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OPENSEQ.org
1jwh_A_C
Genes: A B A+B
Length: 183 328 477
Sequences: 456 30173 126
Seq/Len: 2.49 91.99 0.26
MirrorTree (Pazo et al. 2001) 0.46
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 0.04 0.07 0.02
2 0.05 0.10 0.03
5 0.05 0.12 0.08
10 0.05 0.16 0.15
20 0.05 0.21 0.25
100 0.06 0.30 0.67
∞ 0.08 0.34 0.90
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
91_Y 92_I 1.40 0.32 0.00
96_F 217_G 1.40 0.32 0.00
88_L 48_Y 1.25 0.24 0.00
148_Y 119_F 1.24 0.24 0.00
34_L 137_E 1.24 0.24 0.00
86_Q 110_V 1.14 0.20 0.00
129_K 90_P 1.08 0.17 0.00
80_T 322_F 1.07 0.17 0.00
164_Y 48_Y 1.06 0.16 0.00
113_G 153_R 1.05 0.16 0.00
62_I 184_Q 1.05 0.16 0.00
23_D 225_F 1.04 0.16 0.00
182_I 192_S 1.03 0.15 0.00
134_Y 171_L 1.02 0.15 0.00
93_Q 115_N 1.00 0.14 0.00
87_M 119_F 0.99 0.14 0.00
95_D 112_E 0.97 0.14 0.00
130_C 152_H 0.97 0.14 0.00
91_Y 144_Y 0.97 0.14 0.00
178_Y 53_E 0.96 0.13 0.00
156_M 43_L 0.96 0.13 0.00
117_I 138_I 0.96 0.13 0.00
77_Y 123_Y 0.96 0.13 0.00
178_Y 38_Q 0.95 0.13 0.00
148_Y 245_K 0.95 0.13 0.00
178_Y 208_D 0.94 0.13 0.00
24_Y 111_F 0.93 0.12 0.00
24_Y 226_R 0.93 0.12 0.00
136_P 230_F 0.93 0.12 0.00
93_Q 295_A 0.92 0.12 0.00
10_G 52_F 0.92 0.12 0.00
89_E 138_I 0.92 0.12 0.00
103_Y 43_L 0.91 0.12 0.00
85_A 84_E 0.91 0.12 0.00
112_I 87_R 0.90 0.11 0.00
152_G 298_F 0.89 0.11 0.00
47_M 157_P 0.89 0.11 0.00
144_T 72_K 0.89 0.11 0.00
47_M 111_F 0.88 0.11 0.00
78_I 171_L 0.88 0.11 0.00
123_V 161_M 0.88 0.11 0.00
94_G 193_R 0.88 0.11 0.00
129_K 111_F 0.88 0.11 0.00
91_Y 101_D 0.87 0.11 0.00
161_H 171_L 0.87 0.11 0.00
5_I 59_N 0.87 0.11 0.00
25_I 145_C 0.86 0.10 0.00
94_G 65_V 0.86 0.10 0.00
150_G 152_H 0.86 0.10 0.00
178_Y 228_E 0.86 0.10 0.00
89_E 289_H 0.86 0.10 0.00
120_E 288_Q 0.86 0.10 0.00
117_I 300_D 0.85 0.10 0.00
113_G 79_E 0.85 0.10 0.00
157_L 151_M 0.85 0.10 0.00
126_Y 314_R 0.85 0.10 0.00
149_F 299_L 0.85 0.10 0.00
134_Y 198_P 0.85 0.10 0.00
161_H 221_A 0.85 0.10 0.00
23_D 216_L 0.85 0.10 0.00
124_K 217_G 0.85 0.10 0.00
129_K 299_L 0.85 0.10 0.00
159_M 57_I 0.84 0.10 0.00
71_G 153_R 0.84 0.10 0.00
129_K 65_V 0.84 0.10 0.00
48_I 79_E 0.84 0.10 0.00
72_L 119_F 0.84 0.10 0.00
161_H 148_M 0.84 0.10 0.00
99_C 154_D 0.84 0.10 0.00
99_C 159_N 0.84 0.10 0.00
99_C 310_R 0.84 0.10 0.00
104_C 154_D 0.84 0.10 0.00
104_C 159_N 0.84 0.10 0.00
104_C 310_R 0.84 0.10 0.00
111_P 154_D 0.84 0.10 0.00
111_P 159_N 0.84 0.10 0.00
111_P 310_R 0.84 0.10 0.00
127_C 154_D 0.84 0.10 0.00
127_C 159_N 0.84 0.10 0.00
127_C 310_R 0.84 0.10 0.00
177_L 43_L 0.83 0.10 0.00
20_V 199_E 0.83 0.10 0.00
101_R 146_H 0.83 0.10 0.00
99_C 152_H 0.83 0.10 0.00
104_C 152_H 0.83 0.10 0.00
111_P 152_H 0.83 0.10 0.00
127_C 152_H 0.83 0.10 0.00
173_F 209_Y 0.83 0.10 0.00
77_Y 216_L 0.83 0.10 0.00
133_V 211_L 0.82 0.10 0.00
75_A 92_I 0.82 0.10 0.00
40_H 92_I 0.82 0.10 0.00
129_K 252_L 0.82 0.10 0.00
16_F 63_V 0.81 0.09 0.00
84_I 68_L 0.81 0.09 0.00
161_H 122_L 0.81 0.09 0.00
117_I 109_L 0.80 0.09 0.00
176_R 42_K 0.80 0.09 0.00
89_E 167_R 0.80 0.09 0.00
10_G 301_K 0.80 0.09 0.00
69_L 103_V 0.80 0.09 0.00
34_L 223_M 0.80 0.09 0.00
150_G 154_D 0.79 0.09 0.00
150_G 159_N 0.79 0.09 0.00
150_G 310_R 0.79 0.09 0.00
4_W 51_V 0.79 0.09 0.00
34_L 199_E 0.79 0.09 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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