Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms.

The functional repertoire of a cell is largely embodied in its proteome, the collection of proteins encoded in the genome of an organism. The molecular functions of proteins are the direct consequence of their structure and structure can be inferred from sequence using hidden Markov models of structural recognition. Here we analyze the functional annotation of protein domain structures in almost a thousand sequenced genomes, exploring the functional and structural diversity of proteomes. We find there is a remarkable conservation in the distribution of domains with respect to the molecular functions they perform in the three superkingdoms of life. In general, most of the protein repertoire is spent in functions related to metabolic processes but there are significant differences in the usage of domains for regulatory and extra-cellular processes both within and between superkingdoms. Our results support the hypotheses that the proteomes of superkingdom Eukarya evolved via genome expansion mechanisms that were directed towards innovating new domain architectures for regulatory and extra/intracellular process functions needed for example to maintain the integrity of multicellular structure or to interact with environmental biotic and abiotic factors (e.g., cell signaling and adhesion, immune responses, and toxin production). Proteomes of microbial superkingdoms Archaea and Bacteria retained fewer numbers of domains and maintained simple and smaller protein repertoires. Viruses appear to play an important role in the evolution of superkingdoms. We finally identify few genomic outliers that deviate significantly from the conserved functional design. These include Nanoarchaeum equitans, proteobacterial symbionts of insects with extremely reduced genomes, Tenericutes and Guillardia theta. These organisms spend most of their domains on information functions, including translation and transcription, rather than on metabolism and harbor a domain repertoire characteristic of parasitic organisms. In contrast, the functional repertoire of the proteomes of the Planctomycetes-Verrucomicrobia-Chlamydiae superphylum was no different than the rest of bacteria, failing to support claims of them representing a separate superkingdom. In turn, Protista and Bacteria shared similar functional distribution patterns suggesting an ancestral evolutionary link between these groups.

Introduction

Proteins are active components of molecular machinery that perform vital functions for cellular and organismal life [1,2]. Information in the DNA is copied into messenger RNA that is generally translated into proteins by the ribosome. Nascent polypeptide chains are unfolded random coils but quickly undergo conformational changes to produce characteristic and functional folds. These folds are three-dimensional (3D) structures that define the native state of proteins [3,4]. Biologically active proteins are made up of well-packed structural and functional units referred to as domains. Domains appear either singly or in combination with other domains in a protein and act as modules by engaging in combinatorial interplays that enhance the functional repertoires of cells [5]. While molecular interactions between domains in mutidomain proteins play important roles in the evolution of protein repertoires [6], it is the domain structure that is maintained in proteins for long periods of evolutionary time [7-9]. This is in sharp contrast to amino acid sequence, which is highly variable. For this reason, protein domains are also considered evolutionary units [7,10-12].

Classification of Domains

Domains that are evolutionarily related can be grouped together in hierarchical classifications [1,10,13]. One scheme of classifying protein domains is the well-established “Structural Classification of Proteins” (SCOP). The SCOP database groups domains that have sequence conservation (generally with >30% pairwise amino acid residue identities) into fold families (FFs), FFs with structural and functional evidence of common ancestry into fold superfamilies (FSFs), FSFs with common 3D structural topologies into folds (Fs), and Fs sharing a same general architecture into protein classes [10,14]. SCOP identifies protein domains using concise classification strings (css) (e.g., c.26.1.2, where c represents the protein class, 26 the F, 1 the FSF and 2 the FF). The 97,178 domains indexed in SCOP 1.73 (corresponding to 34,494 PDB entries) are classified into 1,086 F, 1,777 FSFs, and 3,464 FFs. Compared to the number of protein entries in UniProt (531,473 total entries as of July 27, 2011) the number of domain structural designs at these different levels of structural abstraction is quite limited. Their relatively small number suggests that fold space is finite and is evolutionarily highly conserved [1,7,15].

Assigning FSF Structures to Proteomes

Genome-encoded proteins can be scanned against advanced linear hidden Markov models (HMMs) of structural recognition in SUPERFAMILY [16,17]. HMM libraries are generated using the iterative Sequence Alignment and Modeling (SAM) method. SAM is considered one of the most powerful algorithms for detecting remote homologies [18]. The SUPERFAMILY database currently provides FSF structural assignments for a total of 1,245 model organisms including 96 Archaea, 861 Bacteria and 288 Eukarya.

Assigning Functional Categories to Protein Domains

Assigning molecular functions to FSFs is a difficult task since approximately 80% of the FSFs defined in SCOP are multi-functional and highly diverse [19]. For example, most of the ancient FSFs, such as the P-loop-containing NTP hydrolase FSF (c.37.1), are highly abundant in nature and include many FFs (20 in case of c.37.1). Each of those families may have functions that impinge on multiple and distinct pathways or networks. The functional annotation scheme introduced by Vogel and Chothia in SUPERFAMILY is a one-to-one mapping scheme that is based on information from various resources, including the Cluster of Orthologus Groups (COG) and Gene Ontology (GO) databases and manual surveys [20-23]. When a FSF is involved in multiple functions, the most predominant function is assigned to that multi-functional FSF under the assumption that the most dominant function is the most ancient and predominantly present in all proteomes. The error rate in assignments is estimated to be <10% for large FSFs and <20% for all FSFs [23].

The SUPERFAMILY functional classification maps seven general functional categories to 50 detailed functional categories in a two-tier hierarchy (Table 1). The seven general categories include Metabolism, Information, Intracellular processes (ICP), Extracellular processes (ECP), Regulation, General, and Other (we will refer to them as “categories” and “functional repertoires” interchangeably). In this study, we take advantage of this coarse-grained functional annotation scheme to assign individual functional categories to FSFs. We are aware that this one-to-one mapping may not provide a complete profile for multi-functional domains [19]. Dissection of such detailed functions and their comparison across organisms is a difficult problem that we will not address in this study. In contrast, we focus on domains defined at FSF level and use the coarse-grained functional annotation scheme to explore the functional diversity of the proteomes encoded in genomes that have been completely sequenced. Our results yield a global picture of the functional organization of proteomes that is only possible with this classification scheme. Results suggest that the functional structure of proteomes is remarkably conserved across all organisms, ranging from small bacteria to complex eukaryotes. There is also evidence for the existence of few outliers that deviate from global trends. Here we explore what makes these proteomes distinct.

Table 1

Mapping between the general and minor functional categories for 1,781 protein domains defined in structural classification of proteins (SCOP) 1.73 and the number of fold superfamilies (FSFs) corresponding to each minor category in our dataset of 965 organisms. A total of 135 FSFs could not be annotated. m/tr, metabolism and transport.

Functional category	Minor categories	No. of FSF domains
Metabolism (533 FSFs)	Energy	54
	Photosynthesis	20
	E- transfer	31
	Amino acids m/tr	20
	Nitrogen m/tr	1
	Nucleotide m/tr	30
	Carbohydrate m/tr	30
	Polysaccharide m/tr	21
	Storage	0
	Coenzyme m/tr	50
	Lipid m/tr	17
	Cell envelope m/tr	8
	Secondary metabolism	11
	Redox	55
	Transferases	29
	Other enzymes	156
General (131 FSFs)	Small molecule binding	27
	Ion binding	13
	Lipid/membrane binding	4
	Ligand binding	3
	General	28
	Protein interaction	49
	Structural protein	7
Information (201 FSFs)	Chromatin structure	7
	Translation	92
	Transcription	24
	DNA replication/repair	68
	RNA processing	10
	Nuclear structure	0
Other (273 FSFs)	Unknown function	200
	Viral proteins	73
Extracellular processes (95 FSFs)	Cell adhesion	31
	Immune response	19
	Blood clotting	5
	Toxins/defense	40
Intracellular processes (208 FSFs)	Cell cycle, Apoptosis	20
	Phospholipid m/tr	6
	Cell motility	20
	Trafficking/secretion	0
	Protein modification	35
	Proteases	52
	Ion m/tr	21
	Transport	54
Regulation (205 FSFs)	RNA binding, m/tr	19
	DNA-binding	66
	Kinases/phosphatases	15
	Signal transduction	53
	Other regulatory function	34
	Receptor activity	18

Results and Discussion

General Patterns in the Distribution of FSF Domain Functions

We studied the molecular functions of 1,646 domains defined at the FSF level of structural abstraction (SCOP 1.73) that are present in the proteomes of a total of 965 organisms spanning the three superkingdoms. A total of 135 FSFs that could not be annotated were excluded from analysis. For these FSFs, the functional annotation is not available. Out of the 1,646 FSFs studied, approximately one-third (32.38%) performs molecular functions related to Metabolism. Categories Other (16.58%), ICP (12.63%), Regulation (12.45%), and Information (12.21%) are uniformly distributed within proteomes. In contrast, General (7.96%) and ECP (5.77%) are significantly underrepresented compared to the rest (Figure 1(A)). The total number of FSFs in each category exhibits the following decreasing trend: Metabolism > Other > ICP > Regulation > Information > General > ECP. These patterns of FSF number and relative proteome content are for the most part maintained when studying the functional annotation of FSFs belonging to each superkingdom (Figure 1(B)). However, the number of FSFs in each superkingdom varies considerably and increases in the order Archaea, Bacteria and Eukarya, as we have shown in earlier studies [7].

Figure 1

Number of protein FSFs annotated for each functional category defined in SCOP 1.73 (A) and in the three superkingdoms (B). The functional distributions show that coarse-grained functions are conserved across cellular proteomes and Metabolism is the most dominant functional category. Numbers in parentheses indicate the total number of FSFs annotated in each dataset. The number of FSFs increases in the order Archaea, Bacteria and Eukarya.

The significantly higher number of FSFs devoted to Metabolism is an anticipated result given the central importance of metabolic networks. However, the much larger number of FSFs corresponding to Other is quite unexpected. The 273 FSFs belonging to this category include 200 and 73 FSFs in sub-categories unknown functions and viral proteins, respectively. The sub-category unknown function includes FSFs for which the functions are either unknown or are unclassifiable. Viruses are defined as simple biological entities that are considered to be “gene poor” relatives of cellular organisms [24]. However, the number of domains belonging to viral proteins that are present in cellular organisms makes a noteworthy contribution to the total pool of FSFs (4.43%). Thus, viruses have a much more rich and diverse repertoire of domain structures than previously thought and their association with cellular life has contributed considerable structural diversity to the proteomic make up (A. Nasir, K.M. Kim and G. Caetano-Anollés, ms. in preparation).

The numbers of FSFs belonging to categories Regulation, Information, and ICP are uniformly distributed in proteomes. However, the ECP category is the least represented, perhaps because this category is the last to appear in evolution [7,15]. Extra cellular processes are more important to multicellular organisms (mainly eukaryotes) than to unicellular organisms. Multicellular organisms need efficient communication, such as signaling and cell adhesion. They also trigger immune responses and produce toxins when defending from parasites and pathogens. These ECP processes, which are depicted in the minor categories of cell adhesion, immune response, blood clotting and toxins/defense, are needed when interacting with environmental biotic and abiotic factors and for maintaining the integrity of multicellular structure. These categories are also present in the microbial superkingdoms but their functional role may be different than in Eukarya.

We note that current genomic research is highly shifted towards the sequencing of microbial genomes, especially those that hold parasitic lifestyles and are of bacterial origin. In fact, 67% of proteomes in our dataset belong to Bacteria. This bias can affect conclusions drawn from global trends such as those in Figure 1(A), including the under-representation of ECP FFs, because of their decreased representation in microbial proteomes.

Distribution of FSF Domain Functions in the Three Superkingdoms of Life

In order to explore whether the overall distribution of general functional categories differs in organisms belonging to the three superkingdoms, we analyzed proteomes at the species level and calculated both the percentage and actual number of FSFs corresponding to different functional repertoires (Figure 2).

Figure 2

The functional distribution of FSFs in individual proteomes of the three superkingdoms. Both the percentage (A) and actual FSF numbers (B) indicate conservation of functional distributions in proteomes and the existence of considerable functional flexibility between superkingdoms. Dotted vertical lines indicate genomic outliers. Insets highlight the interplay between Metabolism (yellow trend lines) and Information (red trend lines) in N. equitans.

FSF domains follow the following decreasing trend in both the percentage and actual counts of FSFs, and do so consistently for the three superkingdoms: Metabolism > Information > ICP > Regulation > Other > General > ECP. Note that trend lines across proteomes seldom overlap and cross in Figure 2. It is noteworthy however that this trend differs from the decreasing total numbers of FSFs we described above (Figure 1). Thus, no correlation should be expected between the numbers of FSFs for individual proteomes and the total set for each category. This suggests that variation in functional assignments across proteomes of superkingdoms may not necessarily match overall functional patterns.

Proteomes in microbial superkingdoms Archaea and Bacteria exhibit remarkably similar functional distributions of FSFs (Figure 2(A)). The only exception appears to be the slight overrepresentation of Regulation FSFs (green trend lines) and underrepresentation of ICP (black trend lines) in Archaea compared to Bacteria (especially Proteobacteria). These distributions are clearly distinct from those in Eukarya. Proteomic representations of FSFs corresponding to Metabolism and Information are decreased while those of all other five functional categories are significantly and consistently increased (Figure 2(A)). There is also more variation evident in Eukarya; large groups of proteomes exhibit different patterns of functional use (clearly evident in Information; red trend lines in Figure 2(A)).

On the whole, the relative functional make up of the proteomes of individual superkingdoms appear highly conserved (Figure 2(A)). There is however considerable variation in the metabolic functional repertoire of organisms, especially in Bacteria, where Metabolism ranges 30–50% of proteomic content (100–350 FSFs, Table S1 and Table S2). This variation is not present in other functional repertoires.

Table S1

Average number of FSF domains in each phyla/kingdom corresponding to the seven general functional categories. Numbers were rounded up when the decimal value exceeded 0.5 and rounded down otherwise. Nanoarchaeota and Tenericutes have the least number of metabolic domains and are highlighted in bold. Eukaryal kingdoms (Fungi, Metazoa, Plants and Protista) have the richest FSF repertoires compared to the prokaryotes.

