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OPENSEQ.org
McrD-McrG
Genes: A B A+B
Length: 170 248 395
Sequences: 64 58 51
Seq/Len: 0.38 0.23 0.13
MirrorTree (Pazo et al. 2001) 0.80
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 0.08 0.04
2 0.09 0.08 0.12
5 0.09 0.08 0.12
10 0.09 0.08 0.12
20 0.09 0.09 0.12
100 0.12 0.10 0.12
∞ 0.27 0.25 0.12
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
45_V 40_V 2.27 0.62 0.12
139_P 41_L 1.66 0.31 0.03
155_V 64_A 1.55 0.26 0.02
59_G 78_A 1.53 0.26 0.02
59_G 154_A 1.50 0.24 0.02
141_L 32_I 1.47 0.23 0.01
109_L 139_M 1.41 0.21 0.01
133_L 89_A 1.40 0.20 0.01
105_C 8_Y 1.37 0.19 0.01
92_I 140_E 1.36 0.19 0.01
92_I 216_Y 1.35 0.19 0.01
48_P 204_M 1.34 0.18 0.01
93_E 123_I 1.32 0.18 0.01
101_V 166_D 1.30 0.17 0.01
69_R 110_F 1.29 0.17 0.01
113_F 98_T 1.28 0.17 0.01
53_R 183_I 1.27 0.16 0.01
91_E 247_P 1.26 0.16 0.01
111_F 83_V 1.25 0.16 0.01
131_A 104_Y 1.24 0.15 0.01
91_E 81_D 1.23 0.15 0.01
40_I 65_C 1.22 0.15 0.01
34_L 148_L 1.21 0.15 0.01
99_E 52_S 1.21 0.15 0.01
37_V 123_I 1.20 0.14 0.01
111_F 5_A 1.20 0.14 0.01
25_E 245_F 1.20 0.14 0.01
14_I 89_A 1.19 0.14 0.01
144_M 139_M 1.19 0.14 0.01
33_E 223_F 1.19 0.14 0.01
73_Q 32_I 1.19 0.14 0.01
138_D 228_E 1.17 0.14 0.01
110_P 29_L 1.16 0.13 0.01
64_V 113_V 1.16 0.13 0.01
92_I 41_L 1.15 0.13 0.01
24_P 58_A 1.15 0.13 0.01
91_E 14_V 1.15 0.13 0.01
66_H 233_V 1.15 0.13 0.01
34_L 133_Q 1.14 0.13 0.01
100_K 245_F 1.13 0.12 0.01
48_P 143_M 1.13 0.12 0.01
91_E 62_E 1.12 0.12 0.01
113_F 16_A 1.12 0.12 0.00
75_G 68_R 1.12 0.12 0.00
88_I 230_I 1.11 0.12 0.00
15_E 234_H 1.11 0.12 0.00
130_Y 22_M 1.11 0.12 0.00
128_T 150_G 1.10 0.12 0.00
142_L 41_L 1.09 0.12 0.00
71_P 7_Y 1.09 0.12 0.00
103_S 230_I 1.09 0.12 0.00
12_I 21_H 1.09 0.12 0.00
15_E 27_E 1.08 0.12 0.00
139_P 166_D 1.08 0.12 0.00
113_F 199_N 1.08 0.11 0.00
117_E 168_V 1.08 0.11 0.00
145_V 37_L 1.08 0.11 0.00
80_E 245_F 1.07 0.11 0.00
91_E 129_R 1.07 0.11 0.00
60_T 185_M 1.07 0.11 0.00
137_T 39_A 1.06 0.11 0.00
94_N 235_R 1.05 0.11 0.00
61_G 228_E 1.05 0.11 0.00
142_L 223_F 1.05 0.11 0.00
