Category:BM

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==BM: Basic Metabolites 基礎代謝物==
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{{Huge|Basic Metabolism (基礎代謝)}}
 +
 
 +
{{Basic Metabolism/Header}}
 +
=={{Bilingual|概要|Class Overview}}==
 +
{{Twocolumn|
 +
(The following description is translated from an article written by Arita in "Encyclopedia of Bioinformatics" under the publisher's permission, Kyoritsu Co. Ltd.)
 +
<br><br>
 +
Metabolism is the total body of physicochemical reactions inside living systems.  It can be functionally divided into two groups: the basic (or primary) metabolism essential for maintenance of life systems, and the non-essential secondary metabolism.  Basic metabolites therefore include bases, amino acids, sugars, and fatty acids (building blocks  of DNA, protein, carbohydrate, and fat, respectively).  Also included are lignin and cellulose which are essential for plant growth.  On the other hand, the secondary metabolism provides species-specific functions.  It includes medicinal metabolites such as antibiotics and crude drugs.
 +
 
 +
|
 +
 
 +
(以下の情報は共立出版バイオインフォマティクス事典で有田の執筆項目「代謝」より、出版社の許可を得て転載)
 +
<br><br>
 +
代謝とは, 生体内でおこなわれる物理化学反応の総体, または特定の分子に関与する物理化学反応の総体です. 機能の観点から, 生命の維持に必須の物質群に関わる基礎/一次代謝と, 生命維持に必須ではない二次代謝に分けられます. 生命に欠かせない核酸, アミノ酸, 糖, 脂肪酸 (それぞれDNA,タンパク質,炭水化物, 脂質の構成単位) は基礎代謝物とよばれ, また植物に必須のリグニンやセルロースも基礎代謝物に分類されます. これに対し二次代謝は, 生物種に固有の機能を提供する部分です. 抗生物質や生薬など, 人間が利用してきた薬効成分はいずれも二次代謝物に属します.
 +
}}
 +
 
 +
=={{Bilingual|Metabolite Category|代謝物の種類}}==
 +
 
 +
* [[Aritalab:Lecture/Biochem/Amino Acid|アミノ酸]]
 +
* [[Aritalab:Lecture/Biochem/Saccharide|糖]]
 +
* [[Aritalab:Lecture/Biochem/Nucleic Acid|核酸]]
 +
* [[Aritalab:Lecture/Biochem/Lipid|脂質]]
 +
 
 +
==Design of Basic Metabolite ID numbers <small>ID番号の設計</small>==
 +
<center>
 +
12-DIGIT
 +
<table border=1>
 +
<tr>
 +
<td style="background-color:yellowgreen;" width=15px align="center"><big>B</big>
 +
<td style="background-color:yellowgreen;" width=15px align="center"><big>M</big>
 +
<td style="background-color:darkseagreen;" width=15px align="center"><big>''a''</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>''b''</big>
 +
<td style="background-color:tomato; color:white" width=15px align="center"><big>''b''</big>
 +
<td style="background-color:firebrick; color:white" width=15px align="center"><big>''c''</big>
 +
<td style="background-color:firebrick; color:white" width=15px align="center"><big>''c''</big>
 +
<td style="background-color:green; color:white;" width=15px align="center"><big>''d''</big>
 +
<td style="background-color:green; color:white" width=15px align="center"><big>''d''</big>
 +
<td style="background-color:white;" width=15px align="center"><big>''e''</big>
 +
<td style="background-color:white;" width=15px align="center"><big>''e''</big>
 +
</tr>
 +
</table>
 +
</center>
 +
{{Twocolumn|
 +
* ''a'' ... Structure type (Table 1)
 +
* ''b'' ... degree of unsaturation (Table 2)
 +
* ''c'' ... position of n-''z'' (n minus z; also ω-z or omega-z) nomenclature (Table 3)
 +
* ''d'' ... structure type (Table 4)
 +
* ''e'' ... serial number
 +
|
 +
* ''a'' ... 炭素鎖長(Table 1)
 +
* ''b'' ... 不飽和度(Table 2)
 +
* ''c'' ... n-''z'' (またはω-''z''やomega-''z'') における数(Table 3)
 +
* ''d'' ... 骨格のタイプ (Table 4)
 +
* ''e'' ... 通し番号
 +
}}
  
{| style="background-color:transparent;width:100%;border-style:none;border-collapse:collapase"
 
|-
 
| style="width:50%;vertical-align:top;padding-right:0.2em" |
 
<p>
 
(The following description is translated from an article by Arita in "Encyclopedia of Bioinformatics" under the publisher's permission, Kyoritsu Co. Ltd.)
 
</p>
 
<p>
 
Metabolism is the total body of physicochemical reactions inside living systems.  It can be functionally divided into two groups: the basic (or primary) metabolism essential for maintenance of life systems, and the non-essential secondary metabolism.  Basic metabolites therefore include bases, amino acids, sugars, and fatty acids (building blocks  of DNA, protein, carbohydrate, and fat, respectively).  Also included are lignin and cellulose which are essential for plant growth.  On the other hand, the secondary metabolism provides species-specific functions.  It includes medicinal metabolites such as antibiotics and herbal medicines.
 
