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OPENSEQ.org
TssJ-TssM_Pa2
Genes: A B A+B
Length: 168 135 281
Sequences: 645 729 533
Seq/Len: 3.84 5.4 1.9
MirrorTree (Pazo et al. 2001) 0.85
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 0.00 0.00 0.04
2 0.00 0.00 0.11
5 0.00 0.00 1.43
10 0.00 0.00 1.71
20 0.00 0.02 1.76
100 0.02 0.04 1.79
∞ 0.11 0.12 1.80
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
56_P 37_H 1.66 0.95 0.72
131_W 48_P 1.51 0.91 0.60
65_K 126_L 1.49 0.90 0.58
56_P 17_L 1.39 0.85 0.49
73_A 96_V 1.39 0.85 0.49
58_V 10_F 1.28 0.78 0.40
36_L 12_L 1.26 0.77 0.38
56_P 77_W 1.26 0.77 0.38
76_F 39_P 1.26 0.77 0.38
132_R 18_D 1.25 0.76 0.36
82_P 28_F 1.23 0.74 0.34
98_L 25_E 1.22 0.73 0.34
62_F 42_P 1.22 0.73 0.34
58_V 36_R 1.21 0.72 0.32
80_E 41_V 1.16 0.68 0.29
47_N 35_Y 1.16 0.67 0.28
116_Y 26_F 1.15 0.67 0.28
76_F 37_H 1.15 0.67 0.28
32_R 114_A 1.15 0.66 0.28
78_L 120_P 1.15 0.66 0.27
147_L 25_E 1.14 0.66 0.27
91_V 83_F 1.14 0.65 0.27
36_L 126_L 1.12 0.64 0.26
121_A 135_L 1.11 0.63 0.25
124_R 40_I 1.10 0.62 0.24
117_V 99_L 1.10 0.62 0.24
95_E 110_Y 1.09 0.60 0.23
110_V 23_R 1.08 0.59 0.22
95_E 36_R 1.07 0.59 0.22
124_R 22_S 1.07 0.59 0.22
74_D 84_D 1.07 0.58 0.21
57_V 95_D 1.06 0.57 0.21
56_P 76_P 1.05 0.57 0.20
59_V 103_L 1.04 0.55 0.20
22_A 133_V 1.04 0.55 0.19
124_R 18_D 1.03 0.55 0.19
57_V 56_T 1.03 0.55 0.19
74_D 31_Q 1.02 0.53 0.18
56_P 62_K 1.02 0.53 0.18
23_G 112_L 1.01 0.52 0.18
34_T 110_Y 1.01 0.52 0.18
42_A 15_Y 1.01 0.52 0.17
74_D 77_W 1.00 0.51 0.17
55_S 17_L 1.00 0.51 0.17
35_K 114_A 1.00 0.51 0.17
55_S 37_H 0.99 0.50 0.17
70_F 26_F 0.99 0.49 0.16
96_L 86_M 0.98 0.48 0.15
114_S 12_L 0.97 0.48 0.15
154_I 58_L 0.97 0.48 0.15
90_L 44_S 0.97 0.47 0.15
139_A 108_A 0.96 0.47 0.15
101_G 84_D 0.96 0.47 0.15
79_Y 36_R 0.96 0.47 0.15
147_L 89_E 0.96 0.46 0.14
98_L 46_K 0.96 0.46 0.14
156_N 77_W 0.96 0.46 0.14
126_L 18_D 0.95 0.46 0.14
105_E 33_M 0.95 0.46 0.14
116_Y 130_R 0.95 0.46 0.14
120_L 61_E 0.95 0.46 0.14
42_A 21_V 0.93 0.43 0.13
48_P 44_S 0.93 0.43 0.13
114_S 13_E 0.93 0.43 0.13
40_L 26_F 0.93 0.43 0.13
108_L 29_D 0.93 0.43 0.13
118_G 107_R 0.93 0.43 0.13
61_L 88_T 0.92 0.42 0.12
54_P 70_I 0.92 0.42 0.12
25_S 45_F 0.92 0.42 0.12
75_F 39_P 0.92 0.42 0.12
65_K 90_Y 0.92 0.42 0.12
42_A 102_D 0.92 0.42 0.12
36_L 41_V 0.91 0.41 0.12
15_L 45_F 0.91 0.41 0.12
