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OPENSEQ.org
1D09
Genes: A B A+B
Length: 153 311 452
Sequences: 684 5668 567
Seq/Len: 4.47 18.23 1.25
MirrorTree (Pazo et al. 2001) 0.72
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 0.00 0.04 1.20
2 0.00 0.05 1.20
5 0.00 0.07 1.22
10 0.00 0.09 1.23
20 0.00 0.11 1.22
100 0.00 0.13 1.23
∞ 0.00 0.25 1.30
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
115_I 89_L 1.79 0.94 0.61
43_T 133_N 1.53 0.84 0.40
62_E 50_F 1.44 0.79 0.32
9_V 62_T 1.42 0.77 0.30
77_Y 212_L 1.26 0.64 0.19
9_V 76_D 1.25 0.63 0.19
86_I 265_L 1.22 0.60 0.17
53_M 260_A 1.22 0.60 0.17
42_I 305_L 1.22 0.60 0.17
11_A 25_L 1.14 0.52 0.13
61_I 243_N 1.09 0.48 0.11
144_E 69_A 1.09 0.48 0.11
83_V 290_A 1.09 0.48 0.11
107_L 306_N 1.07 0.46 0.10
142_E 20_D 1.07 0.46 0.10
85_R 155_N 1.06 0.45 0.10
62_E 300_L 1.05 0.44 0.10
58_L 115_L 1.05 0.44 0.10
120_P 88_T 1.05 0.44 0.09
7_L 294_I 1.04 0.43 0.09
142_E 114_R 1.04 0.43 0.09
116_S 248_F 1.03 0.42 0.09
18_I 303_L 1.01 0.41 0.08
125_F 103_I 1.01 0.40 0.08
103_I 178_A 1.01 0.40 0.08
9_V 290_A 1.01 0.40 0.08
119_E 80_T 1.00 0.40 0.08
85_R 275_A 1.00 0.39 0.08
104_D 70_S 0.99 0.38 0.07
115_I 17_S 0.98 0.37 0.07
106_V 177_L 0.97 0.36 0.07
76_L 294_I 0.94 0.34 0.06
55_R 18_R 0.94 0.34 0.06
58_L 83_G 0.94 0.34 0.06
48_L 298_Q 0.93 0.33 0.06
55_R 43_K 0.93 0.33 0.06
87_D 182_G 0.93 0.33 0.06
24_Q 145_T 0.93 0.33 0.06
74_L 188_I 0.92 0.32 0.06
27_F 294_I 0.92 0.32 0.06
116_S 231_V 0.92 0.32 0.06
98_S 9_H 0.92 0.32 0.06
49_P 212_L 0.92 0.32 0.06
118_A 50_F 0.92 0.32 0.06
108_V 37_P 0.92 0.32 0.06
12_I 251_R 0.91 0.31 0.05
142_E 96_I 0.91 0.31 0.05
91_V 50_F 0.90 0.31 0.05
7_L 66_R 0.90 0.30 0.05
143_K 11_I 0.90 0.30 0.05
7_L 125_V 0.90 0.30 0.05
78_A 240_E 0.90 0.30 0.05
37_E 155_N 0.90 0.30 0.05
118_A 109_Q 0.90 0.30 0.05
117_H 109_Q 0.90 0.30 0.05
103_I 215_S 0.89 0.30 0.05
29_L 295_F 0.89 0.30 0.05
14_R 72_V 0.89 0.29 0.05
121_V 35_P 0.89 0.29 0.05
117_H 240_E 0.89 0.29 0.05
88_N 75_S 0.89 0.29 0.05
26_G 183_N 0.88 0.29 0.05
80_Q 24_V 0.88 0.29 0.05
18_I 276_T 0.88 0.29 0.05
90_E 189_A 0.88 0.29 0.05
88_N 165_K 0.88 0.29 0.05
43_T 298_Q 0.88 0.28 0.05
7_L 134_Q 0.87 0.28 0.05
55_R 264_V 0.87 0.28 0.05
117_H 242_A 0.87 0.28 0.05
27_F 255_L 0.87 0.28 0.04
28_K 24_V 0.86 0.28 0.04
142_E 133_N 0.86 0.28 0.04
128_R 8_K 0.86 0.27 0.04
120_P 119_F 0.86 0.27 0.04
32_L 50_F 0.85 0.27 0.04
116_S 275_A 0.85 0.26 0.04
88_N 205_E 0.85 0.26 0.04
103_I 260_A 0.85 0.26 0.04
88_N 155_N 0.84 0.26 0.04
62_E 160_M 0.84 0.26 0.04
103_I 13_I 0.84 0.26 0.04
31_S 78_A 0.84 0.26 0.04
4_D 231_V 0.83 0.25 0.04
18_I 156_L 0.83 0.25 0.04
