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OPENSEQ.org
251
Genes: A B A+B
Length: 164 437 596
Sequences: 11633 745 66
Seq/Len: 70.93 1.7 0.11
MirrorTree (Pazo et al. 2001) 0.33
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 0.05 0.03 0.00
2 0.06 0.03 0.01
5 0.08 0.03 0.03
10 0.10 0.03 0.06
20 0.13 0.03 0.11
100 0.23 0.03 0.41
∞ 0.28 0.05 0.71
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
6_L 7_I 1.67 0.28 0.00
144_N 161_Q 1.43 0.19 0.00
148_V 339_V 1.28 0.15 0.00
64_R 282_P 1.27 0.15 0.00
22_V 282_P 1.22 0.14 0.00
5_L 85_A 1.18 0.13 0.00
147_N 94_I 1.18 0.12 0.00
74_A 7_I 1.13 0.12 0.00
4_I 285_I 1.13 0.12 0.00
50_V 201_Q 1.13 0.11 0.00
17_L 177_F 1.13 0.11 0.00
147_N 227_L 1.10 0.11 0.00
33_T 100_R 1.08 0.10 0.00
34_I 204_A 1.08 0.10 0.00
3_K 306_I 1.08 0.10 0.00
117_E 230_M 1.07 0.10 0.00
116_D 217_S 1.07 0.10 0.00
15_S 284_V 1.07 0.10 0.00
122_T 35_Q 1.06 0.10 0.00
159_I 236_L 1.05 0.10 0.00
126_G 85_A 1.05 0.10 0.00
107_Q 275_K 1.05 0.10 0.00
2_I 136_I 1.04 0.10 0.00
43_V 208_F 1.04 0.10 0.00
77_I 155_D 1.04 0.10 0.00
106_A 151_S 1.02 0.09 0.00
88_F 95_H 1.01 0.09 0.00
152_F 179_L 1.01 0.09 0.00
142_A 248_G 1.01 0.09 0.00
18_L 310_N 1.00 0.09 0.00
153_F 284_V 1.00 0.09 0.00
148_V 7_I 0.99 0.09 0.00
107_Q 350_S 0.99 0.09 0.00
113_N 12_G 0.99 0.09 0.00
50_V 313_V 0.99 0.09 0.00
13_G 232_G 0.99 0.09 0.00
14_K 232_G 0.99 0.09 0.00
141_S 145_F 0.99 0.09 0.00
15_S 423_K 0.98 0.09 0.00
113_N 329_S 0.98 0.09 0.00
143_K 23_S 0.98 0.09 0.00
57_T 145_F 0.97 0.09 0.00
150_E 146_L 0.97 0.09 0.00
8_G 232_G 0.96 0.08 0.00
116_D 33_D 0.96 0.08 0.00
116_D 38_Y 0.96 0.08 0.00
116_D 39_G 0.96 0.08 0.00
4_I 246_I 0.96 0.08 0.00
87_T 227_L 0.95 0.08 0.00
102_A 146_L 0.95 0.08 0.00
114_K 248_G 0.95 0.08 0.00
87_T 118_I 0.95 0.08 0.00
4_I 230_M 0.95 0.08 0.00
15_S 260_V 0.95 0.08 0.00
82_I 198_D 0.95 0.08 0.00
56_D 232_G 0.95 0.08 0.00
57_T 354_Y 0.94 0.08 0.00
116_D 10_G 0.94 0.08 0.00
102_A 402_N 0.94 0.08 0.00
75_G 279_F 0.93 0.08 0.00
112_G 354_Y 0.93 0.08 0.00
91_I 284_V 0.93 0.08 0.00
117_E 107_V 0.93 0.08 0.00
109_L 32_I 0.93 0.08 0.00
6_L 55_K 0.92 0.08 0.00
147_N 355_L 0.92 0.08 0.00
15_S 43_A 0.92 0.08 0.00
95_F 282_P 0.91 0.08 0.00
55_W 80_P 0.91 0.08 0.00
114_K 33_D 0.91 0.07 0.00
114_K 38_Y 0.91 0.07 0.00
114_K 39_G 0.91 0.07 0.00
155_L 83_L 0.91 0.07 0.00
45_I 358_I 0.90 0.07 0.00
82_I 406_S 0.90 0.07 0.00
147_N 17_I 0.90 0.07 0.00
76_I 227_L 0.90 0.07 0.00
54_I 352_G 0.90 0.07 0.00
15_S 36_D 0.90 0.07 0.00
87_T 281_A 0.90 0.07 0.00
26_F 72_R 0.90 0.07 0.00
116_D 11_T 0.89 0.07 0.00
134_G 123_A 0.88 0.07 0.00
113_N 292_P 0.88 0.07 0.00
114_K 10_G 0.88 0.07 0.00
17_L 235_E 0.88 0.07 0.00
141_S 238_Q 0.88 0.07 0.00
140_S 85_A 0.87 0.07 0.00
143_K 146_L 0.87 0.07 0.00
54_I 175_Y 0.87 0.07 0.00
122_T 308_I 0.87 0.07 0.00
4_I 376_K 0.87 0.07 0.00
54_I 7_I 0.86 0.07 0.00
152_F 248_G 0.86 0.07 0.00
159_I 355_L 0.86 0.07 0.00
141_S 139_K 0.86 0.07 0.00
91_I 23_S 0.85 0.07 0.00
66_I 313_V 0.85 0.07 0.00
116_D 80_P 0.85 0.07 0.00
139_E 306_I 0.85 0.07 0.00
16_C 270_E 0.85 0.07 0.00
128_A 281_A 0.85 0.07 0.00
99_N 49_Q 0.85 0.07 0.00
87_T 263_K 0.84 0.07 0.00
13_G 242_R 0.84 0.07 0.00
14_K 242_R 0.84 0.07 0.00
159_I 331_L 0.84 0.07 0.00
105_E 236_L 0.83 0.07 0.00
114_K 11_T 0.83 0.07 0.00
12_V 191_M 0.83 0.07 0.00
130_A 313_V 0.83 0.07 0.00
2_I 13_I 0.83 0.06 0.00
107_Q 103_D 0.82 0.06 0.00
47_G 22_L 0.82 0.06 0.00
26_F 51_Y 0.82 0.06 0.00
111_V 135_G 0.82 0.06 0.00
8_G 242_R 0.82 0.06 0.00
13_G 253_L 0.82 0.06 0.00
14_K 253_L 0.82 0.06 0.00
73_G 113_F 0.82 0.06 0.00
138_I 292_P 0.81 0.06 0.00
6_L 308_I 0.81 0.06 0.00
81_D 87_G 0.81 0.06 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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