Superkingdom	Phyla/Kingdom	Metabolism	Information	ICP	Regulation	Other	General	ECP
Archaea	Crenarchaeota	204	85	44	35	30	20	2
	Euryarchaeota	219	96	50	44	32	24	4
	Korarchaeota	178	85	38	37	29	19	2
	Nanoarchaeota	57	76	23	15	16	11	1
	Thaumarchaeota	202	91	49	42	23	25	5
Bacteria	Proteobacteria	274	119	78	52	42	31	7
	Firmicutes	246	117	67	53	35	26	7
	Actinobacteria	275	115	66	50	33	30	7
	Bacteroidetes	251	113	65	43	32	29	9
	Tenericutes	99	90	33	25	13	14	0
	Cyanobacteria	289	112	73	52	39	30	8
	Spirochaetes	171	104	56	41	24	25	5
	Thermotogae	231	110	60	48	36	22	4
	Rest of Bacteria *	255	113	67	48	37	27	6
	PVC	206	110	58	43	28	27	6
Eukarya	Fungi	298	127	105	87	51	52	10
	Metazoa	307	135	136	126	65	75	42
	Plants	332	145	117	87	58	54	14
	Protista	220	117	94	67	39	46	9

Includes proteomes from Chlorobi, Chloroflexi, Aquificae, Deinococcus thermus, Fusobacteria, Acidobacteria, Deferribacters, Dictyoglomi, Elusimicrobia, Synergistetes, Fibrobacters, Gemmatimonadetes, Nitrospirae, and Thermobaculum.

Table S2

Average percentage of FSF domains in each phyla/kingdom corresponding to the seven general functional categories. Numbers were rounded up when the decimal value exceeded 0.5 and rounded down otherwise. Nanoarchaeota (highlighted in bold) is an outlier considering it has the smallest percentage for metabolic domains compared to the rest and this decrease is offset by an increase in the informational FSFs.

Superkingdom	Phyla/Kingdom	Metabolism	Information	ICP	Regulation	Other	General	ECP
Archaea	Crenarchaeota	48	21	10	9	7	5	1
	Euryarchaeota	47	20	11	9	7	5	1
	Korarchaeota	46	22	10	9	7	5	1
	Nanoarchaeota	29	38	12	8	8	6	1
	Thaumarchaeota	46	21	11	10	5	6	1
Bacteria	Proteobacteria	45	20	13	8	7	5	1
	Firmicutes	44	21	12	10	6	5	1
	Actinobacteria	48	20	12	9	6	5	1
	Bacteroidetes	46	22	12	8	6	5	2
	Tenericutes	36	33	12	9	5	5	0
Bacteria	Cyanobacteria	48	19	12	9	6	5	1
	Spirochaetes	39	25	13	10	6	6	1
	Thermotogae	45	22	12	9	7	4	1
	Rest of Bacteria *	46	21	12	9	7	5	1
	PVC	42	24	12	9	6	6	1
Eukarya	Fungi	41	17	14	12	7	7	1
	Metazoa	35	15	15	14	7	8	5
	Plants	41	18	14	11	7	7	2
	Protista	36	20	16	11	6	8	2

Includes proteomes from Chlorobi, Chloroflexi, Aquificae, Deinococcus thermus, Fusobacteria, Acidobacteria, Deferribacters, Dictyoglomi, Elusimicrobia, Synergistetes, Fibrobacters, Gemmatimonadetes, Nitrospirae, and Thermobaculum

Consequently, tendencies of reduction in the metabolic repertoire are generally offset by small increases in the representation of the other six repertoires, with the notable exception of Information. In this particular case, when Metabolism goes down Information goes up. For example, bacterial proteomes with metabolic FSF repertoires of <45% offset their decrease by a corresponding increase in Information FSFs (generally from ∼20% to ∼35%, Figure 2(A)). In all superkingdoms, we identify groups of proteomes or few outliers that deviate from the global trends (vertical dotted lines in Figure 2(A)). As we will discuss below this is generally a consequence of reductive evolution imposed by the lifestyle of organisms (discussed in detail below). Outliers are particularly evident in Bacteria and harbor sharp increases in Information repertoires, not always with corresponding decreases in Metabolism. In Archaea, decreases of Metabolism are generally offset by increases of the Regulation category, with an exception in Nanoarchaeum equitans (see below). In Eukarya, decreases in Metabolism go in hand with decreases in Information, and are correspondingly offset mostly by increases in Regulation and ECP. Apparently, the advantages of regulatory control (e.g., signal transduction and transcriptional and posttranscriptional regulation) and multicellularity counteract the interplay of Metabolism and Information in eukaryotes.

When we look at the actual number of FSFs within each functional repertoire (Figure 2(B)), we observe a clear trend in domain use that matches the total trend for superkingdoms described above (Figure 1). In most cases, the functional repertoires of Archaea are smaller than those of Bacteria, and bacterial repertoires are generally smaller than those of Eukarya (Figure 2(B)). This holds true for all functional categories. However, the numbers of metabolic FSFs vary 1.5–4 fold in proteomes of superkingdoms, the change being maximal in Bacteria. While both proteomes in Eukarya and Bacteria show similar ranges of metabolic FSFs, the repertoire of Archaea is more constrained. Furthermore, FSFs belonging to categories Other and ECP are significantly higher in Eukarya than in the microbial superkingdoms. These remarkable observations suggest high conservation in the make up of proteomes of superkingdoms and at the same time considerable levels of flexibility in the metabolic make-up of organisms. Results also support the evolution of the protein complements of Archaea and Bacteria via reductive evolutionary processes and Eukarya by genome expansion mechanisms [7,25]. Reductive tendencies in microbial superkingdoms do not show bias in favor of any functional category. Furthermore, enrichment of eukaryal proteomes with viral proteins supports theories, which state that viruses have played an important role in the evolution of Eukarya [26].

Distribution of FSF Domain Functions in Individual Phyla/Kingdoms

Figure 2 also describes the functional distribution of FSFs at the phyla/kingdom level for each superkingdom. Plots describing the percentages (Figure 2(A)) and actual number of FSFs in proteomes (Figure 2(B)) highlight the existence of “outliers” (vertical dotted lines in Figure 2(A)) that deviate from the global functional trends that are typical of each superkingdom.

In Archaea, the functional repertoires of the proteomes of Euryarachaeota, Crenarchaeota, Korarcheota and Thaumarchaeota were remarkably conserved and consistent with each other. Only N. equitans could be considered an outlier (insets of Figure 2). Its proteome deviates from the global archaeal signature by reducing its proteomic make up (it has only 200 distinct FSFs) and by exchanging Information for metabolic FSFs. N. equitans is an obligate intracellular parasite [27] that is part of a new phylum of Archaea, the Nanoarchaeota [28]. N. equitans has many atypical features, including the almost complete absence of operons and presence of split genes [29], tRNA genes that code for only half of the tRNA molecule [30], and the complete absence of the nucleic acid processing enzyme RNAse P [31]. Some of these features were used to propose that N. equitans is a living fossil [32], represents the root of superkingdom Archaea and the tree of life [33], and is part of a very ancient and yet to be described superkingdom (M. Di Giulio, personal communication). Phylogenomic analyses of domain structures in proteomes suggest Archaea is the most ancient superkingdom [19,34] and has placed N. equitans at the base of the tree of life together with other archaeal species. Its ancestral nature is therefore in line with the evolutionary and functional uniqueness of N. equitans and the very distinct functional repertoire we here report.

In Bacteria, the functional repertoires of bacterial phyla were also remarkably conserved. Only Information and Metabolism showed significantly distinct patterns and considerable variation in the use of FSFs. Again, decreases in representation of metabolic FSFs were generally offset by increases in informational FSFs (Figure 2(A)). Notable outliers include the Tenericutes and the Spirochetes. As groups, they have the highest relative usage of Information FSFs, which are clearly offset by a decrease in metabolic FSFs. The Tenericutes is a phylum of bacteria that includes class Mollicutes. Members of the Mollicutes are typical obligate parasites of animals and plants (some of medical significance such as Mycoplasma) that lack cell walls and have gliding motility. These organisms are characterized by small genome sizes [35] considered to have evolved via reductive evolutionary processes [36]. Because of its unique properties and history, mycoplasmas have been used recently to produce a completely synthetic genome [37]. There were also clear outliers in the Proteobacteria. These included Candidatus Blochmannia floridanus (symbiont of ants), Baumannia cicadellinicola (symbiont of sharpshooter insect), Candidatus Riesia pediculicola, Candidatus Carsonella ruddii (symbiont of sap-feeding insects) and Candidatus Hodgkinia cicadicola (symbiont of cicadas). These bacteria are generally endosymbionts of insects (e.g., ants, sharpshooters, psyllids, cicadas) that have undergone irreversible specialization to an intracellular lifestyle. Candidatus Carsonella ruddii has the smallest genome of any bacteria [38]. There were also bacterial proteome groups that were expected to be outliers but were no different than the rest. Bacteria belonging to the superphylum Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) are different from other bacterial phyla because they have an “eukaryotic touch” [39]. Indeed, PVC bacteria display genetic and cellular features that are characteristics of Eukarya and Archaea, including the presence of Histone H1, condensed DNA surrounded by membrane, α-helical repeat domains and β-propeller folds that make up eukaryotic-like membrane coats, reproduction by budding, ether lipids and lack of cell walls [40-42]. Due to the unique nature of the PVC superphylum, it was proposed that these organisms be identified as a separate superkingdom that contributed to the evolution of Eukarya and Archaea [40]. However, trees of life generated from domain structures in hundreds of proteomes did not dissect the PVC superphylum into a separate group [7,19,34]. Functional distributions of FSFs now show PVC proteomes appear no different from bacteria (Figure 2). These results do not support PVC-inspired theories that explain the diversification of the three cellular superkingdoms of life.

In contrast to the functional repertoires of bacterial and archaeal phyla, proteomes belonging to individual kingdoms in Eukarya had functional signatures that were highly conserved (Figure 2(A)). However, these signatures differed between groups. Plants and fungi had functional representations that were very similar and showed little diversity. In contrast, Metazoa functional distributions increased the representation of ECP and Regulation FSFs in exchange of FSFs in Metabolism and Information. Protista had patterns that resemble those of Plants and Fungi but had widely varying metabolic repertoires, very much like Bacteria. This possible link between basal eukaryotes and bacteria revealed by our comparative analysis is consistent with the existence of an ancestor of Bacteria and Eukarya and the early rise of Archaea [34]. Only few outliers belonging to kingdoms Fungi (Encephalitozoon cuniculi and Encephalitozoon intestinalis) and Protista (Guillardia theta) were identified. E. cuniculi and E. intestinalis are eukaryotic parasites with highly reduced genomes [43,44]. Similarly, Guillardia theta is a nucleomorph that has a highly compact and reduced genome with loss of nearly all metabolic genes [45].

When we look at the actual number of FSFs in proteomes of phyla and kingdoms (Figure 2(B)) we observe that while the overall patterns match those of FSF representation (Figure 2(A)), FSF number revealed considerable variation in the metabolic repertoire of Protista and Bacteria. FSFs in these groups typically ranged 130–340, with PVC and Spirochetes exhibiting the smallest range (130–300 FSFs). In contrast, metabolic repertoires of Archaea and the other eukaryotic kingdoms typically ranged 200–260 FSFs and 270–350 FSFs, respectively. This observation is significant. It provides comparative information to support a unique evolutionary link of phyla within superkingdoms Eukarya and Bacteria. Plots of FSF number also clarified functional patterns in outliers, revealing they did not have more numbers of FSFs in Information but rather have reduced metabolic repertoires. This shows that parasitic outliers get rid of metabolic domains and become more and more dependent on host cells.

Effect of Organism Lifestyle

The analysis thus far revealed the existence of a small group of outliers within each superkingdom. Manual inspection of lifestyles of these organisms showed that all of these organisms are united by a parasitic or symbiotic lifestyle. For example, N. equitans is the smallest archaeal genome ever sequenced and represents a new phylum, the Nanoarchaeaota [28]. This organism interacts with Ignicoccus hospitalis, establishing the only known parasite/symbiont relationship of Archaea, and harbors a highly reduced genome [29]. Parasitic/symbiotic relationships with various plants and animals can be found in Tenericutes and in the endosymbionts of insects that belong to Proteobacteria. Similarly, the Encephalitozoon species are eukaryotic parasites that lack mitochondria and have highly reduced genomes [43,44]. E. cunniculi has even a chromosomal dispersion of its ribosomal genes, very much like N. equitans, and the rRNA of the large ribosomal subunit reduced to its universal core [46]. Similarly, Guillardia theta is a nucleomorph that has a highly compact and reduced genome with loss of nearly all metabolic genes [45]. Thus, all outliers exhibit extreme or unique cases of genome reduction.

In order to explore whether organisms that engage in parasitic or symbiotic interactions have general tendencies that resemble those of the outliers, we classified organisms into three different lifestyles: free living (FL) (592 proteomes), facultative parasitic (P) (153 proteomes), and obligate parasitic (OP) (158 proteomes). Functional distributions for the seven general functional categories for these proteomic sets explained the role of parasitic life on proteomic constitution (Figure 3). Plots of percentages (Figure 3(A)) and actual number of FSFs in proteomes (Figure 3(B)) showed FSF distribution in FL organisms were remarkably homogenous and that the vast majority of variability within superkingdoms was ascribed to the P and OP lifestyles. This variability was for the most part explained by a sharp decline in the number of metabolic FSFs that are assigned to the Metabolism general category (Figure 3(B)). Plots also support the hypothesis that parasitic organisms have gone the route of massive genome reduction in a tendency to loose all of their metabolic genes. This tendency makes them more and more dependent on host cells for metabolic functions and survival [47,48].

Figure 3

The functional distribution of FSFs with respect to organism lifestyle. Both the percentage (A) and actual FSF numbers (B) indicate that obligate parasitic (OP) and facultative parasitic (P) organisms exhibit considerable variability in their metabolic repertoires (yellow trend lines) that is offset by corresponding increases in the Information FSFs (red trend lines).

The number of domains corresponding to each general functional category in the proteomes of FL organisms increases in the order Archaea, Bacteria and Eukarya (Table S3). When compared to the total proteomic set (Figure 2), Metabolism remains the predominant functional category and a large number of domains in all the proteomes perform metabolic functions. Again, the proteomes of Eukarya have the richest FSF repertoires, and those of Archaea the most simple. Since maximum variability lies within the proteome repertoires of parasitic/symbiotic organisms (Figure 3) and parasitism/symbiosis in these organisms is the result of secondary adaptations, the analysis of proteomic diversity in FL organisms allows us to test if the functional repertoires of superkingdoms are indeed statistically significant. Analysis of variance showed that the number of FSFs for each functional repertoire was consistently different between superkingdoms (p < 0.0001; Table S3). This supports the conclusions drawn from earlier analyses that the microbial superkingdoms followed a genome reduction path while Eukarya expanded their genomic repertoires [7,25].

