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OPENSEQ.org
S4-S5-Madhumita
Genes: A B A+B
Length: 206 167 367
Sequences: 1232 2153 286
Seq/Len: 5.98 12.89 0.78
MirrorTree (Pazo et al. 2001) 0.64
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 0.09 0.07 0.00
2 0.09 0.07 0.00
5 0.09 0.07 0.03
10 0.09 0.07 0.67
20 0.09 0.07 0.77
100 0.09 0.07 1.02
∞ 0.09 0.08 1.61
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
47_R 16_I 1.50 0.69 0.00
139_P 75_A 1.34 0.57 0.00
143_V 142_D 1.27 0.51 0.00
62_R 136_V 1.13 0.39 0.00
62_R 36_L 1.13 0.39 0.00
50_D 14_K 1.11 0.38 0.00
146_R 94_V 1.11 0.38 0.00
47_R 12_Q 1.08 0.35 0.00
136_Q 122_N 1.04 0.32 0.00
67_V 118_A 1.02 0.30 0.00
200_I 32_S 1.02 0.30 0.00
206_K 136_V 1.01 0.29 0.00
117_L 31_F 0.99 0.28 0.00
127_G 74_V 0.99 0.28 0.00
76_Y 34_T 0.96 0.26 0.00
49_S 19_N 0.96 0.26 0.00
9_L 90_T 0.96 0.26 0.00
40_Q 70_N 0.95 0.26 0.00
197_E 21_V 0.95 0.26 0.00
78_E 69_R 0.94 0.25 0.00
52_G 18_V 0.94 0.24 0.00
150_K 11_L 0.94 0.24 0.00
121_K 36_L 0.93 0.24 0.00
62_R 88_V 0.93 0.24 0.00
9_L 91_G 0.92 0.24 0.00
77_K 147_M 0.92 0.24 0.00
14_R 56_V 0.91 0.23 0.00
195_I 114_V 0.91 0.23 0.00
47_R 69_R 0.91 0.23 0.00
102_V 120_V 0.91 0.23 0.00
62_R 76_L 0.90 0.22 0.00
19_L 13_E 0.89 0.22 0.00
57_E 108_G 0.89 0.22 0.00
206_K 60_I 0.89 0.22 0.00
119_S 125_A 0.88 0.21 0.00
188_R 21_V 0.88 0.21 0.00
145_I 80_T 0.88 0.21 0.00
8_K 10_E 0.88 0.21 0.00
102_V 81_L 0.88 0.21 0.00
150_K 123_V 0.87 0.20 0.00
147_E 161_V 0.87 0.20 0.00
153_S 16_I 0.87 0.20 0.00
123_I 15_L 0.86 0.20 0.00
200_I 92_S 0.86 0.20 0.00
113_E 96_M 0.86 0.20 0.00
11_L 163_E 0.85 0.20 0.00
37_A 60_I 0.85 0.19 0.00
70_R 146_N 0.84 0.19 0.00
183_K 122_N 0.84 0.19 0.00
103_Y 80_T 0.84 0.19 0.00
45_K 63_A 0.84 0.19 0.00
78_E 45_R 0.84 0.19 0.00
73_R 120_V 0.84 0.19 0.00
54_Q 60_I 0.84 0.19 0.00
57_E 52_K 0.84 0.19 0.00
8_K 18_V 0.84 0.19 0.00
168_P 85_V 0.84 0.19 0.00
36_Q 18_V 0.83 0.18 0.00
182_F 15_L 0.83 0.18 0.00
124_M 161_V 0.83 0.18 0.00
122_A 82_Q 0.83 0.18 0.00
137_V 68_R 0.83 0.18 0.00
137_V 57_P 0.82 0.18 0.00
123_I 75_A 0.82 0.18 0.00
47_R 82_Q 0.82 0.18 0.00
28_I 93_R 0.82 0.18 0.00
21_L 57_P 0.81 0.17 0.00
25_V 15_L 0.81 0.17 0.00
136_Q 120_V 0.81 0.17 0.00
185_K 32_S 0.81 0.17 0.00
152_Q 13_E 0.80 0.17 0.00
94_L 25_V 0.80 0.17 0.00
54_Q 23_K 0.80 0.17 0.00
45_K 60_I 0.80 0.17 0.00
54_Q 106_I 0.79 0.17 0.00
67_V 63_A 0.79 0.17 0.00
74_N 111_M 0.79 0.17 0.00
178_M 31_F 0.79 0.16 0.00
41_H 113_A 0.79 0.16 0.00
62_R 22_S 0.79 0.16 0.00
150_K 14_K 0.79 0.16 0.00
172_E 117_V 0.79 0.16 0.00
47_R 61_Q 0.79 0.16 0.00
25_V 147_M 0.79 0.16 0.00
6_G 86_K 0.78 0.16 0.00
129_V 111_M 0.78 0.16 0.00
125_V 143_G 0.78 0.16 0.00
8_K 63_A 0.78 0.16 0.00
83_K 100_S 0.78 0.16 0.00
203_L 141_I 0.78 0.16 0.00
203_L 127_A 0.78 0.16 0.00
179_E 93_R 0.77 0.16 0.00
153_S 66_K 0.77 0.16 0.00
6_G 105_I 0.77 0.15 0.00
142_V 43_N 0.77 0.15 0.00
138_S 84_P 0.77 0.15 0.00
206_K 12_Q 0.77 0.15 0.00
140_N 90_T 0.77 0.15 0.00
182_F 68_R 0.77 0.15 0.00
156_K 79_G 0.77 0.15 0.00
47_R 58_A 0.77 0.15 0.00
187_E 120_V 0.77 0.15 0.00
114_A 85_V 0.77 0.15 0.00
47_R 32_S 0.77 0.15 0.00
22_K 57_P 0.76 0.15 0.00
7_P 131_T 0.76 0.15 0.00
70_R 114_V 0.76 0.15 0.00
92_A 96_M 0.76 0.15 0.00
73_R 5_E 0.76 0.15 0.00
133_A 73_N 0.76 0.15 0.00
90_L 154_A 0.75 0.15 0.00
50_D 16_I 0.75 0.15 0.00
82_L 69_R 0.75 0.15 0.00
47_R 68_R 0.75 0.14 0.00
49_S 120_V 0.74 0.14 0.00
188_R 158_G 0.74 0.14 0.00
75_Y 110_A 0.74 0.14 0.00
196_N 123_V 0.74 0.14 0.00
201_V 74_V 0.74 0.14 0.00
123_I 131_T 0.73 0.14 0.00
201_V 78_N 0.73 0.14 0.00
76_Y 50_Y 0.73 0.14 0.00
160_E 77_N 0.73 0.14 0.00
8_K 93_R 0.73 0.14 0.00
75_Y 46_V 0.73 0.14 0.00
155_V 15_L 0.73 0.14 0.00
94_L 53_A 0.73 0.14 0.00
147_E 134_I 0.73 0.14 0.00
123_I 95_F 0.73 0.14 0.00
169_T 43_N 0.73 0.14 0.00
160_E 151_E 0.73 0.14 0.00
62_R 71_M 0.73 0.14 0.00
112_A 121_H 0.72 0.14 0.00
29_D 71_M 0.72 0.13 0.00
110_T 111_M 0.72 0.13 0.00
45_K 130_S 0.72 0.13 0.00
76_Y 96_M 0.72 0.13 0.00
8_K 105_I 0.72 0.13 0.00
168_P 87_G 0.72 0.13 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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