The "Protein Structure Universe" is a representation of the space of known protein structures mapped into 3 dimensions. A more detailed description and references may be found in the New Technologies section of the site.

Picture of the Protein Structure Universe represented by ~2000 unique protein structures, divided by SCOP class	Examples of some of the structures in the Protein Structure Universe

NEAR-COMPLETE Mycoplasma STRUCTURAL PROTEOME:

Progress on M. genitalium proteome: 86% of soluble proteins completed	Progress of M. pneumoniae proteome: 70% of soluble proteins completed

We mapped Mycoplasma protein structures and the structural homologs of other Mycoplasma proteins. 86% of M. genitalium soluble proteins and 70% of M. pneumoniae soluble proteins were mapped. Similarity to homologs was identified through a PSI-BLAST E-value of 10^-4 or better over 50 residues, or by a full-length match against a Pfam family that also matches the PDB entry. This shows where the proteins fit into the Protein Structure Universe map. Mycoplasma proteins and their homologs are shown in red. Transmembrane proteins (from all species) are shown in yellow.

We also mapped Mycoplasma proteins or their homologs of known structure according to their SCOP classification (we required homologous matches to cover at least 75% of the length of the domain):

SCOP classification (class level) of domains from homologs of 687 Mycoplasma pneumoniae proteins	SCOP classification (class level) of domains from homologs of 486 Mycoplasma genitalium proteins

In the above figures, we treated proteins of unknown structure as a single domain.

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The mapping of each protein in Mycoplasma pneumoniae and Mycoplasma genitalium onto known structures is shown in the following two tables:

• Overview of Mycoplasma pneumoniae proteome
• Overview of Mycoplasma genitalium proteome

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Most of the Mycoplasma ORFs (586/687 M. pneumoniae and 464/486 M. genitalium) have been annotated with cellular roles by TIGR. The number of proteins in each role category, and the number with structure, are shown below:

Cellular Function	Proteomes: (total ORFs / ORFs with known protein structure or fold)
	M. pneumoniae	M. genitalium
Amino acid biosynthesis	1 / 1	0 / 0
Biosynthesis of cofactors, prosthetic groups, and carriers	7 / 7	5 / 5
Cell envelope	50 / 15	28 / 7
Cellular processes	6 / 6	6 / 6
Central intermediary metabolism	8 / 8	7 / 7
DNA metabolism	36 / 29	28 / 26
Energy metabolism37/37	32 / 32
Fatty acid and phospholipid metabolism	9 / 7	8/6
Protein fate	22 / 21	20 / 19
Protein synthesis	77 / 74	89 / 86
Purines, pyrimidines, nucleosides, and nucleotides	20 / 20	17 / 17
Regulatory functions	5 / 5	5 / 5
Signal transduction	0 / 0	0 / 0
Transcription	11 / 10	13 / 12
Transport and binding proteins	35 / 24	33 / 23
Hypothetical proteins	88 / 34	160 / 75
Unclassified function	162 / 51	1 / 0
Unknown function	12 / 11	12 / 12
No annotation by TIGR	101 / 31	22 / 10

The SCOP classifications above were broken down according to the cellular functions (according to TIGR role category) of their parent proteins. Structural classifications of proteins from the most populated cellular function categories are shown below:

SCOP classification (class level) of domains from homologs of 50 Mycoplasma pneumoniae proteins from the "Cell envelope" role (TIGR category)	SCOP classification (class level) of domains from homologs of 28 Mycoplasma genitalium proteins from the "Cell envelope" role (TIGR category)
SCOP classification (class level) of domains from homologs of 36 Mycoplasma pneumoniae proteins from the "DNA metabolism" role (TIGR category)	SCOP classification (class level) of domains from homologs of 28 Mycoplasma genitalium proteins from the "DNA metabolism" role (TIGR category)
SCOP classification (class level) of domains from homologs of 37 Mycoplasma pneumoniae proteins from the "Energy metabolism" role (TIGR category)	SCOP classification (class level) of domains from homologs of 32 Mycoplasma genitalium proteins from the "Energy metabolism" role (TIGR category)
SCOP classification (class level) of domains from homologs of 88 Mycoplasma pneumoniae proteins from the "Hypothetical protein" role (TIGR category)	SCOP classification (class level) of domains from homologs of 160 Mycoplasma genitalium proteins from the "Hypothetical protein" role (TIGR category)
SCOP classification (class level) of domains from homologs of 22 Mycoplasma pneumoniae proteins from the "Protein fate" role (TIGR category)	SCOP classification (class level) of domains from homologs of 20 Mycoplasma genitalium proteins from the "Protein fate" role (TIGR category)
SCOP classification (class level) of domains from homologs of 20 Mycoplasma pneumoniae proteins from the "Purines, pyrimidines, nucleosides, and nucleotides" role (TIGR category)	SCOP classification (class level) of domains from homologs of 17 Mycoplasma genitalium proteins from the "Purines, pyrimidines, nucleosides, and nucleotides" role (TIGR category)
SCOP classification (class level) of domains from homologs of 77 Mycoplasma pneumoniae proteins from the "Protein synthesis" role (TIGR category)	SCOP classification (class level) of domains from homologs of 89 Mycoplasma genitalium proteins from the "Protein synthesis" role (TIGR category)
SCOP classification (class level) of domains from homologs of 11 Mycoplasma pneumoniae proteins from the "Transcription" role (TIGR category)	SCOP classification (class level) of domains from homologs of 13 Mycoplasma genitalium proteins from the "Transcription" role (TIGR category)
SCOP classification (class level) of domains from homologs of 35 Mycoplasma pneumoniae proteins from the "Transport and binding proteins" role (TIGR category)	SCOP classification (class level) of domains from homologs of 33 Mycoplasma genitalium proteins from the "Transport and binding proteins" role (TIGR category)

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