Table S3

Comparison of functional categories across superkingdoms using Welch's ANOVA.

Functional category	F-ratio	DF	P-value *
Metabolism	350.21	2	<0.0001
Information	582.28	2	<0.0001
ICP	1271.32	2	<0.0001
Regulation	966.75	2	<0.0001
Other	520.97	2	<0.0001
General	1043.76	2	<0.0001
ECP	263.44	2	<0.0001

All the P-values are statistically significant at 0.05.

Analysis of Minor Functional Categories

The seven general categories of molecular functions map to 50 minor categories (Table 1). We explored the distribution of FSFs corresponding to each minor category in superkingdoms (Figure 4). Only category “not annotated” (NONA) was excluded from analysis. In terms of percentage (Figure 4(A)), the overall functional signature is split into two components: prokaryotic and eukaryotic. Prokaryotes spend most of their domain repertoire on Metabolism and Information whereas Eukarya stand out in ECP (particularly cell adhesion, immune response), Regulation (DNA binding, signal transduction), and all the minor functional categories corresponding to ICP and General.

Figure 4

The percentage (A) and number (B) of FSFs in minor functional categories across superkingdoms. Archaea (A) and Bacteria (B) spend most of their proteomes in functions related to Metabolism and Information whereas Eukarya (E) stand out in the minor categories of Regulation, General, Intracellular processes (ICP) and Extracellular processes (ECP). In turn, the number of FSFs increases in the order Archaea, Bacteria and Eukarya. Eukaryal proteomes have the richest functional repertoires for Regulation, Other, General, ICP and ECP.

In terms of domain counts (Figure 4(B)), proteomes of Eukarya have the richest functional repertoires with a significantly large number of FSFs devoted for each minor functional category. Bacteria and Archaea work with small number of domains. However, the number of FSFs in Bacteria is significantly higher compared to Archaea (supporting results of Figure 1, Figure 2 and Table S3). These results are consistent with the evolutionary trends in proteomes described previously [7,19,25]. Our results support the complex nature of the Last Universal Common Ancestor (LUCA) [19] and are consistent with the evolution of microbial superkingdoms via reductive evolutionary processes and the evolution of eukaryal proteomes by genome expansion [7,25]. It appears that Archaea went on the route of genome reduction very early in evolution and was followed by Bacteria and finally Eukarya. Late in evolution, the eukaryal superkingdom increased the representation of FSFs and developed a rich proteome. This can explain the relatively huge and diverse nature of eukaryal proteomes compared to prokaryotic proteomes. Finally, there appears to be no significant difference in the distributions of FSFs corresponding to Metabolism and Information between Bacteria and Eukarya except for minor category “Translation” (green trend lines in Figure 4(B, Information)) that is significantly higher in Eukarya compared to Bacteria. This shows that Bacteria exhibit incredible metabolic and informational diversity despite their reduced genomic complements. We conclude that the genome expansion in Eukarya occurred primarily for functions related to ECP, ICP, Regulation and General.

Reliability of Functional Annotations and Conclusions of this Study

Our analysis depends upon the accuracy of assigning structures to protein sequences and the SCOP protein classification and SUPERFAMILY functional annotation schemes. Databases such as SCOP and SUPERFAMILY are continuously updated with more and more genomes and new assignments. We therefore ask the reader to focus on the general trends in the data as opposed to the specifics such as the exact percentage or numbers of FSFs in each functional repertoire. Trends related to the number of domains in Archaea relative to Bacteria and Eukarya and the reduction of metabolic repertoires in parasitic organisms should be considered robust since these have been reliably observed in previous studies with more limited datasets [1,7,15,19,34]. Biases in sampling of proteomes in the three superkingdoms is not expected to over or underestimate the remarkably conserved nature of the functional makeup. We show that the conservation of molecular functions in proteomes is only broken in genomic outliers that are united by parasitic lifestyles. Thus equal sampling will not significantly alter the global trends described for individual superkingdoms. In light of our results, organism lifestyle is the only factor affecting the conserved nature of proteomes. Finally, we propose that lower or higher than expected numbers of FSFs in any category (subcategory) can be explained either by possible limitations of the scheme used to annotate molecular functions of FSFs or the simple nature of the functional repertoire. For example, the number of FSFs in subcategory structural proteins (main category General) is 7 (Table 1) despite the importance of structural proteins in cellular organization. Table S4 lists the description of these FSFs and shows that indeed these FSF domains play important structural roles. Their limited number indicates that the structural and functional organization is quite limited and very few folds play important structural roles. Another possibility is the “hidden” overlap between FSFs and molecular functions due to the one-to-one mapping limitations of the SUPERFAMILY functional annotation scheme. Most of the large FSFs include many FFs and participate in multiple pathways; for few FSFs a complete functional profile may not be intuitively obvious. This may be one of the shortcomings of using this functional annotation scheme but dissection of such detailed functions and pathways is a difficult task and is not described in this study. In summary, we do not believe that the classification or annotation schemes, despite their limitations, would undergo serious revisions or weaken our findings.

Table S4

Names and description of FSF domains corresponding to subcategory structural proteins in the main category General.

No.	SCOP Id	FSF Id	Description
1	103589	g.71.1	Mini-collagen I, C-terminal domain
2	49695	b.11.1	Gamma-crystallin-like
3	51269	b.85.1	Anti-freeze protein (AFP) III-like domain
4	56558	d.182.1	Baseplate structural protein gp11
5	58002	h.1.6	Chicken cartilage matrix protein
6	58006	h.1.7	Assembly domain of catrillage oligomeric matrix protein
7	75404	d.213.1	Vesiculovirus (VSV) matrix proteins

Experimental Section

Data Retrieval

We downloaded the protein architecture assignments for a total of 965 organisms including 70 Archaea, 651 Bacteria and 244 Eukarya (Table S5) from SUPERFAMILY ver. 1.73 MySQL [16,17] at an E-value cutoff of 10−4. This cutoff is considered a stringent threshold to eliminate the rate of false positives in HMM assignments [19]. Classification of organisms according to their lifestyles was done manually and resulted in 592 FL, 153 P, and 158 OP organisms.

Table S5

List of organisms analyzed with their taxonomic classifications.