58_V 99_L 0.90 0.40 0.12
64_L 132_P 0.90 0.40 0.12
123_Y 42_P 0.90 0.40 0.12
129_A 37_H 0.90 0.40 0.12
122_A 37_H 0.90 0.40 0.12
77_S 50_D 0.90 0.40 0.12
66_H 83_F 0.90 0.40 0.11
120_L 100_K 0.90 0.40 0.11
95_E 65_G 0.90 0.40 0.11
101_G 120_P 0.89 0.39 0.11
38_L 63_M 0.89 0.39 0.11
42_A 130_R 0.89 0.39 0.11
79_Y 105_G 0.89 0.39 0.11
75_F 85_L 0.89 0.39 0.11
62_F 35_Y 0.89 0.38 0.11
52_G 19_P 0.88 0.38 0.11
123_Y 37_H 0.88 0.38 0.10
21_L 29_D 0.88 0.38 0.10
87_D 103_L 0.87 0.37 0.10
112_E 20_G 0.87 0.37 0.10
61_L 15_Y 0.87 0.37 0.10
56_P 39_P 0.87 0.36 0.10
126_L 42_P 0.87 0.36 0.10
50_L 105_G 0.86 0.36 0.10
72_N 57_S 0.86 0.36 0.10
17_V 87_Q 0.86 0.35 0.10
17_V 12_L 0.85 0.35 0.09
50_L 134_Q 0.85 0.35 0.09
79_Y 29_D 0.85 0.35 0.09
84_E 96_V 0.85 0.35 0.09
40_L 126_L 0.85 0.35 0.09
31_S 82_L 0.85 0.35 0.09
85_T 64_A 0.85 0.35 0.09
82_P 79_L 0.85 0.35 0.09
75_F 127_R 0.84 0.34 0.09
93_S 23_R 0.84 0.34 0.09
62_F 22_S 0.84 0.34 0.09
137_V 38_G 0.84 0.34 0.09
48_P 22_S 0.84 0.34 0.09
70_F 78_S 0.84 0.33 0.09
92_T 33_M 0.83 0.33 0.09
97_E 36_R 0.83 0.33 0.09
125_D 34_E 0.83 0.33 0.09
38_L 71_E 0.83 0.33 0.09
54_P 130_R 0.83 0.33 0.08
131_W 79_L 0.83 0.33 0.08
131_W 58_L 0.83 0.32 0.08
124_R 79_L 0.82 0.32 0.08
83_K 50_D 0.82 0.32 0.08
121_A 30_G 0.82 0.32 0.08
39_A 33_M 0.82 0.31 0.08
70_F 35_Y 0.82 0.31 0.08
134_V 12_L 0.81 0.31 0.08
109_S 114_A 0.81 0.31 0.08
85_T 128_S 0.81 0.30 0.08
24_C 47_W 0.80 0.30 0.08
123_Y 104_G 0.80 0.30 0.07
76_F 18_D 0.80 0.30 0.07
140_K 12_L 0.80 0.30 0.07
98_L 102_D 0.80 0.30 0.07
73_A 7_Q 0.80 0.30 0.07
96_L 84_D 0.80 0.30 0.07
130_S 78_S 0.80 0.30 0.07
129_A 78_S 0.79 0.29 0.07
93_S 52_D 0.79 0.29 0.07
134_V 91_L 0.79 0.29 0.07
78_L 105_G 0.79 0.29 0.07
43_G 38_G 0.79 0.29 0.07
126_L 39_P 0.79 0.29 0.07
97_E 30_G 0.79 0.29 0.07
60_R 11_R 0.79 0.29 0.07
16_A 12_L 0.78 0.28 0.07
56_P 8_V 0.78 0.28 0.07
87_D 121_F 0.78 0.28 0.07
132_R 133_V 0.78 0.28 0.07
154_I 20_G 0.78 0.28 0.07
87_D 114_A 0.78 0.28 0.07
56_P 101_A 0.78 0.28 0.07
65_K 33_M 0.78 0.28 0.07
114_S 131_M 0.78 0.28 0.07
64_L 35_Y 0.78 0.28 0.07
97_E 135_L 0.78 0.28 0.07
123_Y 43_M 0.77 0.27 0.07
131_W 45_F 0.77 0.27 0.06
40_L 20_G 0.77 0.27 0.06
148_K 4_A 0.77 0.27 0.06
147_L 59_V 0.77 0.27 0.06
46_V 28_F 0.77 0.27 0.06
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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