Additional file 1:

Proteins specific to Sulfolobales. These proteins are indicated to be specific for the either all three sequenced Sulfolobus species (S. solfataricus, S. acidocaldarius and S. tokodaii) or two of these based on Blastp and PSI-Blast searches. The proteins only found in a single Sulfolobus species are not listed here.

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Additional file 2:

Proteins specific to Pyrobaculum and Thermofilum. For the proteins listed in this table, significant hits in Blastp and PSI-Blast searches are only observed for Pyrobaculum and Thermofilum. Because the genome of Thermofilum pendens is only partially sequenced, additional proteins of this kind may be found.

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Additional file 3:

Proteins specific for particular groups of methanogens. For the proteins listed in this table, significant hits in Blastp and PSI-Blast searches are only observed for (a) Methanococcales and (b) Methanosarcinaceae.

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Additional file 4:

Proteins specific for Thermococci. The proteins listed in this table are specific for either various (a) Thermococci (i.e. Thermococcus and Pyrococcus) or (b) various Pyrococci.

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Additional file 5:

Proteins specific for various Halobacteria. The proteins listed in this Table are specifically found in various sequenced halobacteria species as determined by Blastp and PSI-Blast searches.

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Additional file 6:

Proteins specific for various Halobacteria. These proteins are also specific for Halobacteria. However, unlike the proteins listed in Additional file 5, they are present in only three of the four sequenced halobacterial genomes.

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Additional file 7:

Proteins specific for various Halobacteria. These proteins are also specific for Halobacteria but they are found in only two of the four sequenced halobacterial genomes.

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Additional file 8:

Proteins specific for Thermoplasmata. These proteins are specific for either (a) all sequenced Thermoplasmata species, or (b) specific for only Thermoplasma, or (c) specific for Picrophilus and Ferroplasma.

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Additional file 9:

Archaeal-specific proteins with sporadic distribution. These proteins are specific for Archaea but they show sporadic distribution in different groups.

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Additional file 10:

List of proteins used in phylogenetic analysis

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