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OPENSEQ.org
MDTRP2A_TRP2B
Genes: A B A+B
Length: 389 258 612
Sequences: 2377 15736 102
Seq/Len: 6.11 60.99 0.17
MirrorTree (Pazo et al. 2001) 0.37
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 0.01
2 0.05 0.03 0.02
5 0.05 0.03 0.04
10 0.05 0.04 0.08
20 0.05 0.05 0.16
100 0.05 0.09 0.55
∞ 0.07 0.18 1.88
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
74_L 180_A 1.54 0.31 0.00
76_I 146_G 1.50 0.29 0.00
314_V 220_V 1.50 0.29 0.00
179_D 79_S 1.39 0.24 0.00
224_L 100_E 1.33 0.21 0.00
193_I 222_E 1.21 0.17 0.00
359_F 58_I 1.19 0.17 0.00
172_L 104_K 1.18 0.16 0.00
331_N 23_E 1.16 0.15 0.00
359_F 207_V 1.15 0.15 0.00
189_I 73_A 1.15 0.15 0.00
301_D 211_I 1.14 0.15 0.00
359_F 200_I 1.12 0.14 0.00
77_R 180_A 1.12 0.14 0.00
178_D 230_L 1.12 0.14 0.00
34_I 58_I 1.11 0.14 0.00
62_F 159_V 1.11 0.14 0.00
154_S 209_A 1.09 0.14 0.00
157_V 12_G 1.09 0.13 0.00
383_A 64_A 1.07 0.13 0.00
73_V 110_R 1.06 0.13 0.00
192_V 146_G 1.06 0.13 0.00
168_R 45_A 1.05 0.12 0.00
286_I 196_C 1.05 0.12 0.00
60_D 104_K 1.05 0.12 0.00
230_L 89_Y 1.04 0.12 0.00
27_E 166_I 1.03 0.12 0.00
172_L 21_F 1.03 0.12 0.00
86_A 221_K 1.02 0.12 0.00
344_K 172_D 1.02 0.12 0.00
331_N 202_K 1.02 0.12 0.00
272_R 177_S 1.01 0.12 0.00
34_I 41_L 1.01 0.12 0.00
88_L 15_F 1.01 0.11 0.00
6_E 199_A 1.01 0.11 0.00
65_I 196_C 1.00 0.11 0.00
370_I 159_V 1.00 0.11 0.00
137_S 220_V 0.99 0.11 0.00
69_P 9_K 0.99 0.11 0.00
34_I 196_C 0.99 0.11 0.00
144_Q 156_P 0.99 0.11 0.00
239_T 34_L 0.99 0.11 0.00
202_Y 153_S 0.98 0.11 0.00
277_I 32_W 0.97 0.11 0.00
367_S 108_E 0.97 0.10 0.00
314_V 82_F 0.96 0.10 0.00
359_F 180_A 0.96 0.10 0.00
28_I 180_A 0.96 0.10 0.00
76_I 41_L 0.96 0.10 0.00
209_T 89_Y 0.95 0.10 0.00
48_S 86_G 0.95 0.10 0.00
359_F 196_C 0.95 0.10 0.00
384_L 207_V 0.94 0.10 0.00
146_I 149_Y 0.94 0.10 0.00
188_R 56_T 0.94 0.10 0.00
44_I 41_L 0.94 0.10 0.00
63_I 170_P 0.93 0.10 0.00
133_V 199_A 0.93 0.10 0.00
352_I 167_K 0.93 0.10 0.00
335_K 175_G 0.93 0.10 0.00
204_I 212_R 0.93 0.10 0.00
185_E 152_K 0.93 0.10 0.00
359_F 89_Y 0.92 0.10 0.00
256_D 74_D 0.92 0.10 0.00
303_I 210_Y 0.92 0.10 0.00
352_I 94_D 0.92 0.10 0.00
71_Q 45_A 0.92 0.10 0.00
90_N 233_A 0.92 0.10 0.00
341_I 195_D 0.92 0.10 0.00
87_E 123_K 0.91 0.09 0.00
81_I 97_K 0.91 0.09 0.00
71_Q 57_A 0.91 0.09 0.00
256_D 180_A 0.91 0.09 0.00
38_S 58_I 0.91 0.09 0.00
192_V 227_L 0.90 0.09 0.00
105_E 45_A 0.90 0.09 0.00
178_D 35_H 0.90 0.09 0.00
189_I 42_N 0.89 0.09 0.00
384_L 227_L 0.89 0.09 0.00
279_K 149_Y 0.89 0.09 0.00
222_E 162_Y 0.89 0.09 0.00
256_D 173_A 0.89 0.09 0.00
224_L 25_I 0.89 0.09 0.00
105_E 233_A 0.89 0.09 0.00
345_L 180_A 0.88 0.09 0.00
115_M 53_E 0.88 0.09 0.00
104_M 38_I 0.88 0.09 0.00
382_A 38_I 0.88 0.09 0.00
34_I 36_K 0.88 0.09 0.00
154_S 138_K 0.88 0.09 0.00
172_L 173_A 0.88 0.09 0.00
148_E 45_A 0.87 0.09 0.00
224_L 232_A 0.87 0.09 0.00
132_R 222_E 0.87 0.09 0.00
183_Y 86_G 0.87 0.09 0.00
179_D 22_D 0.87 0.09 0.00
331_N 188_S 0.87 0.09 0.00
188_R 18_A 0.86 0.09 0.00
204_I 214_A 0.86 0.09 0.00
361_K 128_A 0.86 0.09 0.00
387_L 199_A 0.86 0.09 0.00
138_K 149_Y 0.86 0.08 0.00
192_V 79_S 0.85 0.08 0.00
74_L 209_A 0.85 0.08 0.00
298_E 222_E 0.85 0.08 0.00
63_I 91_K 0.85 0.08 0.00
178_D 94_D 0.85 0.08 0.00
102_A 32_W 0.85 0.08 0.00
305_E 238_A 0.85 0.08 0.00
239_T 100_E 0.85 0.08 0.00
359_F 212_R 0.85 0.08 0.00
140_N 28_Y 0.85 0.08 0.00
77_R 99_I 0.85 0.08 0.00
256_D 133_Y 0.85 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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