</p>
 
| style="width:50%;vertical-align:top;padding-left:0.2em" |
 
<p>
 
(以下の情報は共立出版バイオインフォマティクス事典で有田の執筆項目「代謝」より、出版社の許可を得て転載)</p>
 
<p>
 
代謝とは,生体内でおこなわれる物理化学反応の総体,または特定の分子に関与する物理化学反応の総体である.機能の観点から,生命の維持に必須の物質群に関わる基礎/一次代謝と,生命維持に必須ではない二次代謝に分けられる.生命に欠かせない核酸,アミノ酸,糖,脂肪酸(それぞれDNA,タンパク質,炭水化物,脂質の構成単位)は基礎代謝物とよばれる.また植物に必須のリグニンやセルロースも基礎代謝物に分類される.これに対し二次代謝は,生物種に固有の機能を提供する.抗生物質や生薬など,人間が利用してきた薬効成分はいずれも二次代謝物である.
 
</p>
 
|}
 
 
<center>
 
<center>
 
{| class="wikitable" border="1" cellpadding="2" cellspacing="1" margin: 1em 1em 1em 1em"
 
{| class="wikitable" border="1" cellpadding="2" cellspacing="1" margin: 1em 1em 1em 1em"
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|- valign="top"
 
|- valign="top"
 
|align="center"|[[:Category:BMIO|BMIO: Inorganics]]<br>無機物<br>[[Image:BMIO.png|100px]]<br>metals, phosphates etc.<br>金属、燐酸等
 
|align="center"|[[:Category:BMIO|BMIO: Inorganics]]<br>無機物<br>[[Image:BMIO.png|100px]]<br>metals, phosphates etc.<br>金属、燐酸等
|align="center"|[[:Category:BMAA|BMAA: Amino acids]]<br>アミノ酸<br>[[Image:BMAA.png|100px]]
+
|align="center"|[[:Category:BMAA|BMAA: Amino acids]]<br>アミノ酸<br>[[Image:BMAA.png|100px]]<br>proper amino acids
|align="center"|[[:Category:BMAD|BMAD: Amino acid derivatives]]<br>アミノ酸誘導体<br>[[Image:BMAD.png|120px]]<br>peptides etc.<br>ペプチド等
+
|align="center"|[[:Category:BMAX|BMAX: Amino acid derivatives]]<br>アミノ酸誘導体<br>[[Image:BMAX.png|140px]]<br>peptides etc.<br>修飾物、ペプチド等
 
|- valign="top"
 
|- valign="top"
 
|align="center" valign="center"|
 
|align="center" valign="center"|
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  ! colspan="2"|2nd Class
 
  ! colspan="2"|2nd Class
 
  |-
 
  |-
  |[[:Category:BMIOMT|BMIOMT]]||[[:Category:BMIOMT|Metals and halogens]]<br>[[Image:BMIOMT.png|60px]]
+
  |[[:Category:BMIO|BMIOMT]]||[[:Category:BMIO|Metals and halogens]]<br>[[Image:BMIOMT.png|60px]]
 
  |-
 
  |-
  |[[:Category:BMIONT|BMIONT]]||[[:Category:BMIONT|Nitrogen compounds]]<br>[[Image:BMIONT.png|60px]]
+
  |[[:Category:BMIO|BMIONT]]||[[:Category:BMIO|Nitrogen compounds]]<br>[[Image:BMIONT.png|50px]]
 
  |-
 
  |-
  |[[:Category:BMIOOX|BMIOOX]]||[[:Category:BMIOOX|Oxidized elements]]<br>[[Image:BMIOOX.png|60px]]
+
  |[[:Category:BMIO|BMIOOX]]||[[:Category:BMIO|Oxidized elements]]<br>[[Image:BMIOOX.png|50px]]
 
  |-
 
  |-
  |[[:Category:BMIOPP|BMIOPP]]||[[:Category:BMIOPP|phosphates]] <br>[[Image:BMIOPP.png|60px]]
+
  |[[:Category:BMIO|BMIOPP]]||[[:Category:BMIO|phosphates]] <br>[[Image:BMIOPP.png|80px]]
 
  |-
 
  |-
  |[[:Category:BMIOSF|BMIOSF]]||[[:Category:BMIOSF|sulfates]] <br>[[Image:BMIOSF.png|60px]]
+
  |[[:Category:BMIO|BMIOSF]]||[[:Category:BMIO|sulfates]] <br>[[Image:BMIOSF.png|80px]]
 
  |}
 
  |}
 
|align="center" valign="center"|
 
|align="center" valign="center"|
Line 47: Line 86:
 
  ! colspan="2"|2nd Class
 
  ! colspan="2"|2nd Class
 
  |-
 
  |-
  |[[:Category:BMAA|BMAASn]]||[[:Category:BMAA|Straight chain]]<br>[[Image:BMAASn.png|80px]]
+
  |[[:Category:BMAA|BMAASn]]||[[:Category:BMAA|Straight chain]]<br>[[Image:BMAASn.png|90px]]
 
  |-
 
  |-
  |[[:Category:BMAA|BMAABn]]||[[:Category:BMAA|Branched chain]]<br>[[Image:BMAABn.png|80px]]
+
  |[[:Category:BMAA|BMAABn]]||[[:Category:BMAA|Branched chain]]<br>[[Image:BMAABn.png|110px]]
|-
+
|[[:Category:BMAACC|BMAACC]]||[[:Category:BMAACC|Cyclic]]<br>[[Image:BMAACC.png|90px]]
+
 
  |}
 
  |}
 
|align="center" valign="center"|
 
|align="center" valign="center"|
Line 58: Line 95:
 
