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OPENSEQ.org
3M4W-2
Genes: A B A+B
Length: 273 42 312
Sequences: 499 104 168
Seq/Len: 1.83 2.48 0.54
MirrorTree (Pazo et al. 2001) 0.85
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.00 0.54
2 0.00 0.00 0.53
5 0.00 0.00 0.53
10 0.00 0.00 0.53
20 0.00 0.00 0.53
100 0.00 0.00 0.54
∞ 0.00 0.00 0.54
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
51_M 5_F 1.78 0.77 0.03
41_D 41_E 1.54 0.61 0.01
201_W 35_Q 1.42 0.52 0.01
110_R 35_Q 1.39 0.50 0.01
224_V 6_N 1.30 0.43 0.01
134_W 21_Q 1.29 0.42 0.01
110_R 31_D 1.21 0.36 0.01
45_L 28_M 1.18 0.34 0.01
54_P 31_D 1.16 0.33 0.01
46_A 34_L 1.15 0.32 0.01
272_K 19_L 1.14 0.31 0.01
261_P 22_R 1.14 0.31 0.00
168_D 25_I 1.13 0.31 0.00
114_R 25_I 1.13 0.31 0.00
134_W 35_Q 1.13 0.30 0.00
213_Y 29_L 1.11 0.29 0.00
69_E 12_G 1.11 0.29 0.00
151_D 25_I 1.11 0.29 0.00
10_N 41_E 1.11 0.29 0.00
258_E 26_N 1.09 0.28 0.00
218_F 32_Y 1.08 0.28 0.00
220_F 32_Y 1.08 0.27 0.00
55_R 5_F 1.07 0.27 0.00
264_A 18_S 1.07 0.27 0.00
259_L 6_N 1.06 0.26 0.00
163_F 13_K 1.06 0.26 0.00
5_L 24_R 1.05 0.26 0.00
250_N 10_M 1.05 0.26 0.00
18_Y 36_R 1.05 0.25 0.00
143_M 13_K 1.04 0.25 0.00
134_W 22_R 1.04 0.25 0.00
84_D 36_R 1.04 0.25 0.00
53_G 35_Q 1.04 0.25 0.00
53_G 31_D 1.04 0.25 0.00
221_S 12_G 1.03 0.24 0.00
4_A 26_N 1.03 0.24 0.00
149_D 3_P 1.01 0.23 0.00
71_G 28_M 1.01 0.23 0.00
256_V 22_R 1.00 0.23 0.00
8_Q 27_A 1.00 0.23 0.00
114_R 28_M 0.99 0.22 0.00
1_A 25_I 0.99 0.22 0.00
108_R 38_L 0.99 0.22 0.00
119_I 25_I 0.98 0.22 0.00
129_Y 4_V 0.98 0.21 0.00
268_A 16_P 0.98 0.21 0.00
113_D 1_E 0.97 0.21 0.00
3_G 14_A 0.97 0.21 0.00
137_T 23_R 0.95 0.20 0.00
265_K 27_A 0.95 0.20 0.00
74_P 18_S 0.95 0.20 0.00
144_R 34_L 0.94 0.20 0.00
77_L 40_S 0.94 0.20 0.00
69_E 16_P 0.94 0.19 0.00
65_I 10_M 0.94 0.19 0.00
66_S 33_E 0.93 0.19 0.00
112_A 35_Q 0.93 0.19 0.00
146_D 30_Q 0.93 0.19 0.00
50_Q 5_F 0.92 0.19 0.00
206_F 25_I 0.92 0.19 0.00
121_V 1_E 0.92 0.19 0.00
164_N 25_I 0.92 0.18 0.00
145_V 6_N 0.92 0.18 0.00
100_Y 23_R 0.91 0.18 0.00
259_L 32_Y 0.91 0.18 0.00
103_F 32_Y 0.91 0.18 0.00
221_S 24_R 0.91 0.18 0.00
103_F 40_S 0.90 0.18 0.00
252_E 18_S 0.90 0.17 0.00
161_I 3_P 0.90 0.17 0.00
2_S 41_E 0.89 0.17 0.00
108_R 18_S 0.89 0.17 0.00
150_R 38_L 0.89 0.17 0.00
172_S 41_E 0.89 0.17 0.00
22_F 11_M 0.89 0.17 0.00
255_I 14_A 0.89 0.17 0.00
207_S 23_R 0.89 0.17 0.00
48_L 37_R 0.89 0.17 0.00
75_F 33_E 0.88 0.17 0.00
179_A 38_L 0.88 0.17 0.00
48_L 21_Q 0.88 0.17 0.00
270_N 24_R 0.88 0.17 0.00
117_E 26_N 0.88 0.17 0.00
242_T 3_P 0.88 0.17 0.00
206_F 11_M 0.87 0.16 0.00
123_A 23_R 0.87 0.16 0.00
255_I 16_P 0.87 0.16 0.00
82_I 37_R 0.87 0.16 0.00
170_S 10_M 0.87 0.16 0.00
155_L 38_L 0.86 0.16 0.00
75_F 32_Y 0.86 0.16 0.00
151_D 23_R 0.86 0.16 0.00
178_K 23_R 0.86 0.16 0.00
256_V 38_L 0.86 0.16 0.00
85_S 36_R 0.85 0.16 0.00
273_F 30_Q 0.85 0.15 0.00
62_G 12_G 0.85 0.15 0.00
271_I 14_A 0.85 0.15 0.00
71_G 12_G 0.85 0.15 0.00
262_Q 41_E 0.84 0.15 0.00
74_P 27_A 0.84 0.15 0.00
201_W 21_Q 0.84 0.15 0.00
208_E 6_N 0.84 0.15 0.00
75_F 30_Q 0.84 0.15 0.00
144_R 31_D 0.84 0.15 0.00
272_K 4_V 0.84 0.15 0.00
169_I 26_N 0.84 0.15 0.00
19_E 33_E 0.83 0.15 0.00
145_V 12_G 0.83 0.15 0.00
154_T 5_F 0.83 0.15 0.00
35_Y 30_Q 0.83 0.15 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)
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