No.	Genome Name	Phyla/Kingdom	Superkingdom
1	Malassezia globosa CBS 7966	Fungi	Eukaryota
2	Ustilago maydis	Fungi	Eukaryota
3	Puccinia graminis f. sp. tritici CRL 75-36-700-3	Fungi	Eukaryota
4	Melampsora laricis-populina	Fungi	Eukaryota
5	Sporobolomyces roseus IAM 13481	Fungi	Eukaryota
6	Serpula lacrymans var. lacrymans S7.9	Fungi	Eukaryota
7	Coprinopsis cinerea okayama7 130 v3	Fungi	Eukaryota
8	Pleurotus ostreatus	Fungi	Eukaryota
9	Laccaria bicolor S238N-H82	Fungi	Eukaryota
10	Agaricus bisporus var. bisporus	Fungi	Eukaryota
11	Schizophyllum commune	Fungi	Eukaryota
12	Heterobasidion annosum	Fungi	Eukaryota
13	Phanerochaete chrysosporium RP-78 2.1	Fungi	Eukaryota
14	Postia placenta	Fungi	Eukaryota
15	Tremella mesenterica	Fungi	Eukaryota
16	Cryptococcus neoformans JEC21	Fungi	Eukaryota
17	Magnaporthe grisea 70-15	Fungi	Eukaryota
18	Podospora anserina	Fungi	Eukaryota
19	Sporotrichum thermophile ATCC 42464	Fungi	Eukaryota
20	Thielavia terrestris NRRL 8126	Fungi	Eukaryota
21	Chaetomium globosum CBS 148.51	Fungi	Eukaryota
22	Neurospora tetrasperma	Fungi	Eukaryota
23	Neurospora discreta FGSC 8579	Fungi	Eukaryota
24	Neurospora crassa OR74A	Fungi	Eukaryota
25	Cryphonectria parasitica	Fungi	Eukaryota
26	Verticillium dahliae VdLs.17	Fungi	Eukaryota
27	Verticillium albo-atrum VaMs.102	Fungi	Eukaryota
28	Fusarium oxysporum f. sp. lycopersici 4286	Fungi	Eukaryota
29	Nectria haematococca mpVI	Fungi	Eukaryota
30	Fusarium verticillioides 7600	Fungi	Eukaryota
31	Fusarium graminearum	Fungi	Eukaryota
32	Trichoderma atroviride	Fungi	Eukaryota
33	Trichoderma reesei 1.2	Fungi	Eukaryota
34	Trichoderma virens Gv29-8	Fungi	Eukaryota
35	Botrytis cinerea B05.10	Fungi	Eukaryota
36	Sclerotinia sclerotiorum	Fungi	Eukaryota
37	Alternaria brassicicola	Fungi	Eukaryota
38	Pyrenophora tritici-repentis	Fungi	Eukaryota
39	Cochliobolus heterostrophus	Fungi	Eukaryota
40	Stagonospora nodorum	Fungi	Eukaryota
41	Mycosphaerella fijiensis CIRAD86	Fungi	Eukaryota
42	Mycosphaerella graminicola IPO323	Fungi	Eukaryota
43	Ajellomyces dermatitidis SLH14081	Fungi	Eukaryota
44	Histoplasma capsulatum class NAmI strain WU24	Fungi	Eukaryota
45	Microsporum canis CBS 113480	Fungi	Eukaryota
46	Microsporum gypseum	Fungi	Eukaryota
47	Arthroderma benhamiae CBS 112371	Fungi	Eukaryota
48	Trichophyton equinum CBS 127.97	Fungi	Eukaryota
49	Trichophyton verrucosum HKI 0517	Fungi	Eukaryota
50	Trichophyton tonsurans CBS 112818	Fungi	Eukaryota
51	Trichophyton rubrum CBS 118892	Fungi	Eukaryota
52	Paracoccidioides brasiliensis Pb18	Fungi	Eukaryota
53	Coccidioides posadasii RMSCC 3488	Fungi	Eukaryota
54	Coccidioides immitis RS	Fungi	Eukaryota
55	Uncinocarpus reesii 1704	Fungi	Eukaryota
56	Aspergillus fumigatus Af293	Fungi	Eukaryota
57	Neosartorya fischeri NRRL 181	Fungi	Eukaryota
58	Penicillium chrysogenum Wisconsin 54-1255	Fungi	Eukaryota
59	Penicillium marneffei ATCC 18224	Fungi	Eukaryota
60	Aspergillus carbonarius ITEM 5010	Fungi	Eukaryota
61	Aspergillus terreus NIH2624	Fungi	Eukaryota
62	Aspergillus oryzae RIB40	Fungi	Eukaryota
63	Aspergillus niger ATCC 1015	Fungi	Eukaryota
64	Aspergillus flavus NRRL3357	Fungi	Eukaryota
65	Aspergillus clavatus NRRL 1	Fungi	Eukaryota
66	Aspergillus nidulans FGSC A4	Fungi	Eukaryota
67	Tuber melanosporum Vittad	Fungi	Eukaryota
68	Pichia stipitis CBS 6054	Fungi	Eukaryota
69	Candida guilliermondii ATCC 6260	Fungi	Eukaryota
70	Lodderomyces elongisporus NRRL YB-4239	Fungi	Eukaryota
71	Debaromyces hansenii	Fungi	Eukaryota
72	Candida dubliniensis CD36	Fungi	Eukaryota
73	Candida tropicalis MYA-3404	Fungi	Eukaryota
74	Candida parapsilosis	Fungi	Eukaryota
75	Candida albicans SC5314	Fungi	Eukaryota
76	Yarrowia lipolytica CLIB122	Fungi	Eukaryota
77	Candida lusitaniae ATCC 42720	Fungi	Eukaryota
78	Vanderwaltozyma polyspora DSM 70294	Fungi	Eukaryota
79	Candida glabrata CBS138	Fungi	Eukaryota
80	Kluyveromyces thermotolerans CBS 6340	Fungi	Eukaryota
81	Lachancea kluyveri	Fungi	Eukaryota
82	Kluyveromyces waltii	Fungi	Eukaryota
83	Ashbya gossypii ATCC 10895	Fungi	Eukaryota
84	Zygosaccharomyces rouxii	Fungi	Eukaryota
85	Saccharomyces mikatae MIT	Fungi	Eukaryota
86	Saccharomyces paradoxus MIT	Fungi	Eukaryota
87	Saccharomyces cerevisiae SGD	Fungi	Eukaryota
88	Saccharomyces bayanus MIT	Fungi	Eukaryota
89	Pichia pastoris GS115	Fungi	Eukaryota
90	Kluyveromyces lactis	Fungi	Eukaryota
91	Schizosaccharomyces octosporus yFS286	Fungi	Eukaryota
92	Schizosaccharomyces japonicus yFS275	Fungi	Eukaryota
93	Schizosaccharomyces pombe	Fungi	Eukaryota
94	Allomyces macrogynus ATCC 38327	Fungi	Eukaryota
95	Rhizopus oryzae RA 99-880	Fungi	Eukaryota
96	Phycomyces blakesleeanus	Fungi	Eukaryota
97	Mucor circinelloides	Fungi	Eukaryota
98	Spizellomyces punctatus DAOM BR117	Fungi	Eukaryota
99	Batrachochytrium dendrobatidis JEL423	Fungi	Eukaryota
100	Encephalitozoon cuniculi	Fungi	Eukaryota
101	Encephalitozoon intestinalis	Fungi	Eukaryota
102	Homo sapiens 59_37d (all transcripts)	Metazoa	Eukaryota
103	Pan troglodytes 59_21n (all transcripts)	Metazoa	Eukaryota
104	Gorilla gorilla 59_3b (all transcripts)	Metazoa	Eukaryota
105	Pongo pygmaeus 59_1e (all transcripts)	Metazoa	Eukaryota
106	Macaca mulatta 59_10n (all transcripts)	Metazoa	Eukaryota
107	Callithrix jacchus 59_321a (all transcripts)	Metazoa	Eukaryota
108	Otolemur garnettii 59_1g (all transcripts)	Metazoa	Eukaryota
109	Microcebus murinus 59_1d (all transcripts)	Metazoa	Eukaryota
110	Tarsius syrichta 59_1e (all transcripts)	Metazoa	Eukaryota
111	Rattus norvegicus 59_34a (all transcripts)	Metazoa	Eukaryota
112	Mus musculus 59_37l (all transcripts)	Metazoa	Eukaryota
113	Spermophilus tridecemlineatus 59_1i (all transcripts)	Metazoa	Eukaryota
114	Dipodomys ordii 59_1e (all transcripts)	Metazoa	Eukaryota
115	Cavia porcellus 59_3c (all transcripts)	Metazoa	Eukaryota
116	Oryctolagus cuniculus 59_2b (all transcripts)	Metazoa	Eukaryota
117	Ochotona princeps 59_1e (all transcripts)	Metazoa	Eukaryota
118	Tupaia belangeri 59_1h (all transcripts)	Metazoa	Eukaryota
119	Sus scrofa 59_9c (all transcripts)	Metazoa	Eukaryota
120	Bos taurus 59_4h (all transcripts)	Metazoa	Eukaryota
121	Vicugna pacos 59_1e (all transcripts)	Metazoa	Eukaryota
122	Tursiops truncatus 59_1e (all transcripts)	Metazoa	Eukaryota
123	Canis familiaris 59_2o (all transcripts)	Metazoa	Eukaryota
124	Felis catus 59_1h (all transcripts)	Metazoa	Eukaryota
125	Equus caballus 59_2f (all transcripts)	Metazoa	Eukaryota
126	Myotis lucifugus 59_1i (all transcripts)	Metazoa	Eukaryota
127	Pteropus vampyrus 59_1e (all transcripts)	Metazoa	Eukaryota
128	Sorex araneus 59_1g (all transcripts)	Metazoa	Eukaryota
129	Erinaceus europaeus 59_1g (all transcripts)	Metazoa	Eukaryota
130	Procavia capensis 59_1e (all transcripts)	Metazoa	Eukaryota
131	Loxodonta africana 59_3b (all transcripts)	Metazoa	Eukaryota
132	Echinops telfairi 59_1i (all transcripts)	Metazoa	Eukaryota
133	Dasypus novemcinctus 59_2c (all transcripts)	Metazoa	Eukaryota
134	Macropus eugenii 59_1b (all transcripts)	Metazoa	Eukaryota
135	Monodelphis domestica 59_5k (all transcripts)	Metazoa	Eukaryota
136	Ornithorhynchus anatinus 59_1m (all transcripts)	Metazoa	Eukaryota
137	Anolis carolinensis 59_1c (all transcripts)	Metazoa	Eukaryota
138	Taeniopygia guttata 59_1e (all transcripts)	Metazoa	Eukaryota
139	Meleagris gallopavo 57_2 (all transcripts)	Metazoa	Eukaryota
140	Gallus gallus 59_2o (all transcripts)	Metazoa	Eukaryota
141	Xenopus laevis	Metazoa	Eukaryota
142	Xenopus tropicalis 59_41p (all transcripts)	Metazoa	Eukaryota
143	Danio rerio 59_8e (all transcripts)	Metazoa	Eukaryota
144	Gasterosteus aculeatus 59_1l (all transcripts)	Metazoa	Eukaryota
145	Oryzias latipes 59_1k (all transcripts)	Metazoa	Eukaryota
146	Tetraodon nigroviridis 59_8d (all transcripts)	Metazoa	Eukaryota
147	Takifugu rubripes 59_4m (all transcripts)	Metazoa	Eukaryota
148	Branchiostoma floridae 1.0	Metazoa	Eukaryota
149	Ciona savignyi 59_2j (all transcripts)	Metazoa	Eukaryota
150	Ciona intestinalis 59_2o (all transcripts)	Metazoa	Eukaryota
151	Strongylocentrotus purpuratus	Metazoa	Eukaryota
152	Helobdella robusta	Metazoa	Eukaryota
153	Capitella sp. I	Metazoa	Eukaryota
154	Bombyx mori	Metazoa	Eukaryota
155	Nasonia vitripennis	Metazoa	Eukaryota
156	Apis mellifera 38.2d (all transcripts)	Metazoa	Eukaryota
157	Drosophila grimshawi 1.3	Metazoa	Eukaryota
158	Drosophila willistoni 1.3	Metazoa	Eukaryota
159	Drosophila pseudoobscura 2.13	Metazoa	Eukaryota
160	Drosophila persimilis 1.3	Metazoa	Eukaryota
161	Drosophila yakuba 1.3	Metazoa	Eukaryota
162	Drosophila simulans 1.3	Metazoa	Eukaryota
163	Drosophila sechellia 1.3	Metazoa	Eukaryota
164	Drosophila melanogaster 59_525a (all transcripts)	Metazoa	Eukaryota
165	Drosophila erecta 1.3	Metazoa	Eukaryota
166	Drosophila ananassae 1.3	Metazoa	Eukaryota
167	Drosophila virilis 1.2	Metazoa	Eukaryota
168	Drosophila mojavensis 1.3	Metazoa	Eukaryota
169	Aedes aegypti 55 (all transcripts)	Metazoa	Eukaryota
170	Culex pipiens quinquefasciatus	Metazoa	Eukaryota
171	Anopheles gambiae 49_3j (all transcripts)	Metazoa	Eukaryota
172	Tribolium castaneum 3.0	Metazoa	Eukaryota
173	Pediculus humanus corporis	Metazoa	Eukaryota
174	Acyrthosiphon pisum	Metazoa	Eukaryota
175	Daphnia pulex	Metazoa	Eukaryota
176	Ixodes scapularis	Metazoa	Eukaryota
177	Lottia gigantea	Metazoa	Eukaryota
178	Pristionchus pacificus	Metazoa	Eukaryota
179	Meloidogyne incognita	Metazoa	Eukaryota
180	Brugia malayi WS218	Metazoa	Eukaryota
181	Caenorhabditis japonica	Metazoa	Eukaryota
182	Caenorhabditis brenneri	Metazoa	Eukaryota
183	Caenorhabditis remanei	Metazoa	Eukaryota
184	Caenorhabditis elegans 59_210a (all transcripts)	Metazoa	Eukaryota
185	Caenorhabditis briggsae 2	Metazoa	Eukaryota
186	Schistosoma mansoni	Metazoa	Eukaryota
187	Nematostella vectensis 1.0	Metazoa	Eukaryota
188	Hydra magnipapillata	Metazoa	Eukaryota
189	Trichoplax adhaerens	Metazoa	Eukaryota
190	Giardia lamblia 2.3	Protista	Eukaryota
191	Trypanosoma cruzi strain CL Brener	Protista	Eukaryota
192	Trypanosoma brucei	Protista	Eukaryota
193	Leishmania mexicana 2.4	Protista	Eukaryota
194	Leishmania major strain Friedlin	Protista	Eukaryota
195	Leishmania infantum JPCM5 2.4	Protista	Eukaryota
196	Leishmania braziliensis MHOM/BR/75/M2904 2.4	Protista	Eukaryota
197	Aureococcus anophagefferens	Protista	Eukaryota
198	Phytophthora ramorum 1.1	Protista	Eukaryota
199	Phytophthora sojae 1.1	Protista	Eukaryota
200	Phytophthora infestans T30-4	Protista	Eukaryota
201	Phytophthora capsici	Protista	Eukaryota
202	Paramecium tetraurelia	Protista	Eukaryota
203	Tetrahymena thermophila SB210 1	Protista	Eukaryota
204	Babesia bovis T2Bo	Protista	Eukaryota
205	Theileria parva	Protista	Eukaryota
206	Theileria annulata	Protista	Eukaryota
207	Plasmodium falciparum 3D7	Protista	Eukaryota
208	Plasmodium vivax SaI-1 7.0	Protista	Eukaryota
209	Plasmodium knowlesi strain H	Protista	Eukaryota
210	Plasmodium yoelii ssp. yoelii 1	Protista	Eukaryota
211	Plasmodium chabaudi	Protista	Eukaryota
212	Plasmodium berghei ANKA	Protista	Eukaryota
213	Cryptosporidium hominis	Protista	Eukaryota
214	Cryptosporidium muris	Protista	Eukaryota
215	Cryptosporidium parvum Iowa II	Protista	Eukaryota
216	Neospora caninum Nc-Liverpool 6.2	Protista	Eukaryota
217	Neospora caninum	Protista	Eukaryota
218	Toxoplasma gondii ME49	Protista	Eukaryota
219	Naegleria gruberi	Protista	Eukaryota
220	Guillardia theta	Protista	Eukaryota
221	Arabidopsis lyrata	Plantae	Eukaryota
222	Arabidopsis thaliana 10 (all transcripts)	Plantae	Eukaryota
223	Carica papaya	Plantae	Eukaryota
224	Medicago truncatula	Plantae	Eukaryota
225	Glycine max	Plantae	Eukaryota
226	Cucumis sativus	Plantae	Eukaryota
227	Populus trichocarpa 6.0	Plantae	Eukaryota
228	Vitis vinifera	Plantae	Eukaryota
229	Brachypodium distachyon	Plantae	Eukaryota
230	Oryza sativa ssp. japonica 5.0	Plantae	Eukaryota
231	Zea mays subsp. mays	Plantae	Eukaryota
232	Sorghum bicolor	Plantae	Eukaryota
233	Selaginella moellendorffii	Plantae	Eukaryota
234	Physcomitrella patens subsp. patens	Plantae	Eukaryota
235	Ostreococcus sp. RCC809	Plantae	Eukaryota
236	Ostreococcus lucimarinus CCE9901	Plantae	Eukaryota
237	Ostreococcus tauri	Plantae	Eukaryota
238	Micromonas sp. RCC299	Plantae	Eukaryota
239	Micromonas pusilla CCMP1545	Plantae	Eukaryota
240	Coccomyxa sp. C-169	Plantae	Eukaryota
241	Chlorella sp. NC64A	Plantae	Eukaryota
242	Chlorella vulgaris	Plantae	Eukaryota
243	Volvox carteri f. nagariensis	Plantae	Eukaryota
244	Chlamydomonas reinhardtii 4.0	Plantae	Eukaryota
245	Candidatus Koribacter versatilis Ellin345	Acidobacteria	Bacteria
246	Candidatus Solibacter usitatus Ellin6076	Acidobacteria	Bacteria
247	Acidobacterium capsulatum ATCC 51196	Acidobacteria	Bacteria
248	Gardnerella vaginalis 409-05	Actinobacteria	Bacteria
249	Bifidobacterium longum NCC2705	Actinobacteria	Bacteria
250	Bifidobacterium animalis ssp. lactis AD011	Actinobacteria	Bacteria
251	Bifidobacterium dentium Bd1	Actinobacteria	Bacteria
252	Bifidobacterium adolescentis ATCC 15703	Actinobacteria	Bacteria
253	Kineococcus radiotolerans SRS30216	Actinobacteria	Bacteria
254	Catenulispora acidiphila DSM 44928	Actinobacteria	Bacteria
255	Stackebrandtia nassauensis DSM 44728	Actinobacteria	Bacteria
256	Acidothermus cellulolyticus 11B	Actinobacteria	Bacteria
257	Nakamurella multipartita DSM 44233	Actinobacteria	Bacteria
258	Geodermatophilus obscurus DSM 43160	Actinobacteria	Bacteria
259	Frankia sp. CcI3	Actinobacteria	Bacteria
260	Frankia alni ACN14a	Actinobacteria	Bacteria
261	Thermobifida fusca YX	Actinobacteria	Bacteria
262	Thermomonospora curvata DSM 43183	Actinobacteria	Bacteria
263	Streptosporangium roseum DSM 43021	Actinobacteria	Bacteria
264	Streptomyces griseus ssp. griseus NBRC 13350	Actinobacteria	Bacteria
