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OPENSEQ.org
tfb3kin28
Genes: A B A+B
Length: 306 321 599
Sequences: 59057 256 87
Seq/Len: 193 0.8 0.15
MirrorTree (Pazo et al. 2001) 0.64
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 0.09 0.04 0.02
2 0.12 0.04 0.04
5 0.16 0.04 0.08
10 0.20 0.04 0.11
20 0.24 0.04 0.14
100 0.32 0.04 0.26
∞ 0.34 0.04 0.30
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
188_I 106_Y 1.40 0.22 0.00
198_L 115_D 1.39 0.22 0.00
117_V 296_F 1.33 0.20 0.00
60_E 169_K 1.26 0.17 0.00
19_A 270_F 1.17 0.15 0.00
119_H 63_L 1.12 0.13 0.00
117_V 141_K 1.11 0.13 0.00
167_T 210_E 1.10 0.13 0.00
270_M 57_K 1.10 0.13 0.00
176_L 173_R 1.09 0.13 0.00
151_A 92_F 1.09 0.12 0.00
29_T 126_V 1.08 0.12 0.00
34_A 136_Y 1.05 0.12 0.00
122_R 321_L 1.05 0.12 0.00
117_V 108_K 1.04 0.12 0.00
82_V 43_V 1.04 0.11 0.00
100_L 123_G 1.04 0.11 0.00
124_F 63_L 1.03 0.11 0.00
189_W 107_N 1.03 0.11 0.00
176_L 25_D 1.02 0.11 0.00
99_I 117_I 1.01 0.11 0.00
34_A 312_G 1.01 0.11 0.00
54_E 144_I 1.00 0.11 0.00
288_D 113_V 1.00 0.11 0.00
259_A 296_F 1.00 0.11 0.00
198_L 221_S 1.00 0.10 0.00
190_S 308_E 1.00 0.10 0.00
284_C 86_K 0.99 0.10 0.00
261_E 285_L 0.99 0.10 0.00
94_I 86_K 0.98 0.10 0.00
274_N 41_S 0.98 0.10 0.00
76_Y 82_V 0.97 0.10 0.00
117_V 76_V 0.96 0.10 0.00
21_V 93_N 0.96 0.10 0.00
21_V 99_F 0.96 0.10 0.00
21_V 114_E 0.96 0.10 0.00
21_V 295_G 0.96 0.10 0.00
149_G 93_N 0.96 0.10 0.00
149_G 99_F 0.96 0.10 0.00
149_G 114_E 0.96 0.10 0.00
149_G 295_G 0.96 0.10 0.00
174_E 93_N 0.96 0.10 0.00
174_E 99_F 0.96 0.10 0.00
174_E 114_E 0.96 0.10 0.00
174_E 295_G 0.96 0.10 0.00
187_D 93_N 0.96 0.10 0.00
187_D 99_F 0.96 0.10 0.00
187_D 114_E 0.96 0.10 0.00
187_D 295_G 0.96 0.10 0.00
122_R 115_D 0.96 0.10 0.00
175_L 269_R 0.95 0.10 0.00
56_K 96_I 0.94 0.09 0.00
58_L 87_R 0.94 0.09 0.00
177_F 172_K 0.94 0.09 0.00
82_V 86_K 0.94 0.09 0.00
66_V 60_D 0.94 0.09 0.00
136_L 136_Y 0.93 0.09 0.00
214_M 117_I 0.93 0.09 0.00
286_E 270_F 0.93 0.09 0.00
32_K 224_R 0.93 0.09 0.00
114_L 47_F 0.93 0.09 0.00
219_R 86_K 0.93 0.09 0.00
64_P 98_D 0.92 0.09 0.00
284_C 131_E 0.92 0.09 0.00
122_R 117_I 0.92 0.09 0.00
274_N 77_E 0.92 0.09 0.00
125_I 104_V 0.92 0.09 0.00
139_P 208_T 0.92 0.09 0.00
190_S 309_A 0.92 0.09 0.00
195_F 166_K 0.91 0.09 0.00
127_H 309_A 0.91 0.09 0.00
296_P 136_Y 0.90 0.09 0.00
89_D 297_N 0.89 0.09 0.00
163_S 296_F 0.89 0.09 0.00
81_L 91_V 0.89 0.09 0.00
281_A 192_K 0.89 0.09 0.00
172_A 118_Y 0.89 0.09 0.00
287_S 128_K 0.89 0.08 0.00
22_Y 183_E 0.89 0.08 0.00
14_G 312_G 0.89 0.08 0.00
59_Q 201_T 0.88 0.08 0.00
21_V 85_R 0.88 0.08 0.00
149_G 85_R 0.88 0.08 0.00
174_E 85_R 0.88 0.08 0.00
187_D 85_R 0.88 0.08 0.00
154_I 267_H 0.88 0.08 0.00
66_V 170_L 0.88 0.08 0.00
31_R 113_V 0.88 0.08 0.00
208_Q 201_T 0.88 0.08 0.00
148_F 154_E 0.87 0.08 0.00
89_D 173_R 0.87 0.08 0.00
183_T 174_L 0.87 0.08 0.00
5_M 21_Y 0.86 0.08 0.00
125_I 254_A 0.86 0.08 0.00
287_S 84_I 0.86 0.08 0.00
140_D 105_E 0.86 0.08 0.00
284_C 214_N 0.86 0.08 0.00
128_R 109_Y 0.86 0.08 0.00
10_E 316_V 0.86 0.08 0.00
132_P 140_N 0.86 0.08 0.00
53_R 139_L 0.85 0.08 0.00
19_A 195_V 0.85 0.08 0.00
117_V 102_D 0.85 0.08 0.00
42_E 194_I 0.85 0.08 0.00
85_F 83_D 0.85 0.08 0.00
201_R 107_N 0.84 0.08 0.00
188_I 131_E 0.84 0.08 0.00
126_L 188_E 0.84 0.08 0.00
179_A 188_E 0.84 0.08 0.00
27_H 80_K 0.84 0.08 0.00
39_K 23_S 0.84 0.08 0.00
145_V 127_A 0.83 0.07 0.00
145_V 196_N 0.83 0.07 0.00
78_N 169_K 0.83 0.07 0.00
278_R 93_N 0.83 0.07 0.00
278_R 99_F 0.83 0.07 0.00
278_R 114_E 0.83 0.07 0.00
278_R 295_G 0.83 0.07 0.00
276_Q 153_T 0.82 0.07 0.00
194_I 78_V 0.82 0.07 0.00
170_Y 80_K 0.82 0.07 0.00
266_F 96_I 0.82 0.07 0.00
84_E 21_Y 0.82 0.07 0.00
137_F 115_D 0.82 0.07 0.00
281_A 300_Y 0.82 0.07 0.00
66_V 62_I 0.82 0.07 0.00
175_L 100_N 0.82 0.07 0.00
268_C 37_R 0.82 0.07 0.00
126_L 174_L 0.82 0.07 0.00
7_Y 141_K 0.81 0.07 0.00
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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