Difference between revisions of "TransportSeed-Light"

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(Created page with "Category:reaction == Reaction 2.1.1.5-RXN == * direction: ** left-to-right * common-name: ** betaine-homocysteine s-methyltransferase * ec-number: ** [http://enzyme.expasy...")
(Created page with "Category:reaction == Reaction MALATE-DEH-RXN == * direction: ** reversible * common-name: ** malate dehydrogenase * ec-number: ** [http://enzyme.expasy.org/EC/1.1.1.37 ec-...")
Line 1: Line 1:
 
[[Category:reaction]]
 
[[Category:reaction]]
−
== Reaction 2.1.1.5-RXN ==
+
== Reaction MALATE-DEH-RXN ==
 
* direction:
 
* direction:
−
** left-to-right
+
** reversible
 
* common-name:
 
* common-name:
−
** betaine-homocysteine s-methyltransferase
+
** malate dehydrogenase
 
* ec-number:
 
* ec-number:
−
** [http://enzyme.expasy.org/EC/2.1.1.5 ec-2.1.1.5]
+
** [http://enzyme.expasy.org/EC/1.1.1.37 ec-1.1.1.37]
 +
* synonymous:
 +
** malate dehydrogenation
 
== Reaction formula ==
 
== Reaction formula ==
−
* 1 [[BETAINE]][c] '''+''' 1 [[HOMO-CYS]][c] '''=>''' 1 [[DIMETHYL-GLYCINE]][c] '''+''' 1 [[MET]][c]
+
* 1 [[MAL]][c] '''+''' 1 [[NAD]][c] '''<=>''' 1 [[NADH]][c] '''+''' 1 [[OXALACETIC_ACID]][c] '''+''' 1 [[PROTON]][c]
 
== Gene(s) associated with this reaction  ==
 
== Gene(s) associated with this reaction  ==
−
* Gene: [[SJ07112]]
+
<div class="toccolours mw-collapsible mw-collapsed" style="width:100%; overflow:auto;">
 +
* Gene: [[SJ05075]]
 
** Category: [[annotation]]
 
** Category: [[annotation]]
−
*** Source: [[saccharina_japonica_genome]], Tool: [[pathwaytools]], Assignment: go-term, Comment: n.a
+
*** Source: [[saccharina_japonica_genome]], Tool: [[pathwaytools]], Assignment: ec-number, Comment: n.a
 +
** Category: [[orthology]]
 +
*** Source: [[output_pantograph_nannochloropsis_salina]], Tool: [[pantograph]], Assignment: n.a, Comment: n.a
 +
*** Source: [[output_pantograph_nannochloropsis_salina]], Tool: [[pantograph]], Assignment: n.a, Comment: n.a
 +
*** Source: [[output_pantograph_arabidopsis_thaliana]], Tool: [[pantograph]], Assignment: n.a, Comment: n.a
 +
*** Source: [[output_pantograph_arabidopsis_thaliana]], Tool: [[pantograph]], Assignment: n.a, Comment: n.a
 +
*** Source: [[output_pantograph_arabidopsis_thaliana]], Tool: [[pantograph]], Assignment: n.a, Comment: n.a
 +
*** Source: [[output_pantograph_arabidopsis_thaliana]], Tool: [[pantograph]], Assignment: n.a, Comment: n.a
 +
*** Source: [[output_pantograph_ectocarpus_siliculosus]], Tool: [[pantograph]], Assignment: n.a, Comment: n.a
 +
* Gene: [[SJ15523]]
 +
** Category: [[annotation]]
 +
*** Source: [[saccharina_japonica_genome]], Tool: [[pathwaytools]], Assignment: ec-number, Comment: n.a
 +
** Category: [[orthology]]
 +
*** Source: [[output_pantograph_nannochloropsis_salina]], Tool: [[pantograph]], Assignment: n.a, Comment: n.a
 +
* Gene: [[SJ15746]]
 +
** Category: [[annotation]]
 +
*** Source: [[saccharina_japonica_genome]], Tool: [[pathwaytools]], Assignment: ec-number, Comment: n.a
 +
** Category: [[orthology]]
 +
*** Source: [[output_pantograph_nannochloropsis_salina]], Tool: [[pantograph]], Assignment: n.a, Comment: n.a
 +
*** Source: [[output_pantograph_arabidopsis_thaliana]], Tool: [[pantograph]], Assignment: n.a, Comment: n.a
 +
*** Source: [[output_pantograph_arabidopsis_thaliana]], Tool: [[pantograph]], Assignment: n.a, Comment: n.a
 +
*** Source: [[output_pantograph_arabidopsis_thaliana]], Tool: [[pantograph]], Assignment: n.a, Comment: n.a
 +
*** Source: [[output_pantograph_arabidopsis_thaliana]], Tool: [[pantograph]], Assignment: n.a, Comment: n.a
 +
*** Source: [[output_pantograph_ectocarpus_siliculosus]], Tool: [[pantograph]], Assignment: n.a, Comment: n.a
 +
</div>
 