265	Streptomyces avermitilis MA-4680	Actinobacteria	Bacteria
266	Streptomyces scabiei 87.22	Actinobacteria	Bacteria
267	Streptomyces coelicolor	Actinobacteria	Bacteria
268	Actinosynnema mirum DSM 43827	Actinobacteria	Bacteria
269	Saccharomonospora viridis DSM 43017	Actinobacteria	Bacteria
270	Saccharopolyspora erythraea NRRL 2338	Actinobacteria	Bacteria
271	Kribbella flavida DSM 17836	Actinobacteria	Bacteria
272	Nocardioides sp. JS614	Actinobacteria	Bacteria
273	Propionibacterium acnes KPA171202	Actinobacteria	Bacteria
274	Salinispora arenicola CNS-205	Actinobacteria	Bacteria
275	Salinispora tropica CNB-440	Actinobacteria	Bacteria
276	Gordonia bronchialis DSM 43247	Actinobacteria	Bacteria
277	Rhodococcus jostii RHA1	Actinobacteria	Bacteria
278	Rhodococcus opacus B4	Actinobacteria	Bacteria
279	Rhodococcus erythropolis PR4	Actinobacteria	Bacteria
280	Nocardia farcinica IFM 10152	Actinobacteria	Bacteria
281	Mycobacterium abscessus ATCC 19977	Actinobacteria	Bacteria
282	Mycobacterium sp. MCS	Actinobacteria	Bacteria
283	Mycobacterium avium ssp. paratuberculosis K-10	Actinobacteria	Bacteria
284	Mycobacterium vanbaalenii PYR-1	Actinobacteria	Bacteria
285	Mycobacterium tuberculosis H37Rv	Actinobacteria	Bacteria
286	Mycobacterium bovis AF2122/97	Actinobacteria	Bacteria
287	Mycobacterium ulcerans Agy99	Actinobacteria	Bacteria
288	Mycobacterium gilvum PYR-GCK	Actinobacteria	Bacteria
289	Mycobacterium marinum M	Actinobacteria	Bacteria
290	Mycobacterium smegmatis MC2 155	Actinobacteria	Bacteria
291	Mycobacterium leprae TN	Actinobacteria	Bacteria
292	Corynebacterium aurimucosum ATCC 700975	Actinobacteria	Bacteria
293	Corynebacterium kroppenstedtii DSM 44385	Actinobacteria	Bacteria
294	Corynebacterium efficiens YS-314	Actinobacteria	Bacteria
295	Corynebacterium urealyticum DSM 7109	Actinobacteria	Bacteria
296	Corynebacterium jeikeium K411	Actinobacteria	Bacteria
297	Corynebacterium glutamicum ATCC 13032 Kitasato	Actinobacteria	Bacteria
298	Corynebacterium diphtheriae NCTC 13129	Actinobacteria	Bacteria
299	Tropheryma whipplei Twist	Actinobacteria	Bacteria
300	Sanguibacter keddieii DSM 10542	Actinobacteria	Bacteria
301	Kytococcus sedentarius DSM 20547	Actinobacteria	Bacteria
302	Beutenbergia cavernae DSM 12333	Actinobacteria	Bacteria
303	Leifsonia xyli ssp. xyli CTCB07	Actinobacteria	Bacteria
304	Clavibacter michiganensis ssp. michiganensis NCPPB 382	Actinobacteria	Bacteria
305	Jonesia denitrificans DSM 20603	Actinobacteria	Bacteria
306	Brachybacterium faecium DSM 4810	Actinobacteria	Bacteria
307	Xylanimonas cellulosilytica DSM 15894	Actinobacteria	Bacteria
308	Kocuria rhizophila DC2201	Actinobacteria	Bacteria
309	Rothia mucilaginosa DY-18	Actinobacteria	Bacteria
310	Arthrobacter sp. FB24	Actinobacteria	Bacteria
311	Arthrobacter chlorophenolicus A6	Actinobacteria	Bacteria
312	Arthrobacter aurescens TC1	Actinobacteria	Bacteria
313	Renibacterium salmoninarum ATCC 33209	Actinobacteria	Bacteria
314	Micrococcus luteus NCTC 2665	Actinobacteria	Bacteria
315	Cryptobacterium curtum DSM 15641	Actinobacteria	Bacteria
316	Eggerthella lenta DSM 2243	Actinobacteria	Bacteria
317	Slackia heliotrinireducens DSM 20476	Actinobacteria	Bacteria
318	Atopobium parvulum DSM 20469	Actinobacteria	Bacteria
319	Conexibacter woesei DSM 14684	Actinobacteria	Bacteria
320	Rubrobacter xylanophilus DSM 9941	Actinobacteria	Bacteria
321	Acidimicrobium ferrooxidans DSM 10331	Actinobacteria	Bacteria
322	Sulfurihydrogenibium sp. YO3AOP1	Aquificae	Bacteria
323	Sulfurihydrogenibium azorense Az-Fu1	Aquificae	Bacteria
324	Persephonella marina EX-H1	Aquificae	Bacteria
325	Hydrogenobaculum sp. Y04AAS1	Aquificae	Bacteria
326	Thermocrinis albus DSM 14484	Aquificae	Bacteria
327	Aquifex aeolicus VF5	Aquificae	Bacteria
328	Hydrogenobacter thermophilus TK-6	Aquificae	Bacteria
329	Dyadobacter fermentans DSM 18053	Bacteroidetes	Bacteria
330	Cytophaga hutchinsonii ATCC 33406	Bacteroidetes	Bacteria
331	Spirosoma linguale DSM 74	Bacteroidetes	Bacteria
332	Candidatus Azobacteroides pseudotrichonymphae genomovar.	Bacteroidetes	Bacteria
333	Prevotella ruminicola 23	Bacteroidetes	Bacteria
334	Parabacteroides distasonis ATCC 8503	Bacteroidetes	Bacteria
335	Porphyromonas gingivalis W83	Bacteroidetes	Bacteria
336	Bacteroides vulgatus ATCC 8482	Bacteroidetes	Bacteria
337	Bacteroides thetaiotaomicron VPI-5482	Bacteroidetes	Bacteria
338	Bacteroides fragilis NCTC 9343	Bacteroidetes	Bacteria
339	Candidatus Amoebophilus asiaticus 5a2	Bacteroidetes	Bacteria
340	Salinibacter ruber DSM 13855	Bacteroidetes	Bacteria
341	Rhodothermus marinus DSM 4252	Bacteroidetes	Bacteria
342	Chitinophaga pinensis DSM 2588	Bacteroidetes	Bacteria
343	Pedobacter heparinus DSM 2366	Bacteroidetes	Bacteria
344	Candidatus Sulcia muelleri GWSS	Bacteroidetes	Bacteria
345	Zunongwangia profunda SM-A87	Bacteroidetes	Bacteria
346	Gramella forsetii KT0803	Bacteroidetes	Bacteria
347	Robiginitalea biformata HTCC2501	Bacteroidetes	Bacteria
348	Flavobacteriaceae bacterium 3519-10	Bacteroidetes	Bacteria
349	Capnocytophaga ochracea DSM 7271	Bacteroidetes	Bacteria
350	Flavobacterium psychrophilum JIP02/86	Bacteroidetes	Bacteria
351	Flavobacterium johnsoniae UW101	Bacteroidetes	Bacteria
352	Blattabacterium sp. Bge	Bacteroidetes	Bacteria
353	Candidatus Protochlamydia amoebophila UWE25	Chlamydiae	Bacteria
354	Chlamydophila pneumoniae TW-183	Chlamydiae	Bacteria
355	Chlamydophila caviae GPIC	Chlamydiae	Bacteria
356	Chlamydophila felis Fe/C-56	Chlamydiae	Bacteria
357	Chlamydophila abortus S26/3	Chlamydiae	Bacteria
358	Chlamydia muridarum Nigg	Chlamydiae	Bacteria
359	Chlamydia trachomatis D/UW-3/CX	Chlamydiae	Bacteria
360	Pelodictyon phaeoclathratiforme BU-1	Chlorobi	Bacteria
361	Chlorobium luteolum DSM 273	Chlorobi	Bacteria
362	Chlorobium chlorochromatii CaD3	Chlorobi	Bacteria
363	Chlorobium phaeobacteroides DSM 266	Chlorobi	Bacteria
364	Chlorobium phaeovibrioides DSM 265	Chlorobi	Bacteria
365	Chlorobium limicola DSM 245	Chlorobi	Bacteria
366	Chlorobaculum parvum NCIB 8327	Chlorobi	Bacteria
367	Chlorobium tepidum TLS	Chlorobi	Bacteria
368	Chloroherpeton thalassium ATCC 35110	Chlorobi	Bacteria
369	Prosthecochloris aestuarii DSM 271	Chlorobi	Bacteria
370	Dehalococcoides sp. CBDB1	Chloroflexi	Bacteria
371	Dehalococcoides ethenogenes 195	Chloroflexi	Bacteria
372	Thermomicrobium roseum DSM 5159	Chloroflexi	Bacteria
373	Sphaerobacter thermophilus DSM 20745	Chloroflexi	Bacteria
374	Herpetosiphon aurantiacus ATCC 23779	Chloroflexi	Bacteria
375	Roseiflexus sp. RS-1	Chloroflexi	Bacteria
376	Roseiflexus castenholzii DSM 13941	Chloroflexi	Bacteria
377	Chloroflexus sp. Y-400-fl	Chloroflexi	Bacteria
378	Chloroflexus aggregans DSM 9485	Chloroflexi	Bacteria
379	Chloroflexus aurantiacus J-10-fl	Chloroflexi	Bacteria
380	Gloeobacter violaceus PCC 7421	Cyanobacteria	Bacteria
381	Acaryochloris marina MBIC11017	Cyanobacteria	Bacteria
382	Prochlorococcus marinus MIT 9313	Cyanobacteria	Bacteria
383	Nostoc punctiforme PCC 73102	Cyanobacteria	Bacteria
384	Nostoc sp. PCC 7120	Cyanobacteria	Bacteria
385	Anabaena variabilis ATCC 29413	Cyanobacteria	Bacteria
386	Trichodesmium erythraeum IMS101	Cyanobacteria	Bacteria
387	Thermosynechococcus elongatus BP-1	Cyanobacteria	Bacteria
388	cyanobacterium UCYN-A	Cyanobacteria	Bacteria
389	Cyanothece sp. ATCC 51142	Cyanobacteria	Bacteria
390	Synechocystis sp. PCC 6803	Cyanobacteria	Bacteria
391	Synechococcus elongatus PCC 6301	Cyanobacteria	Bacteria
392	Microcystis aeruginosa NIES-843	Cyanobacteria	Bacteria
393	Denitrovibrio acetiphilus DSM 12809	Deferribacteres	Bacteria
394	Deferribacter desulfuricans SSM1	Deferribacteres	Bacteria
395	Deinococcus deserti VCD115	Deinococcus-Thermus	Bacteria
396	Deinococcus geothermalis DSM 11300	Deinococcus-Thermus	Bacteria
397	Deinococcus radiodurans R1	Deinococcus-Thermus	Bacteria
398	Meiothermus ruber DSM 1279	Deinococcus-Thermus	Bacteria
399	Thermus thermophilus HB27	Deinococcus-Thermus	Bacteria
400	Dictyoglomus turgidum DSM 6724	Dictyoglomi	Bacteria
401	Dictyoglomus thermophilum H-6-12	Dictyoglomi	Bacteria
402	Elusimicrobium minutum Pei191	Elusimicrobia	Bacteria
403	uncultured Termite group 1 bacterium phylotype Rs-D17	Elusimicrobia	Bacteria
404	Fibrobacter succinogenes ssp. succinogenes S85	Fibrobacteres	Bacteria
405	Acidaminococcus fermentans DSM 20731	Firmicutes	Bacteria
406	Veillonella parvula DSM 2008	Firmicutes	Bacteria
407	Natranaerobius thermophilus JW/NM-WN-LF	Firmicutes	Bacteria
408	Symbiobacterium thermophilum IAM 14863	Firmicutes	Bacteria
409	Anaerococcus prevotii DSM 20548	Firmicutes	Bacteria
410	Finegoldia magna ATCC 29328	Firmicutes	Bacteria
411	Clostridiales genomosp. BVAB3 UPII9-5	Firmicutes	Bacteria
412	Candidatus Desulforudis audaxviator MP104C	Firmicutes	Bacteria
413	Pelotomaculum thermopropionicum SI	Firmicutes	Bacteria
414	Desulfitobacterium hafniense Y51	Firmicutes	Bacteria
415	Desulfotomaculum reducens MI-1	Firmicutes	Bacteria
416	Desulfotomaculum acetoxidans DSM 771	Firmicutes	Bacteria
417	Eubacterium rectale ATCC 33656	Firmicutes	Bacteria
418	Eubacterium eligens ATCC 27750	Firmicutes	Bacteria
419	Syntrophomonas wolfei ssp. wolfei Goettingen	Firmicutes	Bacteria
420	Heliobacterium modesticaldum Ice1	Firmicutes	Bacteria
421	Alkaliphilus oremlandii OhILAs	Firmicutes	Bacteria
422	Alkaliphilus metalliredigens QYMF	Firmicutes	Bacteria
423	Clostridium phytofermentans ISDg	Firmicutes	Bacteria
424	Clostridium novyi NT	Firmicutes	Bacteria
425	Clostridium kluyveri DSM 555	Firmicutes	Bacteria
426	Clostridium cellulolyticum H10	Firmicutes	Bacteria
427	Clostridium beijerinckii NCIMB 8052	Firmicutes	Bacteria
428	Clostridium thermocellum ATCC 27405	Firmicutes	Bacteria
429	Clostridium tetani E88	Firmicutes	Bacteria
430	Clostridium perfringens 13	Firmicutes	Bacteria
431	Clostridium difficile 630	Firmicutes	Bacteria
432	Clostridium botulinum A ATCC 3502	Firmicutes	Bacteria
433	Clostridium acetobutylicum ATCC 824	Firmicutes	Bacteria
434	Caldicellulosiruptor saccharolyticus DSM 8903	Firmicutes	Bacteria
435	Anaerocellum thermophilum DSM 6725	Firmicutes	Bacteria
436	Coprothermobacter proteolyticus DSM 5265	Firmicutes	Bacteria
437	Thermoanaerobacter tengcongensis MB4	Firmicutes	Bacteria
438	Carboxydothermus hydrogenoformans Z-2901	Firmicutes	Bacteria
439	Moorella thermoacetica ATCC 39073	Firmicutes	Bacteria
440	Ammonifex degensii KC4	Firmicutes	Bacteria
441	Thermoanaerobacter pseudethanolicus ATCC 33223	Firmicutes	Bacteria
442	Thermoanaerobacter sp. X514	Firmicutes	Bacteria
443	Thermoanaerobacter italicus Ab9	Firmicutes	Bacteria
444	Halothermothrix orenii H 168	Firmicutes	Bacteria
445	Enterococcus faecalis V583	Firmicutes	Bacteria
446	Oenococcus oeni PSU-1	Firmicutes	Bacteria
447	Leuconostoc citreum KM20	Firmicutes	Bacteria
448	Leuconostoc mesenteroides ssp. mesenteroides ATCC 8293	Firmicutes	Bacteria
449	Lactobacillus casei ATCC 334	Firmicutes	Bacteria
450	Lactobacillus crispatus ST1	Firmicutes	Bacteria
451	Lactobacillus rhamnosus GG	Firmicutes	Bacteria
452	Lactobacillus johnsonii NCC 533	Firmicutes	Bacteria
453	Lactobacillus salivarius UCC118	Firmicutes	Bacteria
454	Lactobacillus fermentum IFO 3956	Firmicutes	Bacteria
455	Lactobacillus sakei ssp. sakei 23K	Firmicutes	Bacteria
456	Lactobacillus reuteri DSM 20016	Firmicutes	Bacteria
457	Lactobacillus gasseri ATCC 33323	Firmicutes	Bacteria
458	Lactobacillus plantarum WCFS1	Firmicutes	Bacteria
459	Lactobacillus helveticus DPC 4571	Firmicutes	Bacteria
460	Lactobacillus delbrueckii ssp. bulgaricus ATCC 11842	Firmicutes	Bacteria
461	Lactobacillus brevis ATCC 367	Firmicutes	Bacteria
462	Lactobacillus acidophilus NCFM	Firmicutes	Bacteria
463	Pediococcus pentosaceus ATCC 25745	Firmicutes	Bacteria
464	Lactococcus lactis ssp. lactis Il1403	Firmicutes	Bacteria
465	Streptococcus gallolyticus UCN34	Firmicutes	Bacteria
466	Streptococcus equi ssp. zooepidemicus MGCS10565	Firmicutes	Bacteria
467	Streptococcus dysgalactiae ssp. equisimilis GGS_124	Firmicutes	Bacteria
468	Streptococcus mitis B6	Firmicutes	Bacteria
469	Streptococcus uberis 0140J	Firmicutes	Bacteria
470	Streptococcus pyogenes M1 GAS	Firmicutes	Bacteria
471	Streptococcus pneumoniae TIGR4	Firmicutes	Bacteria
472	Streptococcus agalactiae NEM316	Firmicutes	Bacteria
473	Streptococcus mutans UA159	Firmicutes	Bacteria
474	Streptococcus thermophilus LMG 18311	Firmicutes	Bacteria
475	Streptococcus suis 05ZYH33	Firmicutes	Bacteria
476	Streptococcus sanguinis SK36	Firmicutes	Bacteria
477	Streptococcus gordonii Challis subCH1	Firmicutes	Bacteria
478	Exiguobacterium sp. AT1b	Firmicutes	Bacteria
479	Exiguobacterium sibiricum 255-15	Firmicutes	Bacteria
480	Bacillus tusciae DSM 2912	Firmicutes	Bacteria
481	Alicyclobacillus acidocaldarius ssp. acidocaldarius DSM 446	Firmicutes	Bacteria
482	Brevibacillus brevis NBRC 100599	Firmicutes	Bacteria
483	Paenibacillus sp. JDR-2	Firmicutes	Bacteria
484	Listeria welshimeri ser. 6b SLCC5334	Firmicutes	Bacteria
485	Listeria innocua Clip11262	Firmicutes	Bacteria
486	Listeria seeligeri ser. 1/2b SLCC3954	Firmicutes	Bacteria
487	Listeria monocytogenes EGD-e	Firmicutes	Bacteria
488	Lysinibacillus sphaericus C3-41	Firmicutes	Bacteria
489	Oceanobacillus iheyensis HTE831	Firmicutes	Bacteria
490	Anoxybacillus flavithermus WK1	Firmicutes	Bacteria
491	Geobacillus sp. WCH70	Firmicutes	Bacteria
492	Geobacillus thermodenitrificans NG80-2	Firmicutes	Bacteria
493	Geobacillus kaustophilus HTA426	Firmicutes	Bacteria
494	Bacillus subtilis ssp. subtilis 168	Firmicutes	Bacteria
495	Bacillus licheniformis ATCC 14580	Firmicutes	Bacteria
496	Bacillus amyloliquefaciens FZB42	Firmicutes	Bacteria
497	Bacillus halodurans C-125	Firmicutes	Bacteria
498	Bacillus weihenstephanensis KBAB4	Firmicutes	Bacteria
499	Bacillus thuringiensis ser. konkukian 97-27	Firmicutes	Bacteria