  ! colspan="2"|2nd Class
 
  ! colspan="2"|2nd Class
 
  |-
 
  |-
  |[[:Category:BMAD|BMADSn]]||[[:Category:BMAD|Straight chain]]<br>[[Image:BMADSn.png|90px]]
+
  |[[:Category:BMAX|BMAXSn]]||[[:Category:BMAX|Straight chain]]<br>[[Image:BMAXSn.png|90px]]
 
  |-
 
  |-
  |[[:Category:BMAD|BMADBn]]||[[:Category:BMAD|Branched chain]]<br>[[Image:BMADBn.png|90px]]
+
  |[[:Category:BMAX|BMAXBn]]||[[:Category:BMAX|Branched chain]]<br>[[Image:BMAXBn.png|110px]]
 
  |-
 
  |-
  |[[:Category:BMADCC|BMADCC]]||[[:Category:BMADCC|Cyclic]]<br>[[Image:BMADCC.png|90px]]
+
  |[[:Category:BMAX|BMAXDP]]||[[:Category:BMAX|Dipeptide]]<br>[[Image:BMAXDP.png|130px]]
 
  |-
 
  |-
  |[[:Category:BMADDP|BMADDP]]||[[:Category:BMADDP|Dipeptide]]<br>[[Image:BMADDP.png|120px]]
+
  |[[:Category:BMAX|BMAXTP]]||[[:Category:BMAX|Tripeptide]]<br>[[Image:BMAXTP.png|140px]]
|-
+
|[[:Category:BMADTP|BMADTP]]||[[:Category:BMADTP|Tripeptide]]<br>[[Image:BMADTP.png|120px]]
+
 
  |}
 
  |}
 
|- valign="top"
 
|- valign="top"
|align="center"|[[:Category:BMFY|BMFY: Fatty acyl]]<br>アシル<br>[[Image:BMFY.png|100px]]<br>Tree-shaped<br>樹状のもの
+
|align="center"|[[:Category:BMAC|BMAC: Amino-cyclic]]<br>環をもつアミノ酸<br>[[Image:BMAC.png|120px]]<br>Trp, Pro, His etc.
|align="center"|[[:Category:BMMC|BMMC: Mono-cyclic]]<br>単環<br>[[Image:BMMC.png|60px]]<br>benzene, pyrimidine etc.<br>ベンゼン、ピリミジン環
+
|align="center"|[[:Category:BMMC|BMMC: Mono-cyclic]]<br>単環<br>[[Image:BMMC.png|50px]]<br>benzene, pyrimidine etc.<br>ベンゼン、ピリミジン環
 
|align="center"|[[:Category:BMCC|BMCC: Conjugated cyclic]]<br>複合環<br>[[Image:BMCC.png|100px]]<br>purine, porphyrin etc.<br>プリン、ポルフィリン環
 
|align="center"|[[:Category:BMCC|BMCC: Conjugated cyclic]]<br>複合環<br>[[Image:BMCC.png|100px]]<br>purine, porphyrin etc.<br>プリン、ポルフィリン環
 
|- valign="top"
 
|- valign="top"
Line 76: Line 111:
 
  {| class="collapsible collapsed" border="1" cellspacing="0" width="150"
 
  {| class="collapsible collapsed" border="1" cellspacing="0" width="150"
 
  |-
 
  |-
  ! colspan="2"|2nd Class
+
  ! colspan="4"|2nd Class
 
  |-
 
  |-
  |[[:Category:BMFYSn|BMFYSn]]||[[:Category:BMFYSn|Straight chain]]<br>[[Image:BMFYSn.png|90px]]
+
  |[[:Category:BMAC|BMACBZ]]||[[:Category:BMAC|with benzene]]<br>[[Image:BMACBZ.png|60px]]
 
  |-
 
  |-
  |[[:Category:BMFYBn|BMFYBn]]||[[:Category:BMFYBn|Branched chain]]<br>[[Image:BMFYBn.png|90px]]
+
  |[[:Category:BMAC|BMACID]]||[[:Category:BMAC|with indole]]<br>[[Image:BMACID.png|75px]]
 +
|-
 +
|[[:Category:BMAC|BMACIZ]]||[[:Category:BMAC|with imidazole]]<br>[[Image:BMACIZ.png|65px]]
 +
|-
 +
|[[:Category:BMAC|BMACPL]]||[[:Category:BMAC|with pyrrolidine]]<br>[[Image:BMACPL.png|75px]]
 
  |}
 
  |}
 
|align="center" valign="center"|
 
|align="center" valign="center"|
 
  {| class="collapsible collapsed" border="1" cellspacing="0" width="150"
 