== Pathway(s)  ==
 
== Pathway(s)  ==
−
* [[PWY-3661]], glycine betaine degradation I:
+
<div class="toccolours mw-collapsible mw-collapsed" style="width:100%; overflow:auto;">
−
** '''3''' reactions found over '''7''' reactions in the full pathway
+
* [[PWY-6969]], TCA cycle V (2-oxoglutarate:ferredoxin oxidoreductase):
−
* [[PWY-3661-1]], glycine betaine degradation II (mammalian):
+
** '''10''' reactions found over '''12''' reactions in the full pathway
−
** '''2''' reactions found over '''4''' reactions in the full pathway
+
* [[P23-PWY]], reductive TCA cycle I:
−
* [[ADENOSYLHOMOCYSCAT-PWY]], L-methionine salvage from L-homocysteine:
+
** '''9''' reactions found over '''12''' reactions in the full pathway
−
** '''3''' reactions found over '''3''' reactions in the full pathway
+
* [[FERMENTATION-PWY]], mixed acid fermentation:
 +
** '''11''' reactions found over '''16''' reactions in the full pathway
 +
* [[GLYOXYLATE-BYPASS]], glyoxylate cycle:
 +
** '''6''' reactions found over '''6''' reactions in the full pathway
 +
* [[GLUCONEO-PWY]], gluconeogenesis I:
 +
** '''12''' reactions found over '''13''' reactions in the full pathway
 +
* [[PWY-1622]], formaldehyde assimilation I (serine pathway):
 +
** '''6''' reactions found over '''13''' reactions in the full pathway
 +
* [[PWY-7383]], anaerobic energy metabolism (invertebrates, cytosol):
 +
** '''4''' reactions found over '''7''' reactions in the full pathway
 +
* [[P42-PWY]], incomplete reductive TCA cycle:
 +
** '''5''' reactions found over '''7''' reactions in the full pathway
 +
* [[PWY-5392]], reductive TCA cycle II:
 +
** '''6''' reactions found over '''12''' reactions in the full pathway
 +
* [[PWY-5690]], TCA cycle II (plants and fungi):
 +
** '''8''' reactions found over '''9''' reactions in the full pathway
 +
* [[PWY-7115]], C4 photosynthetic carbon assimilation cycle, NAD-ME type:
 +
** '''9''' reactions found over '''10''' reactions in the full pathway
 +
* [[TCA]], TCA cycle I (prokaryotic):
 +
** '''9''' reactions found over '''10''' reactions in the full pathway
 +
* [[PWY-561]], superpathway of glyoxylate cycle and fatty acid degradation:
 +
** '''6''' reactions found over '''4''' reactions in the full pathway
 +
* [[PWY-5913]], partial TCA cycle (obligate autotrophs):
 +
** '''10''' reactions found over '''11''' reactions in the full pathway
 +
* [[PWY-6728]], methylaspartate cycle:
 +
** '''11''' reactions found over '''19''' reactions in the full pathway
 +
* [[P105-PWY]], TCA cycle IV (2-oxoglutarate decarboxylase):
 +
** '''10''' reactions found over '''11''' reactions in the full pathway
 +
* [[PWY66-398]], TCA cycle III (animals):
 +
** '''10''' reactions found over '''10''' reactions in the full pathway
 +
* [[P108-PWY]], pyruvate fermentation to propanoate I:
 +
** '''2''' reactions found over '''7''' reactions in the full pathway
 +
* [[MALATE-ASPARTATE-SHUTTLE-PWY]], malate/L-aspartate shuttle pathway:
 +
** '''2''' reactions found over '''2''' reactions in the full pathway
 +
* [[PWY66-399]], gluconeogenesis III:
 +
** '''11''' reactions found over '''12''' reactions in the full pathway
 +
</div>
 
