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OPENSEQ.org
Consensus-DUF-N-same-genome
Genes: A B A+B
Length: 145 435 545
Sequences: 253 656 158
Seq/Len: 1.74 1.51 0.29
MirrorTree (Pazo et al. 2001) 0.77
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 0.00 0.00 0.22
2 0.00 0.00 0.22
5 0.00 0.00 0.22
10 0.00 0.00 0.22
20 0.00 0.00 0.22
100 0.00 0.00 0.23
∞ 0.01 0.10 0.27
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
42_L 239_Q 1.21 0.24 0.00
128_A 226_A 1.20 0.23 0.00
109_M 29_A 1.18 0.23 0.00
128_A 61_S 1.17 0.22 0.00
94_V 190_D 1.15 0.21 0.00
38_F 335_L 1.14 0.21 0.00
141_R 182_V 1.14 0.21 0.00
129_A 324_V 1.14 0.21 0.00
12_N 285_F 1.14 0.21 0.00
99_D 181_L 1.13 0.20 0.00
132_G 223_D 1.13 0.20 0.00
69_C 252_D 1.13 0.20 0.00
69_C 326_R 1.13 0.20 0.00
11_Y 318_L 1.12 0.20 0.00
69_C 259_N 1.12 0.20 0.00
75_G 203_R 1.10 0.19 0.00
69_C 332_F 1.10 0.19 0.00
16_F 359_P 1.09 0.19 0.00
95_L 263_F 1.07 0.18 0.00
6_K 55_L 1.06 0.17 0.00
143_A 314_I 1.06 0.17 0.00
72_L 85_S 1.05 0.17 0.00
69_C 255_T 1.05 0.17 0.00
116_G 95_Y 1.05 0.17 0.00
125_L 145_V 1.04 0.17 0.00
42_L 57_A 1.03 0.17 0.00
110_I 227_L 1.03 0.16 0.00
130_R 199_V 1.02 0.16 0.00
42_L 132_P 1.02 0.16 0.00
16_F 214_I 1.01 0.16 0.00
137_S 227_L 1.00 0.15 0.00
97_V 197_H 1.00 0.15 0.00
69_C 299_G 1.00 0.15 0.00
109_M 94_V 0.99 0.15 0.00
57_V 352_I 0.99 0.15 0.00
127_A 122_H 0.99 0.15 0.00
55_I 133_I 0.99 0.15 0.00
32_V 284_L 0.98 0.15 0.00
73_Y 245_L 0.97 0.14 0.00
71_V 371_S 0.96 0.14 0.00
111_C 227_L 0.96 0.14 0.00
18_R 65_E 0.96 0.14 0.00
87_R 108_E 0.96 0.14 0.00
13_F 261_A 0.95 0.14 0.00
69_C 375_G 0.95 0.14 0.00
78_E 321_S 0.95 0.14 0.00
136_S 401_K 0.95 0.14 0.00
47_G 85_S 0.95 0.14 0.00
143_A 246_A 0.94 0.14 0.00
10_L 227_L 0.94 0.14 0.00
104_C 227_L 0.94 0.13 0.00
7_A 230_E 0.94 0.13 0.00
37_P 221_G 0.94 0.13 0.00
76_S 269_R 0.94 0.13 0.00
107_G 94_V 0.93 0.13 0.00
96_T 258_P 0.93 0.13 0.00
96_T 24_G 0.93 0.13 0.00
135_I 372_L 0.92 0.13 0.00
63_A 157_L 0.92 0.13 0.00
91_G 352_I 0.92 0.13 0.00
123_I 352_I 0.91 0.13 0.00
104_C 333_A 0.91 0.12 0.00
94_V 102_L 0.91 0.12 0.00
105_R 286_I 0.91 0.12 0.00
27_P 102_L 0.91 0.12 0.00
139_L 242_N 0.91 0.12 0.00