  {| class="collapsible collapsed" border="1" cellspacing="0" width="150"
 
  |-
 
  |-
  ! colspan="2"|2nd Class
+
  ! colspan="4"|2nd Class
 
  |-
 
  |-
  |[[:Category:BMMCBZ|BMMCBZ]]||[[:Category:BMMCBZ|Benzene]]<br>[[Image:BMMCBZ.png|60px]]
+
  |[[:Category:BMMCBZ|BMMCBZ]]||[[:Category:BMMCBZ|Benzene]]<br>[[Image:BMMCBZ.png|40px]]
 +
 
 +
|[[:Category:BMMCPY|BMMCPY]]||[[:Category:BMMCPY|Pyrimidine]]<br>[[Image:BMMCPY.png|40px]]
 
  |-
 
  |-
  |[[:Category:BMMCPY|BMMCPY]]||[[:Category:BMMCPY|Pyrimidine]]<br>[[Image:BMMCPY.png|60px]]
+
  |[[:Category:BMMC|BMMCPD]]||[[:Category:BMMC|Pyridine]]<br>[[Image:BMMCPD.png|40px]]
 +
 
 +
|[[:Category:BMMC|BMMCIZ]]||[[:Category:BMMC|Imidazole]]<br>[[Image:BMMCIZ.png|40px]]
 
  |-
 
  |-
  |[[:Category:BMMCPD|BMMCPD]]||[[:Category:BMMCPD|Pyridine]]<br>[[Image:BMMCPD.png|90px]]
+
  |[[:Category:BMMC|BMMCQN]]||[[:Category:BMMC|Quinone]]<br>[[Image:BMMCQN.png|40px]]
 +
 
 +
|[[:Category:BMMC|BMMCPL]]||[[:Category:BMMC|Pyrrolidine]]<br>[[Image:BMMCPL.png|40px]]
 
  |-
 
  |-
|[[:Category:BMMCIZ|BMMCIZ]]||[[:Category:BMMCIZ|Imidazole]]<br>[[Image:BMMCIZ.png|90px]]
+
|[[:Category:BMMC|BMMCTZ]]||[[:Category:BMMC|Thiazole]]<br>[[Image:BMMCTZ.png|40px]]
 +
|[[:Category:BMMC|BMMCLA]]||[[:Category:BMMC|Lactone]]<br>[[Image:BMMCLA.png|60px]]
 +
 
 
  |-
 
  |-
  |[[:Category:BMMCQN|BMMCQN]]||[[:Category:BMMCQN|Quinone]]<br>[[Image:BMMCQN.png|90px]]
+
  |[[:Category:BMMC|BMMCAC]]||[[:Category:BMMC|Aliphatic cycle]]<br>[[Image:BMMCAC.png|40px]]
 +
|[[:Category:BMMC|BMMCHC]]||[[:Category:BMMC|Hetero cycle]]<br>[[Image:BMMCHC.png|40px]]
 
  |-
 
  |-
  |[[:Category:BMMCPL|BMMCPL]]||[[:Category:BMMCPL|Pyrrolidine]]<br>[[Image:BMMCPL.png|90px]]
+
  |[[:Category:BMMC|BMMCVA]]
 +
|colspan="3"| [[:Category:BMMC|Retinol]] [[Image:BMMCVA.png|120px]]
 
  |-
 
  |-
|[[:Category:BMMCTZ|BMMCTZ]]||[[:Category:BMMCTZ|Thiazole]]<br>[[Image:BMMCTZ.png|90px]]
+
|[[:Category:BMMC|BMMCAS]]
 +
|colspan="3"|[[:Category:BMMC|Assembled cycle]]<br>[[Image:BMMCAS.png|90px]]
 +
|}
 +
|align="center" valign="center"|
 +
{| class="collapsible collapsed" border="1" cellspacing="0" width="150"
 
  |-
 
  |-
  |[[:Category:BMMCVA|BMMCVA]]||[[:Category:BMMCVA|Retinol]]<br>[[Image:BMMCVA.png|90px]]
+
  ! colspan="4"|2nd Class
 
  |-
 
  |-
  |[[:Category:BMMCLA|BMMCLA]]||[[:Category:BMMCLA|Lactone]]<br>[[Image:BMMCLA.png|90px]]
+
  |[[:Category:BMCCPU|BMCCPU]]
 +
||[[:Category:BMCCPU|Purine]]<br>[[Image:BMCCPU.png|70px]]
 +
|[[:Category:BMCCPT|BMCCPT]]
 +
||[[:Category:BMCCPT|Pteridine]]<br>[[Image:BMCCPT.png|70px]]
 
  |-
 
  |-
  |[[:Category:BMMCAC|BMMCAC]]||[[:Category:BMMCAC|Aliphatic cycle]]<br>[[Image:BMMCAC.png|60px]]
+
  |[[:Category:BMCCPP|BMCCPP]]
 +
||[[:Category:BMCCPP|Porphyrin]]<br>[[Image:BMCCPP.png|70px]]
 +
|[[:Category:BMCC|BMCCID]]
 +
||[[:Category:BMCC|Indole]]<br>[[Image:BMCCID.png|70px]]
 
