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OPENSEQ.org
cI_D_G
Genes: A B A+B
Length: 485 100 574
Sequences: 1691 1241 1480
Seq/Len: 3.49 12.41 2.58
MirrorTree (Pazo et al. 2001) 0.77
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 0.00 0.02
2 0.00 0.00 0.08
5 0.00 0.00 2.31
10 0.00 0.00 2.37
20 0.01 0.00 2.37
100 0.01 0.01 2.44
∞ 0.02 0.02 2.53
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
175_A 45_A 3.38 1.00 1.00
172_F 12_A 2.60 1.00 1.00
179_A 49_A 2.22 1.00 0.99
164_A 35_L 1.94 0.99 0.97
137_L 75_I 1.94 0.99 0.97
168_S 38_M 1.92 0.99 0.97
126_A 46_F 1.74 0.98 0.95
160_T 76_G 1.63 0.97 0.93
153_L 86_R 1.57 0.96 0.91
165_A 19_L 1.48 0.94 0.87
168_S 19_L 1.41 0.92 0.84
171_L 42_S 1.39 0.91 0.82
165_A 22_L 1.32 0.87 0.78
175_A 32_L 1.28 0.85 0.74
172_F 11_A 1.19 0.79 0.67
406_H 84_H 1.15 0.76 0.63
157_I 28_L 1.13 0.74 0.61
126_A 64_L 1.11 0.72 0.58
242_L 32_L 1.07 0.68 0.54
430_V 45_A 1.06 0.67 0.53
314_I 98_M 1.02 0.63 0.48
174_M 61_M 1.02 0.62 0.47
132_I 64_L 1.00 0.60 0.46
178_Y 55_Q 0.99 0.58 0.43
345_S 80_L 0.98 0.58 0.43
125_L 98_M 0.97 0.57 0.42
168_S 92_I 0.96 0.56 0.41
134_L 80_L 0.96 0.56 0.41
91_A 34_G 0.95 0.55 0.40
257_L 11_A 0.95 0.54 0.39
161_I 28_L 0.94 0.53 0.38
330_L 17_L 0.92 0.51 0.36
166_A 100_G 0.92 0.51 0.35
430_V 22_L 0.91 0.49 0.34
430_V 32_L 0.91 0.49 0.34
281_I 63_I 0.90 0.49 0.34
163_S 43_A 0.90 0.48 0.33
184_L 61_M 0.90 0.48 0.33
119_L 23_V 0.89 0.47 0.32
209_L 11_A 0.89 0.47 0.32
450_Y 60_V 0.88 0.46 0.31
139_L 25_R 0.86 0.44 0.29
100_D 75_I 0.86 0.44 0.29
288_A 31_M 0.86 0.43 0.28
114_L 23_V 0.85 0.43 0.28
170_L 65_A 0.85 0.43 0.28
464_V 73_A 0.85 0.42 0.28
280_S 75_I 0.85 0.42 0.28
399_L 29_L 0.85 0.42 0.28
206_G 98_M 0.85 0.42 0.27
183_D 9_I 0.84 0.41 0.27
422_L 68_L 0.82 0.39 0.25
245_A 8_L 0.82 0.39 0.24
134_L 75_I 0.82 0.39 0.24
206_G 81_L 0.81 0.38 0.24
82_L 11_A 0.81 0.38 0.24
172_F 45_A 0.81 0.38 0.23
123_N 17_L 0.81 0.37 0.23
305_H 20_T 0.80 0.37 0.23
347_M 89_N 0.80 0.37 0.23
136_S 35_L 0.79 0.36 0.22
340_A 18_G 0.78 0.35 0.21
212_V 34_G 0.78 0.35 0.21
209_L 34_G 0.78 0.34 0.21
113_A 98_M 0.78 0.34 0.21
207_F 11_A 0.78 0.34 0.20
51_S 13_I 0.78 0.34 0.20
42_V 38_M 0.78 0.34 0.20
183_D 98_M 0.77 0.33 0.20
132_I 39_I 0.77 0.33 0.20
424_Y 74_S 0.77 0.33 0.20
240_T 52_Y 0.76 0.33 0.19
310_L 47_V 0.76 0.32 0.19
161_I 32_L 0.76 0.32 0.19
396_F 31_M 0.76 0.32 0.19
306_L 6_H 0.76 0.32 0.19
276_I 75_I 0.76 0.32 0.19
147_F 45_A 0.75 0.32 0.18
164_A 41_A 0.75 0.32 0.18
407_L 9_I 0.75 0.31 0.18
376_M 1_M 0.75 0.31 0.18
339_G 80_L 0.75 0.31 0.18
465_L 42_S 0.75 0.31 0.18
184_L 57_D 0.75 0.31 0.18
60_A 38_M 0.75 0.31 0.18
309_L 93_D 0.75 0.31 0.18
320_E 2_I 0.75 0.31 0.18
132_I 56_T 0.75 0.31 0.18
380_M 50_G 0.75 0.31 0.18
457_V 11_A 0.75 0.31 0.18
145_Y 66_I 0.75 0.31 0.18
193_L 54_G 0.74 0.31 0.18
275_I 44_L 0.74 0.30 0.17
416_V 98_M 0.73 0.29 0.17
81_L 47_V 0.73 0.29 0.17
160_T 33_I 0.73 0.29 0.17
134_L 29_L 0.73 0.29 0.17
332_G 75_I 0.73 0.29 0.17
151_R 98_M 0.73 0.29 0.16
390_L 89_N 0.73 0.29 0.16
138_P 48_V 0.73 0.29 0.16
456_V 41_A 0.73 0.29 0.16
190_G 82_Q 0.73 0.29 0.16
111_I 81_L 0.72 0.29 0.16
239_S 51_S 0.72 0.28 0.16
278_F 7_G 0.72 0.28 0.16
363_R 11_A 0.72 0.28 0.16
302_S 61_M 0.72 0.28 0.16
172_F 99_R 0.72 0.28 0.16
136_S 73_A 0.72 0.28 0.16
398_V 79_L 0.72 0.28 0.16
178_Y 58_G 0.72 0.28 0.16
285_N 91_N 0.72 0.28 0.16
389_T 3_P 0.72 0.28 0.16
244_T 29_L 0.72 0.28 0.15
41_S 23_V 0.71 0.28 0.15
377_T 44_L 0.71 0.28 0.15
313_L 59_Q 0.71 0.28 0.15
398_V 55_Q 0.71 0.28 0.15
169_F 15_F 0.71 0.28 0.15
112_A 17_L 0.71 0.27 0.15
238_V 55_Q 0.71 0.27 0.15
171_L 78_A 0.70 0.27 0.15
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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