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OPENSEQ.org
1FGN
Genes: A B A+B
Length: 214 214 399
Sequences: 1555 6398 67
Seq/Len: 7.27 29.9 0.17
MirrorTree (Pazo et al. 2001) 0.50
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 0.25 0.42 0.05
2 0.26 0.42 0.07
5 0.27 0.43 0.11
10 0.28 0.44 0.13
20 0.28 0.44 0.16
100 0.29 0.46 0.25
∞ 0.31 0.46 0.30
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
201_V 140_Y 1.55 0.31 0.00
153_P 179_L 1.55 0.31 0.00
36_W 35_W 1.44 0.26 0.00
81_L 73_L 1.41 0.25 0.00
83_L 75_I 1.41 0.25 0.00
203_H 192_Y 1.35 0.22 0.00
153_P 86_Y 1.33 0.21 0.00
120_T 60_S 1.31 0.21 0.00
96_C 88_C 1.30 0.20 0.00
165_S 78_L 1.28 0.20 0.00
90_D 86_Y 1.27 0.19 0.00
86_L 78_L 1.25 0.19 0.00
98_R 31_K 1.25 0.18 0.00
15_G 106_I 1.23 0.18 0.00
96_C 86_Y 1.22 0.17 0.00
119_K 92_G 1.20 0.17 0.00
38_K 196_A 1.20 0.17 0.00
67_K 134_C 1.19 0.17 0.00
113_L 148_W 1.18 0.16 0.00
199_C 194_C 1.16 0.15 0.00
31_D 90_Q 1.16 0.15 0.00
153_P 84_A 1.16 0.15 0.00
142_L 151_D 1.16 0.15 0.00
86_L 61_R 1.15 0.15 0.00
22_C 35_W 1.12 0.14 0.00
103_Y 150_I 1.12 0.14 0.00
144_C 194_C 1.11 0.14 0.00
83_L 181_L 1.10 0.14 0.00
86_L 49_Y 1.10 0.14 0.00
137_N 21_I 1.10 0.14 0.00
96_C 73_L 1.09 0.14 0.00
200_N 37_Q 1.08 0.13 0.00
103_Y 21_I 1.07 0.13 0.00
83_L 130_A 1.06 0.13 0.00
92_A 84_A 1.06 0.13 0.00
24_A 148_W 1.05 0.12 0.00
149_Y 74_T 1.04 0.12 0.00
153_P 23_C 1.04 0.12 0.00
44_G 140_Y 1.04 0.12 0.00
144_C 75_I 1.04 0.12 0.00
48_I 146_V 1.03 0.12 0.00
185_V 19_V 1.03 0.12 0.00
155_T 184_D 1.03 0.12 0.00
144_C 19_V 1.02 0.12 0.00
194_S 82_D 1.00 0.11 0.00
137_N 188_R 1.00 0.11 0.00
43_Q 155_R 1.00 0.11 0.00
71_T 19_V 0.99 0.11 0.00
201_V 77_S 0.99 0.11 0.00
142_L 179_L 0.99 0.11 0.00
22_C 23_C 0.97 0.11 0.00
92_A 188_R 0.97 0.11 0.00
33_Y 41_W 0.96 0.10 0.00
193_P 200_T 0.96 0.10 0.00
194_S 106_I 0.95 0.10 0.00
92_A 148_W 0.95 0.10 0.00
17_L 33_L 0.95 0.10 0.00
131_G 192_Y 0.95 0.10 0.00
81_L 132_V 0.95 0.10 0.00
192_W 92_G 0.94 0.10 0.00
204_P 151_D 0.94 0.10 0.00
22_C 86_Y 0.94 0.10 0.00
201_V 179_L 0.94 0.10 0.00
158_W 35_W 0.94 0.10 0.00
178_L 81_D 0.94 0.10 0.00
165_S 12_Y 0.93 0.10 0.00
134_A 192_Y 0.93 0.10 0.00
156_V 77_S 0.93 0.10 0.00
81_L 86_Y 0.93 0.10 0.00
144_C 134_C 0.93 0.10 0.00
138_S 62_F 0.93 0.10 0.00
90_D 84_A 0.92 0.10 0.00
115_V 106_I 0.92 0.10 0.00
156_V 19_V 0.91 0.09 0.00
18_V 194_C 0.91 0.09 0.00
98_R 183_K 0.91 0.09 0.00
38_K 88_C 0.91 0.09 0.00
78_T 146_V 0.91 0.09 0.00
23_K 155_R 0.91 0.09 0.00
158_W 108_R 0.91 0.09 0.00
199_C 134_C 0.90 0.09 0.00
94_Y 113_P 0.90 0.09 0.00
101_S 101_G 0.90 0.09 0.00
34_M 72_S 0.90 0.09 0.00
43_Q 70_D 0.90 0.09 0.00
144_C 35_W 0.90 0.09 0.00
113_L 180_T 0.89 0.09 0.00
86_L 120_P 0.89 0.09 0.00
132_S 197_T 0.89 0.09 0.00
