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OPENSEQ.org
cIII_cytc1_ISP
Genes: A B A+B
Length: 250 190 419
Sequences: 918 1043 678
Seq/Len: 3.67 5.49 1.62
MirrorTree (Pazo et al. 2001) 0.88
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 0.01 0.01 0.12
2 0.01 0.01 1.44
5 0.01 0.01 1.45
10 0.01 0.01 1.45
20 0.01 0.01 1.45
100 0.01 0.01 1.46
∞ 0.01 0.02 1.54
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
231_L 23_T 1.69 0.94 0.64
141_I 180_E 1.33 0.78 0.34
73_R 55_Q 1.32 0.77 0.32
235_T 19_L 1.31 0.76 0.32
134_G 45_S 1.21 0.68 0.24
235_T 20_Y 1.21 0.68 0.24
95_T 52_A 1.21 0.67 0.24
144_V 153_P 1.15 0.62 0.20
81_I 138_V 1.14 0.61 0.20
78_N 187_I 1.07 0.54 0.15
93_V 49_Q 1.07 0.53 0.15
168_G 74_K 1.06 0.52 0.15
134_G 47_D 1.05 0.52 0.14
217_V 8_A 1.04 0.51 0.14
207_A 125_W 1.04 0.51 0.14
235_T 23_T 1.04 0.50 0.14
41_Y 54_I 1.03 0.50 0.14
129_S 103_Q 1.01 0.48 0.12
54_V 42_M 0.99 0.46 0.12
11_A 28_T 0.99 0.45 0.11
93_V 167_R 0.97 0.44 0.11
122_G 81_R 0.97 0.43 0.11
51_L 142_D 0.97 0.43 0.11
235_T 27_G 0.97 0.43 0.10
236_N 19_L 0.96 0.42 0.10
123_P 50_A 0.95 0.41 0.10
94_P 80_R 0.95 0.41 0.10
229_A 74_K 0.94 0.41 0.10
92_R 40_N 0.94 0.40 0.09
234_L 15_R 0.94 0.40 0.09
219_F 72_L 0.94 0.40 0.09
47_A 42_M 0.93 0.39 0.09
227_V 21_Y 0.92 0.38 0.09
203_L 126_L 0.92 0.38 0.09
225_L 181_F 0.91 0.37 0.08
183_T 124_E 0.91 0.37 0.08
130_Q 33_A 0.90 0.36 0.08
47_A 35_A 0.90 0.36 0.08
34_L 72_L 0.89 0.35 0.08
179_D 125_W 0.86 0.33 0.07
130_Q 30_A 0.86 0.32 0.07
237_K 74_K 0.85 0.32 0.07
116_A 168_G 0.85 0.32 0.07
15_I 96_Q 0.85 0.31 0.06
241_Q 29_V 0.85 0.31 0.06
187_G 117_R 0.84 0.30 0.06
219_F 67_L 0.84 0.30 0.06
231_L 26_A 0.84 0.30 0.06
227_V 30_A 0.83 0.30 0.06
200_A 93_D 0.83 0.30 0.06
61_D 57_D 0.83 0.30 0.06
143_A 76_V 0.83 0.29 0.06
233_Y 29_V 0.83 0.29 0.06
163_N 159_Y 0.83 0.29 0.06
54_V 145_G 0.82 0.29 0.06
9_S 148_G 0.82 0.29 0.06
36_R 34_A 0.82 0.29 0.06
35_Q 44_P 0.82 0.28 0.06
217_V 69_V 0.81 0.28 0.05
212_M 187_I 0.81 0.28 0.05
125_G 189_L 0.81 0.28 0.05
231_L 22_A 0.81 0.28 0.05
118_A 74_K 0.81 0.28 0.05
231_L 24_A 0.80 0.27 0.05
20_F 30_A 0.80 0.27 0.05
196_A 78_I 0.80 0.27 0.05
69_E 101_S 0.80 0.27 0.05
138_P 23_T 0.80 0.27 0.05
108_P 171_P 0.80 0.27 0.05
222_V 33_A 0.80 0.27 0.05
16_E 27_G 0.80 0.27 0.05
207_A 104_N 0.79 0.26 0.05
214_R 168_G 0.79 0.26 0.05
131_L 180_E 0.78 0.25 0.05
59_L 57_D 0.78 0.25 0.05
30_D 85_E 0.78 0.25 0.05
73_R 46_A 0.78 0.25 0.05
139_E 138_V 0.78 0.25 0.05
16_E 54_I 0.78 0.25 0.05
61_D 46_A 0.77 0.25 0.04
174_A 12_G 0.77 0.25 0.04
207_A 36_W 0.77 0.25 0.04
214_R 33_A 0.77 0.25 0.04
192_V 115_E 0.77 0.24 0.04
114_A 70_K 0.77 0.24 0.04
63_G 42_M 0.77 0.24 0.04
143_A 94_L 0.77 0.24 0.04
156_A 28_T 0.77 0.24 0.04
166_F 48_V 0.76 0.24 0.04
163_N 47_D 0.76 0.24 0.04
239_L 13_A 0.76 0.24 0.04
227_V 114_D 0.76 0.24 0.04
68_P 15_R 0.76 0.24 0.04
69_E 29_V 0.76 0.23 0.04
123_P 49_Q 0.76 0.23 0.04
30_D 145_G 0.75 0.23 0.04
228_L 129_I 0.75 0.23 0.04
35_Q 59_S 0.75 0.23 0.04
183_T 9_G 0.75 0.23 0.04
213_D 123_G 0.75 0.23 0.04
33_Q 172_Q 0.75 0.23 0.04
46_S 95_G 0.74 0.23 0.04
193_D 52_A 0.74 0.23 0.04
140_Y 25_G 0.74 0.23 0.04
98_F 50_A 0.74 0.22 0.04
244_K 131_V 0.74 0.22 0.04
26_F 166_R 0.74 0.22 0.04
148_Y 85_E 0.74 0.22 0.04
142_H 35_A 0.73 0.22 0.04
187_G 85_E 0.73 0.22 0.04
222_V 184_D 0.73 0.22 0.04
216_Q 167_R 0.73 0.21 0.04
57_R 46_A 0.73 0.21 0.04
222_V 29_V 0.73 0.21 0.04
238_K 24_A 0.73 0.21 0.04
97_H 43_N 0.73 0.21 0.04
137_G 77_F 0.72 0.21 0.04
44_V 117_R 0.72 0.21 0.04
208_E 181_F 0.72 0.21 0.04
203_L 98_I 0.72 0.21 0.04
50_G 168_G 0.72 0.21 0.04
154_E 145_G 0.72 0.21 0.04
207_A 29_V 0.72 0.21 0.04
185_E 58_V 0.72 0.21 0.04
141_I 96_Q 0.72 0.21 0.04
156_A 31_A 0.72 0.21 0.04
186_D 118_T 0.72 0.21 0.03
208_E 131_V 0.72 0.21 0.03
176_P 78_I 0.71 0.20 0.03
183_T 87_Q 0.71 0.20 0.03
140_Y 107_K 0.71 0.20 0.03
28_K 39_V 0.71 0.20 0.03
208_E 171_P 0.71 0.20 0.03
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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