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OPENSEQ.org
cI_BctermL_cIII_isp
Genes: A B A+B
Length: 170 195 351
Sequences: 2039 974 309
Seq/Len: 11.99 4.99 0.88
MirrorTree (Pazo et al. 2001) 0.58
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 0.00 0.00
2 0.00 0.00 0.00
5 0.00 0.01 0.00
10 0.00 0.01 0.00
20 0.00 0.01 0.01
100 0.01 0.01 0.07
∞ 0.01 0.02 0.85
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
159_A 35_A 1.50 0.73 0.01
148_L 35_A 1.48 0.72 0.01
148_L 33_T 1.33 0.60 0.01
22_T 60_Q 1.30 0.57 0.01
145_N 180_H 1.26 0.53 0.01
108_K 57_A 1.21 0.49 0.00
148_L 101_Q 1.18 0.46 0.00
99_D 169_R 1.16 0.44 0.00
167_M 37_G 1.15 0.43 0.00
145_N 170_I 1.14 0.43 0.00
141_L 50_S 1.14 0.43 0.00
140_L 85_R 1.12 0.41 0.00
99_D 178_N 1.11 0.41 0.00
46_S 92_Q 1.11 0.40 0.00
62_I 51_A 1.10 0.39 0.00
112_G 36_A 1.09 0.39 0.00
167_M 145_I 1.09 0.39 0.00
83_A 40_A 1.09 0.39 0.00
106_F 24_L 1.09 0.39 0.00
147_Y 186_F 1.07 0.37 0.00
58_A 188_D 1.07 0.37 0.00
166_L 136_V 1.06 0.36 0.00
154_S 28_T 1.06 0.36 0.00
156_S 188_D 1.06 0.36 0.00
100_W 109_N 1.03 0.34 0.00
143_S 83_I 1.03 0.34 0.00
145_N 33_T 1.03 0.33 0.00
141_L 52_D 1.02 0.33 0.00
127_N 50_S 1.01 0.32 0.00
156_S 52_D 0.99 0.31 0.00
58_A 146_G 0.99 0.30 0.00
98_F 36_A 0.99 0.30 0.00
153_A 23_F 0.99 0.30 0.00
94_N 79_K 0.98 0.30 0.00
162_V 91_I 0.98 0.30 0.00
97_G 112_K 0.97 0.29 0.00
1_H 60_Q 0.97 0.29 0.00
40_T 189_D 0.97 0.29 0.00
23_F 40_A 0.97 0.29 0.00
14_L 87_T 0.97 0.29 0.00
98_F 173_G 0.97 0.29 0.00
67_W 127_A 0.96 0.28 0.00
138_K 35_A 0.96 0.28 0.00
65_A 64_S 0.96 0.28 0.00
159_A 17_G 0.96 0.28 0.00
161_V 146_G 0.96 0.28 0.00
103_D 192_I 0.96 0.28 0.00
53_T 95_R 0.96 0.28 0.00
2_A 64_S 0.96 0.28 0.00
126_M 106_S 0.95 0.28 0.00
50_L 172_R 0.95 0.28 0.00
101_L 44_V 0.95 0.27 0.00
113_I 135_G 0.95 0.27 0.00
99_D 175_A 0.95 0.27 0.00
99_D 154_G 0.94 0.27 0.00
3_H 33_T 0.94 0.27 0.00
88_L 44_V 0.94 0.27 0.00
99_D 69_G 0.93 0.26 0.00
148_L 190_T 0.92 0.26 0.00
10_H 143_V 0.92 0.26 0.00
9_T 99_L 0.92 0.25 0.00
80_A 63_V 0.92 0.25 0.00
153_A 24_L 0.92 0.25 0.00
163_L 132_V 0.92 0.25 0.00
62_I 194_L 0.92 0.25 0.00
143_S 30_G 0.91 0.25 0.00
133_S 189_D 0.91 0.25 0.00
165_L 45_N 0.91 0.25 0.00
94_N 171_R 0.90 0.24 0.00
103_D 38_A 0.90 0.24 0.00
51_E 54_Q 0.90 0.24 0.00
98_F 90_E 0.90 0.24 0.00
99_D 165_D 0.90 0.24 0.00
27_L 74_V 0.89 0.24 0.00
99_D 86_R 0.89 0.24 0.00
45_G 33_T 0.88 0.23 0.00
52_I 36_A 0.88 0.23 0.00
22_T 194_L 0.88 0.23 0.00
18_L 192_I 0.88 0.23 0.00
27_L 184_A 0.88 0.23 0.00
2_A 71_Q 0.87 0.22 0.00
161_V 45_N 0.87 0.22 0.00
38_Q 64_S 0.86 0.22 0.00
126_M 192_I 0.86 0.22 0.00
14_L 154_G 0.86 0.22 0.00
78_S 27_A 0.86 0.21 0.00
133_S 136_V 0.86 0.21 0.00
28_I 184_A 0.85 0.21 0.00
138_K 63_V 0.85 0.21 0.00
162_V 134_I 0.84 0.21 0.00
73_R 53_V 0.84 0.20 0.00
98_F 138_T 0.84 0.20 0.00
100_W 173_G 0.84 0.20 0.00
42_L 66_V 0.84 0.20 0.00
124_S 78_G 0.83 0.20 0.00
106_F 66_V 0.83 0.20 0.00
58_A 34_V 0.83 0.20 0.00
102_Y 82_F 0.83 0.20 0.00
103_D 168_G 0.83 0.20 0.00
12_L 68_T 0.83 0.20 0.00
77_T 180_H 0.83 0.20 0.00
23_F 172_R 0.83 0.20 0.00
163_L 63_V 0.82 0.20 0.00
52_I 164_Y 0.82 0.19 0.00
154_S 103_I 0.82 0.19 0.00
108_K 63_V 0.82 0.19 0.00
38_Q 92_Q 0.82 0.19 0.00
68_L 194_L 0.82 0.19 0.00
133_S 66_V 0.82 0.19 0.00
102_Y 173_G 0.82 0.19 0.00
40_T 89_D 0.81 0.19 0.00
110_F 79_K 0.81 0.19 0.00
165_L 191_T 0.81 0.19 0.00
104_K 47_M 0.81 0.19 0.00
22_T 179_L 0.81 0.19 0.00
3_H 38_A 0.81 0.19 0.00
99_D 162_S 0.81 0.19 0.00
148_L 46_Q 0.81 0.18 0.00
152_V 69_G 0.80 0.18 0.00
148_L 65_G 0.80 0.18 0.00
60_V 181_I 0.80 0.18 0.00
118_K 127_A 0.80 0.18 0.00
49_T 172_R 0.80 0.18 0.00
143_S 194_L 0.80 0.18 0.00
131_V 132_V 0.80 0.18 0.00
49_T 151_D 0.80 0.18 0.00
105_V 71_Q 0.80 0.18 0.00
49_T 143_V 0.80 0.18 0.00
101_L 46_Q 0.80 0.18 0.00
14_L 175_A 0.79 0.18 0.00
101_L 112_K 0.79 0.17 0.00
48_L 124_M 0.79 0.17 0.00
137_G 43_L 0.79 0.17 0.00
156_S 39_A 0.79 0.17 0.00
168_V 114_D 0.78 0.17 0.00
167_M 65_G 0.78 0.17 0.00
114_A 77_L 0.78 0.17 0.00
125_M 181_I 0.78 0.17 0.00
19_I 177_Q 0.78 0.17 0.00
117_L 185_E 0.78 0.17 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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