== Reconstruction information  ==
 
== Reconstruction information  ==
 +
* category: [[orthology]]; source: [[output_pantograph_nannochloropsis_salina]]; tool: [[pantograph]]; comment: n.a
 +
* category: [[orthology]]; source: [[output_pantograph_ectocarpus_siliculosus]]; tool: [[pantograph]]; comment: n.a
 
* category: [[annotation]]; source: [[saccharina_japonica_genome]]; tool: [[pathwaytools]]; comment: n.a
 
* category: [[annotation]]; source: [[saccharina_japonica_genome]]; tool: [[pathwaytools]]; comment: n.a
 +
* category: [[orthology]]; source: [[output_pantograph_arabidopsis_thaliana]]; tool: [[pantograph]]; comment: n.a
 
== External links  ==
 
== External links  ==
 +
<div class="toccolours mw-collapsible mw-collapsed" style="width:100%; overflow:auto;">
 
* RHEA:
 
* RHEA:
−
** [http://www.ebi.ac.uk/rhea/reaction.xhtml?id=22337 22337]
+
** [http://www.ebi.ac.uk/rhea/reaction.xhtml?id=21435 21435]
 +
* PIR:
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=A32472 A32472]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=A49496 A49496]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=A60689 A60689]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=C64110 C64110]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=D81399 D81399]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=DEBYMC DEBYMC]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=DEBYMM DEBYMM]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=DEBYMP DEBYMP]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=DEEBM DEEBM]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=DEECM DEECM]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=DEMSMC DEMSMC]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=DEMSMM DEMSMM]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=DEPGMM DEPGMM]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=DEPUGW DEPUGW]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=DEPUMW DEPUMW]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=DERTMM DERTMM]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=DETWMA DETWMA]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=F85551 F85551]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=G01650 G01650]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=H64477 H64477]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=I40383 I40383]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=PA0040 PA0040]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=PA0079 PA0079]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=PN0162 PN0162]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=S03352 S03352]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=S03958 S03958]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=S04956 S04956]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=S04957 S04957]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=S04958 S04958]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=S04959 S04959]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=S04960 S04960]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=S04961 S04961]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=S07574 S07574]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=S08981 S08981]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=S44167 S44167]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=S52039 S52039]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=S57958 S57958]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=S61213 S61213]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=S75735 S75735]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=T03272 T03272]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=T06325 T06325]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=T06326 T06326]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=T06327 T06327]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=T06328 T06328]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=T06386 