Category:LBA: Difference between revisions

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=={{Bilingual|ID番号 (ページ名) の設計|Design of Fat acyl Page Titles}}==
=={{Bilingual|ID番号 (ページ名) の設計|Design of Fat acyl Page Titles}}==
{{Twocolumn|
{{Twocolumn|
Each page title contains chain-length, degree of unsaturation, position of double bonds, and backbone structure (branches, peroxidation, or prostanoids etc.).
Each ID contains information on backbone type, chemical modification of polar head, and attached sugars.
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|
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。
各分子のページIDは基本骨格、極性基のタイプ、糖のタイプがコード化されています。
}}
}}
<center>
<center>
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<td style="background-color:yellowgreen;" width=15px align="center"><big>L</big>
<td style="background-color:yellowgreen;" width=15px align="center"><big>L</big>
<td style="background-color:yellowgreen;" width=15px align="center"><big>B</big>
<td style="background-color:yellowgreen;" width=15px align="center"><big>B</big>
<td style="background-color:darkseagreen;" width=15px align="center"><big>F</big>
<td style="background-color:darkseagreen;" width=15px align="center"><big>A</big>
<td style="background-color:tomato; color:white" width=15px align="center"><big>''x''</big>
<td style="background-color:tomato; color:white" width=15px align="center"><big>''x''</big>
<td style="background-color:purple; color:white" width=15px align="center"><big>''y''</big>
<td style="background-color:purple; color:white" width=15px align="center"><big>''y''</big>

Revision as of 06:31, 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


Design of Fat acyl Page Titles

Each ID contains information on backbone type, chemical modification of polar head, and attached sugars.

各分子のページIDは基本骨格、極性基のタイプ、糖のタイプがコード化されています。

9-DIGIT

L B A x y z w c 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 (C20,C20 type below)
File:LBAA.png
H: hydroxy & methoxy archaeol (sn-2-hydroxy below)
File:LBAH.png
U: unsaturated (alkenyl) archaeol
File:LBAU.png
C: caldachaeol (tetraether type)
File:LBAC.png
D: calditocaldarchaeol
File:LBAD.png
Y: cyclic archaeol
File:LBAY.png
Order Backbone Polar-head 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)

}}

Polar-head Type
N: no structure; P: phosphate; C: phosphocholine; E: phosphoethanolamine; I: phosphoinositol; S: phosphoserine; G: phosphoglycerol; A: aminopentanetetrol; X: others
Sugar Type
G: glucose and galactose; M: including mannose; L: including gulose; S: including HSO3; C: including nonitol; X: others;

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