113_F 154_A 1.04 0.11 0.00
13_Q 115_P 1.04 0.11 0.00
139_P 245_F 1.04 0.11 0.00
91_E 79_A 1.03 0.10 0.00
13_Q 104_Y 1.02 0.10 0.00
14_I 233_V 1.02 0.10 0.00
40_I 20_K 1.02 0.10 0.00
98_K 221_V 1.02 0.10 0.00
139_P 190_V 1.02 0.10 0.00
67_P 235_R 1.01 0.10 0.00
64_V 60_M 1.01 0.10 0.00
64_V 21_H 1.01 0.10 0.00
60_T 103_S 1.00 0.10 0.00
44_M 194_L 1.00 0.10 0.00
113_F 190_V 1.00 0.10 0.00
18_P 215_I 1.00 0.10 0.00
133_L 145_D 1.00 0.10 0.00
87_R 27_E 0.99 0.10 0.00
50_L 50_Y 0.99 0.10 0.00
128_T 58_A 0.99 0.10 0.00
84_S 220_N 0.99 0.10 0.00
15_E 126_A 0.99 0.10 0.00
95_A 135_A 0.99 0.10 0.00
76_D 225_D 0.99 0.10 0.00
96_E 40_V 0.98 0.09 0.00
68_L 41_L 0.98 0.09 0.00
100_K 12_T 0.98 0.09 0.00
132_K 98_T 0.98 0.09 0.00
93_E 66_S 0.98 0.09 0.00
56_A 19_R 0.98 0.09 0.00
30_L 74_T 0.97 0.09 0.00
130_Y 228_E 0.97 0.09 0.00
114_E 74_T 0.96 0.09 0.00
13_Q 202_K 0.96 0.09 0.00
147_P 228_E 0.96 0.09 0.00
14_I 206_S 0.96 0.09 0.00
67_P 98_T 0.96 0.09 0.00
139_P 231_E 0.96 0.09 0.00
149_A 179_E 0.96 0.09 0.00
55_S 22_M 0.96 0.09 0.00
135_P 166_D 0.96 0.09 0.00
83_I 210_A 0.95 0.09 0.00
59_G 64_A 0.94 0.09 0.00
93_E 239_Q 0.94 0.09 0.00
117_E 115_P 0.94 0.09 0.00
62_E 52_S 0.94 0.09 0.00
100_K 166_D 0.94 0.09 0.00
77_Q 166_D 0.94 0.09 0.00
31_I 161_V 0.94 0.09 0.00
138_D 155_T 0.94 0.09 0.00
102_R 149_A 0.94 0.09 0.00
138_D 190_V 0.94 0.09 0.00
107_K 205_S 0.94 0.09 0.00
129_D 46_P 0.93 0.09 0.00
98_K 70_A 0.93 0.09 0.00
30_L 68_R 0.93 0.09 0.00
14_I 183_I 0.93 0.09 0.00
39_G 67_I 0.93 0.09 0.00
110_P 12_T 0.93 0.09 0.00
77_Q 72_A 0.92 0.08 0.00
32_S 206_S 0.92 0.08 0.00
133_L 92_M 0.92 0.08 0.00
13_Q 204_M 0.92 0.08 0.00
139_P 220_N 0.92 0.08 0.00
107_K 237_F 0.92 0.08 0.00
79_I 35_E 0.92 0.08 0.00
41_I 168_V 0.92 0.08 0.00
69_R 225_D 0.92 0.08 0.00
87_R 126_A 0.92 0.08 0.00
113_F 78_A 0.91 0.08 0.00
91_E 45_A 0.91 0.08 0.00
40_I 227_A 0.91 0.08 0.00
33_E 212_R 0.91 0.08 0.00
49_R 35_E 0.91 0.08 0.00
66_H 64_A 0.91 0.08 0.00
117_E 124_V 0.91 0.08 0.00
27_A 209_A 0.90 0.08 0.00
95_A 233_V 0.90 0.08 0.00
150_K 133_Q 0.90 0.08 0.00
21_I 223_F 0.90 0.08 0.00
