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OPENSEQ.org
cIm_M_20_1_isp_2_human
Genes: A B A+B
Length: 459 274 611
Sequences: 6342 609 102
Seq/Len: 13.82 2.22 0.17
MirrorTree (Pazo et al. 2001) 0.42
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 0.00 0.00 0.00
2 0.00 0.00 0.00
5 0.00 0.00 0.00
10 0.00 0.00 0.00
20 0.00 0.00 0.00
100 0.00 0.00 0.01
∞ 0.01 0.00 0.14
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
83_H 250_R 1.39 0.24 0.00
103_Q 108_E 1.30 0.20 0.00
163_A 66_A 1.30 0.20 0.00
410_M 126_A 1.29 0.20 0.00
376_L 247_G 1.29 0.20 0.00
226_A 266_T 1.26 0.19 0.00
68_L 247_G 1.24 0.18 0.00
71_W 118_T 1.24 0.18 0.00
386_F 133_V 1.23 0.18 0.00
71_W 128_A 1.22 0.17 0.00
212_L 177_R 1.21 0.17 0.00
268_G 124_G 1.18 0.16 0.00
321_L 66_A 1.17 0.16 0.00
107_I 245_A 1.16 0.16 0.00
339_S 196_R 1.16 0.15 0.00
242_G 266_T 1.14 0.15 0.00
373_I 271_V 1.11 0.14 0.00
282_L 250_R 1.11 0.14 0.00
262_L 248_R 1.10 0.14 0.00
259_Y 207_K 1.10 0.14 0.00
321_L 71_N 1.10 0.14 0.00
186_L 96_V 1.09 0.14 0.00
95_Y 248_R 1.08 0.13 0.00
127_I 200_H 1.07 0.13 0.00
101_S 213_L 1.07 0.13 0.00
93_K 92_R 1.05 0.13 0.00
274_S 218_T 1.05 0.12 0.00
287_A 267_S 1.05 0.12 0.00
62_T 104_R 1.04 0.12 0.00
66_L 113_F 1.02 0.12 0.00
274_S 230_D 1.02 0.12 0.00
261_F 176_V 1.02 0.12 0.00
365_A 112_G 1.01 0.12 0.00
303_I 265_F 1.01 0.12 0.00
257_M 67_S 1.01 0.12 0.00
403_T 216_V 1.00 0.11 0.00
67_M 248_R 1.00 0.11 0.00
361_L 123_V 1.00 0.11 0.00
209_L 201_D 0.99 0.11 0.00
395_L 119_G 0.99 0.11 0.00
410_M 118_T 0.98 0.11 0.00
209_L 203_D 0.98 0.11 0.00
176_I 224_P 0.98 0.11 0.00
134_T 264_E 0.97 0.11 0.00
205_V 71_N 0.97 0.11 0.00
120_I 177_R 0.97 0.11 0.00
205_V 108_E 0.97 0.10 0.00
338_H 250_R 0.96 0.10 0.00
62_T 116_L 0.96 0.10 0.00
382_L 116_L 0.96 0.10 0.00
358_W 79_S 0.96 0.10 0.00
361_L 133_V 0.96 0.10 0.00
67_M 207_K 0.96 0.10 0.00
274_S 259_E 0.96 0.10 0.00
308_S 78_Y 0.96 0.10 0.00
210_Y 208_P 0.95 0.10 0.00
125_T 212_I 0.94 0.10 0.00
65_L 68_V 0.94 0.10 0.00
392_T 248_R 0.94 0.10 0.00
400_M 72_V 0.93 0.10 0.00
325_L 96_V 0.93 0.10 0.00
250_L 146_V 0.93 0.10 0.00
385_T 96_V 0.93 0.10 0.00
310_T 88_F 0.93 0.10 0.00
352_L 174_L 0.93 0.10 0.00
221_V 134_T 0.93 0.10 0.00
140_P 185_E 0.93 0.10 0.00
410_M 64_L 0.92 0.10 0.00
310_T 67_S 0.92 0.10 0.00
