Category:LBA: Difference between revisions

Revision as of 03:33, 9 March 2013

Archaeal Lipid

Upper classes: LB

Class Overview

Archaeal lipid is composed of sn-glycerol 1-phosphate and isoprenoids. This composition is different from lipid in eubacteria and eukaryotes, which comprises of sn-glycerol 3-phosphate and fatty acids. Responsible enzymes are also non-homologous. Archaea also contains tetraether lipid

アーキア古細菌と呼ばれることが多いのですが、真性細菌と明確に区別するためにここではアーキアと記します。の脂質は、 sn-グリセロール1リン酸にイソプレン骨格がエーテル結合しています。これは、グリセロール3リン酸と脂肪酸を利用する真性細菌や真核生物と全く異なる構造で、生合成をおこなう酵素も相同ではありません。またテトラエーテル型と呼ばれるイソプレン骨格が末端で重合した環状脂質も広く存在し、これが単分子膜を形成すると考えられています。

Archaea are separated into two phyla which show three different characters (Table 1: leftmost column).

アーキアの系統はcrenarchaeotaとeuryarchaetaに分かれますが、特徴からみると三通りになります（表の最左カラム）。

Table 1. Clades in Archaea
Character	Phyrum (綱)	Order (目)	Family (科)
Non-methanogenic thermophils	crenarchaeota	desulfurococcales	desulfurococcaceae, pyrodictiaceae
		sulfolobales	sulfolobaceae
		thermoproteales	thermoproteaceae
	euryarchaeota	thermococcales	thermococcaceae
		thermoplasmatales	thermoplasmataceae
Halophils		halobacteriales	halobacteriaceae
Methanogens		methanobacteriales	methanobacteriaceae, methanothermaceae
		methanococcales	methanococcaceae, methanocaldococcaceae
		methanomicrobiales	methanomicrobiaceae, methanospirillaceae
		methanopyrales	methanopyraceae
		methanosarcinales	methanosarcinaceae, methanosaetaceae

Table 2. Genus Names in This Database
Family (科)	Genus (属)
desulfurococcaceae	Aeropyrum, Desulfurococcus
pyrodictiaceae	Pyrolobus
sulfolobales	Acidianus, Sulfolobus
thermoproteaceae	Pyrobaculum, Thermoproteus
thermococcaceae	Pyrococcus, Thermococcus
thermoplasmataceae	Thermoplasma
halobacteriaceae	Haloarcula, Halobacterium, Halococcus, Haloferax, Halorubrum, Natrialba, Natronobacterium, Notronococcus
methanobacteriaceae	Methanobacterium, Methanobrevibacter, Methanosphaera, Methanothermobacter
methanococcaceae	Methanothermococcus, Methanococcus
methanocaldococcaceae	Methanocaldococcus
methanomicrobiaceae	Methanomicrobium
methanospirillaceae	Mehtanospirillum
methanopyraceae	Mehtanospirillum
methanosarcinaceae	Methanococcoides, Methanohalophilus, Methanolobus, Methanosarcina

以下に示す種は名前に気をつけてください。（旧→新）

Methanosaeta concilii → Methanothrix soehngenii (detail)
Halobacterium sodomense → Halorubrum sodomense (detail)
Halobacterium lacusprofundi → Halorubrum lacusprofundi (detail)
Caldariella acidophila → Sulfolobus solfataricus

Design of Fat acyl Page Titles

Each page title contains chain-length, degree of unsaturation, position of double bonds, and backbone structure (branches, peroxidation, or prostanoids etc.).

各分子のページタイトルに鎖長、不飽和度、二重結合の位置、骨格タイプ（分岐や過酸化、プロスタノイドなど）がコード化されています。

9-DIGIT

L

B

F

x

y

z

w

c

x ... backbone type
y ... polar-head type
z ... sugar type
w ... number of sugars
c ... serial number

x ... バックボーンの構造
y ... 極性基（リン酸部分）の構造
z ... 糖のタイプ
w ... 糖の個数
c ... 通し番号

Classification 分類

Backbone Structure 基本構造

Backbone Structure
A: archaeol	H: hydroxy archaeol	U: unsaturated (alkenyl) archaeol
C: caldachaeol	D: calditocaldarchaeol	Y: cyclic archaeol