  |-
 
  |-
  |[[:Category:BMMCHC|BMMCHC]]||[[:Category:BMMCHC|Hetero cycle]]<br>[[Image:BMMCHC.png|60px]]
+
  |[[:Category:BMCC|BMCCQI]]
 +
||[[:Category:BMCC|Quinoline]]<br>[[Image:BMCCQI.png|70px]]
 +
|[[:Category:BMCC|BMCCNP]]
 +
||[[:Category:BMCC|Naphthalen]]<br>[[Image:BMCCNP.png|70px]]
 
  |-
 
  |-
  |[[:Category:BMMCAS|BMMCAS]]||[[:Category:BMMCAS|Assembled cycle]]<br>[[Image:BMMCAS.png|90px]]
+
  |[[:Category:BMCC|BMCCCC]]
 +
||[[:Category:BMCC|Other condensed cycle]]<br>[[Image:BMCCCC.png|70px]]
 +
|[[:Category:BMCC|BMCCBR]]
 +
||[[:Category:BMCC|Bridged cycle]]<br>[[Image:BMCCBR.png|50px]]
 +
|-
 +
|[[:Category:BMCC|BMCCVE]]
 +
|colspan="3"|[[:Category:BMCC|Tocopherol]]<br>[[Image:BMCCVE.png|150px]]
 
  |}
 
  |}
|align="center" valign="center"|
+
|- valign="top"
 +
|align="center"|[[:Category:BMFY|BMFY: Fat acyl]]<br>アシル<br>[[Image:BMFY.png|100px]]<br>Tree-shaped<br>樹状のもの
 +
|align="center"|[[:Category:BMSU|BMSU: Sugar]]<br>炭水化物<br>[[Image:BMSU.png|100px]]<br>mono, disaccharide<br>単糖、二糖
 +
|align="center"|[[:Category:BMXX|BMXX: Others]]<br>その他<br> [[Image:BMXX.png|100px]]
 +
|- valign="top"
 +
|align="center" valign="center"|
 
  {| class="collapsible collapsed" border="1" cellspacing="0" width="150"
 
  {| class="collapsible collapsed" border="1" cellspacing="0" width="150"
 
  |-
 
  |-
 
  ! colspan="2"|2nd Class
 
  ! colspan="2"|2nd Class
 
  |-
 
  |-
  |[[:Category:BMCCPU|BMCCPU]]||[[:Category:BMCCPU|Purine]]<br>[[Image:BMCCPU.png|90px]]
+
  |[[:Category:BMFY|BMFYSn]]||[[:Category:BMFY|Straight chain]]<br>[[Image:BMFYSn.png|70px]]
 
  |-
 
  |-
  |[[:Category:BMCCPT|BMCCPT]]||[[:Category:BMCCPT|Pteridine]]<br>[[Image:BMCCPT.png|90px]]
+
  |[[:Category:BMFY|BMFYBn]]||[[:Category:BMFY|Branched chain]]<br>[[Image:BMFYBn.png|80px]]
 +
|}
 +
|align="center" valign="center"|
 +
{| class="collapsible collapsed" border="1" cellspacing="0" width="150"
 
  |-
 
  |-
  |[[:Category:BMCCPP|BMCCPP]]||[[:Category:BMCCPP|Porphyrin]]<br>[[Image:BMCCPP.png|90px]]
+
  ! colspan="2"|2nd Class
 
  |-
 
  |-
  |[[:Category:BMCCID|BMCCID]]||[[:Category:BMCCID|Indole]]<br>[[Image:BMCCID.png|90px]]
+
  |[[:Category:BMSU|BMSUM4]]||[[:Category:BMSU|Monosaccharide (C4)]]<br>[[Image:BMSUM4.png|70px]]
 
  |-
 
  |-
  |[[:Category:BMCCVE|BMCCVE]]||[[:Category:BMCCVE|Tocopherol]]<br>[[Image:BMCCVE.png|90px]]
+
  |[[:Category:BMSU|BMSUM5]]||[[:Category:BMSU|Monosaccharide (C5)]]<br>[[Image:BMSUM5.png|70px]]
 
  |-
 
  |-
  |[[:Category:BMCCQI|BMCCQI]]||[[:Category:BMCCQI|Quinoline]]<br>[[Image:BMCCQI.png|90px]]
+
  |[[:Category:BMSU|BMSUM6]]||[[:Category:BMSU|Monosaccharide (C6)]]<br>[[Image:BMSUM6.png|70px]]
 
  |-
 
  |-
  |[[:Category:BMCCNP|BMCCNP]]||[[:Category:BMCCNP|Naphthalen]]<br>[[Image:BMCCNP.png|90px]]
+
  |[[:Category:BMSU|BMSUM7]]||[[:Category:BMSU|Monosaccharide (C >7 )]]<br>[[Image:BMSUM7.png|70px]]
|-
+
|[[:Category:BMCCCC|BMCCCC]]||[[:Category:BMCCCC|Condensed cycle]]<br>[[Image:BMCCCC.png|90px]]
+
|-
+
|[[:Category:BMCCBR|BMCCBR]]||[[:Category:BMCCBR|Bridged cycle]]<br>[[Image:BMCCBR.png|90px]]
+
 
  |}
 
  |}
|- valign="top"
+
|align="center" valign="center"|
|align="center"|[[:Category:BMXX|BMXX: Others]]<br>その他<br>[[Image:BMXX.png|100px]]<br><br>
+
|align="center"|[[:Category:|:]]<br><br>[[Image: .png|100px]]<br><br>
+
|align="center"|[[:Category:|:]]<br><br>[[Image: .png|75px]]<br><br>
+
|- valign="top"
+
|
+
 
