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OPENSEQ.org
821P_ Ras GTPase GTN 1E8Z_A PIP3 kinase
Genes: A B A+B
Length: 166 966 1095
Sequences: 7568 400 67
Seq/Len: 45.59 0.41 0.06
MirrorTree (Pazo et al. 2001) 0.31
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.11 0.02 0.01
2 0.12 0.02 0.01
5 0.14 0.03 0.02
10 0.16 0.03 0.04
20 0.18 0.03 0.06
100 0.23 0.03 0.14
∞ 0.26 0.05 0.19
Paired alignment generation
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Sequence A E-value:
Iterations:
Sequence B E-value:
Iterations:
Δgene MSA
Figure 1: The effect of Δgene on ratio of paralogs in the genome for each gene, and the number of sequences in the resulting joined alignment. Figure 2: Distribution of Δgene across all genomes. Figure 3: Current parameters. You can use the form to adjust the parameters and resubmit the job!
GREMLIN results (Scaled_score > 1):
Figure 4: The darker and larger the blue dots, the higher strength in coevolution. 		Inter Residue pairs sorted by strength in coevolution signal:
i j Scaled Score Prob I_Prob
112_V 257_T 1.59 0.17 0.00
60_G 789_S 1.34 0.12 0.00
64_Y 151_V 1.29 0.11 0.00
57_D 691_K 1.26 0.10 0.00
57_D 695_D 1.26 0.10 0.00
57_D 699_D 1.26 0.10 0.00
57_D 804_D 1.26 0.10 0.00
57_D 805_R 1.26 0.10 0.00
57_D 806_H 1.26 0.10 0.00
57_D 809_N 1.26 0.10 0.00
57_D 822_D 1.26 0.10 0.00
119_D 691_K 1.26 0.10 0.00
119_D 695_D 1.26 0.10 0.00
119_D 699_D 1.26 0.10 0.00
119_D 804_D 1.26 0.10 0.00
119_D 805_R 1.26 0.10 0.00
119_D 806_H 1.26 0.10 0.00
119_D 809_N 1.26 0.10 0.00
119_D 822_D 1.26 0.10 0.00
17_S 546_N 1.25 0.10 0.00
151_G 320_Y 1.15 0.09 0.00
120_L 810_I 1.14 0.09 0.00
147_K 413_L 1.14 0.08 0.00
152_V 270_V 1.13 0.08 0.00
57_D 668_P 1.13 0.08 0.00
119_D 668_P 1.13 0.08 0.00
115_G 488_L 1.12 0.08 0.00
138_G 677_D 1.12 0.08 0.00
142_I 778_K 1.11 0.08 0.00
19_L 848_D 1.11 0.08 0.00
84_I 877_A 1.11 0.08 0.00
57_D 735_G 1.10 0.08 0.00
119_D 735_G 1.10 0.08 0.00
113_L 749_I 1.10 0.08 0.00
156_F 845_L 1.10 0.08 0.00
82_F 945_F 1.10 0.08 0.00
57_D 843_F 1.10 0.08 0.00
119_D 843_F 1.10 0.08 0.00
82_F 470_A 1.08 0.08 0.00
17_S 543_G 1.08 0.08 0.00
24_I 741_K 1.07 0.08 0.00
152_V 845_L 1.07 0.08 0.00
89_S 672_E 1.07 0.08 0.00
152_V 885_L 1.06 0.07 0.00
53_L 845_L 1.06 0.07 0.00
9_V 145_I 1.05 0.07 0.00
19_L 540_L 1.05 0.07 0.00
152_V 139_L 1.05 0.07 0.00
84_I 853_M 1.04 0.07 0.00
86_N 627_Q 1.04 0.07 0.00
151_G 800_L 1.04 0.07 0.00
