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OPENSEQ.org
Sudipto
Genes: A B A+B
Length: 477 128 578
Sequences: 529 344 159
Seq/Len: 1.11 2.69 0.28
MirrorTree (Pazo et al. 2001) 0.87
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 0.00 0.03 0.23
2 0.00 0.04 0.26
5 0.00 0.04 0.26
10 0.00 0.04 0.26
20 0.01 0.05 0.26
100 0.01 0.05 0.26
∞ 0.03 0.08 0.26
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
320_M 103_F 1.84 0.62 0.00
429_Q 25_D 1.76 0.57 0.00
153_H 17_Y 1.68 0.52 0.00
145_S 99_R 1.49 0.39 0.00
288_G 110_Q 1.36 0.32 0.00
142_P 100_I 1.34 0.30 0.00
182_A 17_Y 1.32 0.29 0.00
371_M 17_Y 1.32 0.29 0.00
394_F 31_E 1.29 0.27 0.00
153_H 110_Q 1.25 0.26 0.00
286_D 83_L 1.25 0.25 0.00
182_A 110_Q 1.24 0.25 0.00
426_A 99_R 1.22 0.24 0.00
271_T 108_Q 1.21 0.24 0.00
326_I 115_I 1.21 0.23 0.00
288_G 108_Q 1.21 0.23 0.00
320_M 99_R 1.20 0.23 0.00
118_T 17_Y 1.19 0.23 0.00
223_E 69_W 1.18 0.22 0.00
182_A 103_F 1.16 0.21 0.00
418_A 90_K 1.16 0.21 0.00
372_P 110_Q 1.15 0.21 0.00
220_F 39_V 1.15 0.21 0.00
350_R 73_M 1.14 0.20 0.00
200_T 69_W 1.13 0.20 0.00
130_L 82_V 1.10 0.19 0.00
284_C 33_L 1.10 0.19 0.00
373_G 108_Q 1.10 0.19 0.00
400_L 21_L 1.10 0.19 0.00
396_D 115_I 1.10 0.19 0.00
227_K 101_I 1.10 0.19 0.00
372_P 103_F 1.10 0.18 0.00
183_K 73_M 1.10 0.18 0.00
182_A 39_V 1.09 0.18 0.00
463_K 76_C 1.09 0.18 0.00
157_V 103_F 1.09 0.18 0.00
213_R 17_Y 1.09 0.18 0.00
183_K 99_R 1.08 0.18 0.00
288_G 103_F 1.08 0.18 0.00
372_P 108_Q 1.08 0.18 0.00
373_G 110_Q 1.07 0.18 0.00
452_S 110_Q 1.07 0.18 0.00
129_A 81_Q 1.07 0.17 0.00
220_F 14_T 1.07 0.17 0.00
461_I 103_F 1.06 0.17 0.00
163_N 110_Q 1.05 0.17 0.00
110_E 109_V 1.04 0.17 0.00
223_E 113_S 1.04 0.16 0.00
460_E 17_Y 1.04 0.16 0.00
469_F 90_K 1.03 0.16 0.00
174_I 69_W 1.03 0.16 0.00
414_A 110_Q 1.03 0.16 0.00
289_L 17_Y 1.03 0.16 0.00
153_H 108_Q 1.03 0.16 0.00
161_K 110_Q 1.03 0.16 0.00
310_H 73_M 1.03 0.16 0.00
288_G 17_Y 1.02 0.16 0.00
13_F 103_F 1.02 0.16 0.00
469_F 102_G 1.01 0.15 0.00
450_K 25_D 1.01 0.15 0.00
132_A 86_L 1.01 0.15 0.00
342_T 99_R 1.01 0.15 0.00
165_Y 25_D 1.00 0.15 0.00
391_T 22_T 1.00 0.15 0.00
357_D 92_A 1.00 0.15 0.00
350_R 99_R 1.00 0.15 0.00
182_A 108_Q 0.99 0.15 0.00
25_Y 93_Y 0.99 0.15 0.00
81_K 110_Q 0.99 0.15 0.00
460_E 102_G 0.99 0.14 0.00
365_T 83_L 0.98 0.14 0.00
118_T 25_D 0.98 0.14 0.00
213_R 105_N 0.98 0.14 0.00
456_A 102_G 0.98 0.14 0.00
310_H 99_R 0.98 0.14 0.00
224_A 14_T 0.97 0.14 0.00
118_T 110_Q 0.97 0.14 0.00
249_E 44_F 0.97 0.14 0.00
160_D 62_D 0.97 0.14 0.00
454_E 83_L 0.96 0.14 0.00