142_L 174_A 0.91 0.12 0.00
29_R 390_L 0.91 0.12 0.00
97_V 20_R 0.91 0.12 0.00
137_S 105_W 0.90 0.12 0.00
4_Q 203_R 0.90 0.12 0.00
97_V 195_V 0.90 0.12 0.00
39_A 149_G 0.90 0.12 0.00
96_T 265_G 0.90 0.12 0.00
82_L 314_I 0.90 0.12 0.00
71_V 201_R 0.89 0.12 0.00
29_R 96_D 0.89 0.12 0.00
118_R 174_A 0.89 0.12 0.00
73_Y 52_N 0.88 0.12 0.00
104_C 69_V 0.88 0.12 0.00
130_R 37_V 0.88 0.12 0.00
34_G 188_P 0.87 0.12 0.00
128_A 206_E 0.87 0.11 0.00
59_R 266_R 0.87 0.11 0.00
14_A 288_S 0.87 0.11 0.00
98_S 314_I 0.87 0.11 0.00
142_L 328_G 0.87 0.11 0.00
114_L 145_V 0.87 0.11 0.00
115_E 102_L 0.86 0.11 0.00
72_L 347_R 0.86 0.11 0.00
141_R 301_A 0.86 0.11 0.00
32_V 335_L 0.86 0.11 0.00
143_A 336_L 0.86 0.11 0.00
30_L 138_Q 0.86 0.11 0.00
89_L 64_V 0.86 0.11 0.00
122_E 285_F 0.86 0.11 0.00
55_I 391_H 0.86 0.11 0.00
96_T 370_T 0.86 0.11 0.00
15_K 306_V 0.86 0.11 0.00
75_G 75_A 0.86 0.11 0.00
71_V 137_G 0.85 0.11 0.00
117_G 145_V 0.85 0.11 0.00
8_A 52_N 0.85 0.11 0.00
39_A 137_G 0.85 0.11 0.00
73_Y 16_R 0.85 0.11 0.00
143_A 311_A 0.85 0.11 0.00
53_R 160_F 0.85 0.11 0.00
13_F 140_I 0.85 0.11 0.00
27_P 213_G 0.85 0.11 0.00
98_S 173_G 0.84 0.11 0.00
121_F 149_G 0.84 0.11 0.00
137_S 63_T 0.84 0.11 0.00
84_Q 238_L 0.84 0.10 0.00
137_S 155_F 0.84 0.10 0.00
69_C 329_G 0.84 0.10 0.00
143_A 378_L 0.83 0.10 0.00
93_P 71_G 0.83 0.10 0.00
54_P 117_E 0.83 0.10 0.00
16_F 195_V 0.83 0.10 0.00
30_L 101_T 0.83 0.10 0.00
91_G 311_A 0.83 0.10 0.00
143_A 209_V 0.83 0.10 0.00
28_L 270_A 0.83 0.10 0.00
127_A 325_A 0.83 0.10 0.00
124_N 68_V 0.83 0.10 0.00
139_L 52_N 0.83 0.10 0.00
73_Y 66_A 0.83 0.10 0.00
137_S 75_A 0.82 0.10 0.00
90_A 382_H 0.82 0.10 0.00
101_E 13_S 0.82 0.10 0.00
140_L 255_T 0.82 0.10 0.00
20_P 359_P 0.82 0.10 0.00
85_L 359_P 0.82 0.10 0.00
122_E 231_L 0.82 0.10 0.00
31_C 252_D 0.82 0.10 0.00
31_C 326_R 0.82 0.10 0.00
61_S 339_L 0.82 0.10 0.00
32_V 265_G 0.82 0.10 0.00
83_Q 348_I 0.81 0.10 0.00
128_A 21_A 0.81 0.10 0.00
137_S 218_S 0.81 0.10 0.00
135_I 227_L 0.81 0.10 0.00
89_L 42_L 0.81 0.10 0.00
125_L 309_N 0.81 0.10 0.00
31_C 259_N 0.81 0.10 0.00
36_D 125_L 0.81 0.10 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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