Polar-head Types
N: no structure	A: aminopentanetetrol	C: phosphocholine
E: phosphoethanolamine	I: phosphoinositol	P: phosphate
S: phosphoserine	G: phosphoglycerol	X: others

Sugar Types
G: glucose and galactose	M: including mannose	L: including gulose
S: including HSO3	C: including nonitol	X: others

Order

Backbone

Polar-group

Sugar

{{#lua:

 desulfurococcales ={{},{},{}}
 sulfolobales ={{},{},{}}
 thermoproteales ={{},{},{}}
 thermococcales ={{},{},{}}
 thermoplasmatales ={{},{},{}}
 halobacteriales ={{},{},{}}
 methanobacteriales ={{},{},{}}
 methanococcales ={{},{},{}}
 methanomicrobiales ={{},{},{}}
 methanopyrales ={{},{},{}}
 methanosarcinales ={{},{},{}}

 function printtable(name, T) print("\n|-\n|"..name.." || ") for k,v in pairs(T[1]) do print(k) end print(" || ") for k,v in pairs(T[2]) do print(k) end print(" || ") for k,v in pairs(T[3]) do print(k) end end
 function register(T, id) T[1][string.sub(id,4,4)] = true T[2][string.sub(id,5,5)] = true T[3][string.sub(id,6,6)] = true end

 for ref, sp, id in stdin:gmatch("|?|?([%w\. ]+)||([%w\., ]+)||([^\n]+)") do
   if (string.match(sp,"Aeropyrum") or string.match(sp,"Desulfurococcus") or string.match(sp,"Pyrolobus"))
     then register(desulfurococcales, id)
   elseif (string.match(sp,"Acidianus") or string.match(sp,"Sulfolobus"))
     then register(sulfolobales, id)
   elseif (string.match(sp,"Pyrobaculum") or string.match(sp,"Thermoproteus"))
     then register(thermoproteales, id)
   elseif (string.match(sp,"Pyrococcus") or string.match(sp,"Thermococcus"))
     then register(thermococcales, id)
   elseif (string.match(sp,"Thermoplasma"))
     then register(thermoplasmatales, id)
   elseif (string.match(sp,"Haloarcula") or string.match(sp,"Halobacterium") or string.match(sp,"Halococcus") or string.match(sp,"Haloferax") or string.match(sp,"Halorubrum") or string.match(sp,"Natrialba") or string.match(sp,"Natronobacterium") or string.match(sp,"Natronococcus"))
     then register(halobacteriales, id)
   elseif (string.match(sp,"Methanobacterium") or string.match(sp,"Methanobrevibacter") or string.match(sp,"Methanosphaera") or string.match(sp,"Methanothermobacter"))
     then register(methanobacteriales, id)
   elseif (string.match(sp,"Methanothermococcus") or string.match(sp,"Methanococcus") or string.match(sp,"Methanocaldococcus"))
     then register(methanococcales, id)
   elseif (string.match(sp,"Methanomicrobium") or string.match(sp,"Methanospirillum"))
     then register(methanomicrobiales, id)
   elseif (string.match(sp,"Methanopyrus"))
     then register(methanopyrales, id)
   elseif (string.match(sp,"Methanococcoides") or string.match(sp,"Methanohalophilus") or string.match(sp,"Methanolobus") or string.match(sp,"Methanosarcina"))
     then register(methanosarcinales, id)
   end
 end
 printtable("desulfurococcales", desulfurococcales)
 printtable("sulfolobales",sulfolobales)
 printtable("thermoproteales",thermoproteales)
 printtable("thermococcales",thermococcales)
 printtable("thermoplasmatales",thermoplasmatales)
 printtable("halobacteriales",halobacteriales)
 printtable("methanobacteriales",methanobacteriales)
 printtable("methanococcales",methanococcales)
 printtable("methanomicrobiales",methanomicrobiales)
 printtable("methanopyrales",methanopyrales)
 printtable("mehtanosarcinales",methanosarcinales)

}}

This category currently contains no pages or media.

