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OPENSEQ.org
m-l
Genes: A B A+B
Length: 514 215 706
Sequences: 252 206 216
Seq/Len: 0.49 0.96 0.31
MirrorTree (Pazo et al. 2001) 0.72
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 0.00 0.00 0.30
2 0.00 0.00 0.30
5 0.00 0.00 0.30
10 0.00 0.00 0.30
20 0.00 0.00 0.30
100 0.00 0.00 0.30
∞ 0.00 0.00 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
17_M 24_A 1.58 0.48 0.00
121_R 18_A 1.51 0.43 0.00
383_A 147_E 1.46 0.40 0.00
94_I 141_Q 1.40 0.36 0.00
25_L 52_I 1.32 0.31 0.00
93_Y 28_I 1.31 0.30 0.00
206_S 194_T 1.27 0.28 0.00
127_D 32_E 1.26 0.28 0.00
352_V 170_S 1.22 0.26 0.00
234_Y 52_I 1.22 0.26 0.00
21_F 33_I 1.21 0.25 0.00
172_K 111_G 1.21 0.25 0.00
83_V 148_M 1.20 0.25 0.00
483_G 159_N 1.19 0.24 0.00
25_L 55_L 1.17 0.23 0.00
121_R 190_M 1.16 0.23 0.00
329_I 147_E 1.13 0.21 0.00
360_S 44_I 1.11 0.20 0.00
133_G 46_L 1.09 0.20 0.00
329_I 69_L 1.09 0.19 0.00
483_G 24_A 1.08 0.19 0.00
25_L 46_L 1.08 0.19 0.00
63_D 18_A 1.08 0.19 0.00
60_T 119_N 1.07 0.19 0.00
24_M 34_G 1.07 0.19 0.00
244_D 189_Q 1.07 0.19 0.00
235_S 148_M 1.07 0.19 0.00
227_A 22_V 1.06 0.18 0.00
449_V 18_A 1.06 0.18 0.00
386_S 188_E 1.06 0.18 0.00
47_A 19_V 1.05 0.18 0.00
360_S 77_G 1.05 0.18 0.00
206_S 29_T 1.05 0.18 0.00
260_L 144_Y 1.05 0.18 0.00
493_T 172_N 1.05 0.18 0.00
502_L 55_L 1.04 0.18 0.00
212_V 136_D 1.04 0.17 0.00
502_L 3_L 1.03 0.17 0.00
40_M 137_S 1.03 0.17 0.00
139_N 18_A 1.02 0.17 0.00
359_A 168_S 1.02 0.17 0.00
211_D 212_S 1.01 0.16 0.00
87_S 18_A 1.01 0.16 0.00
387_V 129_K 1.01 0.16 0.00
165_I 41_M 1.01 0.16 0.00
220_Y 48_T 1.00 0.16 0.00
371_G 33_I 1.00 0.16 0.00
330_S 148_M 1.00 0.16 0.00
437_K 29_T 1.00 0.16 0.00
99_T 19_V 0.99 0.16 0.00
315_S 209_S 0.99 0.16 0.00
40_M 103_M 0.99 0.16 0.00
240_I 209_S 0.99 0.16 0.00
22_I 47_L 0.98 0.15 0.00
488_I 18_A 0.98 0.15 0.00
428_N 32_E 0.98 0.15 0.00
481_G 198_A 0.98 0.15 0.00
346_S 59_E 0.98 0.15 0.00
396_K 18_A 0.98 0.15 0.00
238_Q 55_L 0.98 0.15 0.00
479_R 179_I 0.98 0.15 0.00
127_D 29_T 0.97 0.15 0.00
202_A 166_L 0.97 0.15 0.00
131_G 5_S 0.97 0.15 0.00
70_K 19_V 0.97 0.15 0.00
483_G 74_L 0.97 0.15 0.00
376_S 46_L 0.96 0.15 0.00
27_M 41_M 0.96 0.15 0.00
199_I 42_L 0.96 0.15 0.00
50_S 175_A 0.96 0.15 0.00
402_T 44_I 0.96 0.14 0.00
264_D 12_A 0.96 0.14 0.00
208_W 48_T 0.96 0.14 0.00
307_G 170_S 0.95 0.14 0.00
58_L 33_I 0.95 0.14 0.00
22_I 33_I 0.95 0.14 0.00
83_V 197_I 0.95 0.14 0.00
280_N 141_Q 0.94 0.14 0.00
481_G 68_T 0.94 0.14 0.00
446_G 188_E 0.94 0.14 0.00
193_F 139_A 0.94 0.14 0.00
467_N 131_I 0.93 0.14 0.00
348_S 207_M 0.93 0.14 0.00
96_T 140_G 0.93 0.14 0.00
372_K 191_A 0.92 0.13 0.00
206_S 203_V 0.92 0.13 0.00
424_G 194_T 0.92 0.13 0.00
259_V 165_Q 0.92 0.13 0.00
460_P 183_A 0.92 0.13 0.00
381_T 64_E 0.92 0.13 0.00
80_A 41_M 0.92 0.13 0.00
165_I 48_T 0.92 0.13 0.00
79_T 155_M 0.92 0.13 0.00
490_E 193_M 0.92 0.13 0.00
188_Y 148_M 0.92 0.13 0.00
145_I 48_T 0.91 0.13 0.00
259_V 127_A 0.91 0.13 0.00
47_A 170_S 0.91 0.13 0.00
303_F 83_E 0.91 0.13 0.00
483_G 203_V 0.91 0.13 0.00
502_L 213_N 0.91 0.13 0.00
104_G 19_V 0.91 0.13 0.00
331_A 57_A 0.91 0.13 0.00
