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OPENSEQ.org
SMC_CTH_SCPA_GREM
Genes: A B A+B
Length: 155 251 386
Sequences: 2381 2308 1117
Seq/Len: 15.36 9.2 2.89
MirrorTree (Pazo et al. 2001) 0.85
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 0.01 0.02 0.27
2 0.01 0.02 0.27
5 0.01 0.02 0.30
10 0.01 0.02 0.34
20 0.02 0.02 0.43
100 0.03 0.02 0.72
∞ 0.05 0.02 2.75
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
126_A 204_L 1.56 0.96 0.80
45_A 183_A 1.52 0.96 0.77
29_R 199_I 1.44 0.94 0.71
102_Q 229_V 1.43 0.94 0.71
143_I 231_I 1.41 0.93 0.69
140_S 222_E 1.38 0.92 0.66
22_G 41_Y 1.35 0.91 0.64
144_S 233_Q 1.34 0.91 0.63
51_K 24_R 1.30 0.89 0.59
88_V 121_R 1.19 0.82 0.48
114_I 235_H 1.16 0.79 0.45
100_F 33_P 1.16 0.79 0.45
84_V 161_L 1.14 0.78 0.43
49_G 74_L 1.13 0.77 0.42
114_I 224_M 1.13 0.77 0.42
16_V 57_S 1.11 0.75 0.40
84_V 99_E 1.11 0.75 0.40
106_K 159_K 1.09 0.73 0.38
16_V 118_E 1.09 0.73 0.38
116_I 160_V 1.08 0.72 0.37
88_V 56_A 1.08 0.72 0.37
142_V 9_D 1.08 0.72 0.37
149_E 185_M 1.07 0.71 0.36
34_N 41_Y 1.07 0.71 0.36
23_G 21_L 1.06 0.70 0.35
6_F 45_V 1.05 0.69 0.34
24_G 233_Q 1.05 0.69 0.34
72_F 41_Y 1.05 0.69 0.34
88_V 59_Y 1.02 0.66 0.31
29_R 112_K 1.02 0.65 0.31
117_T 28_D 1.01 0.64 0.30
129_L 111_A 1.00 0.64 0.30
95_A 181_I 0.99 0.62 0.28
80_V 53_L 0.99 0.62 0.28
11_S 196_G 0.99 0.62 0.28
120_K 177_Q 0.98 0.61 0.28
95_A 9_D 0.97 0.61 0.27
82_F 24_R 0.97 0.60 0.27
134_M 19_L 0.96 0.59 0.26
35_D 237_F 0.96 0.59 0.26
9_I 54_D 0.96 0.59 0.26
68_I 50_V 0.96 0.59 0.26
132_V 202_M 0.96 0.59 0.26
24_G 21_L 0.96 0.59 0.26
129_L 60_L 0.96 0.58 0.25
39_S 50_V 0.95 0.58 0.25
6_F 190_H 0.95 0.57 0.24
116_I 177_Q 0.94 0.56 0.24
88_V 151_Y 0.94 0.56 0.24
120_K 100_K 0.94 0.56 0.24
144_S 28_D 0.94 0.56 0.24
69_A 106_K 0.93 0.56 0.23
108_S 176_R 0.93 0.55 0.23
5_T 26_E 0.92 0.55 0.23
122_T 97_L 0.92 0.54 0.23
120_K 38_T 0.92 0.54 0.23
138_G 13_G 0.92 0.54 0.22
48_P 71_S 0.92 0.54 0.22
76_K 108_K 0.91 0.53 0.22
135_Q 224_M 0.91 0.53 0.22
108_S 231_I 0.91 0.53 0.21
39_S 227_Q 0.91 0.53 0.21
30_L 152_D 0.91 0.52 0.21
94_E 211_E 0.90 0.52 0.21
55_L 155_G 0.90 0.52 0.21
57_L 101_L 0.90 0.52 0.21
58_L 35_A 0.90 0.51 0.21
82_F 217_F 0.90 0.51 0.20
63_R 57_S 0.90 0.51 0.20
70_L 114_L 0.89 0.50 0.20
114_I 37_I 0.88 0.49 0.19
117_T 11_F 0.88 0.49 0.19
84_V 98_I 0.88 0.49 0.19
32_D 26_E 0.88 0.49 0.19
74_I 125_F 0.88 0.49 0.19
40_G 21_L 0.87 0.48 0.19
91_A 56_A 0.87 0.48 0.19
118_H 13_G 0.87 0.47 0.18
78_R 65_T 0.87 0.47 0.18
21_F 13_G 0.87 0.47 0.18
126_A 233_Q 0.86 0.47 0.18
43_I 211_E 0.86 0.47 0.18
51_K 17_L 0.86 0.47 0.18
145_V 55_I 0.86 0.47 0.18
82_F 37_I 0.86 0.47 0.18
42_E 109_D 0.86 0.47 0.18
99_R 215_V 0.86 0.47 0.18
