1 acetate kinase ATP:acetate phosphotransferase
2.7.2.7 butyrate kinase ATP:butanoate 1-phosphotransferase
2.8.3.9 butyrate-acetoacetate CoA-transferase butanoyl-CoA:acetoacetate CoA-transferase
4.1.1.4 acetoacetate decarboxylase acetoacetate carboxy-lyase (acetone-forming)
4.2.1.150 short-chain-enoyl-CoA hydratase short-chain-(3S)-3-hydroxyacyl-CoA hydro-lyase


Pathway Source

Organism Taxonomy Group Enzyme List Source Ratio
Clostridium acetobutylicum ATCC 824 MAGs 1.1.1.- / 1.1.1.1 / 1.1.1.157 / 1.2.1.3 / 1.3.8.1 / 2.3.1.19 / 2.3.1.8 / 2.3.1.9 / 2.7.2.1 / 2.7.2.7 / 2.8.3.9 / 4.1.1.4 / 4.2.1.150 100.00%
Bacillus cereus ATCC 14579 MAGs 1.1.1.- / 1.1.1.1 / 1.1.1.157 / 1.2.1.3 / 1.3.8.1 / 2.3.1.19 / 2.3.1.8 / 2.3.1.9 / 2.7.2.1 / 2.7.2.7 76.92%
Clostridium botulinum A str. ATCC 3502 MAGs 1.1.1.- / 1.1.1.1 / 1.1.1.157 / 1.2.1.3 / 1.3.8.1 / 2.3.1.19 / 2.3.1.8 / 2.3.1.9 / 2.7.2.1 / 2.7.2.7 76.92%
Paraburkholderia graminis bacteria 1.1.1.- / 1.1.1.1 / 1.1.1.157 / 1.2.1.3 / 1.3.8.1 / 2.3.1.8 / 2.3.1.9 / 2.7.2.1 / 4.1.1.4 / 4.2.1.150 76.92%
Clostridium butyricum 5521 MAGs 1.1.1.- / 1.1.1.1 / 1.1.1.157 / 1.2.1.3 / 2.3.1.19 / 2.3.1.8 / 2.3.1.9 / 2.7.2.1 / 2.7.2.7 69.23%
Geobacillus kaustophilus HTA426 MAGs 1.1.1.- / 1.1.1.1 / 1.1.1.157 / 1.2.1.3 / 2.3.1.19 / 2.3.1.8 / 2.3.1.9 / 2.7.2.1 / 2.7.2.7 69.23%
Bacillus subtilis subsp. subtilis str. 168 MAGs 1.1.1.- / 1.1.1.1 / 1.1.1.157 / 1.2.1.3 / 2.3.1.19 / 2.3.1.8 / 2.3.1.9 / 2.7.2.1 / 2.7.2.7 69.23%
Bordetella avium 197N MAGs 1.1.1.- / 1.1.1.1 / 1.1.1.157 / 1.2.1.3 / 1.3.8.1 / 2.3.1.8 / 2.3.1.9 / 2.7.2.1 / 4.1.1.4 69.23%
Staphylococcus carnosus subsp. carnosus TM300 MAGs 1.1.1.- / 1.1.1.1 / 1.2.1.3 / 2.3.1.19 / 2.3.1.8 / 2.3.1.9 / 2.7.2.1 / 2.7.2.7 / 4.1.1.4 69.23%
Clostridium perfringens ATCC 13124 MAGs 1.1.1.- / 1.1.1.1 / 1.1.1.157 / 1.3.8.1 / 2.3.1.19 / 2.3.1.8 / 2.7.2.1 / 2.7.2.7 61.54%
Bradyrhizobium sp. BTAi1 bacteria 1.1.1.- / 1.1.1.1 / 1.2.1.3 / 1.3.8.1 / 2.3.1.19 / 2.3.1.9 / 2.7.2.1 / 4.1.1.4 61.54%
Mycobacterium tuberculosis H37Rv MAGs 1.1.1.- / 1.1.1.1 / 1.1.1.157 / 1.2.1.3 / 1.3.8.1 / 2.3.1.8 / 2.3.1.9 / 2.7.2.1 61.54%
Cupriavidus taiwanensis bacteria 1.1.1.- / 1.1.1.1 / 1.1.1.157 / 1.2.1.3 / 1.3.8.1 / 2.3.1.8 / 2.3.1.9 / 2.7.2.1 61.54%
Clostridium tetani E88 MAGs 1.1.1.- / 1.1.1.1 / 1.1.1.157 / 1.2.1.3 / 2.3.1.8 / 2.3.1.9 / 2.7.2.1 / 2.7.2.7 61.54%
Chromobacterium violaceum ATCC 12472 MAGs 1.1.1.- / 1.1.1.1 / 1.1.1.157 / 1.2.1.3 / 2.3.1.8 / 2.3.1.9 / 2.7.2.1 / 4.1.1.4 61.54%
Clostridium kluyveri DSM 555 MAGs 1.1.1.- / 1.1.1.1 / 1.1.1.157 / 1.2.1.3 / 1.3.8.1 / 2.3.1.8 / 2.3.1.9 / 2.7.2.1 61.54%
Rhodospirillum rubrum ATCC 11170 MAGs 1.1.1.1 / 1.2.1.3 / 1.3.8.1 / 2.3.1.19 / 2.3.1.8 / 2.3.1.9 / 2.7.2.1 / 2.8.3.9 61.54%
Renibacterium salmoninarum ATCC 33209 MAGs 1.1.1.- / 1.1.1.1 / 1.1.1.157 / 1.2.1.3 / 2.3.1.9 / 2.7.2.1 / 4.1.1.4 53.85%
Bordetella bronchiseptica RB50 MAGs 1.1.1.- / 1.1.1.1 / 1.1.1.157 / 1.2.1.3 / 2.3.1.19 / 2.3.1.9 / 2.7.2.1 53.85%
Mycobacterium tuberculosis CDC1551 MAGs 1.1.1.- / 1.1.1.1 / 1.1.1.157 / 1.2.1.3 / 2.3.1.8 / 2.3.1.9 / 2.7.2.1 53.85%