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OPENSEQ.org
cI_F_cIII_isp
Genes: A B A+B
Length: 184 195 365
Sequences: 2037 974 301
Seq/Len: 11.07 4.99 0.82
MirrorTree (Pazo et al. 2001) 0.50
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 0.00 0.00 0.00
2 0.00 0.00 0.00
5 0.00 0.01 0.00
10 0.00 0.01 0.00
20 0.00 0.01 0.01
100 0.01 0.01 0.07
∞ 0.02 0.02 0.79
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
98_I 36_A 1.50 0.71 0.01
52_G 17_G 1.50 0.71 0.01
57_I 83_I 1.40 0.64 0.01
52_G 79_K 1.35 0.59 0.00
97_A 66_V 1.29 0.54 0.00
24_N 35_A 1.28 0.53 0.00
56_I 60_Q 1.28 0.53 0.00
13_I 66_V 1.27 0.53 0.00
41_G 30_G 1.23 0.49 0.00
10_L 181_I 1.23 0.49 0.00
29_L 27_A 1.22 0.47 0.00
33_I 155_W 1.20 0.46 0.00
129_V 164_Y 1.18 0.45 0.00
57_I 82_F 1.17 0.44 0.00
156_F 64_S 1.16 0.43 0.00
175_S 77_L 1.15 0.42 0.00
156_F 161_G 1.14 0.41 0.00
120_D 89_D 1.12 0.40 0.00
51_A 121_N 1.12 0.39 0.00
7_I 156_F 1.11 0.38 0.00
96_P 83_I 1.11 0.38 0.00
15_A 149_A 1.10 0.38 0.00
86_Q 194_L 1.10 0.38 0.00
101_A 36_A 1.10 0.38 0.00
147_L 191_T 1.09 0.37 0.00
19_V 167_S 1.09 0.37 0.00
57_I 90_E 1.08 0.36 0.00
154_V 170_I 1.07 0.36 0.00
46_L 47_M 1.07 0.35 0.00
35_S 89_D 1.07 0.35 0.00
149_L 161_G 1.06 0.34 0.00
51_A 53_V 1.04 0.33 0.00
16_T 96_E 1.04 0.33 0.00
146_M 190_T 1.04 0.33 0.00
102_I 189_D 1.04 0.33 0.00
82_E 60_Q 1.03 0.32 0.00
57_I 53_V 1.03 0.32 0.00
29_L 91_I 1.03 0.32 0.00
163_R 34_V 1.02 0.31 0.00
138_V 177_Q 1.02 0.31 0.00
13_I 24_L 1.02 0.31 0.00
35_S 63_V 1.01 0.31 0.00
70_V 42_T 1.01 0.31 0.00
155_A 32_G 1.01 0.30 0.00
174_D 46_Q 1.01 0.30 0.00
123_P 100_G 1.00 0.30 0.00
67_F 178_N 1.00 0.30 0.00
140_A 63_V 1.00 0.30 0.00
52_G 20_R 1.00 0.30 0.00
13_I 100_G 1.00 0.30 0.00
52_G 191_T 1.00 0.30 0.00
121_G 194_L 0.99 0.29 0.00
136_P 65_G 0.99 0.29 0.00
23_T 181_I 0.99 0.29 0.00
103_M 83_I 0.98 0.29 0.00
173_D 188_D 0.98 0.28 0.00
138_V 95_R 0.97 0.28 0.00
10_L 126_E 0.97 0.28 0.00
120_D 180_H 0.97 0.27 0.00
124_I 194_L 0.96 0.27 0.00
176_A 35_A 0.96 0.27 0.00
95_G 36_A 0.96 0.27 0.00
176_A 66_V 0.96 0.27 0.00
141_V 21_R 0.96 0.27 0.00
80_E 181_I 0.95 0.26 0.00
35_S 187_L 0.94 0.26 0.00
133_L 36_A 0.94 0.26 0.00
67_F 169_R 0.94 0.26 0.00
105_V 192_I 0.94 0.26 0.00
128_A 150_G 0.94 0.26 0.00
8_C 68_T 0.94 0.25 0.00
141_V 23_F 0.94 0.25 0.00
82_E 30_G 0.94 0.25 0.00
46_L 79_K 0.94 0.25 0.00
172_K 39_A 0.93 0.25 0.00
93_W 17_G 0.93 0.25 0.00
7_I 189_D 0.92 0.24 0.00
67_F 162_S 0.92 0.24 0.00
151_G 89_D 0.92 0.24 0.00
138_V 70_T 0.92 0.24 0.00
146_M 186_F 0.91 0.24 0.00
101_A 88_E 0.91 0.24 0.00
142_E 91_I 0.91 0.24 0.00
79_S 83_I 0.91 0.23 0.00
141_V 24_L 0.90 0.23 0.00
66_L 165_D 0.89 0.23 0.00
38_A 48_N 0.89 0.23 0.00
112_L 32_G 0.89 0.23 0.00
89_K 129_E 0.89 0.23 0.00
85_R 63_V 0.88 0.22 0.00
89_K 31_A 0.88 0.22 0.00
9_G 152_F 0.87 0.21 0.00
41_G 173_G 0.87 0.21 0.00
54_L 63_V 0.87 0.21 0.00
37_L 153_G 0.87 0.21 0.00
67_F 175_A 0.86 0.21 0.00
135_G 184_A 0.86 0.21 0.00
57_I 155_W 0.86 0.21 0.00
16_T 85_R 0.86 0.21 0.00
132_T 123_T 0.86 0.20 0.00
165_G 38_A 0.86 0.20 0.00
31_Y 35_A 0.85 0.20 0.00
47_G 23_F 0.85 0.20 0.00
54_L 134_I 0.85 0.20 0.00
31_Y 188_D 0.85 0.20 0.00
21_T 17_G 0.84 0.20 0.00
142_E 19_T 0.84 0.20 0.00
70_V 162_S 0.84 0.20 0.00
64_M 22_D 0.84 0.20 0.00
19_V 194_L 0.84 0.19 0.00
169_S 35_A 0.83 0.19 0.00
7_I 123_T 0.83 0.19 0.00
95_G 19_T 0.83 0.19 0.00
129_V 31_A 0.83 0.19 0.00
126_A 70_T 0.82 0.18 0.00
97_A 61_V 0.82 0.18 0.00
3_F 164_Y 0.82 0.18 0.00
121_G 193_K 0.82 0.18 0.00
132_T 93_A 0.82 0.18 0.00
3_F 110_S 0.82 0.18 0.00
3_F 62_D 0.81 0.18 0.00
14_L 83_I 0.81 0.18 0.00
21_T 103_I 0.81 0.18 0.00
97_A 97_V 0.81 0.18 0.00
61_G 165_D 0.81 0.18 0.00
89_K 56_L 0.81 0.18 0.00
99_L 63_V 0.80 0.18 0.00
103_M 97_V 0.80 0.18 0.00
40_S 187_L 0.80 0.18 0.00
30_L 86_R 0.80 0.17 0.00
28_A 145_I 0.80 0.17 0.00
166_E 134_I 0.80 0.17 0.00
85_R 60_Q 0.80 0.17 0.00
35_S 27_A 0.80 0.17 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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