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OPENSEQ.org
821P_ Ras GTPase GTN 1E8Z_A PIP3 kinase
Genes: A B A+B
Length: 166 966 1100
Sequences: 39542 221 59
Seq/Len: 238.2 0.23 0.05
MirrorTree (Pazo et al. 2001) 0.38
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 0.15 0.01 0.01
2 0.16 0.01 0.01
5 0.19 0.03 0.02
10 0.21 0.03 0.03
20 0.24 0.03 0.05
100 0.30 0.03 0.11
∞ 0.32 0.04 0.12
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
19_L 241_V 1.55 0.14 0.00
112_V 257_T 1.40 0.12 0.00
10_G 691_K 1.22 0.09 0.00
10_G 737_I 1.18 0.08 0.00
57_D 668_P 1.17 0.08 0.00
57_D 695_D 1.17 0.08 0.00
57_D 699_D 1.17 0.08 0.00
57_D 735_G 1.17 0.08 0.00
57_D 789_S 1.17 0.08 0.00
57_D 801_G 1.17 0.08 0.00
57_D 804_D 1.17 0.08 0.00
57_D 805_R 1.17 0.08 0.00
57_D 806_H 1.17 0.08 0.00
57_D 809_N 1.17 0.08 0.00
57_D 816_G 1.17 0.08 0.00
57_D 822_D 1.17 0.08 0.00
64_Y 855_T 1.16 0.08 0.00
15_G 803_G 1.15 0.08 0.00
16_K 803_G 1.15 0.08 0.00
18_A 688_I 1.13 0.08 0.00
119_D 664_S 1.11 0.07 0.00
15_G 691_K 1.09 0.07 0.00
16_K 691_K 1.09 0.07 0.00
60_G 845_L 1.09 0.07 0.00
57_D 691_K 1.08 0.07 0.00
18_A 643_V 1.08 0.07 0.00
58_T 802_I 1.08 0.07 0.00
10_G 668_P 1.07 0.07 0.00
10_G 695_D 1.07 0.07 0.00
10_G 699_D 1.07 0.07 0.00
10_G 735_G 1.07 0.07 0.00
10_G 789_S 1.07 0.07 0.00
10_G 801_G 1.07 0.07 0.00
10_G 804_D 1.07 0.07 0.00
10_G 805_R 1.07 0.07 0.00
10_G 806_H 1.07 0.07 0.00
10_G 809_N 1.07 0.07 0.00
10_G 816_G 1.07 0.07 0.00
10_G 822_D 1.07 0.07 0.00
19_L 525_V 1.06 0.07 0.00
96_Y 151_V 1.06 0.07 0.00
60_G 765_L 1.06 0.07 0.00
20_T 245_I 1.05 0.07 0.00
57_D 644_P 1.05 0.07 0.00
10_G 803_G 1.04 0.07 0.00
119_D 867_F 1.02 0.06 0.00
145_S 879_R 1.01 0.06 0.00
57_D 879_R 1.00 0.06 0.00
79_L 450_L 1.00 0.06 0.00
143_E 943_N 1.00 0.06 0.00
15_G 821_I 1.00 0.06 0.00
16_K 821_I 1.00 0.06 0.00
64_Y 151_V 0.99 0.06 0.00
60_G 871_C 0.98 0.06 0.00
57_D 820_H 0.97 0.06 0.00
15_G 737_I 0.97 0.06 0.00
16_K 737_I 0.97 0.06 0.00
119_D 668_P 0.97 0.06 0.00
119_D 695_D 0.97 0.06 0.00
119_D 699_D 0.97 0.06 0.00
119_D 735_G 0.97 0.06 0.00
119_D 789_S 0.97 0.06 0.00
119_D 801_G 0.97 0.06 0.00
119_D 804_D 0.97 0.06 0.00
119_D 805_R 0.97 0.06 0.00
119_D 806_H 0.97 0.06 0.00
119_D 809_N 0.97 0.06 0.00
119_D 816_G 0.97 0.06 0.00
119_D 822_D 0.97 0.06 0.00
19_L 761_K 0.96 0.06 0.00
57_D 740_V 0.96 0.06 0.00
59_A 802_I 0.96 0.06 0.00
15_G 668_P 0.96 0.06 0.00
15_G 695_D 0.96 0.06 0.00
15_G 699_D 0.96 0.06 0.00
