Selected Subsystem Examples, Notes and Illustrations

A collection of essays presented below illustrates the type of analysis that can be performed in SEED, the logics of subsystems-based approach, and the type of insight that can be gained by its application. Just as much, it illustrates the philosophy of the SEED project, an effort to support individuals annotating specific subsystems (SSs) across a collection of genomes. Voluntary contribution by such individuals, from graduate students to established experts in various fields of biology, sharing the results of their analysis with the community is a key impact on the content and functionality of the SEED. We consider a variety of strategies and styles in using SEED to be the strength of our project, which allows biologists to capture their diverse expertise and views in an unconstrained intuitive format.

In our view, a mission of this section of the Supplementary materials is to faithfully reflect upon this key aspect of the SEED project. Each contribution (a "story") in the collection below is an independent mini-publication by one or two individuals who invested their time in encoding and analysis of a particular SS. Various individuals in this heterogeneous group of contributors were driven by different research interests: from testing tools to in-depth understanding, from gene discovery to metabolic engineering, etc. Each contribution is a snapshot of an independent research project at different levels of expertise and completion, presented in an individual style without any imposed standards.

However, each essay invariably contains the key components, such as: (i) a list of functional roles included in a SS (ii) a fragment of SS spreadsheet illustrating variations between genomes, (iii) a simple diagram providing connections between functional roles, and, importantly, (iv) notes often pointing to open problems, "missing" genes, and conjectures generated using a variety of tools implemented in SEED. We believe that some of these conjectures will stimulate and provide an effective guidance for experimental efforts in the broad research community.

The links [Notes and Illustrations] and [PDF] point to the web-based and printable versions of each essay. The name of each story is a link leading to the actual populated subsystem available on one of the SEED servers ( When activated, the link will open the corresponding subsystem spreadsheet with the genomes (rows) sorted by phylogeny and the cells colored to display gene clustering on a chromosome (cells within the same row highlighted by a matching color contain genes located in close vicinity of each other).

Ammonia assimilation   [Notes and Illustrations]   [pdf]

Biotin_biosynthesis   [Notes and Illustrations]   [pdf]

Carotenoids   [Comments]  [Notes and Illustrations]   [pdf]

Chlorophyll_Biosynthesis   [Notes and Illustrations]  [pdf]

Coenzyme A Biosynthesis   [Notes and Illustrations]   [pdf]

DNA_Repair_Base_Excision   [Comments]   [Notes and Illustrations]

Embden-Meyerhof and Gluconeogenesis  [Summary]   [pdf]

Fatty Acid Biosynthesis FASII   [Notes and Illustrations]   [pdf]

Fe-S_cluster_assembly   [Notes and Illustrations]   [pdf]

FMN_and_FAD_biosynthesis   [Notes and Illustrations]   [pdf]

Folate_Biosynthesis   [Notes and Illustrations]   [pdf]

General_secretory_pathway   [Notes and Illustrations]   [pdf]

Glycerolipid and glycerphospholipid metabolism   [Notes and Illustrations]   [pdf]

Histidine_Biosynthesis   [Comments]   [Notes and Illustrations]

Histidine_Degradation   [Comments]   [Notes and Illustrations]

InorgAnic_Sulfur_Assimilation   [Notes and Illustrations]   [pdf]

Isoprenoid_Biosynthesis   [Notes and Illustrations]   [pdf]

Lysine Biosynthesis DAP Pathway   [Notes and Illustration]   [pdf]

Methionine_Biosynthesis   [Notes and Illustrations]   [pdf]

Methylcitrate cycle   [Notes and Illustrations]   [pdf]

N-Acetyl-D-Glucosamine_Utilization   [Notes and Illustrations]   [pdf]

NAD_and_NADP_cofactor_biosynthesis_global   [Notes and Illustrations]   [pdf]

Nickel and Cobalt Transport   [Notes and Illustrations]   [pdf]

Nitrogen Oxides Metabolism  [Summary]   [pdf]

Peptidoglycan Biosynthesis   [Comments]  [Notes and Illustrations]   [pdf]

Phenylalanine synthesis   [Comments]

Phycobilisome   [Notes and Illustrations]   [pdf]

Porphyrin, Heme, and Siroheme Biosynthesis   [Notes and Illustrations]   [pdf]

Pterin_biosynthesis   [Notes and Illustrations]   [pdf]

Queuosine-Archaeosine Biosynthesis   [Notes and Illustrations]   [pdf]

Ribonucleotide_reduction   [Notes and Illustrations]   [pdf]

Ribosomal_proteins  [Summary]

Siderophore Enterobactin  [Summary]  [pdf]

Succinate_dehydrogenase   [Comments]   [Notes and Illustrations]   [pdf]

TCA Cycle   [Comments]   [Notes and Illustrations]   [pdf]

Terminal Cytochrome Oxidases  [Summary]  [pdf]

Thiamin_biosynthesis   [Notes and Illustrations]   [pdf]

Ubiquinone_Biosynthesis   [Notes and Illustrations]   [pdf]

UDP-N-acetylmuramate_from_Fructose-6-phosphate   [Notes and Illustrations]   [pdf]