197_V 64_G 0.88 0.09 0.00
123_P 179_L 0.88 0.09 0.00
94_Y 23_C 0.88 0.09 0.00
180_T 119_P 0.88 0.09 0.00
12_V 75_I 0.88 0.09 0.00
116_S 11_M 0.88 0.09 0.00
87_T 205_I 0.88 0.09 0.00
158_W 43_S 0.87 0.09 0.00
7_S 110_D 0.87 0.09 0.00
187_V 191_S 0.87 0.09 0.00
84_S 26_S 0.87 0.09 0.00
95_Y 13_A 0.87 0.09 0.00
92_A 23_C 0.87 0.09 0.00
71_T 75_I 0.86 0.09 0.00
203_H 75_I 0.86 0.09 0.00
86_L 138_N 0.86 0.09 0.00
144_C 43_S 0.86 0.09 0.00
95_Y 38_Q 0.86 0.08 0.00
12_V 19_V 0.86 0.08 0.00
199_C 19_V 0.86 0.08 0.00
90_D 104_L 0.86 0.08 0.00
94_Y 32_Y 0.86 0.08 0.00
199_C 196_A 0.85 0.08 0.00
153_P 148_W 0.85 0.08 0.00
85_S 19_V 0.85 0.08 0.00
153_P 198_H 0.85 0.08 0.00
83_L 86_Y 0.85 0.08 0.00
96_C 35_W 0.85 0.08 0.00
10_E 11_M 0.84 0.08 0.00
96_C 84_A 0.84 0.08 0.00
67_K 148_W 0.84 0.08 0.00
144_C 196_A 0.84 0.08 0.00
181_L 102_T 0.84 0.08 0.00
193_P 75_I 0.84 0.08 0.00
125_V 103_K 0.84 0.08 0.00
42_E 132_V 0.84 0.08 0.00
103_Y 151_D 0.84 0.08 0.00
115_V 57_G 0.83 0.08 0.00
148_G 104_L 0.83 0.08 0.00
94_Y 86_Y 0.83 0.08 0.00
201_V 20_T 0.83 0.08 0.00
120_T 143_D 0.83 0.08 0.00
81_L 163_W 0.83 0.08 0.00
140_V 192_Y 0.83 0.08 0.00
96_C 71_Y 0.83 0.08 0.00
97_A 183_K 0.83 0.08 0.00
201_V 201_S 0.82 0.08 0.00
81_L 194_C 0.82 0.08 0.00
195_E 196_A 0.82 0.08 0.00
158_W 75_I 0.82 0.08 0.00
24_A 174_S 0.82 0.08 0.00
20_L 130_A 0.81 0.08 0.00
22_C 88_C 0.81 0.08 0.00
203_H 140_Y 0.81 0.08 0.00
24_A 155_R 0.81 0.08 0.00
195_E 184_D 0.81 0.08 0.00
113_L 194_C 0.81 0.07 0.00
85_S 127_S 0.81 0.07 0.00
151_P 113_P 0.81 0.07 0.00
199_C 86_Y 0.81 0.07 0.00
123_P 187_E 0.80 0.07 0.00
201_V 198_H 0.80 0.07 0.00
24_A 156_Q 0.80 0.07 0.00
199_C 132_V 0.80 0.07 0.00
83_L 134_C 0.80 0.07 0.00
149_Y 150_I 0.80 0.07 0.00
81_L 177_S 0.80 0.07 0.00
183_S 82_D 0.80 0.07 0.00
14_P 179_L 0.80 0.07 0.00
12_V 13_A 0.80 0.07 0.00
46_E 42_K 0.80 0.07 0.00
140_V 148_W 0.80 0.07 0.00
151_P 35_W 0.79 0.07 0.00
170_F 115_V 0.79 0.07 0.00
50_L 86_Y 0.79 0.07 0.00
66_G 185_E 0.79 0.07 0.00
166_G 73_L 0.79 0.07 0.00
134_A 106_I 0.79 0.07 0.00
131_G 124_Q 0.79 0.07 0.00
90_D 75_I 0.79 0.07 0.00
86_L 82_D 0.79 0.07 0.00
132_S 46_T 0.79 0.07 0.00
180_T 191_S 0.79 0.07 0.00
86_L 55_A 0.79 0.07 0.00
113_L 162_S 0.79 0.07 0.00
155_T 29_I 0.79 0.07 0.00
201_V 112_A 0.78 0.07 0.00
16_A 111_A 0.78 0.07 0.00
22_C 73_L 0.78 0.07 0.00
177_D 147_K 0.78 0.07 0.00
20_L 137_N 0.78 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)
WARNING: The input alignment may be corrupted!
  • For sequence B, there is a high ratio (0.44 > 0.4) of paralogs.
ID Seq/Len Name Options I_Prob Status
8907 0.17 1FGN Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
8881 0 1FGN Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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