107_I 113_F 0.92 0.10 0.00
108_M 112_G 0.92 0.10 0.00
183_A 270_M 0.91 0.09 0.00
373_I 100_T 0.91 0.09 0.00
101_S 123_V 0.91 0.09 0.00
400_M 211_V 0.91 0.09 0.00
291_I 208_P 0.91 0.09 0.00
81_Q 134_T 0.90 0.09 0.00
250_L 156_L 0.90 0.09 0.00
235_L 121_T 0.90 0.09 0.00
106_L 266_T 0.90 0.09 0.00
352_L 234_Y 0.90 0.09 0.00
168_H 95_E 0.90 0.09 0.00
99_L 127_Y 0.90 0.09 0.00
191_A 81_T 0.90 0.09 0.00
82_R 250_R 0.90 0.09 0.00
186_L 95_E 0.90 0.09 0.00
189_S 92_R 0.90 0.09 0.00
312_A 117_V 0.89 0.09 0.00
153_T 266_T 0.89 0.09 0.00
67_M 108_E 0.89 0.09 0.00
313_V 78_Y 0.89 0.09 0.00
329_L 130_K 0.89 0.09 0.00
155_V 202_L 0.89 0.09 0.00
181_L 266_T 0.89 0.09 0.00
383_V 108_E 0.89 0.09 0.00
263_V 170_R 0.88 0.09 0.00
155_V 267_S 0.88 0.09 0.00
308_S 199_Q 0.88 0.09 0.00
335_E 92_R 0.88 0.09 0.00
109_T 266_T 0.88 0.09 0.00
342_M 248_R 0.87 0.09 0.00
253_L 123_V 0.87 0.09 0.00
163_A 199_Q 0.87 0.09 0.00
348_L 140_M 0.87 0.09 0.00
212_L 201_D 0.87 0.09 0.00
103_Q 138_S 0.86 0.09 0.00
103_Q 109_A 0.86 0.09 0.00
113_T 79_S 0.86 0.08 0.00
334_Y 108_E 0.86 0.08 0.00
321_L 173_P 0.86 0.08 0.00
121_F 116_L 0.86 0.08 0.00
270_I 133_V 0.85 0.08 0.00
95_Y 255_P 0.85 0.08 0.00
212_L 247_G 0.85 0.08 0.00
80_S 136_F 0.85 0.08 0.00
362_A 155_K 0.85 0.08 0.00
95_Y 216_V 0.85 0.08 0.00
313_V 136_F 0.85 0.08 0.00
270_I 64_L 0.85 0.08 0.00
314_I 166_A 0.85 0.08 0.00
133_I 250_R 0.85 0.08 0.00
354_L 79_S 0.85 0.08 0.00
250_L 184_I 0.84 0.08 0.00
224_P 100_T 0.84 0.08 0.00
335_E 270_M 0.84 0.08 0.00
127_I 179_R 0.84 0.08 0.00
274_S 214_I 0.84 0.08 0.00
286_I 117_V 0.84 0.08 0.00
405_L 88_F 0.84 0.08 0.00
283_K 255_P 0.84 0.08 0.00
358_W 112_G 0.84 0.08 0.00
238_L 212_I 0.83 0.08 0.00
324_S 116_L 0.83 0.08 0.00
132_I 250_R 0.83 0.08 0.00
192_N 270_M 0.83 0.08 0.00
67_M 265_F 0.83 0.08 0.00
288_Y 99_S 0.83 0.08 0.00
257_M 247_G 0.83 0.08 0.00
362_A 79_S 0.83 0.08 0.00
274_S 95_E 0.83 0.08 0.00
409_Y 155_K 0.83 0.08 0.00
219_A 184_I 0.83 0.08 0.00
343_I 272_I 0.82 0.08 0.00
266_L 76_V 0.82 0.08 0.00
90_S 267_S 0.82 0.08 0.00
423_I 70_L 0.82 0.08 0.00
301_I 228_A 0.82 0.08 0.00
410_M 92_R 0.82 0.08 0.00
419_L 188_A 0.82 0.08 0.00
274_S 93_R 0.82 0.08 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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