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OPENSEQ.org
Manon
Genes: A B A+B
Length: 316 446 735
Sequences: 4372 2576 58
Seq/Len: 13.84 5.78 0.08
MirrorTree (Pazo et al. 2001) 0.13
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 0.07 0.09 0.01
2 0.07 0.09 0.01
5 0.07 0.09 0.02
10 0.07 0.09 0.04
20 0.07 0.09 0.08
100 0.08 0.09 0.31
∞ 0.13 0.11 1.56
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
289_V 33_F 1.54 0.19 0.00
174_V 256_A 1.47 0.17 0.00
204_I 25_D 1.40 0.15 0.00
48_T 214_N 1.25 0.12 0.00
276_G 165_S 1.23 0.11 0.00
200_L 190_L 1.22 0.11 0.00
23_I 185_N 1.19 0.11 0.00
131_V 189_A 1.17 0.10 0.00
200_L 324_K 1.13 0.10 0.00
43_G 79_L 1.11 0.09 0.00
199_P 203_E 1.10 0.09 0.00
126_T 283_T 1.09 0.09 0.00
247_A 248_V 1.07 0.09 0.00
302_F 54_N 1.07 0.09 0.00
286_V 348_K 1.06 0.09 0.00
191_R 246_G 1.06 0.09 0.00
276_G 122_M 1.04 0.08 0.00
276_G 259_F 1.04 0.08 0.00
313_K 248_V 1.04 0.08 0.00
200_L 320_E 1.04 0.08 0.00
42_Q 368_E 1.02 0.08 0.00
121_F 233_D 1.01 0.08 0.00
247_A 362_S 1.01 0.08 0.00
240_A 369_A 1.01 0.08 0.00
49_S 248_V 1.00 0.08 0.00
277_T 362_S 1.00 0.08 0.00
77_I 378_W 0.99 0.08 0.00
160_K 301_I 0.99 0.08 0.00
143_P 49_L 0.98 0.07 0.00
215_E 30_V 0.97 0.07 0.00
113_I 322_I 0.97 0.07 0.00
109_I 111_K 0.97 0.07 0.00
61_V 77_P 0.96 0.07 0.00
143_P 24_V 0.96 0.07 0.00
163_I 90_I 0.96 0.07 0.00
7_I 301_I 0.96 0.07 0.00
272_N 46_Y 0.96 0.07 0.00
187_V 381_M 0.96 0.07 0.00
250_Y 371_L 0.95 0.07 0.00
290_I 357_V 0.95 0.07 0.00
143_P 119_A 0.95 0.07 0.00
165_Q 376_N 0.95 0.07 0.00
247_A 187_K 0.95 0.07 0.00
157_S 142_Q 0.94 0.07 0.00
17_G 126_R 0.94 0.07 0.00
61_V 35_A 0.94 0.07 0.00
303_D 79_L 0.94 0.07 0.00
274_F 49_L 0.94 0.07 0.00
43_G 13_I 0.94 0.07 0.00
168_N 277_D 0.94 0.07 0.00
18_V 248_V 0.94 0.07 0.00
173_D 60_L 0.94 0.07 0.00
289_V 348_K 0.93 0.07 0.00
83_T 14_L 0.93 0.07 0.00
146_K 131_A 0.92 0.07 0.00
142_V 335_V 0.92 0.07 0.00
239_P 287_L 0.92 0.07 0.00
283_G 230_E 0.92 0.07 0.00
140_S 124_V 0.92 0.07 0.00
163_I 54_N 0.92 0.07 0.00
67_Y 111_K 0.91 0.07 0.00
121_F 171_L 0.91 0.07 0.00
140_S 240_K 0.91 0.07 0.00
160_K 250_I 0.91 0.07 0.00
72_G 95_V 0.91 0.07 0.00
164_S 382_V 0.91 0.07 0.00
160_K 248_V 0.91 0.07 0.00
163_I 348_K 0.91 0.07 0.00
113_I 392_V 0.91 0.07 0.00
133_V 313_E 0.90 0.07 0.00
119_N 71_I 0.90 0.07 0.00
179_V 239_I 0.90 0.07 0.00
23_I 214_N 0.90 0.06 0.00
222_V 214_N 0.90 0.06 0.00
146_K 184_P 0.90 0.06 0.00
197_G 221_F 0.89 0.06 0.00
193_I 155_V 0.89 0.06 0.00
168_N 6_T 0.89 0.06 0.00
272_N 239_I 0.89 0.06 0.00
168_N 375_K 0.89 0.06 0.00
288_Q 325_D 0.89 0.06 0.00
145_N 85_R 0.89 0.06 0.00
293_Q 324_K 0.88 0.06 0.00
53_V 320_E 0.88 0.06 0.00
259_V 241_S 0.88 0.06 0.00
5_P 214_N 0.88 0.06 0.00
78_V 221_F 0.88 0.06 0.00
171_P 382_V 0.87 0.06 0.00
171_P 256_A 0.87 0.06 0.00
146_K 186_F 0.87 0.06 0.00
202_E 153_L 0.87 0.06 0.00
177_L 241_S 0.86 0.06 0.00
193_I 341_I 0.86 0.06 0.00
217_I 368_E 0.86 0.06 0.00
36_V 160_V 0.86 0.06 0.00
239_P 87_Q 0.86 0.06 0.00
24_V 35_A 0.86 0.06 0.00
116_L 122_M 0.85 0.06 0.00
156_T 339_T 0.85 0.06 0.00
302_F 197_Y 0.85 0.06 0.00
312_M 362_S 0.85 0.06 0.00
145_N 207_K 0.85 0.06 0.00
8_V 286_E 0.85 0.06 0.00
255_K 111_K 0.85 0.06 0.00
21_T 250_I 0.85 0.06 0.00
167_L 233_D 0.85 0.06 0.00
272_N 232_L 0.85 0.06 0.00
174_V 33_F 0.85 0.06 0.00
193_I 78_K 0.84 0.06 0.00
103_N 346_E 0.84 0.06 0.00
11_G 242_A 0.84 0.06 0.00
13_G 242_A 0.84 0.06 0.00
16_G 242_A 0.84 0.06 0.00
239_P 256_A 0.84 0.06 0.00
242_A 252_M 0.84 0.06 0.00
293_Q 252_M 0.84 0.06 0.00
257_V 317_K 0.84 0.06 0.00
268_Y 324_K 0.84 0.06 0.00
129_V 244_Y 0.84 0.06 0.00
53_V 363_I 0.83 0.06 0.00
33_M 302_S 0.83 0.06 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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