132_A 34_L 0.96 0.14 0.00
73_G 73_M 0.95 0.14 0.00
84_C 82_V 0.95 0.13 0.00
229_Q 92_A 0.95 0.13 0.00
310_H 104_D 0.95 0.13 0.00
338_E 15_L 0.95 0.13 0.00
445_I 118_K 0.94 0.13 0.00
165_Y 110_Q 0.94 0.13 0.00
373_G 39_V 0.94 0.13 0.00
245_G 87_E 0.94 0.13 0.00
213_R 73_M 0.93 0.13 0.00
64_G 13_E 0.93 0.13 0.00
30_E 73_M 0.93 0.13 0.00
89_P 73_M 0.92 0.12 0.00
157_V 110_Q 0.92 0.12 0.00
426_A 104_D 0.92 0.12 0.00
140_I 33_L 0.92 0.12 0.00
460_E 110_Q 0.92 0.12 0.00
357_D 37_K 0.92 0.12 0.00
129_A 79_A 0.91 0.12 0.00
414_A 108_Q 0.91 0.12 0.00
37_L 73_M 0.91 0.12 0.00
279_S 38_W 0.91 0.12 0.00
371_M 21_L 0.90 0.12 0.00
258_R 89_A 0.90 0.12 0.00
100_Y 37_K 0.90 0.12 0.00
25_Y 17_Y 0.90 0.12 0.00
51_E 30_I 0.89 0.12 0.00
37_L 111_L 0.89 0.12 0.00
223_E 92_A 0.89 0.12 0.00
200_T 71_L 0.88 0.12 0.00
67_T 16_S 0.88 0.12 0.00
72_D 16_S 0.88 0.12 0.00
25_Y 100_I 0.88 0.11 0.00
224_A 115_I 0.88 0.11 0.00
450_K 41_C 0.87 0.11 0.00
9_A 99_R 0.87 0.11 0.00
461_I 73_M 0.86 0.11 0.00
51_E 42_L 0.86 0.11 0.00
326_I 100_I 0.86 0.11 0.00
140_I 107_R 0.86 0.11 0.00
224_A 73_M 0.86 0.11 0.00
13_F 110_Q 0.85 0.11 0.00
213_R 64_R 0.85 0.11 0.00
216_D 73_M 0.85 0.11 0.00
206_V 61_Y 0.85 0.11 0.00
44_P 16_S 0.85 0.11 0.00
31_T 96_A 0.85 0.11 0.00
213_R 71_L 0.85 0.11 0.00
415_P 118_K 0.85 0.11 0.00
183_K 106_V 0.85 0.11 0.00
463_K 34_L 0.85 0.10 0.00
51_E 73_M 0.85 0.10 0.00
84_C 39_V 0.85 0.10 0.00
59_A 70_K 0.84 0.10 0.00
110_E 25_D 0.84 0.10 0.00
452_S 102_G 0.84 0.10 0.00
452_S 108_Q 0.84 0.10 0.00
46_P 71_L 0.84 0.10 0.00
165_Y 108_Q 0.84 0.10 0.00
51_E 33_L 0.84 0.10 0.00
362_I 41_C 0.84 0.10 0.00
394_F 87_E 0.84 0.10 0.00
41_R 97_F 0.84 0.10 0.00
68_T 70_K 0.84 0.10 0.00
157_V 111_L 0.84 0.10 0.00
11_V 100_I 0.83 0.10 0.00
225_I 89_A 0.83 0.10 0.00
89_P 44_F 0.83 0.10 0.00
399_V 25_D 0.83 0.10 0.00
323_G 70_K 0.83 0.10 0.00
450_K 120_P 0.83 0.10 0.00
99_A 25_D 0.83 0.10 0.00
331_V 87_E 0.83 0.10 0.00
372_P 17_Y 0.83 0.10 0.00
83_R 70_K 0.83 0.10 0.00
43_T 86_L 0.83 0.10 0.00
411_W 73_M 0.83 0.10 0.00
450_K 31_E 0.83 0.10 0.00
227_K 102_G 0.82 0.10 0.00
42_V 73_M 0.82 0.10 0.00
363_F 17_Y 0.82 0.10 0.00
372_P 14_T 0.82 0.10 0.00
221_C 37_K 0.82 0.10 0.00
314_L 108_Q 0.82 0.10 0.00
271_T 17_Y 0.82 0.10 0.00
387_M 21_L 0.82 0.10 0.00
297_M 62_D 0.81 0.10 0.00
172_C 46_K 0.81 0.10 0.00
387_M 71_L 0.81 0.10 0.00
245_G 67_T 0.81 0.10 0.00
229_Q 82_V 0.81 0.10 0.00
223_E 98_V 0.81 0.10 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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