T06386]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=T08015 T08015]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=T08077 T08077]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=T08177 T08177]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=T09228 T09228]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=T09263 T09263]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=T09286 T09286]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=T09291 T09291]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=T09294 T09294]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=T12433 T12433]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=T18570 T18570]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=T45206 T45206]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=T45208 T45208]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=T49932 T49932]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=T51311 T51311]
 +
** [http://pir.georgetown.edu/cgi-bin/nbrfget?uid=T51862 T51862]
 +
* UNIPROT:
 +
** [http://www.uniprot.org/uniprot/Q07841 Q07841]
 +
** [http://www.uniprot.org/uniprot/P33163 P33163]
 +
** [http://www.uniprot.org/uniprot/P44427 P44427]
 +
** [http://www.uniprot.org/uniprot/Q9PHY2 Q9PHY2]
 +
** [http://www.uniprot.org/uniprot/P22133 P22133]
 +
** [http://www.uniprot.org/uniprot/P17505 P17505]
 +
** [http://www.uniprot.org/uniprot/P32419 P32419]
 +
** [http://www.uniprot.org/uniprot/P25077 P25077]
 +
** [http://www.uniprot.org/uniprot/P14152 P14152]
 +
** [http://www.uniprot.org/uniprot/Q8R1P0 Q8R1P0]
 +
** [http://www.uniprot.org/uniprot/P19446 P19446]
 +
** [http://www.uniprot.org/uniprot/P17783 P17783]
 +
** [http://www.uniprot.org/uniprot/P04636 P04636]
 +
** [http://www.uniprot.org/uniprot/P58408 P58408]
 +
** [http://www.uniprot.org/uniprot/Q58820 Q58820]
 +
** [http://www.uniprot.org/uniprot/P49814 P49814]
 +
** [http://www.uniprot.org/uniprot/Q93ZA7 Q93ZA7]
 +
** [http://www.uniprot.org/uniprot/Q7M4Y9 Q7M4Y9]
 +
** [http://www.uniprot.org/uniprot/Q7M4Z0 Q7M4Z0]
 +
** [http://www.uniprot.org/uniprot/P10887 P10887]
 +
** [http://www.uniprot.org/uniprot/P11386 P11386]
 +
** [http://www.uniprot.org/uniprot/P19983 P19983]
 +
** [http://www.uniprot.org/uniprot/P19981 P19981]
 +
** [http://www.uniprot.org/uniprot/P19979 P19979]
 +
** [http://www.uniprot.org/uniprot/P19977 P19977]
 +
** [http://www.uniprot.org/uniprot/P19982 P19982]
 +
** [http://www.uniprot.org/uniprot/P19978 P19978]
 +
** [http://www.uniprot.org/uniprot/P19980 P19980]
 +
** [http://www.uniprot.org/uniprot/P16142 P16142]
 +
** [http://www.uniprot.org/uniprot/P46487 P46487]
 +
** [http://www.uniprot.org/uniprot/P46488 P46488]
 +
** [http://www.uniprot.org/uniprot/Q43744 Q43744]
 +
** [http://www.uniprot.org/uniprot/Q59202 Q59202]
 +
** [http://www.uniprot.org/uniprot/Q55383 Q55383]
 +
** [http://www.uniprot.org/uniprot/Q42972 Q42972]
 +
** [http://www.uniprot.org/uniprot/O81278 O81278]
 +
** [http://www.uniprot.org/uniprot/O81279 O81279]
 +
** [http://www.uniprot.org/uniprot/O65363 O65363]
 +
** [http://www.uniprot.org/uniprot/O65364 O65364]
 +
** [http://www.uniprot.org/uniprot/O81609 O81609]
 +
** [http://www.uniprot.org/uniprot/Q43743 Q43743]
 +
** [http://www.uniprot.org/uniprot/Q42686 Q42686]
 +
** [http://www.uniprot.org/uniprot/P93106 P93106]
 +
** [http://www.uniprot.org/uniprot/Q04820 Q04820]
 +
** [http://www.uniprot.org/uniprot/O48903 O48903]
 +
** [http://www.uniprot.org/uniprot/O48904 O48904]
 +
** [http://www.uniprot.org/uniprot/O48905 O48905]
 +
** [http://www.uniprot.org/uniprot/O48906 O48906]
 +
** [http://www.uniprot.org/uniprot/O24047 O24047]
 +
** [http://www.uniprot.org/uniprot/Q9XTB4 Q9XTB4]
 +
** [http://www.uniprot.org/uniprot/P50917 P50917]
 +
** [http://www.uniprot.org/uniprot/Q49981 Q49981]
 +
** [http://www.uniprot.org/uniprot/Q9ZP05 Q9ZP05]
 +
** [http://www.uniprot.org/uniprot/Q9ZP06 Q9ZP06]
 +
** [http://www.uniprot.org/uniprot/Q9SN86 Q9SN86]
 
* LIGAND-RXN:
 
