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OPENSEQ.org
2611_vs_2613 (A, 30-164) (B, 50-275)
Genes: A B A+B
Length: 135 226 356
Sequences: 618 116 81
Seq/Len: 4.58 0.51 0.23
MirrorTree (Pazo et al. 2001) 0.51
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 0.04 0.03 0.02
2 0.05 0.03 0.19
5 0.06 0.04 0.22
10 0.06 0.05 0.22
20 0.06 0.05 0.22
100 0.07 0.06 0.23
∞ 0.08 0.07 0.24
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
34_G 148_Y 1.43 0.31 0.00
8_G 167_M 1.40 0.30 0.00
37_A 143_S 1.21 0.20 0.00
61_A 85_F 1.18 0.20 0.00
57_A 118_G 1.15 0.18 0.00
34_G 91_M 1.14 0.18 0.00
34_G 118_G 1.11 0.17 0.00
79_Y 118_G 1.11 0.17 0.00
34_G 98_R 1.08 0.16 0.00
135_Y 17_K 1.04 0.15 0.00
34_G 147_A 1.03 0.14 0.00
65_C 74_C 1.03 0.14 0.00
112_C 74_C 1.03 0.14 0.00
97_G 23_Q 1.02 0.14 0.00
78_V 205_G 1.01 0.14 0.00
82_Q 148_Y 1.01 0.14 0.00
70_A 25_V 1.00 0.13 0.00
79_Y 167_M 0.99 0.13 0.00
54_E 83_S 0.97 0.12 0.00
47_T 167_M 0.97 0.12 0.00
125_S 23_Q 0.97 0.12 0.00
56_K 135_D 0.95 0.12 0.00
55_D 135_D 0.95 0.12 0.00
39_S 55_A 0.95 0.12 0.00
34_G 199_A 0.93 0.12 0.00
6_Q 199_A 0.92 0.11 0.00
73_C 74_C 0.92 0.11 0.00
120_C 118_G 0.92 0.11 0.00
105_I 207_F 0.92 0.11 0.00
102_E 201_A 0.92 0.11 0.00
53_S 205_G 0.92 0.11 0.00
29_W 109_R 0.92 0.11 0.00
3_G 135_D 0.92 0.11 0.00
120_C 74_C 0.91 0.11 0.00
100_T 16_T 0.91 0.11 0.00
98_S 194_G 0.91 0.11 0.00
124_Y 142_E 0.91 0.11 0.00
122_V 56_A 0.91 0.11 0.00
98_S 25_V 0.90 0.11 0.00
127_C 74_C 0.90 0.11 0.00
87_V 35_G 0.90 0.11 0.00
66_S 26_G 0.89 0.11 0.00
70_A 111_K 0.89 0.10 0.00
83_C 74_C 0.88 0.10 0.00
106_D 5_W 0.88 0.10 0.00
74_K 194_G 0.88 0.10 0.00
50_G 112_I 0.86 0.10 0.00
57_A 159_Q 0.86 0.10 0.00
12_G 134_M 0.86 0.10 0.00
82_Q 204_K 0.86 0.10 0.00
108_A 88_M 0.85 0.10 0.00
61_A 74_C 0.85 0.10 0.00
125_S 205_G 0.85 0.10 0.00
6_Q 190_L 0.85 0.10 0.00
6_Q 53_G 0.84 0.10 0.00
58_K 110_K 0.84 0.10 0.00
84_A 20_L 0.84 0.09 0.00
126_G 201_A 0.84 0.09 0.00
79_Y 85_F 0.84 0.09 0.00
39_S 78_Q 0.83 0.09 0.00
87_V 144_A 0.83 0.09 0.00
99_A 68_D 0.83 0.09 0.00
100_T 171_E 0.82 0.09 0.00
108_A 12_L 0.82 0.09 0.00
101_K 195_K 0.82 0.09 0.00
81_N 202_V 0.82 0.09 0.00
113_K 100_E 0.82 0.09 0.00
86_L 47_K 0.82 0.09 0.00
48_A 95_T 0.81 0.09 0.00
33_W 120_L 0.81 0.09 0.00
7_C 70_Q 0.81 0.09 0.00
89_T 170_K 0.81 0.09 0.00
108_A 110_K 0.81 0.09 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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