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OPENSEQ.org
2d1p_I_H
Genes: A B A+B
Length: 95 119 214
Sequences: 505 508 466
Seq/Len: 5.32 4.27 2.18
MirrorTree (Pazo et al. 2001) 0.75
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 0.04 0.05 2.18
2 0.04 0.05 2.18
5 0.04 0.05 2.18
10 0.04 0.05 2.18
20 0.04 0.05 2.18
100 0.04 0.05 2.18
∞ 0.04 0.05 2.21
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
16_A 41_A 1.74 0.97 0.87
1_M 21_G 1.52 0.93 0.75
28_L 63_A 1.35 0.86 0.61
38_V 66_K 1.34 0.85 0.60
77_I 15_T 1.32 0.84 0.58
20_L 106_L 1.27 0.81 0.54
47_L 79_C 1.25 0.79 0.51
32_D 42_D 1.23 0.78 0.49
93_M 7_V 1.21 0.76 0.47
32_D 14_G 1.18 0.73 0.43
10_W 86_R 1.11 0.67 0.37
29_L 65_F 1.08 0.63 0.34
67_T 105_A 1.06 0.62 0.32
62_I 52_K 1.04 0.59 0.30
32_D 86_R 1.03 0.58 0.29
87_V 94_F 1.02 0.57 0.28
67_T 90_P 1.01 0.57 0.28
19_R 81_A 0.99 0.53 0.25
28_L 36_A 0.98 0.53 0.25
37_A 7_V 0.97 0.51 0.23
38_V 57_L 0.96 0.50 0.23
34_V 119_F 0.96 0.50 0.23
31_Q 38_F 0.94 0.48 0.21
15_A 35_L 0.94 0.47 0.21
38_V 45_F 0.92 0.46 0.20
6_H 60_D 0.92 0.46 0.20
79_Y 87_G 0.92 0.46 0.20
92_Q 32_T 0.92 0.45 0.19
6_H 79_C 0.91 0.45 0.19
4_T 97_E 0.91 0.45 0.19
8_S 86_R 0.90 0.44 0.18
33_G 78_V 0.90 0.43 0.18
94_A 31_L 0.90 0.43 0.18
56_A 62_I 0.89 0.43 0.18
78_D 43_G 0.89 0.43 0.18
34_V 14_G 0.89 0.42 0.18
31_Q 79_C 0.89 0.42 0.17
63_A 56_V 0.88 0.41 0.17
27_L 117_L 0.88 0.41 0.17
81_D 20_E 0.88 0.41 0.17
19_R 103_A 0.88 0.41 0.17
33_G 114_D 0.87 0.41 0.16
26_E 56_V 0.87 0.40 0.16
92_Q 67_L 0.87 0.40 0.16
87_V 46_Q 0.87 0.40 0.16
61_L 60_D 0.87 0.40 0.16
30_L 11_A 0.86 0.39 0.16
95_W 98_A 0.86 0.39 0.15
31_Q 16_A 0.86 0.39 0.15
92_Q 20_E 0.86 0.39 0.15
27_L 100_P 0.86 0.39 0.15
14_F 88_L 0.86 0.39 0.15
46_S 37_V 0.85 0.38 0.15
8_S 42_D 0.85 0.38 0.15
49_N 89_D 0.84 0.37 0.14
82_F 13_H 0.84 0.37 0.14
93_M 24_A 0.84 0.37 0.14
85_L 46_Q 0.83 0.36 0.14
65_G 100_P 0.83 0.36 0.14
25_D 23_D 0.83 0.36 0.14
9_P 86_R 0.83 0.36 0.14
20_L 40_I 0.83 0.36 0.14
22_S 97_E 0.83 0.36 0.14
54_V 107_R 0.82 0.35 0.13
62_I 55_A 0.82 0.35 0.13
79_Y 37_V 0.82 0.35 0.13
92_Q 6_F 0.82 0.34 0.13
87_V 10_T 0.82 0.34 0.13
74_I 115_V 0.81 0.34 0.13
2_L 39_F 0.81 0.34 0.12
31_Q 31_L 0.81 0.34 0.12
28_L 116_I 0.81 0.33 0.12
16_A 9_S 0.81 0.33 0.12
7_R 36_A 0.80 0.33 0.12
10_W 43_G 0.80 0.33 0.12
33_G 71_Y 0.80 0.32 0.12
91_S 115_V 0.79 0.32 0.12
27_L 95_V 0.79 0.32 0.12
35_T 26_L 0.79 0.32 0.11
70_I 105_A 0.79 0.32 0.11
40_G 11_A 0.79 0.31 0.11
54_V 111_A 0.78 0.31 0.11
77_I 50_G 0.78 0.31 0.11
53_K 102_E 0.78 0.31 0.11
28_L 89_D 0.78 0.30 0.11
65_G 29_S 0.77 0.30 0.11
27_L 91_Q 0.77 0.30 0.11
10_W 77_W 0.77 0.30 0.10
24_G 50_G 0.77 0.30 0.10
75_I 73_I 0.77 0.29 0.10
6_H 27_A 0.76 0.29 0.10
79_Y 82_S 0.76 0.29 0.10
41_N 68_L 0.76 0.29 0.10
48_R 105_A 0.76 0.29 0.10
14_F 4_I 0.76 0.29 0.10
31_Q 9_S 0.76 0.28 0.10
14_F 118_R 0.76 0.28 0.10
1_M 24_A 0.75 0.28 0.10
27_L 105_A 0.75 0.28 0.10
21_L 100_P 0.75 0.28 0.09
1_M 57_L 0.75 0.28 0.09
31_Q 5_A 0.75 0.28 0.09
67_T 53_P 0.75 0.28 0.09
1_M 6_F 0.74 0.28 0.09
84_R 66_K 0.74 0.27 0.09
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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