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OPENSEQ.org
1FQ1
Genes: A B A+B
Length: 212 298 476
Sequences: 591 61003 102
Seq/Len: 2.79 204.71 0.21
MirrorTree (Pazo et al. 2001) 0.07
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 0.10 0.01
2 0.01 0.12 0.02
5 0.02 0.16 0.07
10 0.02 0.20 0.11
20 0.02 0.24 0.20
100 0.02 0.31 0.42
∞ 0.03 0.34 0.54
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
171_L 143_L 1.39 0.27 0.00
75_I 46_S 1.36 0.26 0.00
71_G 143_L 1.31 0.24 0.00
136_T 194_A 1.24 0.21 0.00
68_K 281_L 1.23 0.20 0.00
75_I 15_Y 1.22 0.20 0.00
136_T 19_Y 1.12 0.16 0.00
143_G 145_D 1.10 0.16 0.00
76_F 110_Q 1.09 0.15 0.00
143_G 274_R 1.07 0.15 0.00
101_I 188_S 1.06 0.14 0.00
164_P 114_G 1.05 0.14 0.00
143_G 125_H 1.05 0.14 0.00
154_L 91_M 1.04 0.14 0.00
167_A 60_H 1.02 0.13 0.00
72_I 266_M 1.02 0.13 0.00
29_I 78_L 1.02 0.13 0.00
136_T 195_E 1.02 0.13 0.00
143_G 33_K 1.01 0.13 0.00
21_E 114_G 0.98 0.12 0.00
140_S 145_D 0.98 0.12 0.00
143_G 172_E 0.97 0.12 0.00
143_G 127_D 0.97 0.12 0.00
119_C 266_M 0.97 0.12 0.00
71_G 255_L 0.97 0.12 0.00
143_G 51_E 0.96 0.12 0.00
110_D 119_H 0.96 0.12 0.00
124_E 133_L 0.96 0.12 0.00
143_G 185_D 0.96 0.12 0.00
149_L 279_A 0.96 0.12 0.00
143_G 132_N 0.95 0.11 0.00
140_S 274_R 0.94 0.11 0.00
76_F 14_T 0.94 0.11 0.00
136_T 98_G 0.94 0.11 0.00
76_F 85_Q 0.93 0.11 0.00
143_G 190_G 0.93 0.11 0.00
143_G 147_G 0.92 0.11 0.00
189_L 7_V 0.92 0.11 0.00
164_P 170_A 0.91 0.10 0.00
143_G 171_P 0.91 0.10 0.00
140_S 125_H 0.91 0.10 0.00
195_K 114_G 0.91 0.10 0.00
138_I 78_L 0.90 0.10 0.00
100_G 63_I 0.90 0.10 0.00
75_I 199_R 0.90 0.10 0.00
105_H 82_F 0.89 0.10 0.00
175_R 145_D 0.89 0.10 0.00
146_R 145_D 0.89 0.10 0.00
140_S 33_K 0.88 0.10 0.00
32_L 70_I 0.88 0.10 0.00
157_Y 193_F 0.87 0.10 0.00
75_I 28_E 0.87 0.10 0.00
175_R 274_R 0.86 0.09 0.00
193_R 115_L 0.86 0.09 0.00
136_T 275_I 0.86 0.09 0.00
146_R 274_R 0.86 0.09 0.00
78_F 81_E 0.85 0.09 0.00
140_S 127_D 0.84 0.09 0.00
127_T 107_Y 0.84 0.09 0.00
97_Q 54_L 0.84 0.09 0.00
100_G 146_F 0.84 0.09 0.00
110_D 274_R 0.84 0.09 0.00
69_S 135_I 0.83 0.09 0.00
140_S 51_E 0.83 0.09 0.00
71_G 35_I 0.83 0.09 0.00
143_G 18_V 0.83 0.09 0.00
197_A 133_L 0.83 0.09 0.00
189_L 181_S 0.83 0.09 0.00
140_S 185_D 0.82 0.09 0.00
140_S 172_E 0.82 0.09 0.00
159_S 112_L 0.82 0.09 0.00
112_G 123_V 0.82 0.09 0.00
140_S 132_N 0.81 0.08 0.00
199_H 187_W 0.81 0.08 0.00
146_R 125_H 0.81 0.08 0.00
175_R 125_H 0.81 0.08 0.00
139_H 145_D 0.81 0.08 0.00
64_T 188_S 0.81 0.08 0.00
143_G 13_G 0.81 0.08 0.00
72_I 99_I 0.81 0.08 0.00
167_A 127_D 0.80 0.08 0.00
105_H 76_L 0.80 0.08 0.00
41_Q 92_D 0.80 0.08 0.00
192_F 32_L 0.80 0.08 0.00
124_E 184_V 0.80 0.08 0.00
64_T 236_Y 0.80 0.08 0.00
102_I 143_L 0.79 0.08 0.00
76_F 155_P 0.79 0.08 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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