41_I 220_N 0.90 0.08 0.00
102_R 227_A 0.90 0.08 0.00
91_E 63_P 0.90 0.08 0.00
15_E 247_P 0.90 0.08 0.00
124_K 230_I 0.90 0.08 0.00
9_E 69_E 0.89 0.08 0.00
10_D 227_A 0.89 0.08 0.00
19_S 202_K 0.89 0.08 0.00
65_E 123_I 0.89 0.08 0.00
123_R 33_S 0.89 0.08 0.00
131_A 58_A 0.89 0.08 0.00
131_A 204_M 0.89 0.08 0.00
85_V 4_E 0.88 0.08 0.00
122_R 110_F 0.88 0.08 0.00
16_I 147_A 0.88 0.08 0.00
64_V 217_R 0.88 0.08 0.00
146_D 117_T 0.88 0.08 0.00
146_D 160_S 0.88 0.08 0.00
146_D 170_F 0.88 0.08 0.00
146_D 171_D 0.88 0.08 0.00
147_P 36_D 0.88 0.08 0.00
83_I 248_K 0.88 0.08 0.00
83_I 183_I 0.88 0.08 0.00
96_E 221_V 0.88 0.08 0.00
48_P 32_I 0.88 0.08 0.00
139_P 94_N 0.88 0.08 0.00
103_S 221_V 0.88 0.08 0.00
44_M 7_Y 0.88 0.08 0.00
37_V 225_D 0.87 0.08 0.00
94_N 75_P 0.87 0.08 0.00
68_L 220_N 0.87 0.08 0.00
98_K 200_L 0.87 0.08 0.00
136_E 188_D 0.87 0.08 0.00
139_P 192_I 0.87 0.07 0.00
104_V 31_E 0.87 0.07 0.00
21_I 166_D 0.87 0.07 0.00
103_S 70_A 0.86 0.07 0.00
76_D 65_C 0.86 0.07 0.00
67_P 69_E 0.86 0.07 0.00
140_R 190_V 0.86 0.07 0.00
94_N 222_A 0.86 0.07 0.00
96_E 225_D 0.86 0.07 0.00
131_A 115_P 0.85 0.07 0.00
13_Q 41_L 0.85 0.07 0.00
148_K 94_N 0.85 0.07 0.00
53_R 40_V 0.85 0.07 0.00
61_G 155_T 0.85 0.07 0.00
144_M 238_D 0.85 0.07 0.00
16_I 5_A 0.85 0.07 0.00
57_G 21_H 0.85 0.07 0.00
58_P 21_H 0.85 0.07 0.00
33_E 225_D 0.85 0.07 0.00
60_T 38_T 0.85 0.07 0.00
34_L 150_G 0.84 0.07 0.00
40_I 39_A 0.84 0.07 0.00
29_K 94_N 0.84 0.07 0.00
101_V 222_A 0.84 0.07 0.00
131_A 65_C 0.84 0.07 0.00
27_A 58_A 0.84 0.07 0.00
105_C 247_P 0.84 0.07 0.00
117_E 103_S 0.84 0.07 0.00
33_E 48_S 0.84 0.07 0.00
125_P 26_L 0.83 0.07 0.00
127_V 58_A 0.83 0.07 0.00
92_I 33_S 0.83 0.07 0.00
148_K 33_S 0.83 0.07 0.00
82_K 225_D 0.83 0.07 0.00
55_S 124_V 0.83 0.07 0.00
116_R 66_S 0.83 0.07 0.00
121_L 103_S 0.82 0.07 0.00
144_M 95_A 0.82 0.07 0.00
73_Q 177_R 0.82 0.07 0.00
13_Q 247_P 0.82 0.07 0.00
153_Q 217_R 0.82 0.07 0.00
15_E 63_P 0.82 0.07 0.00
75_G 104_Y 0.82 0.07 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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