5_K 820_H 1.04 0.07 0.00
145_S 816_G 1.03 0.07 0.00
53_L 413_L 1.03 0.07 0.00
6_L 281_L 1.02 0.07 0.00
89_S 875_Y 1.02 0.07 0.00
17_S 850_L 1.01 0.07 0.00
57_D 816_G 1.01 0.07 0.00
119_D 816_G 1.01 0.07 0.00
48_G 705_I 1.01 0.07 0.00
10_G 820_H 1.00 0.07 0.00
159_L 857_G 1.00 0.07 0.00
9_V 840_R 1.00 0.07 0.00
84_I 834_L 1.00 0.07 0.00
34_P 720_L 0.99 0.07 0.00
125_V 112_K 0.99 0.07 0.00
17_S 799_V 0.99 0.07 0.00
145_S 691_K 0.99 0.07 0.00
145_S 695_D 0.99 0.07 0.00
145_S 699_D 0.99 0.07 0.00
145_S 804_D 0.99 0.07 0.00
145_S 805_R 0.99 0.07 0.00
145_S 806_H 0.99 0.07 0.00
145_S 809_N 0.99 0.07 0.00
145_S 822_D 0.99 0.07 0.00
109_V 210_V 0.99 0.07 0.00
100_I 803_G 0.98 0.07 0.00
15_G 821_I 0.98 0.07 0.00
16_K 821_I 0.98 0.07 0.00
57_D 725_Y 0.97 0.06 0.00
119_D 725_Y 0.97 0.06 0.00
57_D 821_I 0.97 0.06 0.00
119_D 821_I 0.97 0.06 0.00
10_G 737_I 0.96 0.06 0.00
117_K 691_K 0.96 0.06 0.00
117_K 695_D 0.96 0.06 0.00
117_K 699_D 0.96 0.06 0.00
117_K 804_D 0.96 0.06 0.00
117_K 805_R 0.96 0.06 0.00
117_K 806_H 0.96 0.06 0.00
117_K 809_N 0.96 0.06 0.00
117_K 822_D 0.96 0.06 0.00
129_Q 571_F 0.96 0.06 0.00
57_D 820_H 0.95 0.06 0.00
119_D 820_H 0.95 0.06 0.00
39_S 151_V 0.95 0.06 0.00
35_T 468_L 0.95 0.06 0.00
10_G 691_K 0.95 0.06 0.00
10_G 695_D 0.95 0.06 0.00
10_G 699_D 0.95 0.06 0.00
10_G 804_D 0.95 0.06 0.00
10_G 805_R 0.95 0.06 0.00
10_G 806_H 0.95 0.06 0.00
10_G 809_N 0.95 0.06 0.00
10_G 822_D 0.95 0.06 0.00
56_L 629_L 0.95 0.06 0.00
57_D 801_G 0.95 0.06 0.00
119_D 801_G 0.95 0.06 0.00
15_G 691_K 0.94 0.06 0.00
15_G 695_D 0.94 0.06 0.00
15_G 699_D 0.94 0.06 0.00
15_G 804_D 0.94 0.06 0.00
15_G 805_R 0.94 0.06 0.00
15_G 806_H 0.94 0.06 0.00
15_G 809_N 0.94 0.06 0.00
15_G 822_D 0.94 0.06 0.00
16_K 691_K 0.94 0.06 0.00
16_K 695_D 0.94 0.06 0.00
16_K 699_D 0.94 0.06 0.00
16_K 804_D 0.94 0.06 0.00
16_K 805_R 0.94 0.06 0.00
16_K 806_H 0.94 0.06 0.00
16_K 809_N 0.94 0.06 0.00
16_K 822_D 0.94 0.06 0.00
93_I 767_H 0.94 0.06 0.00
64_Y 263_T 0.94 0.06 0.00
160_V 506_L 0.93 0.06 0.00
64_Y 881_H 0.93 0.06 0.00
10_G 725_Y 0.93 0.06 0.00
62_E 333_L 0.93 0.06 0.00
62_E 323_N 0.92 0.06 0.00
112_V 673_F 0.92 0.06 0.00
5_K 737_I 0.92 0.06 0.00
57_D 738_E 0.92 0.06 0.00
119_D 738_E 0.92 0.06 0.00
130_A 690_F 0.91 0.06 0.00
17_S 800_L 0.91 0.06 0.00
17_S 406_P 0.91 0.06 0.00
60_G 821_I 0.90 0.06 0.00
153_E 378_L 0.90 0.06 0.00
9_V 662_M 0.90 0.06 0.00
75_G 947_H 0.90 0.06 0.00