500	Bacillus cereus ATCC 14579	Firmicutes	Bacteria
501	Bacillus anthracis Ames Ancestor	Firmicutes	Bacteria
502	Bacillus pseudofirmus OF4	Firmicutes	Bacteria
503	Bacillus clausii KSM-K16	Firmicutes	Bacteria
504	Bacillus pumilus SAFR-032	Firmicutes	Bacteria
505	Bacillus megaterium QM B1551	Firmicutes	Bacteria
506	Macrococcus caseolyticus JCSC5402	Firmicutes	Bacteria
507	Staphylococcus saprophyticus ssp. saprophyticus ATCC 15305	Firmicutes	Bacteria
508	Staphylococcus lugdunensis HKU09-01	Firmicutes	Bacteria
509	Staphylococcus haemolyticus JCSC1435	Firmicutes	Bacteria
510	Staphylococcus epidermidis RP62A	Firmicutes	Bacteria
511	Staphylococcus carnosus ssp. carnosus TM300	Firmicutes	Bacteria
512	Staphylococcus aureus ssp. aureus NCTC 8325	Firmicutes	Bacteria
513	Streptobacillus moniliformis DSM 12112	Fusobacteria	Bacteria
514	Sebaldella termitidis ATCC 33386	Fusobacteria	Bacteria
515	Leptotrichia buccalis C-1013-b	Fusobacteria	Bacteria
516	Fusobacterium nucleatum ssp. nucleatum ATCC 25586	Fusobacteria	Bacteria
517	Gemmatimonas aurantiaca T-27	Gemmatimonadetes	Bacteria
518	Thermodesulfovibrio yellowstonii DSM 11347	Nitrospirae	Bacteria
519	Rhodopirellula baltica SH 1	Planctomycetes	Bacteria
520	Pirellula staleyi DSM 6068	Planctomycetes	Bacteria
521	Nautilia profundicola AmH	Proteobacteria	Bacteria
522	Sulfurospirillum deleyianum DSM 6946	Proteobacteria	Bacteria
523	Arcobacter butzleri RM4018	Proteobacteria	Bacteria
524	Campylobacter hominis ATCC BAA-381	Proteobacteria	Bacteria
525	Campylobacter lari RM2100	Proteobacteria	Bacteria
526	Campylobacter curvus 525.92	Proteobacteria	Bacteria
527	Campylobacter concisus 13826	Proteobacteria	Bacteria
528	Campylobacter jejuni ssp. jejuni NCTC 11168	Proteobacteria	Bacteria
529	Campylobacter fetus ssp. fetus 82-40	Proteobacteria	Bacteria
530	Sulfurimonas denitrificans DSM 1251	Proteobacteria	Bacteria
531	Wolinella succinogenes DSM 1740	Proteobacteria	Bacteria
532	Helicobacter hepaticus ATCC 51449	Proteobacteria	Bacteria
533	Helicobacter mustelae 12198	Proteobacteria	Bacteria
534	Helicobacter acinonychis Sheeba	Proteobacteria	Bacteria
535	Helicobacter pylori 26695	Proteobacteria	Bacteria
536	Nitratiruptor sp. SB155-2	Proteobacteria	Bacteria
537	Sulfurovum sp. NBC37-1	Proteobacteria	Bacteria
538	Bdellovibrio bacteriovorus HD100	Proteobacteria	Bacteria
539	Syntrophus aciditrophicus SB	Proteobacteria	Bacteria
540	Syntrophobacter fumaroxidans MPOB	Proteobacteria	Bacteria
541	Desulfotalea psychrophila LSv54	Proteobacteria	Bacteria
542	Desulfatibacillum alkenivorans AK-01	Proteobacteria	Bacteria
543	Desulfobacterium autotrophicum HRM2	Proteobacteria	Bacteria
544	Desulfococcus oleovorans Hxd3	Proteobacteria	Bacteria
545	Desulfohalobium retbaense DSM 5692	Proteobacteria	Bacteria
546	Desulfomicrobium baculatum DSM 4028	Proteobacteria	Bacteria
547	Lawsonia intracellularis PHE/MN1-00	Proteobacteria	Bacteria
548	Desulfovibrio magneticus RS-1	Proteobacteria	Bacteria
549	Desulfovibrio vulgaris Hildenborough	Proteobacteria	Bacteria
550	Desulfovibrio salexigens DSM 2638	Proteobacteria	Bacteria
551	Desulfovibrio desulfuricans ssp. desulfuricans G20	Proteobacteria	Bacteria
552	Pelobacter propionicus DSM 2379	Proteobacteria	Bacteria
553	Pelobacter carbinolicus DSM 2380	Proteobacteria	Bacteria
554	Geobacter uraniireducens Rf4	Proteobacteria	Bacteria
555	Geobacter sp. FRC-32	Proteobacteria	Bacteria
556	Geobacter lovleyi SZ	Proteobacteria	Bacteria
557	Geobacter bemidjiensis Bem	Proteobacteria	Bacteria
558	Geobacter sulfurreducens PCA	Proteobacteria	Bacteria
559	Geobacter metallireducens GS-15	Proteobacteria	Bacteria
560	Haliangium ochraceum DSM 14365	Proteobacteria	Bacteria
561	Sorangium cellulosum So ce 56	Proteobacteria	Bacteria
562	Anaeromyxobacter sp. Fw109-5	Proteobacteria	Bacteria
563	Anaeromyxobacter dehalogenans 2CP-C	Proteobacteria	Bacteria
564	Myxococcus xanthus DK 1622	Proteobacteria	Bacteria
565	Magnetococcus sp. MC-1	Proteobacteria	Bacteria
566	Sideroxydans lithotrophicus ES-1	Proteobacteria	Bacteria
567	Aromatoleum aromaticum EbN1	Proteobacteria	Bacteria
568	Dechloromonas aromatica RCB	Proteobacteria	Bacteria
569	Thauera sp. MZ1T	Proteobacteria	Bacteria
570	Laribacter hongkongensis HLHK9	Proteobacteria	Bacteria
571	Chromobacterium violaceum ATCC 12472	Proteobacteria	Bacteria
572	Neisseria meningitidis Z2491	Proteobacteria	Bacteria
573	Neisseria gonorrhoeae FA 1090	Proteobacteria	Bacteria
574	Methylotenera mobilis JLW8	Proteobacteria	Bacteria
575	Methylovorus sp. SIP3-4	Proteobacteria	Bacteria
576	Methylobacillus flagellatus KT	Proteobacteria	Bacteria
577	Thiobacillus denitrificans ATCC 25259	Proteobacteria	Bacteria
578	Candidatus Accumulibacter phosphatis clade IIA UW-1	Proteobacteria	Bacteria
579	Methylibium petroleiphilum PM1	Proteobacteria	Bacteria
580	Leptothrix cholodnii SP-6	Proteobacteria	Bacteria
581	Ralstonia eutropha JMP134	Proteobacteria	Bacteria
582	Cupriavidus taiwanensis	Proteobacteria	Bacteria
583	Cupriavidus metallidurans CH34	Proteobacteria	Bacteria
584	Ralstonia pickettii 12J	Proteobacteria	Bacteria
585	Ralstonia solanacearum GMI1000	Proteobacteria	Bacteria
586	Polynucleobacter necessarius ssp. asymbioticus QLW-P1DMWA-1	Proteobacteria	Bacteria
587	Burkholderia phytofirmans PsJN	Proteobacteria	Bacteria
588	Burkholderia phymatum STM815	Proteobacteria	Bacteria
589	Burkholderia thailandensis E264	Proteobacteria	Bacteria
590	Burkholderia pseudomallei K96243	Proteobacteria	Bacteria
591	Burkholderia mallei ATCC 23344	Proteobacteria	Bacteria
592	Burkholderia sp. 383	Proteobacteria	Bacteria
593	Burkholderia ambifaria AMMD	Proteobacteria	Bacteria
594	Burkholderia cenocepacia AU 1054	Proteobacteria	Bacteria
595	Burkholderia multivorans ATCC 17616	Proteobacteria	Bacteria
596	Burkholderia vietnamiensis G4	Proteobacteria	Bacteria
597	Burkholderia xenovorans LB400	Proteobacteria	Bacteria
598	Burkholderia glumae BGR1	Proteobacteria	Bacteria
599	Rhodoferax ferrireducens T118	Proteobacteria	Bacteria
600	Verminephrobacter eiseniae EF01-2	Proteobacteria	Bacteria
601	Delftia acidovorans SPH-1	Proteobacteria	Bacteria
602	Polaromonas sp. JS666	Proteobacteria	Bacteria
603	Polaromonas naphthalenivorans CJ2	Proteobacteria	Bacteria
604	Variovorax paradoxus S110	Proteobacteria	Bacteria
605	Acidovorax ebreus TPSY	Proteobacteria	Bacteria
606	Acidovorax sp. JS42	Proteobacteria	Bacteria
607	Acidovorax citrulli AAC00-1	Proteobacteria	Bacteria
608	Herminiimonas arsenicoxydans	Proteobacteria	Bacteria
609	Janthinobacterium sp. Marseille	Proteobacteria	Bacteria
610	Bordetella petrii DSM 12804	Proteobacteria	Bacteria
611	Bordetella avium 197N	Proteobacteria	Bacteria
612	Bordetella pertussis Tohama I	Proteobacteria	Bacteria
613	Bordetella parapertussis 12822	Proteobacteria	Bacteria
614	Bordetella bronchiseptica RB50	Proteobacteria	Bacteria
615	Nitrosospira multiformis ATCC 25196	Proteobacteria	Bacteria
616	Nitrosomonas eutropha C91	Proteobacteria	Bacteria
617	Nitrosomonas europaea ATCC 19718	Proteobacteria	Bacteria
618	Caulobacter sp. K31	Proteobacteria	Bacteria
619	Caulobacter crescentus CB15	Proteobacteria	Bacteria
620	Caulobacter segnis ATCC 21756	Proteobacteria	Bacteria
621	Phenylobacterium zucineum HLK1	Proteobacteria	Bacteria
622	Erythrobacter litoralis HTCC2594	Proteobacteria	Bacteria
623	Sphingopyxis alaskensis RB2256	Proteobacteria	Bacteria
624	Novosphingobium aromaticivorans DSM 12444	Proteobacteria	Bacteria
625	Sphingobium japonicum UT26S	Proteobacteria	Bacteria
626	Sphingomonas wittichii RW1	Proteobacteria	Bacteria
627	Zymomonas mobilis ssp. mobilis ZM4	Proteobacteria	Bacteria
628	Maricaulis maris MCS10	Proteobacteria	Bacteria
629	Hirschia baltica ATCC 49814	Proteobacteria	Bacteria
630	Hyphomonas neptunium ATCC 15444	Proteobacteria	Bacteria
631	Dinoroseobacter shibae DFL 12	Proteobacteria	Bacteria
632	Jannaschia sp. CCS1	Proteobacteria	Bacteria
633	Ruegeria sp. TM1040	Proteobacteria	Bacteria
634	Ruegeria pomeroyi DSS-3	Proteobacteria	Bacteria
635	Roseobacter denitrificans OCh 114	Proteobacteria	Bacteria
636	Rhodobacter sphaeroides 2.4.1	Proteobacteria	Bacteria
637	Rhodobacter capsulatus SB 1003	Proteobacteria	Bacteria
638	Paracoccus denitrificans PD1222	Proteobacteria	Bacteria
639	Magnetospirillum magneticum AMB-1	Proteobacteria	Bacteria
640	Rhodospirillum centenum SW	Proteobacteria	Bacteria
641	Rhodospirillum rubrum ATCC 11170	Proteobacteria	Bacteria
642	Azospirillum sp. B510	Proteobacteria	Bacteria
643	Granulibacter bethesdensis CGDNIH1	Proteobacteria	Bacteria
644	Gluconacetobacter diazotrophicus PAl 5	Proteobacteria	Bacteria
645	Gluconobacter oxydans 621H	Proteobacteria	Bacteria
646	Acetobacter pasteurianus IFO 3283-01	Proteobacteria	Bacteria
647	Candidatus Puniceispirillum marinum IMCC1322	Proteobacteria	Bacteria
648	Candidatus Pelagibacter ubique HTCC1062	Proteobacteria	Bacteria
649	Neorickettsia sennetsu Miyayama	Proteobacteria	Bacteria
650	Neorickettsia risticii Illinois	Proteobacteria	Bacteria
651	Wolbachia endosymbiont of Culex_quinquefasciatus Pel	Proteobacteria	Bacteria
652	Wolbachia endosymbiont of Drosophila melanogaster	Proteobacteria	Bacteria
653	Wolbachia endosymbiont TRS of Brugia malayi	Proteobacteria	Bacteria
654	Wolbachia sp. wRi	Proteobacteria	Bacteria
655	Ehrlichia chaffeensis Arkansas	Proteobacteria	Bacteria
656	Ehrlichia canis Jake	Proteobacteria	Bacteria
657	Ehrlichia ruminantium Welgevonden	Proteobacteria	Bacteria
658	Anaplasma phagocytophilum HZ	Proteobacteria	Bacteria
659	Anaplasma marginale St. Maries	Proteobacteria	Bacteria
660	Anaplasma centrale Israel	Proteobacteria	Bacteria
661	Orientia tsutsugamushi Boryong	Proteobacteria	Bacteria
662	Rickettsia bellii RML369-C	Proteobacteria	Bacteria
663	Rickettsia canadensis McKiel	Proteobacteria	Bacteria
664	Rickettsia typhi Wilmington	Proteobacteria	Bacteria
665	Rickettsia prowazekii Madrid E	Proteobacteria	Bacteria
666	Rickettsia peacockii Rustic	Proteobacteria	Bacteria
667	Rickettsia felis URRWXCal2	Proteobacteria	Bacteria
668	Rickettsia massiliae MTU5	Proteobacteria	Bacteria
669	Rickettsia africae ESF-5	Proteobacteria	Bacteria
670	Rickettsia akari Hartford	Proteobacteria	Bacteria
671	Rickettsia rickettsii Sheila Smith	Proteobacteria	Bacteria
672	Rickettsia conorii Malish 7	Proteobacteria	Bacteria
673	Xanthobacter autotrophicus Py2	Proteobacteria	Bacteria
674	Azorhizobium caulinodans ORS 571	Proteobacteria	Bacteria
675	Methylobacterium chloromethanicum CM4	Proteobacteria	Bacteria
676	Methylobacterium extorquens PA1	Proteobacteria	Bacteria
677	Methylobacterium sp. 4-46	Proteobacteria	Bacteria
678	Methylobacterium populi BJ001	Proteobacteria	Bacteria
679	Methylobacterium nodulans ORS 2060	Proteobacteria	Bacteria
680	Methylobacterium radiotolerans JCM 2831	Proteobacteria	Bacteria
681	Candidatus Hodgkinia cicadicola Dsem	Proteobacteria	Bacteria
682	Ochrobactrum anthropi ATCC 49188	Proteobacteria	Bacteria
683	Brucella microti CCM 4915	Proteobacteria	Bacteria
684	Brucella canis ATCC 23365	Proteobacteria	Bacteria
685	Brucella suis 1330	Proteobacteria	Bacteria
686	Brucella melitensis bv. 1 16M	Proteobacteria	Bacteria
687	Brucella ovis ATCC 25840	Proteobacteria	Bacteria
688	Brucella abortus bv. 1 9-941	Proteobacteria	Bacteria
689	Rhizobium sp. NGR234	Proteobacteria	Bacteria
690	Sinorhizobium medicae WSM419	Proteobacteria	Bacteria
691	Sinorhizobium meliloti 1021	Proteobacteria	Bacteria
692	Rhizobium etli CFN 42	Proteobacteria	Bacteria
693	Rhizobium leguminosarum bv. viciae 3841	Proteobacteria	Bacteria
694	Agrobacterium vitis S4	Proteobacteria	Bacteria
695	Agrobacterium radiobacter K84	Proteobacteria	Bacteria
696	Agrobacterium tumefaciens C58	Proteobacteria	Bacteria
697	Candidatus Liberibacter asiaticus psy62	Proteobacteria	Bacteria
698	Chelativorans sp. BNC1	Proteobacteria	Bacteria
699	Parvibaculum lavamentivorans DS-1	Proteobacteria	Bacteria
700	Mesorhizobium loti MAFF303099	Proteobacteria	Bacteria
701	Methylocella silvestris BL2	Proteobacteria	Bacteria
702	Beijerinckia indica ssp. indica ATCC 9039	Proteobacteria	Bacteria
703	Oligotropha carboxidovorans OM5	Proteobacteria	Bacteria
704	Rhodopseudomonas palustris CGA009	Proteobacteria	Bacteria
705	Nitrobacter winogradskyi Nb-255	Proteobacteria	Bacteria
706	Nitrobacter hamburgensis X14	Proteobacteria	Bacteria
707	Bradyrhizobium sp. ORS278	Proteobacteria	Bacteria
708	Bradyrhizobium japonicum USDA 110	Proteobacteria	Bacteria
709	Bartonella tribocorum CIP 105476	Proteobacteria	Bacteria
710	Bartonella henselae Houston-1	Proteobacteria	Bacteria
711	Bartonella grahamii as4aup	Proteobacteria	Bacteria
712	Bartonella quintana Toulouse	Proteobacteria	Bacteria
713	Bartonella bacilliformis KC583	Proteobacteria	Bacteria
714	Acidithiobacillus ferrooxidans ATCC 23270	Proteobacteria	Bacteria
715	Mannheimia succiniciproducens MBEL55E	Proteobacteria	Bacteria
716	Aggregatibacter aphrophilus NJ8700	Proteobacteria	Bacteria
717	Aggregatibacter actinomycetemcomitans D11S-1	Proteobacteria	Bacteria
718	Haemophilus somnus 129PT	Proteobacteria	Bacteria
719	Pasteurella multocida ssp. multocida Pm70	Proteobacteria	Bacteria
720	Haemophilus parasuis SH0165	Proteobacteria	Bacteria
721	Haemophilus ducreyi 35000HP	Proteobacteria	Bacteria
722	Haemophilus influenzae Rd KW20	Proteobacteria	Bacteria
723	Actinobacillus succinogenes 130Z	Proteobacteria	Bacteria
724	Actinobacillus pleuropneumoniae L20	Proteobacteria	Bacteria
725	Tolumonas auensis DSM 9187	Proteobacteria	Bacteria
726	Aeromonas salmonicida ssp. salmonicida A449	Proteobacteria	Bacteria
727	Aeromonas hydrophila ssp. hydrophila ATCC 7966	Proteobacteria	Bacteria
728	Aliivibrio salmonicida LFI1238	Proteobacteria	Bacteria
729	Vibrio fischeri ES114	Proteobacteria	Bacteria