15_G 735_G 0.96 0.06 0.00
15_G 789_S 0.96 0.06 0.00
15_G 801_G 0.96 0.06 0.00
15_G 804_D 0.96 0.06 0.00
15_G 805_R 0.96 0.06 0.00
15_G 806_H 0.96 0.06 0.00
15_G 809_N 0.96 0.06 0.00
15_G 816_G 0.96 0.06 0.00
15_G 822_D 0.96 0.06 0.00
16_K 668_P 0.96 0.06 0.00
16_K 695_D 0.96 0.06 0.00
16_K 699_D 0.96 0.06 0.00
16_K 735_G 0.96 0.06 0.00
16_K 789_S 0.96 0.06 0.00
16_K 801_G 0.96 0.06 0.00
16_K 804_D 0.96 0.06 0.00
16_K 805_R 0.96 0.06 0.00
16_K 806_H 0.96 0.06 0.00
16_K 809_N 0.96 0.06 0.00
16_K 816_G 0.96 0.06 0.00
16_K 822_D 0.96 0.06 0.00
55_I 553_L 0.96 0.06 0.00
119_D 800_L 0.96 0.06 0.00
23_L 431_E 0.95 0.06 0.00
151_G 729_S 0.95 0.06 0.00
151_G 151_V 0.95 0.06 0.00
10_G 839_E 0.95 0.06 0.00
89_S 875_Y 0.94 0.06 0.00
110_P 769_L 0.94 0.06 0.00
135_R 450_L 0.94 0.06 0.00
19_L 477_Q 0.94 0.06 0.00
151_G 543_G 0.94 0.06 0.00
17_S 799_V 0.94 0.06 0.00
57_D 725_Y 0.94 0.06 0.00
116_N 791_A 0.94 0.06 0.00
11_A 219_F 0.93 0.06 0.00
111_M 494_S 0.93 0.06 0.00
141_Y 769_L 0.93 0.06 0.00
119_D 535_L 0.93 0.06 0.00
123_R 730_T 0.92 0.06 0.00
141_Y 498_V 0.92 0.06 0.00
35_T 644_P 0.92 0.06 0.00
57_D 791_A 0.92 0.06 0.00
151_G 391_Q 0.92 0.06 0.00
17_S 258_S 0.91 0.06 0.00
10_G 725_Y 0.91 0.05 0.00
112_V 592_Q 0.91 0.05 0.00
100_I 722_L 0.91 0.05 0.00
64_Y 881_H 0.91 0.05 0.00
57_D 821_I 0.90 0.05 0.00
10_G 521_L 0.90 0.05 0.00
165_Q 836_I 0.90 0.05 0.00
110_P 486_M 0.90 0.05 0.00
20_T 729_S 0.90 0.05 0.00
10_G 842_P 0.90 0.05 0.00
57_D 664_S 0.90 0.05 0.00
9_V 264_E 0.89 0.05 0.00
119_D 749_I 0.89 0.05 0.00
84_I 450_L 0.88 0.05 0.00
57_D 867_F 0.88 0.05 0.00
135_R 897_M 0.88 0.05 0.00
86_N 137_E 0.88 0.05 0.00
151_G 412_Q 0.88 0.05 0.00
57_D 843_F 0.87 0.05 0.00
10_G 694_D 0.87 0.05 0.00
119_D 745_T 0.87 0.05 0.00
116_N 600_L 0.87 0.05 0.00
119_D 691_K 0.87 0.05 0.00
129_Q 571_F 0.87 0.05 0.00
35_T 511_D 0.87 0.05 0.00
46_I 530_Y 0.87 0.05 0.00
5_K 165_L 0.87 0.05 0.00
93_I 845_L 0.87 0.05 0.00
62_E 802_I 0.86 0.05 0.00
149_R 913_L 0.86 0.05 0.00
128_R 103_L 0.86 0.05 0.00
117_K 664_S 0.86 0.05 0.00
57_D 842_P 0.86 0.05 0.00
85_N 802_I 0.86 0.05 0.00
10_G 879_R 0.86 0.05 0.00
123_R 291_I 0.86 0.05 0.00
119_D 738_E 0.86 0.05 0.00
116_N 520_Q 0.85 0.05 0.00
89_S 501_I 0.85 0.05 0.00
81_V 821_I 0.85 0.05 0.00
10_G 820_H 0.85 0.05 0.00
93_I 798_F 0.85 0.05 0.00
7_V 706_L 0.85 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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