135_Q 245_S 0.86 0.47 0.18
54_N 179_I 0.86 0.46 0.18
94_E 26_E 0.85 0.46 0.17
115_V 122_Q 0.85 0.46 0.17
104_L 95_E 0.85 0.46 0.17
39_S 220_V 0.85 0.46 0.17
146_K 49_R 0.85 0.46 0.17
46_Q 32_I 0.85 0.45 0.17
8_Q 160_V 0.85 0.45 0.17
11_S 186_N 0.85 0.45 0.17
141_K 8_I 0.85 0.45 0.17
120_K 181_I 0.85 0.45 0.17
85_L 223_L 0.84 0.45 0.17
90_A 13_G 0.84 0.45 0.17
63_R 30_Y 0.84 0.44 0.17
75_L 4_Y 0.84 0.44 0.16
20_L 181_I 0.83 0.43 0.16
6_F 152_D 0.83 0.43 0.16
27_E 2_E 0.83 0.43 0.16
146_K 227_Q 0.82 0.42 0.15
95_A 12_E 0.82 0.42 0.15
146_K 4_Y 0.82 0.42 0.15
95_A 159_K 0.82 0.42 0.15
108_S 45_V 0.82 0.42 0.15
106_K 50_V 0.82 0.42 0.15
15_Q 241_Y 0.82 0.42 0.15
141_K 35_A 0.82 0.41 0.15
83_C 72_R 0.82 0.41 0.15
99_R 214_V 0.81 0.41 0.15
31_T 29_I 0.81 0.41 0.15
13_F 173_T 0.81 0.41 0.15
11_S 79_E 0.81 0.41 0.15
12_H 155_G 0.81 0.41 0.15
10_R 79_E 0.81 0.41 0.15
68_I 132_L 0.81 0.41 0.14
40_G 60_L 0.81 0.41 0.14
149_E 209_Q 0.81 0.40 0.14
113_F 72_R 0.81 0.40 0.14
97_V 34_V 0.81 0.40 0.14
29_R 203_D 0.81 0.40 0.14
124_E 185_M 0.81 0.40 0.14
126_A 238_S 0.80 0.40 0.14
79_P 37_I 0.80 0.40 0.14
126_A 53_L 0.80 0.40 0.14
8_Q 208_E 0.80 0.40 0.14
116_I 27_I 0.80 0.39 0.14
42_E 117_R 0.80 0.39 0.14
5_T 23_N 0.80 0.39 0.14
104_L 7_K 0.80 0.39 0.14
18_R 228_L 0.80 0.39 0.14
68_I 29_I 0.80 0.39 0.14
116_I 45_V 0.80 0.39 0.14
11_S 155_G 0.80 0.39 0.14
88_V 212_H 0.79 0.38 0.13
71_L 30_Y 0.79 0.38 0.13
140_S 148_V 0.79 0.38 0.13
9_I 234_E 0.79 0.38 0.13
73_S 211_E 0.79 0.38 0.13
152_E 120_E 0.79 0.38 0.13
84_V 119_E 0.79 0.38 0.13
105_K 83_F 0.79 0.38 0.13
91_A 13_G 0.79 0.38 0.13
120_K 215_V 0.79 0.38 0.13
135_Q 231_I 0.79 0.38 0.13
8_Q 154_I 0.79 0.38 0.13
117_T 240_I 0.79 0.38 0.13
73_S 170_M 0.78 0.37 0.13
14_D 210_K 0.78 0.37 0.13
70_L 48_M 0.78 0.37 0.13
45_A 240_I 0.78 0.37 0.13
55_L 23_N 0.78 0.37 0.13
140_S 225_K 0.78 0.37 0.13
94_E 222_E 0.78 0.36 0.12
43_I 43_L 0.77 0.36 0.12
120_K 93_P 0.77 0.36 0.12
51_K 97_L 0.77 0.36 0.12
64_A 33_P 0.77 0.36 0.12
116_I 239_D 0.77 0.36 0.12
42_E 245_S 0.77 0.36 0.12
100_F 184_R 0.77 0.36 0.12
38_H 199_I 0.77 0.36 0.12
101_A 185_M 0.77 0.36 0.12
63_R 67_L 0.77 0.36 0.12
20_L 57_S 0.77 0.36 0.12
46_Q 105_R 0.77 0.36 0.12
43_I 26_E 0.77 0.36 0.12
126_A 128_P 0.77 0.36 0.12
124_E 176_R 0.76 0.35 0.12
38_H 229_V 0.76 0.35 0.12
63_R 29_I 0.76 0.35 0.12
57_L 71_S 0.76 0.35 0.12
42_E 209_Q 0.76 0.35 0.12
22_G 40_Q 0.76 0.35 0.12
5_T 96_E 0.76 0.35 0.12
21_F 222_E 0.76 0.35 0.12
122_T 27_I 0.76 0.35 0.12
151_K 80_E 0.76 0.35 0.12
41_V 225_K 0.76 0.35 0.12
105_K 193_K 0.76 0.35 0.12
17_F 18_L 0.76 0.35 0.12
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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