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OPENSEQ.org
TGD1 and TGD2
Genes: A B A+B
Length: 252 296 522
Sequences: 2590 5277 1591
Seq/Len: 10.28 17.83 3.05
MirrorTree (Pazo et al. 2001) 0.75
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 0.12 0.23 0.95
2 0.12 0.23 2.80
5 0.13 0.23 2.86
10 0.13 0.24 2.89
20 0.14 0.24 2.90
100 0.15 0.24 2.94
∞ 0.22 0.28 3.23
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
142_F 23_G 1.37 0.92 0.45
236_V 28_A 1.14 0.79 0.26
103_A 69_V 1.04 0.69 0.20
227_L 55_A 1.03 0.68 0.19
208_T 48_T 0.98 0.62 0.16
145_L 30_S 0.96 0.61 0.15
87_V 120_P 0.95 0.60 0.14
238_S 115_M 0.93 0.56 0.13
104_E 15_G 0.91 0.55 0.12
211_G 15_G 0.90 0.53 0.12
110_V 118_I 0.90 0.53 0.12
30_L 30_S 0.89 0.52 0.11
107_T 52_L 0.88 0.50 0.11
44_C 189_V 0.87 0.49 0.11
152_M 110_L 0.85 0.47 0.10
138_L 246_T 0.85 0.47 0.10
222_A 66_I 0.84 0.46 0.10
188_I 267_V 0.84 0.46 0.10
179_R 71_V 0.84 0.46 0.10
132_R 84_I 0.84 0.46 0.09
163_Y 106_N 0.82 0.43 0.09
151_G 167_I 0.81 0.42 0.08
129_I 237_L 0.81 0.42 0.08
188_I 87_V 0.81 0.41 0.08
46_L 57_G 0.80 0.41 0.08
48_S 88_A 0.80 0.41 0.08
12_A 230_L 0.79 0.39 0.08
104_E 103_V 0.79 0.39 0.08
169_I 69_V 0.78 0.39 0.07
188_I 269_S 0.77 0.37 0.07
66_L 161_V 0.77 0.37 0.07
88_I 157_L 0.77 0.37 0.07
86_P 112_M 0.76 0.36 0.07
170_I 110_L 0.76 0.36 0.07
133_V 199_K 0.76 0.36 0.07
129_I 207_A 0.76 0.36 0.07
101_F 107_Q 0.75 0.35 0.07
236_V 195_P 0.75 0.35 0.07
194_G 67_R 0.75 0.35 0.07
214_G 114_T 0.75 0.34 0.06
113_Q 280_D 0.74 0.34 0.06
84_L 69_V 0.74 0.34 0.06
64_T 18_L 0.74 0.34 0.06
190_S 147_Q 0.74 0.34 0.06
222_A 79_P 0.74 0.34 0.06
233_A 124_I 0.74 0.34 0.06
230_I 8_K 0.74 0.34 0.06
155_S 77_V 0.74 0.33 0.06
232_I 204_A 0.73 0.33 0.06
29_T 76_R 0.73 0.33 0.06
90_S 116_I 0.73 0.33 0.06
29_T 222_E 0.73 0.33 0.06
200_I 184_E 0.73 0.32 0.06
29_T 119_M 0.73 0.32 0.06
206_V 61_G 0.72 0.32 0.06
60_V 204_A 0.72 0.32 0.06
200_I 86_A 0.72 0.32 0.06
187_M 166_R 0.72 0.32 0.06
53_M 20_I 0.71 0.31 0.06
30_L 16_V 0.71 0.31 0.05
238_S 33_W 0.71 0.30 0.05
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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