730	Vibrio parahaemolyticus RIMD 2210633	Proteobacteria	Bacteria
731	Vibrio harveyi ATCC BAA-1116	Proteobacteria	Bacteria
732	Vibrio sp. Ex25	Proteobacteria	Bacteria
733	Vibrio splendidus LGP32	Proteobacteria	Bacteria
734	Vibrio vulnificus YJ016	Proteobacteria	Bacteria
735	Vibrio cholerae O1 biov. El Tor N16961	Proteobacteria	Bacteria
736	Photobacterium profundum SS9	Proteobacteria	Bacteria
737	Psychromonas ingrahamii 37	Proteobacteria	Bacteria
738	Idiomarina loihiensis L2TR	Proteobacteria	Bacteria
739	Shewanella piezotolerans WP3	Proteobacteria	Bacteria
740	Shewanella loihica PV-4	Proteobacteria	Bacteria
741	Shewanella halifaxensis HAW-EB4	Proteobacteria	Bacteria
742	Shewanella sediminis HAW-EB3	Proteobacteria	Bacteria
743	Shewanella denitrificans OS217	Proteobacteria	Bacteria
744	Shewanella pealeana ATCC 700345	Proteobacteria	Bacteria
745	Shewanella oneidensis MR-1	Proteobacteria	Bacteria
746	Shewanella baltica OS155	Proteobacteria	Bacteria
747	Shewanella woodyi ATCC 51908	Proteobacteria	Bacteria
748	Shewanella sp. MR-7	Proteobacteria	Bacteria
749	Shewanella amazonensis SB2B	Proteobacteria	Bacteria
750	Shewanella violacea DSS12	Proteobacteria	Bacteria
751	Shewanella frigidimarina NCIMB 400	Proteobacteria	Bacteria
752	Shewanella putrefaciens CN-32	Proteobacteria	Bacteria
753	Colwellia psychrerythraea 34H	Proteobacteria	Bacteria
754	Pseudoalteromonas atlantica T6c	Proteobacteria	Bacteria
755	Pseudoalteromonas haloplanktis TAC125	Proteobacteria	Bacteria
756	Teredinibacter turnerae T7901	Proteobacteria	Bacteria
757	Saccharophagus degradans 2-40	Proteobacteria	Bacteria
758	Marinobacter aquaeolei VT8	Proteobacteria	Bacteria
759	Alteromonas macleodii Deep ecotype	Proteobacteria	Bacteria
760	Hahella chejuensis KCTC 2396	Proteobacteria	Bacteria
761	Kangiella koreensis DSM 16069	Proteobacteria	Bacteria
762	Alcanivorax borkumensis SK2	Proteobacteria	Bacteria
763	Marinomonas sp. MWYL1	Proteobacteria	Bacteria
764	Chromohalobacter salexigens DSM 3043	Proteobacteria	Bacteria
765	Methylococcus capsulatus Bath	Proteobacteria	Bacteria
766	Dichelobacter nodosus VCS1703A	Proteobacteria	Bacteria
767	Stenotrophomonas maltophilia R551-3	Proteobacteria	Bacteria
768	Xylella fastidiosa 9a5c	Proteobacteria	Bacteria
769	Xanthomonas axonopodis pv. citri 306	Proteobacteria	Bacteria
770	Xanthomonas albilineans	Proteobacteria	Bacteria
771	Xanthomonas oryzae pv. oryzae KACC10331	Proteobacteria	Bacteria
772	Xanthomonas campestris pv. campestris ATCC 33913	Proteobacteria	Bacteria
773	Halothiobacillus neapolitanus c2	Proteobacteria	Bacteria
774	Alkalilimnicola ehrlichii MLHE-1	Proteobacteria	Bacteria
775	Thioalkalivibrio sp. HL-EbGR7	Proteobacteria	Bacteria
776	Halorhodospira halophila SL1	Proteobacteria	Bacteria
777	Allochromatium vinosum DSM 180	Proteobacteria	Bacteria
778	Nitrosococcus halophilus Nc4	Proteobacteria	Bacteria
779	Nitrosococcus oceani ATCC 19707	Proteobacteria	Bacteria
780	Coxiella burnetii RSA 493	Proteobacteria	Bacteria
781	Legionella longbeachae NSW150	Proteobacteria	Bacteria
782	Legionella pneumophila ssp. pneumophila Philadelphia 1	Proteobacteria	Bacteria
783	Baumannia cicadellinicola Hc	Proteobacteria	Bacteria
784	Candidatus Carsonella ruddii PV	Proteobacteria	Bacteria
785	Candidatus Vesicomyosocius okutanii HA	Proteobacteria	Bacteria
786	Candidatus Ruthia magnifica Cm	Proteobacteria	Bacteria
787	Cronobacter turicensis z3032	Proteobacteria	Bacteria
788	Cronobacter sakazakii ATCC BAA-894	Proteobacteria	Bacteria
789	Candidatus Riesia pediculicola USDA	Proteobacteria	Bacteria
790	Dickeya zeae Ech1591	Proteobacteria	Bacteria
791	Dickeya dadantii Ech703	Proteobacteria	Bacteria
792	Candidatus Hamiltonella defensa 5AT	Proteobacteria	Bacteria
793	Candidatus Blochmannia floridanus	Proteobacteria	Bacteria
794	Pectobacterium wasabiae WPP163	Proteobacteria	Bacteria
795	Pectobacterium atrosepticum SCRI1043	Proteobacteria	Bacteria
796	Pectobacterium carotovorum ssp. carotovorum PC1	Proteobacteria	Bacteria
797	Sodalis glossinidius morsitans	Proteobacteria	Bacteria
798	Pantoea ananatis LMG 20103	Proteobacteria	Bacteria
799	Wigglesworthia glossinidia	Proteobacteria	Bacteria
800	Buchnera aphidicola APS	Proteobacteria	Bacteria
801	Photorhabdus asymbiotica	Proteobacteria	Bacteria
802	Photorhabdus luminescens ssp. laumondii TTO1	Proteobacteria	Bacteria
803	Edwardsiella ictaluri 93-146	Proteobacteria	Bacteria
804	Edwardsiella tarda EIB202	Proteobacteria	Bacteria
805	Yersinia pseudotuberculosis IP 32953	Proteobacteria	Bacteria
806	Yersinia pestis CO92	Proteobacteria	Bacteria
807	Yersinia enterocolitica ssp. enterocolitica 8081	Proteobacteria	Bacteria
808	Xenorhabdus bovienii SS-2004	Proteobacteria	Bacteria
809	Shigella sonnei Ss046	Proteobacteria	Bacteria
810	Shigella flexneri 2a 2457T	Proteobacteria	Bacteria
811	Shigella dysenteriae Sd197	Proteobacteria	Bacteria
812	Shigella boydii Sb227	Proteobacteria	Bacteria
813	Serratia proteamaculans 568	Proteobacteria	Bacteria
814	Salmonella enterica ssp. enterica ser. Typhimurium LT2	Proteobacteria	Bacteria
815	Proteus mirabilis HI4320	Proteobacteria	Bacteria
816	Klebsiella variicola At-22	Proteobacteria	Bacteria
817	Klebsiella pneumoniae ssp. pneumoniae MGH 78578	Proteobacteria	Bacteria
818	Escherichia fergusonii ATCC 35469	Proteobacteria	Bacteria
819	Escherichia coli K-12 subMG1655	Proteobacteria	Bacteria
820	Erwinia tasmaniensis Et1/99	Proteobacteria	Bacteria
821	Erwinia pyrifoliae Ep1/96	Proteobacteria	Bacteria
822	Erwinia amylovora ATCC 49946	Proteobacteria	Bacteria
823	Enterobacter sp. 638	Proteobacteria	Bacteria
824	Citrobacter rodentium ICC168	Proteobacteria	Bacteria
825	Citrobacter koseri ATCC BAA-895	Proteobacteria	Bacteria
826	Azotobacter vinelandii DJ	Proteobacteria	Bacteria
827	Pseudomonas entomophila L48	Proteobacteria	Bacteria
828	Pseudomonas syringae pv. tomato DC3000	Proteobacteria	Bacteria
829	Pseudomonas stutzeri A1501	Proteobacteria	Bacteria
830	Pseudomonas putida KT2440	Proteobacteria	Bacteria
831	Pseudomonas fluorescens Pf-5	Proteobacteria	Bacteria
832	Pseudomonas mendocina ymp	Proteobacteria	Bacteria
833	Pseudomonas aeruginosa PAO1	Proteobacteria	Bacteria
834	Cellvibrio japonicus Ueda107	Proteobacteria	Bacteria
835	Psychrobacter sp. PRwf-1	Proteobacteria	Bacteria
836	Psychrobacter arcticus 273-4	Proteobacteria	Bacteria
837	Psychrobacter cryohalolentis K5	Proteobacteria	Bacteria
838	Acinetobacter baumannii ATCC 17978	Proteobacteria	Bacteria
839	Acinetobacter sp. ADP1	Proteobacteria	Bacteria
840	Thiomicrospira crunogena XCL-2	Proteobacteria	Bacteria
841	Francisella philomiragia ssp. philomiragia ATCC 25017	Proteobacteria	Bacteria
842	Francisella tularensis ssp. tularensis SCHU S4	Proteobacteria	Bacteria
843	Brachyspira hyodysenteriae WA1	Spirochaetes	Bacteria
844	Leptospira borgpetersenii ser. Hardjo-bovis L550	Spirochaetes	Bacteria
845	Leptospira interrogans ser. Lai 56601	Spirochaetes	Bacteria
846	Leptospira biflexa ser. Patoc Patoc 1 (Paris)	Spirochaetes	Bacteria
847	Treponema pallidum ssp. pallidum Nichols	Spirochaetes	Bacteria
848	Treponema denticola ATCC 35405	Spirochaetes	Bacteria
849	Borrelia garinii PBi	Spirochaetes	Bacteria
850	Borrelia afzelii PKo	Spirochaetes	Bacteria
851	Borrelia burgdorferi B31	Spirochaetes	Bacteria
852	Borrelia recurrentis A1	Spirochaetes	Bacteria
853	Borrelia duttonii Ly	Spirochaetes	Bacteria
854	Borrelia turicatae 91E135	Spirochaetes	Bacteria
855	Borrelia hermsii DAH	Spirochaetes	Bacteria
856	Aminobacterium colombiense DSM 12261	Synergistetes	Bacteria
857	Thermanaerovibrio acidaminovorans DSM 6589	Synergistetes	Bacteria
858	Candidatus Phytoplasma mali	Tenericutes	Bacteria
859	Aster yellows witches-broom phytoplasma AYWB	Tenericutes	Bacteria
860	Onion yellows phytoplasma OY-M	Tenericutes	Bacteria
861	Acholeplasma laidlawii PG-8A	Tenericutes	Bacteria
862	Mesoplasma florum L1	Tenericutes	Bacteria
863	Ureaplasma parvum ser. 3 ATCC 700970	Tenericutes	Bacteria
864	Ureaplasma urealyticum ser. 10 ATCC 33699	Tenericutes	Bacteria
865	Mycoplasma mycoides ssp. mycoides SC PG1	Tenericutes	Bacteria
866	Mycoplasma capricolum ssp. capricolum ATCC 27343	Tenericutes	Bacteria
867	Mycoplasma crocodyli MP145	Tenericutes	Bacteria
868	Mycoplasma conjunctivae HRC/581	Tenericutes	Bacteria
869	Mycoplasma penetrans HF-2	Tenericutes	Bacteria
870	Mycoplasma mobile 163K	Tenericutes	Bacteria
871	Mycoplasma arthritidis 158L3-1	Tenericutes	Bacteria
872	Mycoplasma agalactiae PG2	Tenericutes	Bacteria
873	Mycoplasma synoviae 53	Tenericutes	Bacteria
874	Mycoplasma pulmonis UAB CTIP	Tenericutes	Bacteria
875	Mycoplasma pneumoniae M129	Tenericutes	Bacteria
876	Mycoplasma hyopneumoniae 232	Tenericutes	Bacteria
877	Mycoplasma hominis	Tenericutes	Bacteria
878	Mycoplasma genitalium G37	Tenericutes	Bacteria
879	Mycoplasma gallisepticum R(low)	Tenericutes	Bacteria
880	Kosmotoga olearia TBF 19.5.1	Thermotogae	Bacteria
881	Petrotoga mobilis SJ95	Thermotogae	Bacteria
882	Fervidobacterium nodosum Rt17-B1	Thermotogae	Bacteria
883	Thermosipho melanesiensis BI429	Thermotogae	Bacteria
884	Thermosipho africanus TCF52B	Thermotogae	Bacteria
885	Thermotoga lettingae TMO	Thermotogae	Bacteria
886	Thermotoga sp. RQ2	Thermotogae	Bacteria
887	Thermotoga naphthophila RKU-10	Thermotogae	Bacteria
888	Thermotoga petrophila RKU-1	Thermotogae	Bacteria
889	Thermotoga neapolitana DSM 4359	Thermotogae	Bacteria
890	Thermotoga maritima MSB8	Thermotogae	Bacteria
891	Coraliomargarita akajimensis DSM 45221	Verrucomicrobia	Bacteria
892	Opitutus terrae PB90-1	Verrucomicrobia	Bacteria
893	Methylacidiphilum infernorum V4	Verrucomicrobia	Bacteria
894	Akkermansia muciniphila ATCC BAA-835	Verrucomicrobia	Bacteria
895	Thermobaculum terrenum ATCC BAA-798		Bacteria
896	Hyperthermus butylicus DSM 5456	Crenarchaeota	Archaea
897	Aeropyrum pernix K1	Crenarchaeota	Archaea
898	Ignicoccus hospitalis KIN4/I	Crenarchaeota	Archaea
899	Staphylothermus marinus F1	Crenarchaeota	Archaea
900	Desulfurococcus kamchatkensis 1221n	Crenarchaeota	Archaea
901	Metallosphaera sedula DSM 5348	Crenarchaeota	Archaea
902	Sulfolobus tokodaii 7	Crenarchaeota	Archaea
903	Sulfolobus islandicus Y.N.15.51	Crenarchaeota	Archaea
904	Sulfolobus solfataricus P2	Crenarchaeota	Archaea
905	Sulfolobus acidocaldarius DSM 639	Crenarchaeota	Archaea
906	Thermofilum pendens Hrk 5	Crenarchaeota	Archaea
907	Caldivirga maquilingensis IC-167	Crenarchaeota	Archaea
908	Pyrobaculum calidifontis JCM 11548	Crenarchaeota	Archaea
909	Pyrobaculum arsenaticum DSM 13514	Crenarchaeota	Archaea
910	Pyrobaculum aerophilum IM2	Crenarchaeota	Archaea
911	Pyrobaculum islandicum DSM 4184	Crenarchaeota	Archaea
912	Thermoproteus neutrophilus V24Sta	Crenarchaeota	Archaea
913	Methanocella paludicola SANAE	Euryarchaeota	Archaea
914	Methanosaeta thermophila PT	Euryarchaeota	Archaea
915	Methanococcoides burtonii DSM 6242	Euryarchaeota	Archaea
916	Methanosarcina acetivorans C2A	Euryarchaeota	Archaea
917	Methanosarcina mazei Go1	Euryarchaeota	Archaea
918	Methanosarcina barkeri Fusaro	Euryarchaeota	Archaea
919	Methanohalophilus mahii DSM 5219	Euryarchaeota	Archaea
920	Methanosphaerula palustris E1-9c	Euryarchaeota	Archaea
921	Candidatus Methanoregula boonei 6A8	Euryarchaeota	Archaea
922	Methanospirillum hungatei JF-1	Euryarchaeota	Archaea
923	Methanocorpusculum labreanum Z	Euryarchaeota	Archaea
924	Methanoculleus marisnigri JR1	Euryarchaeota	Archaea
925	Methanopyrus kandleri AV19	Euryarchaeota	Archaea
926	Ferroglobus placidus DSM 10642	Euryarchaeota	Archaea
927	Archaeoglobus profundus DSM 5631	Euryarchaeota	Archaea
928	Archaeoglobus fulgidus DSM 4304	Euryarchaeota	Archaea
929	Thermococcus onnurineus NA1	Euryarchaeota	Archaea
930	Thermococcus kodakarensis KOD1	Euryarchaeota	Archaea
931	Thermococcus gammatolerans EJ3	Euryarchaeota	Archaea
932	Thermococcus sibiricus MM 739	Euryarchaeota	Archaea
933	Pyrococcus horikoshii OT3	Euryarchaeota	Archaea
934	Pyrococcus abyssi GE5	Euryarchaeota	Archaea
935	Pyrococcus furiosus DSM 3638	Euryarchaeota	Archaea
936	Thermoplasma volcanium GSS1	Euryarchaeota	Archaea
937	Thermoplasma acidophilum DSM 1728	Euryarchaeota	Archaea
938	Picrophilus torridus DSM 9790	Euryarchaeota	Archaea
939	Haloquadratum walsbyi DSM 16790	Euryarchaeota	Archaea
940	Halomicrobium mukohataei DSM 12286	Euryarchaeota	Archaea
941	Halorhabdus utahensis DSM 12940	Euryarchaeota	Archaea
942	Haloterrigena turkmenica DSM 5511	Euryarchaeota	Archaea
943	Natronomonas pharaonis DSM 2160	Euryarchaeota	Archaea
944	Natrialba magadii ATCC 43099	Euryarchaeota	Archaea
945	Halorubrum lacusprofundi ATCC 49239	Euryarchaeota	Archaea
946	Haloferax volcanii DS2	Euryarchaeota	Archaea
947	Halobacterium salinarum R1	Euryarchaeota	Archaea
948	Halobacterium sp. NRC-1	Euryarchaeota	Archaea
949	Haloarcula marismortui ATCC 43049	Euryarchaeota	Archaea
950	Methanocaldococcus sp. FS406-22	Euryarchaeota	Archaea
951	Methanocaldococcus fervens AG86	Euryarchaeota	Archaea
952	Methanocaldococcus vulcanius M7	Euryarchaeota	Archaea
953	Methanocaldococcus jannaschii DSM 2661	Euryarchaeota	Archaea
954	Methanococcus aeolicus Nankai-3	Euryarchaeota	Archaea
955	Methanococcus maripaludis S2	Euryarchaeota	Archaea
956	Methanococcus vannielii SB	Euryarchaeota	Archaea
957	Methanothermobacter thermautotrophicus Delta H	Euryarchaeota	Archaea
958	Methanosphaera stadtmanae DSM 3091	Euryarchaeota	Archaea
959	Methanobrevibacter ruminantium M1	Euryarchaeota	Archaea
960	Methanobrevibacter smithii ATCC 35061	Euryarchaeota	Archaea
961	uncultured methanogenic archaeon RC-I	Euryarchaeota	Archaea
962	Aciduliprofundum boonei T469	Euryarchaeota	Archaea
963	Candidatus Korarchaeum cryptofilum OPF8	Korarchaeota	Archaea
964	Nanoarchaeum equitans Kin4-M	Nanoarchaeota	Archaea
965	Nitrosopumilus maritimus SCM1	Thaumarchaeota	Archaea