10_G 789_S 0.89 0.06 0.00
114_V 302_K 0.89 0.06 0.00
57_D 839_E 0.89 0.06 0.00
119_D 839_E 0.89 0.06 0.00
142_I 646_D 0.89 0.06 0.00
115_G 836_I 0.89 0.06 0.00
160_V 845_L 0.88 0.06 0.00
5_K 694_D 0.88 0.06 0.00
60_G 823_F 0.88 0.06 0.00
130_A 714_E 0.88 0.06 0.00
9_V 98_T 0.88 0.06 0.00
60_G 691_K 0.88 0.06 0.00
60_G 695_D 0.88 0.06 0.00
60_G 699_D 0.88 0.06 0.00
60_G 804_D 0.88 0.06 0.00
60_G 805_R 0.88 0.06 0.00
60_G 806_H 0.88 0.06 0.00
60_G 809_N 0.88 0.06 0.00
60_G 822_D 0.88 0.06 0.00
58_T 845_L 0.88 0.06 0.00
19_L 289_L 0.88 0.06 0.00
28_F 722_L 0.88 0.06 0.00
89_S 600_L 0.88 0.06 0.00
57_D 867_F 0.87 0.06 0.00
119_D 867_F 0.87 0.06 0.00
35_T 738_E 0.87 0.06 0.00
151_G 598_E 0.87 0.06 0.00
87_T 430_K 0.87 0.05 0.00
117_K 801_G 0.87 0.05 0.00
152_V 700_M 0.87 0.05 0.00
62_E 89_Q 0.87 0.05 0.00
90_F 340_L 0.87 0.05 0.00
57_D 786_F 0.86 0.05 0.00
119_D 786_F 0.86 0.05 0.00
10_G 871_C 0.86 0.05 0.00
80_C 504_Q 0.86 0.05 0.00
42_K 836_I 0.85 0.05 0.00
62_E 712_I 0.85 0.05 0.00
57_D 789_S 0.85 0.05 0.00
119_D 789_S 0.85 0.05 0.00
57_D 737_I 0.85 0.05 0.00
119_D 737_I 0.85 0.05 0.00
145_S 668_P 0.85 0.05 0.00
141_Y 919_E 0.84 0.05 0.00
159_L 840_R 0.84 0.05 0.00
62_E 643_V 0.84 0.05 0.00
28_F 486_M 0.84 0.05 0.00
159_L 645_Y 0.84 0.05 0.00
146_A 644_P 0.83 0.05 0.00
48_G 739_I 0.83 0.05 0.00
9_V 848_D 0.83 0.05 0.00
145_S 735_G 0.83 0.05 0.00
110_P 593_Q 0.83 0.05 0.00
93_I 890_S 0.83 0.05 0.00
114_V 287_L 0.83 0.05 0.00
82_F 877_A 0.83 0.05 0.00
59_A 879_R 0.82 0.05 0.00
80_C 677_D 0.82 0.05 0.00
114_V 845_L 0.82 0.05 0.00
25_Q 799_V 0.82 0.05 0.00
117_K 668_P 0.82 0.05 0.00
160_V 849_F 0.82 0.05 0.00
89_S 881_H 0.82 0.05 0.00
42_K 155_L 0.82 0.05 0.00
125_V 109_K 0.82 0.05 0.00
151_G 518_L 0.82 0.05 0.00
144_T 400_R 0.82 0.05 0.00
19_L 713_W 0.82 0.05 0.00
5_K 878_L 0.82 0.05 0.00
60_G 488_L 0.82 0.05 0.00
114_V 846_T 0.82 0.05 0.00
Figure 5: The i (protein A) and j (protein B) are positions as given in the query sequences.

Scaled Score = raw_score/average(raw_scores)
Prob = P(contact | scaled_score, seq/len)
I_Prob = P(contact | scaled_score, seq/len, top_inter_score)
ID Seq/Len Name Options I_Prob Status
4114 0.06 821P_ Ras GTPase GTN 1E8Z_A PIP3 kinase Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4077 0.05 821P_ Ras GTPase GTN 1E8Z_A PIP3 kinase Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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