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OPENSEQ.org
cIp_5_Ndelta50_2_cIV_3_2
Genes: A B A+B
Length: 216 261 455
Sequences: 1038 2963 351
Seq/Len: 4.81 11.35 0.77
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 0.00 0.00 0.01
2 0.00 0.00 0.02
5 0.01 0.00 0.05
10 0.01 0.00 0.08
20 0.01 0.00 0.12
100 0.02 0.00 0.19
∞ 0.05 0.01 0.74
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
125_M 21_A 1.52 0.71 0.01
105_I 206_L 1.29 0.52 0.00
40_I 206_L 1.22 0.46 0.00
17_V 25_L 1.22 0.46 0.00
139_I 248_V 1.21 0.46 0.00
134_P 116_W 1.20 0.44 0.00
113_K 69_G 1.19 0.44 0.00
182_F 256_I 1.19 0.43 0.00
36_L 55_Y 1.18 0.43 0.00
17_V 178_A 1.18 0.43 0.00
42_P 52_L 1.17 0.42 0.00
181_E 198_F 1.17 0.41 0.00
21_L 10_M 1.15 0.40 0.00
95_V 116_W 1.12 0.38 0.00
97_T 198_F 1.09 0.35 0.00
111_V 41_A 1.08 0.34 0.00
139_I 44_M 1.06 0.33 0.00
102_L 132_L 1.05 0.32 0.00
108_A 144_I 1.02 0.30 0.00
97_T 42_L 1.01 0.30 0.00
123_W 190_D 1.00 0.29 0.00
157_S 13_P 1.00 0.29 0.00
38_V 150_S 0.99 0.28 0.00
34_N 229_S 0.96 0.26 0.00
62_S 209_I 0.95 0.25 0.00
80_I 122_T 0.94 0.25 0.00
93_I 47_L 0.94 0.25 0.00
26_Q 20_G 0.93 0.24 0.00
38_V 40_M 0.92 0.23 0.00
125_M 172_Y 0.91 0.23 0.00
93_I 22_L 0.91 0.23 0.00
156_L 116_W 0.91 0.23 0.00
38_V 162_A 0.91 0.23 0.00
109_V 19_T 0.90 0.22 0.00
126_F 171_L 0.88 0.21 0.00
108_A 20_G 0.88 0.21 0.00
177_E 183_E 0.88 0.21 0.00
172_V 21_A 0.87 0.20 0.00
17_V 54_M 0.86 0.20 0.00
66_L 45_L 0.86 0.20 0.00
60_F 132_L 0.85 0.19 0.00
136_L 39_S 0.85 0.19 0.00
123_W 7_A 0.85 0.19 0.00
108_A 147_A 0.84 0.19 0.00
69_V 150_S 0.84 0.18 0.00
122_I 224_M 0.83 0.18 0.00
99_T 19_T 0.83 0.18 0.00
109_V 44_M 0.83 0.18 0.00
109_V 176_L 0.82 0.18 0.00
93_I 156_R 0.82 0.17 0.00
80_I 179_S 0.81 0.17 0.00
111_V 165_I 0.81 0.17 0.00
22_P 233_F 0.81 0.17 0.00
22_P 143_S 0.81 0.17 0.00
162_L 124_L 0.81 0.17 0.00
111_V 212_S 0.80 0.17 0.00
128_V 164_L 0.80 0.17 0.00
116_N 139_A 0.80 0.17 0.00
126_F 67_Y 0.80 0.17 0.00
108_A 164_L 0.80 0.17 0.00
123_W 97_F 0.80 0.17 0.00
58_A 114_G 0.80 0.17 0.00
172_V 171_L 0.80 0.17 0.00
132_N 103_H 0.80 0.17 0.00
171_V 13_P 0.80 0.17 0.00
95_V 18_L 0.79 0.16 0.00
168_V 225_F 0.79 0.16 0.00
81_V 138_L 0.79 0.16 0.00
146_E 124_L 0.79 0.16 0.00
97_T 164_L 0.79 0.16 0.00
44_G 52_L 0.79 0.16 0.00
53_R 192_I 0.79 0.16 0.00
157_S 231_H 0.79 0.16 0.00
109_V 187_T 0.79 0.16 0.00
77_R 116_W 0.79 0.16 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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