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OPENSEQ.org
L5-vs-S4
Genes: A B A+B
Length: 179 206 384
Sequences: 2042 1236 711
Seq/Len: 11.41 6 1.85
MirrorTree (Pazo et al. 2001) 0.69
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 0.09 0.00
2 0.09 0.09 0.01
5 0.09 0.09 0.02
10 0.09 0.09 0.12
20 0.09 0.09 0.90
100 0.09 0.09 1.24
∞ 0.09 0.09 1.85
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
79_I 75_Y 1.23 0.73 0.02
111_I 174_D 1.12 0.62 0.01
26_M 54_Q 1.11 0.61 0.01
87_C 200_I 1.03 0.53 0.01
9_K 146_R 1.03 0.53 0.01
136_I 121_K 1.00 0.51 0.01
28_V 88_E 1.00 0.50 0.01
61_S 85_N 0.97 0.47 0.01
102_R 81_R 0.97 0.47 0.01
71_R 78_E 0.96 0.46 0.01
164_E 189_S 0.92 0.42 0.01
21_N 103_Y 0.91 0.41 0.01
153_D 8_K 0.91 0.40 0.01
132_V 28_I 0.89 0.39 0.01
48_K 10_K 0.89 0.38 0.01
68_T 110_T 0.89 0.38 0.01
162_S 127_G 0.87 0.36 0.01
27_Q 187_E 0.87 0.36 0.01
56_D 154_R 0.86 0.35 0.01
163_D 189_S 0.85 0.35 0.01
95_R 119_S 0.84 0.33 0.01
155_T 146_R 0.84 0.33 0.01
105_T 85_N 0.83 0.33 0.01
24_S 167_K 0.83 0.33 0.01
81_Q 117_L 0.83 0.32 0.01
67_I 123_I 0.83 0.32 0.01
174_D 3_R 0.82 0.32 0.01
125_R 127_G 0.82 0.31 0.01
150_R 15_E 0.81 0.31 0.01
79_I 161_L 0.80 0.29 0.01
30_R 128_R 0.80 0.29 0.01
143_Y 64_I 0.80 0.29 0.01
85_I 160_E 0.79 0.28 0.01
1_M 19_L 0.78 0.28 0.01
87_C 172_E 0.78 0.28 0.01
73_S 206_K 0.77 0.27 0.01
160_A 172_E 0.77 0.26 0.01
75_A 168_P 0.76 0.26 0.01
67_I 143_V 0.76 0.26 0.01
67_I 167_K 0.75 0.25 0.01
70_A 118_V 0.75 0.25 0.01
66_L 76_Y 0.75 0.25 0.01
41_G 115_R 0.75 0.25 0.01
82_G 108_G 0.74 0.25 0.01
37_N 94_L 0.74 0.25 0.01
30_R 181_T 0.74 0.24 0.01
61_S 92_A 0.74 0.24 0.01
71_R 93_L 0.74 0.24 0.01
108_V 206_K 0.74 0.24 0.01
137_I 67_V 0.74 0.24 0.01
71_R 85_N 0.73 0.23 0.01
87_C 75_Y 0.73 0.23 0.01
9_K 143_V 0.73 0.23 0.00
42_E 56_R 0.73 0.23 0.00
137_I 188_R 0.73 0.23 0.00
179_K 74_N 0.73 0.23 0.00
73_S 107_F 0.72 0.23 0.00
51_D 53_V 0.72 0.23 0.00
55_A 159_L 0.71 0.22 0.00
24_S 76_Y 0.71 0.22 0.00
148_R 173_V 0.71 0.22 0.00
58_A 143_V 0.71 0.22 0.00
36_L 52_G 0.71 0.22 0.00
122_F 202_E 0.70 0.22 0.00
54_A 138_S 0.70 0.21 0.00
153_D 184_R 0.70 0.21 0.00
163_D 127_G 0.70 0.21 0.00
74_V 119_S 0.70 0.21 0.00
146_V 45_K 0.70 0.21 0.00
36_L 159_L 0.69 0.21 0.00
12_V 48_L 0.69 0.21 0.00
119_A 167_K 0.69 0.21 0.00
136_I 50_D 0.69 0.21 0.00
31_V 162_A 0.69 0.21 0.00
98_E 206_K 0.69 0.20 0.00
125_R 118_V 0.69 0.20 0.00
130_M 43_A 0.69 0.20 0.00
7_Y 200_I 0.68 0.20 0.00
13_V 142_V 0.68 0.20 0.00
146_V 78_E 0.68 0.20 0.00
46_D 5_L 0.68 0.20 0.00
25_V 178_M 0.67 0.19 0.00
159_T 113_E 0.67 0.19 0.00
128_Y 37_A 0.67 0.19 0.00
13_V 63_R 0.67 0.19 0.00
15_K 77_K 0.67 0.19 0.00
156_I 12_S 0.67 0.19 0.00
56_D 155_V 0.67 0.19 0.00
171_A 171_L 0.67 0.19 0.00
144_D 38_P 0.66 0.19 0.00
84_P 87_G 0.66 0.19 0.00
159_T 5_L 0.66 0.19 0.00
60_I 90_L 0.66 0.19 0.00
17_M 123_I 0.66 0.18 0.00
26_M 118_V 0.66 0.18 0.00
149_V 86_T 0.66 0.18 0.00
55_A 179_E 0.66 0.18 0.00
47_K 110_T 0.66 0.18 0.00
21_N 140_N 0.66 0.18 0.00
71_R 151_K 0.66 0.18 0.00
26_M 201_V 0.65 0.18 0.00
83_Y 34_I 0.65 0.18 0.00
139_P 72_F 0.65 0.18 0.00
48_K 54_Q 0.65 0.18 0.00
133_R 128_R 0.65 0.18 0.00
69_K 150_K 0.65 0.18 0.00
60_I 56_R 0.65 0.18 0.00
173_F 179_E 0.65 0.18 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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