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OPENSEQ.org
1ep3 chain A vs B
Genes: A B A+B
Length: 311 262 554
Sequences: 4241 8476 1057
Seq/Len: 13.64 32.35 1.91
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 0.05 0.02 1.76
2 0.05 0.02 1.79
5 0.05 0.02 1.80
10 0.05 0.03 1.81
20 0.05 0.04 1.84
100 0.06 0.07 2.15
∞ 0.12 0.17 3.97
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
70_M 225_A 1.53 0.91 0.45
271_T 50_L 1.48 0.90 0.41
74_I 233_A 1.44 0.88 0.38
36_Y 95_M 1.28 0.78 0.25
60_T 245_A 1.15 0.67 0.17
299_L 251_D 1.11 0.63 0.15
63_V 233_A 1.08 0.59 0.14
49_A 232_Y 1.05 0.56 0.12
36_Y 228_I 1.02 0.53 0.11
285_D 42_L 0.97 0.48 0.09
275_A 50_L 0.95 0.46 0.09
271_T 97_P 0.93 0.43 0.08
62_R 53_R 0.93 0.43 0.08
251_A 50_L 0.93 0.43 0.08
64_A 223_R 0.92 0.43 0.08
33_Y 95_M 0.87 0.37 0.06
274_F 225_A 0.85 0.34 0.06
60_T 222_S 0.83 0.33 0.05
271_T 195_Y 0.82 0.32 0.05
105_V 235_V 0.82 0.32 0.05
81_L 67_C 0.82 0.32 0.05
76_L 118_G 0.81 0.31 0.05
77_Q 247_K 0.80 0.30 0.05
27_F 230_A 0.80 0.30 0.05
104_N 230_A 0.79 0.29 0.04
234_H 40_L 0.79 0.29 0.04
288_P 220_M 0.77 0.27 0.04
295_R 136_G 0.77 0.27 0.04
51_T 55_I 0.77 0.27 0.04
105_V 34_D 0.76 0.26 0.04
203_R 123_P 0.75 0.26 0.04
252_N 12_S 0.75 0.25 0.04
291_M 93_D 0.75 0.25 0.04
175_V 40_L 0.74 0.25 0.04
194_T 127_E 0.74 0.25 0.04
8_S 173_S 0.73 0.24 0.04
269_V 81_Y 0.73 0.24 0.04
193_L 45_P 0.73 0.24 0.03
214_A 235_V 0.73 0.24 0.03
44_S 195_Y 0.73 0.24 0.03
9_V 36_P 0.73 0.24 0.03
150_E 42_L 0.72 0.23 0.03
17_K 228_I 0.72 0.23 0.03
291_M 113_I 0.71 0.23 0.03
73_A 168_A 0.71 0.23 0.03
122_D 182_M 0.71 0.23 0.03
291_M 141_I 0.71 0.22 0.03
269_V 100_N 0.71 0.22 0.03
80_G 221_E 0.71 0.22 0.03
67_A 48_A 0.70 0.22 0.03
181_I 170_D 0.70 0.22 0.03
65_E 53_R 0.70 0.22 0.03
286_K 228_I 0.70 0.22 0.03
116_V 235_V 0.70 0.21 0.03
223_P 50_L 0.69 0.21 0.03
126_V 57_I 0.69 0.21 0.03
49_A 235_V 0.69 0.21 0.03
35_K 250_E 0.69 0.21 0.03
74_I 232_Y 0.69 0.21 0.03
76_L 199_A 0.68 0.20 0.03
61_P 235_V 0.68 0.20 0.03
229_A 124_P 0.68 0.20 0.03
103_A 233_A 0.68 0.20 0.03
283_I 185_N 0.68 0.20 0.03
10_K 208_K 0.68 0.20 0.03
274_F 228_I 0.68 0.20 0.03
269_V 257_G 0.68 0.20 0.03
194_T 230_A 0.67 0.20 0.03
74_I 237_H 0.67 0.19 0.03
65_E 79_G 0.66 0.19 0.02
6_R 105_A 0.66 0.19 0.02
220_L 220_M 0.66 0.18 0.02
62_R 79_G 0.66 0.18 0.02
68_S 47_G 0.66 0.18 0.02
175_V 55_I 0.65 0.18 0.02
137_N 53_R 0.65 0.18 0.02
274_F 232_Y 0.64 0.18 0.02
101_I 140_T 0.64 0.18 0.02
110_E 228_I 0.64 0.18 0.02
60_T 235_V 0.64 0.17 0.02
252_N 256_L 0.64 0.17 0.02
76_L 178_G 0.64 0.17 0.02
62_R 51_L 0.64 0.17 0.02
74_I 8_M 0.64 0.17 0.02
15_D 90_A 0.63 0.17 0.02
77_Q 235_V 0.63 0.17 0.02
286_K 225_A 0.63 0.17 0.02
289_E 204_K 0.63 0.17 0.02
33_Y 10_V 0.63 0.17 0.02
33_Y 228_I 0.63 0.17 0.02
115_A 9_T 0.63 0.17 0.02
44_S 128_L 0.63 0.17 0.02
111_A 12_S 0.63 0.17 0.02
155_L 70_L 0.63 0.17 0.02
228_V 23_M 0.63 0.17 0.02
42_L 230_A 0.63 0.17 0.02
10_K 155_N 0.62 0.17 0.02
39_L 203_L 0.62 0.17 0.02
76_L 169_T 0.62 0.16 0.02
109_E 125_L 0.62 0.16 0.02
48_K 54_P 0.62 0.16 0.02
253_A 94_V 0.62 0.16 0.02
94_E 87_E 0.62 0.16 0.02
78_N 118_G 0.62 0.16 0.02
63_V 223_R 0.62 0.16 0.02
83_V 242_E 0.62 0.16 0.02
41_K 215_R 0.62 0.16 0.02
192_G 126_Y 0.61 0.16 0.02
116_V 251_D 0.61 0.16 0.02
193_L 194_L 0.61 0.16 0.02
244_I 200_P 0.61 0.16 0.02
250_V 93_D 0.61 0.16 0.02
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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