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OPENSEQ.org
Domain_Domain_coupling
Genes: A B A+B
Length: 459 286 635
Sequences: 4599 21695 163
Seq/Len: 10.02 75.86 0.26
MirrorTree (Pazo et al. 2001) 0.82
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 0.01 0.10 0.16
2 0.01 0.11 0.18
5 0.01 0.12 0.19
10 0.01 0.13 0.21
20 0.01 0.15 0.22
100 0.02 0.18 0.32
∞ 0.07 0.22 0.52
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
295_I 18_R 1.33 0.28 0.00
265_Y 90_I 1.25 0.24 0.00
135_I 114_A 1.19 0.21 0.00
113_G 105_V 1.18 0.21 0.00
296_A 18_R 1.14 0.19 0.00
71_S 101_A 1.10 0.18 0.00
272_L 18_R 1.10 0.18 0.00
277_S 91_R 1.09 0.17 0.00
276_F 218_N 1.08 0.17 0.00
151_K 105_V 1.07 0.17 0.00
279_A 114_A 1.07 0.17 0.00
166_E 162_L 1.06 0.17 0.00
88_R 77_E 1.04 0.16 0.00
76_N 101_A 1.03 0.15 0.00
85_V 105_V 1.02 0.15 0.00
286_I 77_E 1.00 0.14 0.00
67_V 224_G 0.99 0.14 0.00
379_S 67_N 0.99 0.14 0.00
169_K 229_R 0.97 0.14 0.00
341_P 162_L 0.96 0.13 0.00
139_G 45_F 0.96 0.13 0.00
103_I 178_D 0.96 0.13 0.00
360_R 64_T 0.95 0.13 0.00
151_K 97_A 0.95 0.13 0.00
63_N 92_E 0.95 0.13 0.00
114_E 229_R 0.95 0.13 0.00
61_D 162_L 0.94 0.12 0.00
229_L 224_G 0.93 0.12 0.00
326_H 31_P 0.92 0.12 0.00
352_E 237_V 0.92 0.12 0.00
67_V 97_A 0.92 0.12 0.00
249_G 180_E 0.92 0.12 0.00
365_E 96_K 0.92 0.12 0.00
178_S 224_G 0.91 0.12 0.00
242_R 97_A 0.91 0.12 0.00
187_I 47_L 0.91 0.12 0.00
96_K 71_I 0.91 0.12 0.00
177_A 163_L 0.90 0.12 0.00
276_F 32_D 0.90 0.12 0.00
265_Y 31_P 0.90 0.12 0.00
382_E 99_Q 0.90 0.12 0.00
96_K 204_I 0.90 0.12 0.00
86_K 91_R 0.89 0.11 0.00
277_S 97_A 0.89 0.11 0.00
168_T 230_E 0.89 0.11 0.00
252_F 8_D 0.89 0.11 0.00
356_G 230_E 0.89 0.11 0.00
170_I 8_D 0.88 0.11 0.00
61_D 208_T 0.88 0.11 0.00
410_A 224_G 0.88 0.11 0.00
286_I 224_G 0.87 0.11 0.00
224_P 71_I 0.87 0.11 0.00
333_T 198_D 0.86 0.11 0.00
418_L 99_Q 0.86 0.10 0.00
286_I 227_A 0.86 0.10 0.00
398_V 170_K 0.86 0.10 0.00
328_I 90_I 0.85 0.10 0.00
229_L 158_M 0.85 0.10 0.00
81_I 218_N 0.85 0.10 0.00
114_E 195_L 0.85 0.10 0.00
295_I 53_V 0.85 0.10 0.00
131_E 156_D 0.84 0.10 0.00
165_G 90_I 0.84 0.10 0.00
276_F 105_V 0.84 0.10 0.00
138_P 60_K 0.83 0.10 0.00
190_E 67_N 0.83 0.10 0.00
326_H 136_S 0.83 0.10 0.00
330_I 97_A 0.82 0.10 0.00
241_A 224_G 0.82 0.10 0.00
153_V 105_V 0.82 0.10 0.00
271_K 118_G 0.81 0.09 0.00
260_I 178_D 0.81 0.09 0.00
197_E 98_K 0.81 0.09 0.00
280_E 229_R 0.81 0.09 0.00