* LIGAND-RXN:
−
** [http://www.genome.jp/dbget-bin/www_bget?R02821 R02821]
+
** [http://www.genome.jp/dbget-bin/www_bget?R00342 R00342]
−
{{#set: direction=left-to-right}}
+
</div>
−
{{#set: common-name=betaine-homocysteine s-methyltransferase}}
+
{{#set: direction=reversible}}
−
{{#set: ec-number=ec-2.1.1.5}}
+
{{#set: common-name=malate dehydrogenase}}
−
{{#set: nb gene associated=1}}
+
{{#set: ec-number=ec-1.1.1.37}}
−
{{#set: nb pathway associated=3}}
+
{{#set: synonymous=malate dehydrogenation}}
−
{{#set: reconstruction category=annotation}}
+
{{#set: nb gene associated=3}}
−
{{#set: reconstruction tool=pathwaytools}}
+
{{#set: nb pathway associated=20}}
 +
{{#set: reconstruction category=annotation|orthology}}
 +
{{#set: reconstruction tool=pathwaytools|pantograph}}
 
{{#set: reconstruction comment=n.a}}
 
{{#set: reconstruction comment=n.a}}
−
{{#set: reconstruction source=saccharina_japonica_genome}}
+
{{#set: reconstruction source=output_pantograph_nannochloropsis_salina|output_pantograph_arabidopsis_thaliana|saccharina_japonica_genome|output_pantograph_ectocarpus_siliculosus}}

Revision as of 11:27, 15 January 2021

Reaction MALATE-DEH-RXN

  • direction:
    • reversible
  • common-name:
    • malate dehydrogenase
  • ec-number:
  • synonymous:
    • malate dehydrogenation

Reaction formula

Gene(s) associated with this reaction

Pathway(s)

  • PWY-6969, TCA cycle V (2-oxoglutarate:ferredoxin oxidoreductase):
    • 10 reactions found over 12 reactions in the full pathway
  • P23-PWY, reductive TCA cycle I:
    • 9 reactions found over 12 reactions in the full pathway
  • FERMENTATION-PWY, mixed acid fermentation:
    • 11 reactions found over 16 reactions in the full pathway
  • GLYOXYLATE-BYPASS, glyoxylate cycle:
    • 6 reactions found over 6 reactions in the full pathway
  • GLUCONEO-PWY, gluconeogenesis I:
    • 12 reactions found over 13 reactions in the full pathway
  • PWY-1622, formaldehyde assimilation I (serine pathway):
    • 6 reactions found over 13 reactions in the full pathway
  • PWY-7383, anaerobic energy metabolism (invertebrates, cytosol):
    • 4 reactions found over 7 reactions in the full pathway
  • P42-PWY, incomplete reductive TCA cycle:
    • 5 reactions found over 7 reactions in the full pathway
  • PWY-5392, reductive TCA cycle II:
    • 6 reactions found over 12 reactions in the full pathway
  • PWY-5690, TCA cycle II (plants and fungi):
    • 8 reactions found over 9 reactions in the full pathway
  • PWY-7115, C4 photosynthetic carbon assimilation cycle, NAD-ME type:
    • 9 reactions found over 10 reactions in the full pathway
  • TCA, TCA cycle I (prokaryotic):
    • 9 reactions found over 10 reactions in the full pathway
  • PWY-561, superpathway of glyoxylate cycle and fatty acid degradation:
    • 6 reactions found over 4 reactions in the full pathway
  • PWY-5913, partial TCA cycle (obligate autotrophs):
    • 10 reactions found over 11 reactions in the full pathway
  • PWY-6728, methylaspartate cycle:
    • 11 reactions found over 19 reactions in the full pathway
  • P105-PWY, TCA cycle IV (2-oxoglutarate decarboxylase):
    • 10 reactions found over 11 reactions in the full pathway
  • PWY66-398, TCA cycle III (animals):
    • 10 reactions found over 10 reactions in the full pathway
  • P108-PWY, pyruvate fermentation to propanoate I:
    • 2 reactions found over 7 reactions in the full pathway
  • MALATE-ASPARTATE-SHUTTLE-PWY, malate/L-aspartate shuttle pathway:
    • 2 reactions found over 2 reactions in the full pathway
  • PWY66-399, gluconeogenesis III:
    • 11 reactions found over 12 reactions in the full pathway

Reconstruction information

External links






Retrieved from "https://gem-aureme.genouest.org/sjapgem/index.php?title=TransportSeed-Light&oldid=116834"