  {| class="collapsible collapsed" border="1" cellspacing="0" width="150"
 
  {| class="collapsible collapsed" border="1" cellspacing="0" width="150"
 
  |-
 
  |-
 
  ! colspan="2"|2nd Class
 
  ! colspan="2"|2nd Class
 
  |-
 
  |-
  |[[:Category:BMXXSx|BMXXSx]]||[[:Category:BMXXSx| ]]<br>[[Image:BMXXSX.png|60px]]
+
  |[[:Category:BMXX|BMXXSx]]||[[:Category:BMXX|Straight]]<br>[[Image:BMXXSX.png|60px]]
 
  |-
 
  |-
  |[[:Category:BMXXBx|BMXXBx]]||[[:Category:BMXXBx| ]]<br>[[Image:BMXXBX.png|60px]]
+
  |[[:Category:BMXX|BMXXBx]]||[[:Category:BMXX|Branched]]<br>[[Image:BMXXBX.png|60px]]
  |}
+
  |}  
||
+
||
+
 
|}
 
|}
 
</center>
 
</center>
Line 155: Line 220:
 
<!--- Class Information (Do not delete. It is used by Template:Hierarchy.)
 
<!--- Class Information (Do not delete. It is used by Template:Hierarchy.)
 
&&BM&&Basic Metabolites&&
 
&&BM&&Basic Metabolites&&
&&BMIO&&Inorganics&&
+
&&BMIO&&Inorganics 無機物&&
&&BMAA&&Amino acids&&
+
&&BMIOOX&&oxidized elements 酸化物(no C)&&
&&BMAD&&Amino acid derivatives&&
+
&&BMIOMT&&metals and halogens 金属、ハロゲン&&
&&BMFY&&Fatty acyl&&
+
&&BMIONT&&nitrogen compounds 窒素&&
&&BMCC&&Conjugated cycle&&
+
&&BMIOPP&&phosphates リン酸&&
&&BMMC&&mono- or assembled cycle&&
+
&&BMIOSF&&sulfates 硫黄&&
&&BMXX&&Others&&
+
 
 +
&&BMAA&&Amino acids アミノ酸&&
 +
&&BMAAS&&straight chain 鎖状&&
 +
&&BMAAB&&branched chain 分岐&&
 +
 
 +
&&BMAX&&Amino acid derivatives アミノ酸誘導体&&
 +
&&BMAXS&&straight chain 鎖状&&
 +
&&BMAXB&&branched chain 分岐&&
 +
&&BMAXDP&&di-peptide ジペプチド&&
 +
&&BMAXTP&&tri-peptide トリペプチド&&
 +
 
 +
&&BMAC&&Cyclic amino acids 環状アミノ酸&&
 +
&&BMACBZ&&benzene ring ベンゼン&&
 +
&&BMACID&&indole ring インドール&&
 +
&&BMACPL&&pyrrolidine ring ピロリジン&&
 +
&&BMACIZ&&imidazole ring イミダゾール&&
 +
 
 +
&&BMFY&&Fatty acyl 脂肪酸&&
 +
&&BMFYS&&straight chain 鎖状&&
 +
&&BMFYB&&branched chain 分岐&&
 +
 
 +
&&BMMC&&mono- or assembled cycle 単、複合環&&
 +
&&BMMCBZ&&benzene ring ベンゼン環&&
 +
&&BMMCBZ1S&&0-1 substitution&&
 +
&&BMMCBZ2O&&2 substitutions (ortho)&&
 +
&&BMMCBZ2M&&with 2 substitutions (meta)&&
 +
&&BMMCBZ2P&&with 2 substitutions (para)&&
 +
&&BMMCBZ3S&&with 3 substitutions&&
 +
&&BMMCBZ4S&&with 4-6 substitutions&&
 +
 
 +
&&BMMCPY&&pyrimidine ring ピリミジン環&&
 +
&&BMMCPYCT&&cytosine シトシン&&
 +
&&BMMCPYTY&&thymine チミン&&
 +
&&BMMCPYUR&&uracil ウラシル&&
 +
&&BMMCPYXX&&others その他&&
 +
 
 +
&&BMMCPD&&pyridine ring ピリジン環&&
 +
&&BMMCIZ&&imidazole ring イミダゾール環&&
 +
&&BMMCTZ&&thiazole ring チアゾール環&&
 +
&&BMMCQN&&quinone ring キノン環&&
 +
&&BMMCVA&&retinol ring レチノール環&&
 +
&&BMMCPL&&pyrrolidine ring ピロリジン環&&
 +
&&BMMCLA&&lacton ラクトン&&
 +
&&BMMCAC&&aliphatic cycle 脂肪族環&&
 +
&&BMMCACCH&&cyclohexane シクロヘキサン&&
 +
&&BMMCACEN&&cyclohexene シクロヘキセン&&
 +
&&BMMCACDE&&cyclohexadiene シクロヘキサジエン&&
 +
&&BMMCACXX&&others その他&&
 +
&&BMMCHC&&hetero cyclic ヘテロ環&&
 +
&&BMMCAS&&assembled 複合環&&
 +
 