@@ Line 147: / Line 147: @@
 <center>
 {| class="wikitable" border="1" cellpadding="2" cellspacing="1" margin: 1em 1em 1em 1em"
+|+ Backbone Structure
 |- valign="top"
 |align="center"| A: archaeol
@@ Line 157: / Line 158: @@
 |}
+{| class="wikitable" border="1" cellpadding="2" cellspacing="1" margin: 1em 1em 1em 1em"
+|+ Polar-head Types
+|- valign="top"
+|align="center"| N: no structure
+|align="center"| A: aminopentanetetrol
+|align="center"| C: phosphocholine
+|-
+|align="center"| E: phosphoethanolamine
+|align="center"| I: phosphoinositol
+|align="center"| P: phosphate
+|-
+|align="center"| S: phosphoserine
+|align="center"| G: phosphoglycerol
+|align="center"| X: others
+|}
+{| class="wikitable" border="1" cellpadding="2" cellspacing="1" margin: 1em 1em 1em 1em"
+|+ Sugar Types
+|- valign="top"
+|align="center"| G: glucose and galactose
+|align="center"| M: including mannose
+|align="center"| L: including gulose
+|-
+|align="center"| S: including HSO3
+|align="center"| C: including nonitol
+|align="center"| X: others
+|}
+</center>
+<center>
 {| class="wikitable"
+! Order || Backbone || Polar-group || Sugar
 {{#replace:
 {{#lua:
-   desulfurococcales = {A=false,H=false,U=false,C=false,D=false,Y=false}
+   desulfurococcales ={{},{},{}}
-   sulfolobales = {A=false,H=false,U=false,C=false,D=false,Y=false}
+   sulfolobales ={{},{},{}}
-   thermoproteales = {A=false,H=false,U=false,C=false,D=false,Y=false}
+   thermoproteales ={{},{},{}}
-   thermococcales = {A=false,H=false,U=false,C=false,D=false,Y=false}
+   thermococcales ={{},{},{}}
-   thermoplasmatales = {A=false,H=false,U=false,C=false,D=false,Y=false}
+   thermoplasmatales ={{},{},{}}
-   halobacteriales = {A=false,H=false,U=false,C=false,D=false,Y=false}
+   halobacteriales ={{},{},{}}
-   methanobacteriales = {A=false,H=false,U=false,C=false,D=false,Y=false}
+   methanobacteriales ={{},{},{}}
-   methanococcales = {A=false,H=false,U=false,C=false,D=false,Y=false}
+   methanococcales ={{},{},{}}
-   methanomicrobiales = {A=false,H=false,U=false,C=false,D=false,Y=false}
+   methanomicrobiales ={{},{},{}}
-   methanopyrales = {A=false,H=false,U=false,C=false,D=false,Y=false}
+  methanopyrales ={{},{},{}}
-   methanosarcinales = {A=false,H=false,U=false,C=false,D=false,Y=false}
+   methanosarcinales ={{},{},{}}
+  function printtable(name, T) print("\n&-\n&"..name.." && ") for k,v in pairs(T[1]) do print(k) end print(" && ") for k,v in pairs(T[2]) do print(k) end print(" && ") for k,v in pairs(T[3]) do print(k) end end
+   function register(T, id) T[1][string.sub(id,4,4)] = true T[2][string.sub(id,5,5)] = true T[3][string.sub(id,6,6)] = true end
    for ref, sp, id in stdin:gmatch("&?&?([%w\. ]+)&&([%w\., ]+)&&([^\n]+)") do
      if (string.match(sp,"Aeropyrum") or string.match(sp,"Desulfurococcus") or string.match(sp,"Pyrolobus"))
-       then desulfurococcales[ string.sub(id,4,4) ] = true
+       then register(desulfurococcales, id)
      elseif (string.match(sp,"Acidianus") or string.match(sp,"Sulfolobus"))
-       then sulfolobales[ string.sub(id,4,4) ] = true
+       then register(sulfolobales, id)
      elseif (string.match(sp,"Pyrobaculum") or string.match(sp,"Thermoproteus"))
-       then thermoproteales[ string.sub(id,4,4) ] = true
+       then register(thermoproteales, id)
      elseif (string.match(sp,"Pyrococcus") or string.match(sp,"Thermococcus"))
-       then thermococcales[ string.sub(id,4,4) ] = true
+       then register(thermococcales, id)
      elseif (string.match(sp,"Thermoplasma"))