The most recent domain functional annotation file for SCOP 1.73 was downloaded from the SUPERFAMILY webserver [23]. For each genome we extracted the set of unique FSFs present and then mapped them to the 7 general and 50 detailed functional categories. We calculated both the percentage and actual number of domains using programming implementations in Python 3.1 (http://www.python.org/download/).

Statistical Analysis

The statistical significance between the numbers of functional FSFs in FL organisms of superkingdoms was evaluated by Welch's ANOVA in SAS (http://www.sas.com/software/sas9), which is the appropriate test to detect differences between means for groups having unequal variances [49]. We excluded organisms with P and OP lifestyles in order to remove noise from the data. Additionally, in order to meet asymptotic normality, we used the Log10 transformation and rescaled the data to 0–7 using the following formula, where Nxy is the count of a FSF in x functional category in y superkingdom; N is the largest value in the matrix and N is the normalized and scaled score for FSF x in y superkingdom.

Conclusions

Our analysis revealed a remarkable conservation in the functional distribution of protein domains in superkingdoms for proteomes for which we have structural assignments. Figure S1 showcases average distribution of FSFs in phyla, kingdoms, and superkingdoms. The biggest proportion of each proteome is devoted in all cases to functions related to Metabolism. Phylogenomic analysis has shown that Metabolism appeared earlier than other functional groups and their structures were the first to spread in life [1,50]. This would explain the relative large representation of Metabolism in the functional toolkit of cells. Usage of domains related to ECP and Regulation is significantly higher in Metazoa compared to the rest. This showcases the importance of regulation signal transduction mechanisms for eukaryotic organisms [51,52]. Our results support the view that prokaryotes evolved via reductive evolutionary processes whereas genome expansion was the route taken by eukaryotic organisms. Genome expansion in Eukarya seems to be directed towards innovation of FSF architectures, especially those linked to Regulation, ECP and General. Finally, viral structures make up a substantial proportion of cellular proteomes and appear to have played an important role in the evolution of cellular life.

Figure S1

Average distribution of FSFs in phyla, kingdom, and superkingdoms suggest conservation of functional design in proteomes. Numbers in parentheses indicate total number of proteomes analyzed for each phyla/kingdom.

Organisms with parasitic lifestyles have simple and reduced proteomes and rely on host cells for metabolic functions. Tenericutes are unique in this regard. They spend most of their proteomic resources in functions linked to Information (e.g., translation, replication). Remarkably, we find that the conservation of molecular functions in proteomes is only broken in “outliers” with parasitic lifestyles that do not obey the global trends. We conclude that organism lifestyle is a crucial factor in shaping the nature of proteomes.