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Table 4 The transitions of the model.

From: Application of Petri net based analysis techniques to signal transduction pathways

ID

Transition name

Biological event

1

MATalpha_cell(surroundings)

a near MATα cell secretes its mating pheromone

2

binding_factor _to_receptor

the α-factor binds to the Ste2 receptor

3

receptor_synthesis

synthesis of the cell surface receptor Sst2

4

receptor _conformation_change

conformation change of the receptor

5

division(in_alpha_subunit:GDP->GTP)

dissociation of the Gα subunit of the G-protein

6

hydrolysis_GTP->GDP

hydrolysis reassociates Gα with Gβγ

7

interact_through_Far1

Gβγ interacts Far1 transmitted with Cdc24

8

Cdc42:GDP->GTP

Cdc24 supported activation of Cdc42

9

active_Cdc42_constitutive_at_pm

constitutive active Cdc42 attending the processes

10

binding_to_Ste20

Gβγ binds Ste20

11

Ste20_activated

Cdc42 at plasma membrane activates Ste20

12

binding_to_Ste5

Gβγ binds Ste5

13

Ste5_binds_Ste11

Ste5 binds Ste11

14

Fus3_synth

synthesis of kinase Fus3

15

Fus3_binds_Ste7

Ste7 binds Fus3

16

complex-formation

Ste5/Ste11 binds Ste7/Fus3

17

Ste20_phos_Ste11

phosphorylation of Ste11 by Ste20

18

Ste11_phos_Ste7

phosphorylation of Ste7 by Ste11

19

Ste7_phos_Fus3

phosphorylation of Fus3 by Ste7

20

Fus3PP-release

release of activated Fus3 out of the MAPK complex

21

binding_free_Fus3

remaining MAPK complex binds Fus3

22

Ste12_inhibit _phos

phosphorylation of Ste12 inhibitors Dig1/Dig2 by Fus3PP

23

Ste12-release

release of Ste12 out of the repression complex

24

Ste12_phos

phosphorylation of Ste12 by Fus3PP

25

transcr_activation

transcription activation of pheromone regulated genes

26

Fus3PP_dephos

dephosphorylation of Fus3PP by Msg5

27

repression_through_Fus3

Ste12 repression through inactive Fus3 and Dig1/Dig2

28

cell_fusion

processes leading to the fusion of the two haploid cells

29

transport_out_of_cell

Bar1 transport into the cell environment

30

factor _destruction

Bar1 transmitted destruction of the α-factor

31

Far1_phos

phosphorylation of Far1 by Fus3PP

32

cell_cycle_arrest in_G1

Far1 caused arrest in the cell cycle phase G1

33

transport_out_of_nucleus

Far1 transport out of the nucleus

34

Sst2_phos

phosphorylation of Sst2 by Fus3PP

35

transport_out_of_nucleus

Sst2 transport out of the nucleus

36

accelerated_hydr_GTP->GDP

accelerated hydrolysis reassociates the G-protein

37

Ste11_neg_phos

Fus3PP labels the MAPK complex at Ste11 for degradation

38

degradation

degradation of the MAPK complex

39

Ste7_neg_phos

Fus3PP labels the MAPK complex at Ste7 for degradation

40

Ste7_phos_Kss1

phosphorylation of Kss1 by Ste7

41

accelerated-dephos_Kss1

deactivation of phosphorylated Kss1 by Fus3PP

42

Kss1_dephos

dephosphorylation of phosphorylated Kss1 by Msg5

43

repression_through_Kss1

Ste12 repression through inactive Kss1 and Dig1/Dig2

44

techn_input

technical: the repressed Ste12 complex assumed to be present

45

Akr1_synthesis

synthesis of Akr1

46

Akr1_binds_Yck1/Yck2

Akr1 binds Yck1/Yck2

47

receptor_phos

labelling of Ste2 for degradation

48

ubiquit_endocytosis

ubiquitination and endocytosis of the receptor

  1. The transitions of the model, see Figure 7, each listed with its name, its ID and the biological event represented by this node.