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OPENSEQ.org
hcp_tsse
Genes: A B A+B
Length: 172 145 300
Sequences: 934 678 438
Seq/Len: 5.43 4.68 1.46
MirrorTree (Pazo et al. 2001) 0.68
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 0.00 0.47
2 0.01 0.00 0.71
5 0.03 0.00 0.97
10 0.04 0.00 1.21
20 0.10 0.00 1.38
100 0.12 0.01 1.42
∞ 0.20 0.10 1.53
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
105_G 113_L 1.60 0.90 0.34
146_L 39_E 1.33 0.75 0.17
78_V 65_V 1.31 0.73 0.16
145_S 62_L 1.27 0.70 0.15
120_I 113_L 1.26 0.69 0.14
161_S 88_C 1.24 0.67 0.13
133_P 48_I 1.21 0.65 0.12
37_D 105_Q 1.20 0.64 0.12
44_F 117_I 1.19 0.62 0.11
144_V 84_A 1.18 0.62 0.11
94_V 96_L 1.18 0.62 0.11
31_F 117_I 1.16 0.60 0.10
37_D 76_D 1.14 0.58 0.10
77_A 102_R 1.14 0.57 0.10
168_K 19_L 1.12 0.56 0.09
61_G 92_Y 1.11 0.55 0.09
13_T 48_I 1.07 0.51 0.08
115_L 85_I 1.07 0.50 0.07
84_A 66_D 1.06 0.50 0.07
7_I 140_R 1.01 0.45 0.06
70_F 51_T 0.99 0.42 0.06
163_S 19_L 0.98 0.41 0.05
50_V 44_N 0.97 0.41 0.05
120_I 70_A 0.97 0.41 0.05
121_V 87_Q 0.97 0.40 0.05
53_D 144_V 0.96 0.40 0.05
63_R 92_Y 0.94 0.37 0.05
72_V 66_D 0.94 0.37 0.04
144_V 60_P 0.94 0.37 0.04
120_I 99_V 0.94 0.37 0.04
45_D 118_T 0.93 0.37 0.04
11_G 18_R 0.93 0.36 0.04
150_K 62_L 0.92 0.36 0.04
79_P 9_S 0.92 0.36 0.04
110_F 100_L 0.91 0.35 0.04
77_A 126_L 0.90 0.34 0.04
120_I 75_L 0.89 0.33 0.04
37_D 136_L 0.89 0.33 0.04
153_W 54_G 0.89 0.32 0.04
79_P 113_L 0.89 0.32 0.04
95_E 48_I 0.88 0.32 0.04
44_F 132_F 0.86 0.30 0.03
119_S 41_I 0.86 0.30 0.03
125_C 96_L 0.85 0.30 0.03
96_L 128_E 0.85 0.29 0.03
72_V 140_R 0.85 0.29 0.03
123_I 15_F 0.85 0.29 0.03
41_V 126_L 0.84 0.29 0.03
119_S 96_L 0.84 0.29 0.03
140_Q 9_S 0.84 0.28 0.03
155_H 138_Q 0.83 0.28 0.03
63_R 52_R 0.83 0.28 0.03
66_K 118_T 0.82 0.27 0.03
56_S 49_L 0.82 0.26 0.03
148_Y 107_S 0.81 0.26 0.03
122_D 17_E 0.81 0.26 0.03
60_S 109_N 0.81 0.26 0.03
68_F 112_T 0.81 0.26 0.03
41_V 103_A 0.80 0.26 0.03
96_L 73_E 0.80 0.25 0.03
72_V 40_S 0.80 0.25 0.03
8_S 17_E 0.80 0.25 0.03
77_A 119_A 0.80 0.25 0.03
112_T 103_A 0.80 0.25 0.03
168_K 21_A 0.79 0.24 0.02
84_A 101_V 0.79 0.24 0.02
100_R 45_V 0.78 0.24 0.02
77_A 105_Q 0.78 0.24 0.02
154_D 89_L 0.78 0.24 0.02
19_A 50_N 0.78 0.24 0.02
81_L 126_L 0.78 0.24 0.02
108_E 57_Q 0.78 0.23 0.02
95_E 112_T 0.78 0.23 0.02
142_V 74_T 0.78 0.23 0.02
12_Q 19_L 0.78 0.23 0.02
52_T 62_L 0.78 0.23 0.02
83_N 12_G 0.78 0.23 0.02
63_R 109_N 0.77 0.23 0.02
82_Y 16_F 0.77 0.23 0.02
48_V 89_L 0.77 0.23 0.02
43_Q 117_I 0.77 0.23 0.02
155_H 13_V 0.77 0.23 0.02
145_S 112_T 0.77 0.23 0.02
149_R 70_A 0.76 0.22 0.02
63_R 136_L 0.76 0.22 0.02
123_I 135_L 0.76 0.22 0.02
151_I 85_I 0.76 0.22 0.02
6_Y 41_I 0.76 0.22 0.02
95_E 56_A 0.75 0.22 0.02
120_I 117_I 0.75 0.21 0.02
119_S 23_A 0.75 0.21 0.02
84_A 40_S 0.75 0.21 0.02
71_T 101_V 0.75 0.21 0.02
61_G 93_E 0.75 0.21 0.02
148_Y 116_H 0.75 0.21 0.02
113_T 114_R 0.75 0.21 0.02
9_I 106_D 0.75 0.21 0.02
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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