-       then thermoplasmatales[ string.sub(id,4,4) ] = true
+       then register(thermoplasmatales, id)
      elseif (string.match(sp,"Haloarcula") or string.match(sp,"Halobacterium") or string.match(sp,"Halococcus") or string.match(sp,"Haloferax") or string.match(sp,"Halorubrum") or string.match(sp,"Natrialba") or string.match(sp,"Natronobacterium") or string.match(sp,"Natronococcus"))
-       then halobacteriales[ string.sub(id,4,4) ] = true
+       then register(halobacteriales, id)
      elseif (string.match(sp,"Methanobacterium") or string.match(sp,"Methanobrevibacter") or string.match(sp,"Methanosphaera") or string.match(sp,"Methanothermobacter"))
-       then methanobacteriales[ string.sub(id,4,4) ] = true
+       then register(methanobacteriales, id)
      elseif (string.match(sp,"Methanothermococcus") or string.match(sp,"Methanococcus") or string.match(sp,"Methanocaldococcus"))
-       then methanococcales[ string.sub(id,4,4) ] = true
+       then register(methanococcales, id)
      elseif (string.match(sp,"Methanomicrobium") or string.match(sp,"Methanospirillum"))
-       then methanomicrobiales[ string.sub(id,4,4) ] = true
+       then register(methanomicrobiales, id)
      elseif (string.match(sp,"Methanopyrus"))
-       then methanopyrales[ string.sub(id,4,4) ] = true
+       then register(methanopyrales, id)
      elseif (string.match(sp,"Methanococcoides") or string.match(sp,"Methanohalophilus") or string.match(sp,"Methanolobus") or string.match(sp,"Methanosarcina"))
-       then methanosarcinales[ string.sub(id,4,4) ] = true
+       then register(methanosarcinales, id)
      end
    end
-   print("\n&-\n&desulfurococcales && ") for k,v in pairs(desulfurococcales) do print(k,v) end
+   printtable("desulfurococcales", desulfurococcales)
-   print("\n&-\n&sulfolobales && ") for k,v in pairs(sulfolobales) do print(k,v) end
+   printtable("sulfolobales",sulfolobales)
-   print("\n&-\n&thermoproteales && ") for k,v in pairs(thermoproteales) do print(k,v) end
+   printtable("thermoproteales",thermoproteales)
-   print("\n&-\n&thermococcales && ") for k,v in pairs(thermococcales) do print(k,v) end
+   printtable("thermococcales",thermococcales)
-   print("\n&-\n&thermoplasmatales && ") for k,v in pairs(thermoplasmatales) do print(k,v) end
+   printtable("thermoplasmatales",thermoplasmatales)
-   print("\n&-\n&halobacteriales && ") for k,v in pairs(halobacteriales) do print(k,v) end
+   printtable("halobacteriales",halobacteriales)
-   print("\n&-\n&methanobacteriales && ") for k,v in pairs(methanobacteriales) do print(k,v) end
+   printtable("methanobacteriales",methanobacteriales)
-   print("\n&-\n&methanococcales && ") for k,v in pairs(methanococcales) do print(k,v) end
+   printtable("methanococcales",methanococcales)
-   print("\n&-\n&methanomicrobiales && ") for k,v in pairs(methanomicrobiales) do print(k,v) end
+   printtable("methanomicrobiales",methanomicrobiales)
-   print("\n&-\n&methanopyrales && ") for k,v in pairs(methanopyrales) do print(k,v) end
+   printtable("methanopyrales",methanopyrales)
-   print("\n&-\n&mehtanosarcinales && ") for k,v in pairs(methanosarcinales) do print(k,v) end
+   printtable("mehtanosarcinales",methanosarcinales)
 |
 {{#SearchLine:&&LBA|Reference}}
@@ Line 213: / Line 248: @@
 |&|{{#bar:}}}}
 |}
 </center>

Category:LBA: Difference between revisions

Revision as of 03:33, 9 March 2013

Contents

Class Overview

Design of Fat acyl Page Titles

Classification 分類

Backbone Structure 基本構造

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