248_S 224_G 0.81 0.09 0.00
168_T 99_Q 0.81 0.09 0.00
388_E 187_K 0.80 0.09 0.00
117_E 99_Q 0.80 0.09 0.00
342_A 18_R 0.80 0.09 0.00
97_K 220_C 0.80 0.09 0.00
365_E 231_N 0.80 0.09 0.00
271_K 90_I 0.80 0.09 0.00
321_M 110_I 0.79 0.09 0.00
414_L 113_I 0.79 0.09 0.00
197_E 207_R 0.79 0.09 0.00
123_A 21_K 0.79 0.09 0.00
59_P 208_T 0.79 0.09 0.00
415_R 14_E 0.78 0.09 0.00
388_E 220_C 0.78 0.09 0.00
330_I 136_S 0.78 0.09 0.00
326_H 224_G 0.78 0.09 0.00
170_I 41_P 0.78 0.09 0.00
175_E 19_E 0.78 0.09 0.00
377_G 38_G 0.78 0.09 0.00
121_Q 113_I 0.77 0.09 0.00
365_E 37_L 0.77 0.09 0.00
419_P 183_L 0.77 0.09 0.00
110_L 230_E 0.77 0.09 0.00
246_N 21_K 0.77 0.09 0.00
279_A 91_R 0.77 0.08 0.00
62_E 175_P 0.77 0.08 0.00
113_G 207_R 0.77 0.08 0.00
322_K 8_D 0.77 0.08 0.00
181_L 105_V 0.77 0.08 0.00
333_T 145_G 0.77 0.08 0.00
122_R 199_V 0.77 0.08 0.00
196_S 48_Y 0.77 0.08 0.00
169_K 65_E 0.76 0.08 0.00
158_S 118_G 0.76 0.08 0.00
81_I 101_A 0.76 0.08 0.00
331_G 25_E 0.76 0.08 0.00
370_H 15_D 0.76 0.08 0.00
113_G 101_A 0.76 0.08 0.00
297_P 163_L 0.76 0.08 0.00
336_I 207_R 0.76 0.08 0.00
76_N 94_F 0.75 0.08 0.00
391_A 21_K 0.75 0.08 0.00
267_Q 31_P 0.75 0.08 0.00
62_E 90_I 0.75 0.08 0.00
330_I 224_G 0.75 0.08 0.00
249_G 38_G 0.75 0.08 0.00
405_L 102_P 0.75 0.08 0.00
59_P 60_K 0.75 0.08 0.00
111_K 67_N 0.75 0.08 0.00
361_N 105_V 0.74 0.08 0.00
352_E 14_E 0.74 0.08 0.00
417_Y 184_S 0.74 0.08 0.00
103_I 237_V 0.74 0.08 0.00
219_L 97_A 0.74 0.08 0.00
149_L 90_I 0.74 0.08 0.00
186_R 36_R 0.74 0.08 0.00
111_K 71_I 0.74 0.08 0.00
227_V 47_L 0.73 0.08 0.00
182_E 175_P 0.73 0.08 0.00
112_F 71_I 0.73 0.08 0.00
157_P 163_L 0.73 0.08 0.00
361_N 31_P 0.73 0.08 0.00
336_I 229_R 0.73 0.08 0.00
138_P 94_F 0.73 0.08 0.00
267_Q 184_S 0.73 0.08 0.00
187_I 18_R 0.73 0.08 0.00
252_F 67_N 0.73 0.08 0.00
359_D 119_T 0.73 0.08 0.00
93_E 224_G 0.72 0.08 0.00
286_I 58_L 0.72 0.08 0.00
110_L 60_K 0.72 0.08 0.00
386_F 21_K 0.72 0.07 0.00
240_I 99_Q 0.72 0.07 0.00
180_V 103_A 0.72 0.07 0.00
155_T 64_T 0.72 0.07 0.00
278_K 90_I 0.72 0.07 0.00
330_I 197_P 0.72 0.07 0.00
108_Q 220_C 0.72 0.07 0.00
248_S 114_A 0.72 0.07 0.00
338_A 105_V 0.72 0.07 0.00
109_R 60_K 0.71 0.07 0.00
331_G 136_S 0.71 0.07 0.00
283_A 25_E 0.71 0.07 0.00
60_E 39_I 0.71 0.07 0.00
403_A 97_A 0.71 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)
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