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OPENSEQ.org
JModell-1
Genes: A B A+B
Length: 289 113 387
Sequences: 1857 852 793
Seq/Len: 6.43 7.54 2.05
MirrorTree (Pazo et al. 2001) 0.94
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 0.01 0.01 1.94
2 0.01 0.01 1.96
5 0.02 0.01 1.98
10 0.02 0.02 1.98
20 0.02 0.02 1.97
100 0.04 0.02 1.97
∞ 0.10 0.04 1.99
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
19_N 34_S 2.35 1.00 0.99
20_N 34_S 1.56 0.93 0.86
237_P 64_E 1.49 0.91 0.82
19_N 30_K 1.27 0.79 0.66
54_L 30_K 1.27 0.79 0.66
110_I 64_E 1.24 0.77 0.62
92_G 8_M 1.18 0.72 0.56
122_G 82_F 1.13 0.67 0.50
262_L 82_F 1.07 0.61 0.44
136_L 67_P 1.07 0.61 0.44
226_V 62_L 1.05 0.59 0.41
37_E 47_K 1.04 0.58 0.41
24_F 67_P 1.03 0.57 0.39
185_L 79_E 1.03 0.56 0.39
67_F 37_F 1.00 0.53 0.36
184_L 57_A 0.96 0.49 0.31
66_I 11_M 0.96 0.48 0.31
24_F 105_F 0.95 0.48 0.30
215_A 10_L 0.94 0.47 0.30
196_G 36_G 0.94 0.47 0.29
117_Q 15_P 0.94 0.47 0.29
257_G 67_P 0.94 0.46 0.29
257_G 72_I 0.94 0.46 0.29
183_L 84_R 0.93 0.46 0.28
269_Y 26_R 0.93 0.45 0.28
138_H 68_N 0.92 0.44 0.27
157_F 7_R 0.92 0.44 0.27
25_K 72_I 0.91 0.43 0.26
153_A 15_P 0.91 0.43 0.26
51_S 97_A 0.91 0.42 0.26
286_E 98_N 0.91 0.42 0.26
251_D 79_E 0.90 0.42 0.25
269_Y 105_F 0.89 0.41 0.24
50_L 11_M 0.89 0.41 0.24
181_Y 36_G 0.87 0.39 0.22
128_E 67_P 0.87 0.38 0.22
23_I 28_F 0.86 0.38 0.22
258_K 20_E 0.86 0.38 0.22
10_N 8_M 0.86 0.38 0.21
180_G 79_E 0.85 0.37 0.21
180_G 82_F 0.85 0.37 0.21
180_G 15_P 0.85 0.36 0.20
55_V 65_H 0.84 0.36 0.20
157_F 79_E 0.84 0.35 0.20
33_I 68_N 0.84 0.35 0.20
269_Y 25_Y 0.83 0.35 0.19
84_R 49_L 0.83 0.35 0.19
278_N 99_S 0.83 0.35 0.19
7_V 20_E 0.83 0.35 0.19
238_F 63_R 0.83 0.34 0.19
253_F 8_M 0.83 0.34 0.19
113_K 36_G 0.82 0.34 0.18
130_S 22_R 0.82 0.34 0.18
199_T 71_N 0.82 0.33 0.18
193_V 65_H 0.82 0.33 0.18
125_S 80_K 0.81 0.33 0.18
37_E 48_L 0.81 0.32 0.17
70_D 44_I 0.81 0.32 0.17
193_V 77_V 0.80 0.32 0.17
108_T 18_T 0.80 0.32 0.17
106_W 47_K 0.80 0.32 0.17
50_L 60_G 0.80 0.32 0.17
95_M 11_M 0.80 0.32 0.17
180_G 67_P 0.80 0.31 0.16
277_L 58_M 0.80 0.31 0.16
45_T 86_I 0.79 0.31 0.16
62_N 63_R 0.79 0.31 0.16
144_D 79_E 0.79 0.30 0.16
225_L 62_L 0.79 0.30 0.16
185_L 47_K 0.79 0.30 0.16
135_D 23_K 0.79 0.30 0.16
286_E 46_S 0.79 0.30 0.15
219_M 53_T 0.79 0.30 0.15
46_T 42_F 0.78 0.30 0.15
136_L 28_F 0.78 0.30 0.15
6_T 16_T 0.78 0.29 0.15
54_L 90_G 0.77 0.29 0.15
84_R 60_G 0.77 0.29 0.14
139_G 27_K 0.77 0.29 0.14
63_V 33_L 0.77 0.28 0.14
243_R 104_V 0.77 0.28 0.14
138_H 64_E 0.77 0.28 0.14
140_L 93_N 0.77 0.28 0.14
178_D 88_L 0.76 0.28 0.14
106_W 23_K 0.76 0.28 0.14
105_V 93_N 0.76 0.28 0.14
127_F 44_I 0.76 0.28 0.14
144_D 18_T 0.76 0.28 0.14
218_I 68_N 0.76 0.28 0.14
155_I 64_E 0.76 0.28 0.14
9_V 31_F 0.76 0.28 0.14
42_L 61_R 0.76 0.28 0.14
145_P 66_N 0.76 0.28 0.14
48_I 61_R 0.76 0.28 0.14
100_T 53_T 0.76 0.28 0.14
183_L 15_P 0.76 0.28 0.14
256_N 26_R 0.76 0.28 0.14
286_E 24_A 0.76 0.27 0.14
242_K 96_I 0.76 0.27 0.13
23_I 9_I 0.75 0.27 0.13
17_Y 82_F 0.75 0.27 0.13
133_I 9_I 0.75 0.27 0.13
135_D 22_R 0.75 0.27 0.13
56_K 87_Y 0.75 0.27 0.13
117_Q 67_P 0.75 0.27 0.13
182_T 68_N 0.75 0.27 0.13
45_T 105_F 0.74 0.26 0.13
10_N 89_H 0.74 0.26 0.13
53_M 42_F 0.74 0.26 0.13
5_R 8_M 0.74 0.26 0.12
230_V 30_K 0.74 0.26 0.12
36_S 35_E 0.74 0.26 0.12
49_V 42_F 0.74 0.26 0.12
164_D 20_E 0.74 0.26 0.12
120_Y 89_H 0.73 0.26 0.12
13_S 55_N 0.73 0.25 0.12
3_G 95_C 0.73 0.25 0.12
246_F 92_R 0.73 0.25 0.12
158_N 68_N 0.72 0.25 0.12
284_V 103_L 0.72 0.24 0.11
86_D 73_T 0.72 0.24 0.11
4_W 85_M 0.72 0.24 0.11
256_N 59_I 0.72 0.24 0.11
19_N 33_L 0.72 0.24 0.11
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)
ID Seq/Len Name Options I_Prob Status
9323 2.05 JModell-1 Δgene:(1, 20) A:(1E-04, 4) B:(1E-04, 4) msa: HHblits (2015_06) 0.99 Done
4585 0.96 c1-c2 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.46 Done - Shared
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