 +
&&BMCC&&Conjugated cycle 共役環&&
 +
&&BMCCPU&&purine ring プリン環&&
 +
&&BMCCPUAD&&アデニン(アデニン、ヌクレオシド)&&
 +
&&BMCCPUAP&&アデニン(ヌクレオチド)&&
 +
&&BMCCPUGU&&グアニン(グアノシン)&&
 +
&&BMCCPUXA&&キサンチン&&
 +
&&BMCCPT&&pteridine ring プテリジン環&&
 +
&&BMCCPTFL&&flavin フラビン&&
 +
&&BMCCPTFO&&folic acid 葉酸&&
 +
&&BMCCPTPT&&others その他のプテリジン類&&
 +
&&BMCCPP&&porphyrin ring ポルフィリン環&&
 +
&&BMCCPPPO&&pyrrole ピロール&&
 +
&&BMCCPPPR&&porphyrinogen ポルフィリノーゲン&&
 +
&&BMCCPPHM&&heme ヘム&&
 +
&&BMCCPPPC&&precorrin プレコリン&&
 +
&&BMCCPPCB&&cobalamin コバラミン&&
 +
&&BMCCPPCL&&chlorophyl クロロフィル&&
 +
&&BMCCPPBL&&bilirubin ビリルビン&&
 +
&&BMCCID&&indole インドール&&
 +
&&BMCCVE&&tocopherol トコフェロール(ビタミンE)&&
 +
&&BMCCQI&&quinoline キノリン&&
 +
&&BMCCNP&&naphthalen ナフタレン&&
 +
&&BMCCCC&&condensed rings その他の縮合環&&
 +
&&BMCCBR&&bridged structure 架橋環構造&&
 +
 
 +
&&BMSUM4&&monosaccharide (4 carbons) 単糖(4炭素)&&
 +
&&BMSUM4A&&aldose アルドース&&
 +
&&BMSUM4K&&ketose ケトース&&
 +
&&BMSUM4H&&sugar alcohol 糖アルコール&&
 +
 
 +
&&BMSUM5&&monosaccharide (5 carbons) 単糖(5炭素)&&
 +
&&BMSUM5A&&aldose アルドース&&
 +
&&BMSUM5K&&ketose ケトース&&
 +
&&BMSUM5H&&sugar alcohol 糖アルコール&&
 +
&&BMSUM5N&&amino sugar アミノ糖&&
 +
&&BMSUM5U&&uronic acid ウロン酸&&
 +
&&BMSUM5L&&saccharic lactone 糖ラクトン&&
 +
 
 +
&&BMSUM6&&monosaccharide (6 carbons) 単糖(6炭素)&&
 +
&&BMSUM6A&&aldose アルドース&&
 +
&&BMSUM6K&&ketose ケトース&&
 +
&&BMSUM6H&&sugar alcohol 糖アルコール&&
 +
&&BMSUM6N&&amino sugar アミノ糖&&
 +
&&BMSUM6U&&uronic acid ウロン酸&&
 +
&&BMSUM6L&&saccharic lactone 糖ラクトン&&
 +
 
 +
&&BMSUM7&&monosaccharide (7 carbons) 単糖(7炭素)&&
 +
&&BMSUM7A&&aldose アルドース&&
 +
&&BMSUM7K&&ketose ケトース&&
 +
&&BMSUM7U&&uronic acid ウロン酸&&
 +
 
 +
&&BMSUM8&&monosaccharide (8 carbons) 単糖(8炭素)&&
 +
&&BMSUM8A&&aldose アルドース&&
 +
&&BMSUM8K&&ketose ケトース&&
 +
&&BMSUM8U&&uronic acid ウロン酸&&
 +
 
 +
&&BMSUM9&&monosaccharide (9 carbons) 単糖(9炭素)&&
 +
&&BMSUM9A&&aldose アルドース&&
 +
&&BMSUM9K&&ketose ケトース&&
 +
&&BMSUM9U&&uronic acid ウロン酸&&
 +
 
 +
&&BMSUD2&&disaccharide (12 carbons) 二糖(12炭素)&&
 +
&&BMSUD2A&&aldose アルドース&&
 +
&&BMSUD2K&&ketose ケトース&&
 +
&&BMSUD2H&&sugar alcohol 糖アルコール&&
 +
&&BMSUD2N&&amino sugar アミノ糖&&
 +
 
 +
&&BMSUPn&&polysaccharide 多糖&&
 +
&&BMSUP2A&&aldose アルドース&&
 +
&&BMSUP2K&&ketose ケトース&&
 +
&&BMSUP2N&&amino sugar アミノ糖&&
 +
 
 +
&&BMXX&&Others その他&&
 +
&&BMXXS&&straight chain 鎖状&&
 +
&&BMXXB&&branched chain 分岐&&
 
--->
 
--->
  
==Biosynthesis 生合成==
+
{{Doc:SysName}}

Latest revision as of 13:46, 2 June 2011

Basic Metabolism (基礎代謝)

Basic Metabolism Top
(代謝トップ)
Molecule Index
(化合物索引)
EC classes
( EC分類)
Input New Data
(新規入力)

Contents

[edit] Class Overview

(The following description is translated from an article written by Arita in "Encyclopedia of Bioinformatics" under the publisher's permission, Kyoritsu Co. Ltd.)

