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OPENSEQ.org
1SVD_complex
Genes: A B A+B
Length: 444 108 546
Sequences: 727 454 150
Seq/Len: 1.64 4.2 0.27
MirrorTree (Pazo et al. 2001) 0.83
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 0.09 0.10 0.24
2 0.09 0.10 0.27
5 0.09 0.11 0.27
10 0.09 0.11 0.27
20 0.10 0.11 0.27
100 0.10 0.11 0.27
∞ 0.12 0.14 0.27
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
297_L 87_K 1.77 0.56 0.00
122_V 87_K 1.72 0.53 0.00
130_H 16_Y 1.71 0.52 0.00
406_E 24_R 1.60 0.45 0.00
159_A 16_Y 1.36 0.30 0.00
106_A 69_N 1.34 0.30 0.00
297_L 91_Y 1.34 0.29 0.00
107_V 70_V 1.28 0.26 0.00
438_T 91_Y 1.25 0.25 0.00
265_G 16_Y 1.20 0.23 0.00
287_H 61_F 1.18 0.21 0.00
177_T 87_K 1.17 0.21 0.00
265_G 91_Y 1.16 0.21 0.00
160_K 61_F 1.16 0.21 0.00
142_Y 24_R 1.16 0.21 0.00
266_V 16_Y 1.10 0.18 0.00
159_A 91_Y 1.09 0.18 0.00
197_F 24_R 1.09 0.18 0.00
95_T 16_Y 1.09 0.18 0.00
261_C 32_A 1.08 0.17 0.00
201_A 105_Y 1.08 0.17 0.00
159_A 38_S 1.06 0.17 0.00
348_M 16_Y 1.05 0.16 0.00
350_G 38_S 1.03 0.16 0.00
267_L 91_Y 1.03 0.16 0.00
190_R 93_N 1.02 0.15 0.00
349_P 91_Y 1.02 0.15 0.00
50_L 93_N 1.01 0.15 0.00
117_F 32_A 1.01 0.15 0.00
137_D 50_M 1.00 0.15 0.00
303_L 103_V 1.00 0.15 0.00
438_T 61_F 1.00 0.15 0.00
200_D 57_W 0.99 0.14 0.00
206_E 80_A 0.98 0.14 0.00
119_L 88_L 0.98 0.14 0.00
340_F 16_Y 0.96 0.14 0.00
190_R 16_Y 0.96 0.13 0.00
327_R 87_K 0.96 0.13 0.00
427_Q 24_R 0.96 0.13 0.00
242_I 67_V 0.95 0.13 0.00
190_R 61_F 0.95 0.13 0.00
76_A 24_R 0.95 0.13 0.00
137_D 96_Q 0.94 0.13 0.00
41_G 12_E 0.94 0.13 0.00
129_P 69_N 0.94 0.13 0.00
351_V 13_T 0.94 0.13 0.00
371_F 30_K 0.93 0.12 0.00
134_V 97_S 0.92 0.12 0.00
123_K 102_F 0.92 0.12 0.00
50_L 61_F 0.92 0.12 0.00
66_D 68_D 0.92 0.12 0.00
391_A 87_K 0.90 0.12 0.00
151_I 59_L 0.90 0.12 0.00
388_W 61_F 0.90 0.12 0.00
107_V 67_V 0.90 0.12 0.00
197_F 38_S 0.90 0.12 0.00
58_K 16_Y 0.90 0.12 0.00
291_L 50_M 0.90 0.12 0.00
95_T 24_R 0.90 0.12 0.00
201_A 61_F 0.89 0.12 0.00
106_A 67_V 0.89 0.12 0.00
41_G 48_N 0.89 0.12 0.00
117_F 97_S 0.89 0.12 0.00
177_T 59_L 0.89 0.11 0.00
395_A 78_R 0.89 0.11 0.00
58_K 91_Y 0.88 0.11 0.00
248_T 16_Y 0.88 0.11 0.00
287_H 69_N 0.88 0.11 0.00
61_A 70_V 0.88 0.11 0.00
222_P 55_Y 0.88 0.11 0.00
350_G 16_Y 0.87 0.11 0.00
134_V 91_Y 0.87 0.11 0.00
442_I 79_S 0.87 0.11 0.00
65_E 36_G 0.87 0.11 0.00
138_K 16_Y 0.87 0.11 0.00
193_D 97_S 0.87 0.11 0.00
334_D 80_A 0.87 0.11 0.00
190_R 52_Q 0.87 0.11 0.00
405_V 80_A 0.87 0.11 0.00
134_V 98_L 0.87 0.11 0.00
349_P 16_Y 0.86 0.11 0.00
159_A 87_K 0.86 0.11 0.00
350_G 91_Y 0.85 0.10 0.00
438_T 84_H 0.85 0.10 0.00
403_A 92_D 0.85 0.10 0.00
328_E 92_D 0.84 0.10 0.00
322_W 67_V 0.84 0.10 0.00
298_S 10_K 0.84 0.10 0.00
142_Y 13_T 0.84 0.10 0.00
361_V 61_F 0.84 0.10 0.00
198_V 87_K 0.84 0.10 0.00
440_K 33_I 0.83 0.10 0.00
103_G 59_L 0.83 0.10 0.00
291_L 96_Q 0.83 0.10 0.00
274_M 96_Q 0.83 0.10 0.00
376_V 24_R 0.83 0.10 0.00
106_A 72_A 0.83 0.10 0.00
222_P 61_F 0.83 0.10 0.00
376_V 34_A 0.83 0.10 0.00
286_I 87_K 0.82 0.10 0.00
151_I 57_W 0.82 0.10 0.00
226_E 27_A 0.82 0.10 0.00
5_E 81_Y 0.81 0.10 0.00
59_G 51_N 0.81 0.10 0.00
120_A 91_Y 0.81 0.10 0.00
274_M 50_M 0.81 0.10 0.00
106_A 93_N 0.81 0.10 0.00
349_P 13_T 0.81 0.10 0.00
267_L 38_S 0.81 0.09 0.00
125_C 85_Q 0.80 0.09 0.00
50_L 99_G 0.80 0.09 0.00
134_V 99_G 0.80 0.09 0.00
334_D 36_G 0.80 0.09 0.00
348_M 38_S 0.80 0.09 0.00
44_T 15_S 0.80 0.09 0.00
49_D 15_S 0.80 0.09 0.00
197_F 13_T 0.80 0.09 0.00
265_G 90_A 0.80 0.09 0.00
193_D 61_F 0.80 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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