291_G 48_T 0.91 0.13 0.00
486_V 153_A 0.91 0.13 0.00
171_K 189_Q 0.90 0.13 0.00
40_M 136_D 0.90 0.13 0.00
402_T 153_A 0.90 0.13 0.00
182_E 51_L 0.90 0.13 0.00
203_A 175_A 0.90 0.13 0.00
399_D 153_A 0.90 0.13 0.00
502_L 209_S 0.90 0.12 0.00
135_T 134_T 0.90 0.12 0.00
471_A 79_A 0.90 0.12 0.00
25_L 45_G 0.89 0.12 0.00
481_G 193_M 0.89 0.12 0.00
271_S 12_A 0.89 0.12 0.00
245_K 19_V 0.89 0.12 0.00
350_A 137_S 0.89 0.12 0.00
234_Y 48_T 0.89 0.12 0.00
59_L 59_E 0.89 0.12 0.00
471_A 18_A 0.89 0.12 0.00
25_L 12_A 0.89 0.12 0.00
281_G 196_N 0.89 0.12 0.00
206_S 44_I 0.88 0.12 0.00
186_E 18_A 0.88 0.12 0.00
75_K 112_E 0.88 0.12 0.00
55_N 18_A 0.88 0.12 0.00
284_V 29_T 0.88 0.12 0.00
296_D 102_A 0.88 0.12 0.00
127_D 35_P 0.88 0.12 0.00
502_L 8_V 0.88 0.12 0.00
502_L 18_A 0.87 0.12 0.00
278_I 19_V 0.87 0.12 0.00
444_E 188_E 0.87 0.12 0.00
23_A 24_A 0.87 0.12 0.00
22_I 52_I 0.87 0.12 0.00
495_L 163_K 0.87 0.12 0.00
85_A 129_K 0.87 0.12 0.00
43_K 186_L 0.87 0.12 0.00
412_T 51_L 0.87 0.12 0.00
33_V 25_L 0.87 0.12 0.00
359_A 120_S 0.86 0.12 0.00
232_A 140_G 0.86 0.12 0.00
213_K 187_K 0.86 0.12 0.00
22_I 24_A 0.86 0.12 0.00
387_V 137_S 0.86 0.12 0.00
84_Q 191_A 0.86 0.12 0.00
198_A 148_M 0.86 0.11 0.00
138_G 44_I 0.86 0.11 0.00
27_M 60_P 0.86 0.11 0.00
223_A 136_D 0.86 0.11 0.00
242_V 193_M 0.86 0.11 0.00
444_E 199_S 0.85 0.11 0.00
447_L 163_K 0.85 0.11 0.00
57_S 44_I 0.85 0.11 0.00
66_A 71_Y 0.85 0.11 0.00
69_A 54_A 0.85 0.11 0.00
154_A 19_V 0.85 0.11 0.00
71_G 18_A 0.85 0.11 0.00
484_D 71_Y 0.85 0.11 0.00
96_T 195_A 0.85 0.11 0.00
260_L 67_W 0.85 0.11 0.00
390_T 214_K 0.85 0.11 0.00
407_G 197_I 0.85 0.11 0.00
21_F 207_M 0.85 0.11 0.00
472_Q 169_A 0.85 0.11 0.00
490_E 50_A 0.85 0.11 0.00
488_I 206_G 0.84 0.11 0.00
78_E 44_I 0.84 0.11 0.00
384_T 209_S 0.84 0.11 0.00
387_V 24_A 0.84 0.11 0.00
411_P 163_K 0.84 0.11 0.00
145_I 124_F 0.84 0.11 0.00
220_Y 39_T 0.84 0.11 0.00
303_F 196_N 0.84 0.11 0.00
493_T 2_A 0.84 0.11 0.00
423_K 211_M 0.84 0.11 0.00
191_Y 147_E 0.84 0.11 0.00
34_I 158_L 0.84 0.11 0.00
254_V 22_V 0.84 0.11 0.00
399_D 207_M 0.84 0.11 0.00
439_L 174_Q 0.84 0.11 0.00
45_E 64_E 0.84 0.11 0.00
417_G 51_L 0.83 0.11 0.00
182_E 33_I 0.83 0.11 0.00
445_V 150_M 0.83 0.11 0.00
401_K 158_L 0.83 0.11 0.00
305_E 127_A 0.83 0.11 0.00
389_G 159_N 0.83 0.11 0.00
63_D 41_M 0.83 0.11 0.00
244_D 213_N 0.83 0.11 0.00
510_I 214_K 0.83 0.11 0.00
199_I 34_G 0.83 0.11 0.00
51_S 184_A 0.83 0.11 0.00
196_F 176_N 0.83 0.11 0.00
156_L 109_V 0.83 0.11 0.00
359_A 127_A 0.83 0.11 0.00
62_L 186_L 0.83 0.11 0.00
328_T 148_M 0.83 0.11 0.00
514_Q 172_N 0.83 0.11 0.00
202_A 19_V 0.82 0.11 0.00
427_S 65_L 0.82 0.11 0.00
227_A 64_E 0.82 0.10 0.00
97_L 102_A 0.82 0.10 0.00
150_S 174_Q 0.82 0.10 0.00
449_V 57_A 0.82 0.10 0.00
253_K 214_K 0.82 0.10 0.00
25_L 48_T 0.82 0.10 0.00
145_I 191_A 0.82 0.10 0.00
332_D 124_F 0.82 0.10 0.00
25_L 7_K 0.82 0.10 0.00
120_D 127_A 0.82 0.10 0.00
142_I 189_Q 0.82 0.10 0.00
294_E 181_E 0.81 0.10 0.00
459_Q 127_A 0.81 0.10 0.00
179_K 4_L 0.81 0.10 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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