Metabolism is the total body of physicochemical reactions inside living systems. It can be functionally divided into two groups: the basic (or primary) metabolism essential for maintenance of life systems, and the non-essential secondary metabolism. Basic metabolites therefore include bases, amino acids, sugars, and fatty acids (building blocks of DNA, protein, carbohydrate, and fat, respectively). Also included are lignin and cellulose which are essential for plant growth. On the other hand, the secondary metabolism provides species-specific functions. It includes medicinal metabolites such as antibiotics and crude drugs.

[edit] 代謝物の種類

[edit] Design of Basic Metabolite ID numbers ID番号の設計

12-DIGIT

B M a a b b c c d d e e

  • a ... Structure type (Table 1)
  • b ... degree of unsaturation (Table 2)
  • c ... position of n-z (n minus z; also ω-z or omega-z) nomenclature (Table 3)
  • d ... structure type (Table 4)
  • e ... serial number

Table 1. Classification of Basic Metabolites
1st Class
BMIO: Inorganics
無機物
BMIO.png
metals, phosphates etc.
金属、燐酸等
BMAA: Amino acids
アミノ酸
BMAA.png
proper amino acids
BMAX: Amino acid derivatives
アミノ酸誘導体
BMAX.png
peptides etc.
修飾物、ペプチド等
BMAC: Amino-cyclic
環をもつアミノ酸
BMAC.png
Trp, Pro, His etc.
BMMC: Mono-cyclic
単環
BMMC.png
benzene, pyrimidine etc.
ベンゼン、ピリミジン環
BMCC: Conjugated cyclic
複合環
BMCC.png
purine, porphyrin etc.
プリン、ポルフィリン環
BMFY: Fat acyl
アシル
BMFY.png
Tree-shaped
樹状のもの
BMSU: Sugar
炭水化物
100px
mono, disaccharide
単糖、二糖
BMXX: Others
その他
BMXX.png


[edit] Systematic Name of Enzymes (酵素のシステム名)

EC (Enzyme Commission) number is assigned according to the type of reaction catalysed (EC level 1) and the type(s) of the substrate(s). Since reactions are written for the purpose of classification, the direction does not reflect the actually demonstrated catalysis. The systematic name always reflects the first enzyme-catalysed step, and subsequent transformations are written in parentheses, e.g. acetyl-CoA:glyoxylate C-acetyltransferase (thioester-hydrolysing, carboxymethyl-forming) (EC 2.3.3.9).

EC class 1 Oxidoreductase (酸化還元酵素)

In this class, a substrate is oxidized as hydrogen donor. The systematic name is donor:acceptor oxidoreductase. The common name is usually dehydrogenase, reductase (when reverse reaction is demonstrated), or oxydase (only when O2 is the acceptor).

EC class 2 Tranferase (転移酵素)

In this class, a chemical 'group' is transferred from a 'donor' to an 'acceptor'. The systematic name is donor:acceptor grouptransferase. The common name is usually acceptor grouptransferase, donor grouptransferase, or phosphorylase (when phosphate is an acceptor). Transaminase is formally considered as the combination of oxidative deamination of the donor followed by reductive amination of the acceptor, but is classified in this class (EC 2.6.1).

EC class 3 Hydrolase (加水分解酵素)

In this class, hydrolytic cleavage of C-O, C-N, C-C and some other bonds occurs. The systematic name is hydrolase. The common name is usually the substrate name with -ase. Hydrolase is formally considered as tranfer of a specific group to water as acceptor. The names of peptide hydrolases (proteinase) is based on their 'esterolytic' action.

EC class 4 Lyase (除去付加酵素)

In this class, C-C, C-O, C-N, and other bonds are cleaved by elimination, leaving double bonds or rings. The systematic name is substrate group-lyase. Major common names are decarboxylase, aldolase, and dehydratase. When reverse reaction is demonstrated, synthase (not synthetase) may be used. Pyridoxal-phosphate enzymes usually replace the eliminated substituent by some other group, and therefore, may be formally considered as alkyl-transferase.

EC class 5 Isomerase (異性化酵素)

In this class, geometry or structure is changed within one molecule. Common names include racemase, epimerase, (cis-trans-)isomerase, tautomerase, mutase or cycloisomerase.

EC class 6 Ligase (合成酵素)

In this class, two substrates are joined with the hydrolysis of ATP. The systematic name is X:Y ligase (ADP-forming). An obsolete common name is synthetase (not synthase in EC4).

[edit] Systematic Name of Metabolites (代謝物のシステム名)

準備中

Subcategories

This category has the following 8 subcategories, out of 8 total.

B

  • [×] BMAA(empty)
  • [×] BMAC(empty)
  • [×] BMAX(empty)

B cont.

  • BMCC(3 C)
  • [×] BMFY(empty)
  • [×] BMIO(empty)

B cont.

Pages in category "BM"

The following 2 pages are in this category, out of 2 total.

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