64_T 244_V 0.83 0.25 0.04
14_R 41_K 0.83 0.25 0.04
36_T 80_T 0.83 0.25 0.04
143_K 239_S 0.83 0.25 0.04
76_L 66_R 0.83 0.25 0.04
10_E 294_I 0.83 0.25 0.04
22_P 265_L 0.82 0.24 0.04
63_N 140_L 0.82 0.24 0.04
120_P 66_R 0.82 0.24 0.04
106_V 94_S 0.82 0.24 0.04
11_A 228_M 0.82 0.24 0.04
48_L 248_F 0.82 0.24 0.04
49_P 207_G 0.82 0.24 0.04
103_I 9_H 0.81 0.24 0.04
17_V 176_A 0.81 0.24 0.04
86_I 165_K 0.81 0.24 0.04
16_T 244_V 0.81 0.23 0.04
106_V 57_R 0.81 0.23 0.03
142_E 140_L 0.81 0.23 0.03
90_E 117_T 0.81 0.23 0.03
113_N 166_Y 0.81 0.23 0.03
77_Y 175_Q 0.81 0.23 0.03
97_P 256_H 0.80 0.23 0.03
45_G 48_C 0.80 0.23 0.03
48_L 187_F 0.80 0.23 0.03
59_I 76_D 0.80 0.23 0.03
88_N 288_Q 0.80 0.23 0.03
43_T 265_L 0.80 0.23 0.03
55_R 221_A 0.80 0.23 0.03
127_V 44_V 0.79 0.22 0.03
124_S 118_E 0.79 0.22 0.03
78_A 113_A 0.79 0.22 0.03
108_V 251_R 0.79 0.22 0.03
63_N 100_V 0.79 0.22 0.03
150_V 258_A 0.79 0.22 0.03
118_A 265_L 0.79 0.22 0.03
57_D 22_N 0.79 0.22 0.03
48_L 247_Q 0.79 0.22 0.03
92_V 197_Q 0.79 0.22 0.03
59_I 185_F 0.79 0.22 0.03
43_T 132_S 0.78 0.22 0.03
43_T 188_I 0.78 0.22 0.03
123_S 177_L 0.78 0.22 0.03
89_Y 237_D 0.78 0.22 0.03
44_I 102_A 0.78 0.21 0.03
82_T 137_T 0.78 0.21 0.03
57_D 216_I 0.78 0.21 0.03
68_E 264_V 0.78 0.21 0.03
83_V 24_V 0.78 0.21 0.03
24_Q 216_I 0.78 0.21 0.03
101_E 218_E 0.78 0.21 0.03
71_V 180_F 0.78 0.21 0.03
132_N 233_K 0.78 0.21 0.03
112_S 48_C 0.78 0.21 0.03
88_N 117_T 0.78 0.21 0.03
52_E 140_L 0.78 0.21 0.03
23_A 79_N 0.78 0.21 0.03
36_T 238_P 0.78 0.21 0.03
143_K 50_F 0.78 0.21 0.03
61_I 38_E 0.78 0.21 0.03
145_F 296_A 0.77 0.21 0.03
78_A 98_T 0.77 0.21 0.03
112_S 192_A 0.77 0.21 0.03
91_V 40_L 0.77 0.21 0.03
13_K 155_N 0.77 0.21 0.03
144_E 64_M 0.77 0.21 0.03
89_Y 183_N 0.77 0.21 0.03
92_V 26_A 0.77 0.21 0.03
93_G 19_D 0.77 0.21 0.03
99_L 188_I 0.77 0.20 0.03
102_R 46_A 0.77 0.20 0.03
88_N 122_N 0.76 0.20 0.03
142_E 160_M 0.76 0.20 0.03
48_L 272_D 0.76 0.20 0.03
28_K 79_N 0.76 0.20 0.03
39_D 88_T 0.76 0.20 0.03
108_V 211_S 0.76 0.20 0.03
116_S 304_V 0.76 0.20 0.03
105_N 43_K 0.76 0.20 0.03
93_G 126_L 0.76 0.20 0.03
7_L 262_M 0.75 0.20 0.03
58_L 211_S 0.75 0.19 0.03
88_N 70_S 0.75 0.19 0.03
46_L 288_Q 0.75 0.19 0.03
75_A 13_I 0.74 0.19 0.03
55_R 114_R 0.74 0.19 0.03
103_I 148_E 0.74 0.19 0.03
26_G 76_D 0.74 0.19 0.03
125_F 114_R 0.74 0.19 0.03
97_P 154_D 0.74 0.19 0.03
32_L 21_L 0.74 0.19 0.03
63_N 25_L 0.74 0.19 0.03
135_A 80_T 0.74 0.19 0.03
57_D 258_A 0.74 0.19 0.03
116_S 192_A 0.74 0.19 0.03
132_N 214_S 0.74 0.19 0.03
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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