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1 s that differ as to polypeptide length and C domain combination.

2 and regulatory-ATPase and ATPase-DNA binding domain combinations.

3 in PCBPs indicated an additive effect of two-domain combinations.

4 s is due to frequent duplication of specific domain combinations.

5 in organizations derived from those specific domain combinations.

6 udopodia, and myosins with three contrasting domain combinations and putative functions.

7 the resulting emergence of proteins with new domain combinations, and thus potentially novel function

8 same time, they support a scenario in which domain combinations are formed only once during the evol

9 t cases where structures with both AB and BA domain combinations are known.

10 in nature, will depend on selection for the domain combination based on its function.

11 b-server that allows comparative analysis of domain combinations between plant and other 55 organisms

12 Finally, we report on the specific domain combinations characterizing the three kingdoms of

13 up of large response regulators with complex domain combinations containing at least two receiver dom

14 ein domains are represented as vertices, and domain combinations, defined as instances of two domains

15 ails for all protein assignments, searchable domain combinations, domain occurrence network visualiza

16 o present individual examples of independent domain combination evolution.

17 The ways in which these domain combinations evolve tend to be specific to the or

18 dual species, with, for instance, 70% of the domain combinations found in the human genome having evo

19 latively small pool of evolutionarily stable domain combinations from which numerous rare architectur

20 ate that about 25% of all currently observed domain combinations have evolved multiple times.

21 ylogeny and taxonomic distribution of myosin domain combinations identified five innovations that str

22 , this percentage is even higher for sets of domain combinations in individual species, with, for ins

23 domain repeats and we compare the set of the domain combinations in the genomes to those in PDB, and

24 Finally, we compare the set of the domain combinations in the genomes to those in the RCSB

25 rocess of independent emergence of identical domain combination is widespread, not limited to domains

26 tions, we show that independent evolution of domain combinations is significantly more prevalent than

27 The phylogenetic distribution of domain combinations is surveyed, to establish the extent

28 We found that 9% of domain combinations observed in non-redundant PDB are in

29 e structures are multi-domain proteins; each domain combination occurring once per dataset.

30 We found 37 different protein domain combinations, often lineage-specific, and many pr

31 parallel evolution to the development of the domain combination repertoire in extant genomes has prof

32 microscope images of the ATPase-DNA-binding domain combination show formation of oligomeric rings.

33 structure of the unactivated receiver-ATPase domain combination shows a partially disrupted interface

34 chitectures and the abundance of alternative domain combinations suggest that fusions between the REC

35 Some of the pair-wise domain combinations that are highly duplicated also recu

36 sine interaction in cytoplasmic kinases, and domain combinations that link kinases to small GTPase si

37 We found two-domain and three-domain combinations that recur in different protein cont

38 ied some 1400 (1203 two-domain and 166 three-domain) combinations that are statistically significantl

39 onserved effector domains and discovered new domain combinations, which allowed the inference of as y

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