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OPENSEQ.org
cIV_A_80_cI_J_20_human
Genes: A B A+B
Length: 513 174 676
Sequences: 3020 1614 492
Seq/Len: 5.89 9.28 0.73
MirrorTree (Pazo et al. 2001) 0.54
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 0.01
5 0.01 0.00 0.03
10 0.01 0.00 0.69
20 0.01 0.00 0.72
100 0.02 0.00 0.72
∞ 0.05 0.00 0.72
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
359_A 27_Y 2.25 0.96 0.86
35_L 170_I 1.70 0.80 0.50
271_M 52_G 1.69 0.80 0.49
168_I 30_L 1.68 0.80 0.49
410_A 36_G 1.59 0.74 0.41
434_S 55_V 1.53 0.70 0.35
357_V 150_R 1.50 0.68 0.33
1_M 17_V 1.44 0.64 0.28
168_I 51_M 1.36 0.57 0.22
109_L 30_L 1.34 0.55 0.21
73_I 146_Y 1.27 0.49 0.17
35_L 22_K 1.27 0.49 0.17
4_D 165_Y 1.25 0.47 0.16
198_S 24_S 1.25 0.47 0.16
253_M 27_Y 1.23 0.45 0.14
416_I 170_I 1.22 0.45 0.14
336_A 68_G 1.19 0.42 0.13
393_F 10_V 1.18 0.41 0.12
258_V 51_M 1.17 0.40 0.12
468_M 28_G 1.16 0.40 0.11
20_L 27_Y 1.16 0.40 0.11
116_A 162_V 1.16 0.39 0.11
357_V 7_L 1.16 0.39 0.11
177_T 7_L 1.15 0.39 0.11
404_T 51_M 1.15 0.39 0.11
365_I 156_T 1.14 0.38 0.10
141_A 13_V 1.14 0.38 0.10
168_I 159_T 1.13 0.38 0.10
297_M 163_G 1.13 0.37 0.10
307_S 52_G 1.12 0.36 0.10
496_Y 142_A 1.11 0.36 0.09
258_V 37_V 1.11 0.36 0.09
403_Y 154_V 1.11 0.36 0.09
231_Y 161_F 1.11 0.35 0.09
173_P 81_A 1.10 0.35 0.09
155_V 142_A 1.10 0.35 0.09
434_S 167_V 1.09 0.34 0.09
279_S 29_G 1.09 0.34 0.09
259_T 58_I 1.08 0.34 0.08
168_I 170_I 1.08 0.34 0.08
274_V 70_T 1.08 0.34 0.08
327_L 171_A 1.08 0.33 0.08
413_H 89_L 1.08 0.33 0.08
116_A 163_G 1.08 0.33 0.08
155_V 52_G 1.08 0.33 0.08
279_S 138_D 1.07 0.33 0.08
279_S 27_Y 1.07 0.33 0.08
314_I 58_I 1.06 0.32 0.08
109_L 144_A 1.06 0.32 0.08
189_L 142_A 1.05 0.31 0.07
109_L 20_S 1.05 0.31 0.07
505_F 29_G 1.05 0.31 0.07
481_K 171_A 1.03 0.30 0.07
262_S 51_M 1.03 0.30 0.07
133_A 44_L 1.03 0.30 0.07
401_S 171_A 1.02 0.29 0.07
359_A 76_E 1.01 0.29 0.06
459_F 82_W 1.01 0.28 0.06
231_Y 36_G 1.01 0.28 0.06
109_L 156_T 1.01 0.28 0.06
467_L 162_V 1.01 0.28 0.06
204_A 20_S 1.00 0.28 0.06
274_V 157_G 1.00 0.28 0.06
168_I 75_I 1.00 0.28 0.06
448_T 104_L 1.00 0.27 0.06
87_I 27_Y 0.99 0.27 0.06
419_I 70_T 0.99 0.27 0.06
40_E 156_T 0.99 0.27 0.06
1_M 19_F 0.98 0.27 0.06
505_F 156_T 0.98 0.26 0.05
42_G 161_F 0.98 0.26 0.05
31_T 45_N 0.98 0.26 0.05
136_Y 8_L 0.98 0.26 0.05
179_Y 20_S 0.97 0.26 0.05
139_P 49_G 0.97 0.26 0.05
24_A 11_G 0.97 0.26 0.05
447_Y 57_L 0.97 0.25 0.05
356_I 135_I 0.96 0.25 0.05
318_V 95_G 0.96 0.25 0.05
168_I 156_T 0.96 0.25 0.05
477_A 155_V 0.95 0.24 0.05
185_V 155_V 0.94 0.24 0.05
218_T 106_V 0.94 0.24 0.05
505_F 37_V 0.94 0.24 0.04
128_V 158_W 0.94 0.24 0.04
168_I 71_T 0.94 0.24 0.04
336_A 22_K 0.94 0.23 0.04
21_L 52_G 0.94 0.23 0.04
413_H 27_Y 0.93 0.23 0.04
332_M 156_T 0.93 0.23 0.04
406_D 60_L 0.93 0.23 0.04
108_S 34_V 0.92 0.23 0.04
356_I 89_L 0.92 0.23 0.04
467_L 105_W 0.92 0.23 0.04
502_Y 74_A 0.92 0.23 0.04
434_S 73_M 0.92 0.23 0.04
448_T 135_I 0.91 0.22 0.04
462_L 71_T 0.91 0.22 0.04
187_S 145_L 0.91 0.22 0.04
307_S 1_M 0.90 0.22 0.04
254_I 54_M 0.90 0.22 0.04
413_H 75_I 0.90 0.21 0.04
410_A 29_G 0.90 0.21 0.04
406_D 124_W 0.90 0.21 0.04
495_L 1_M 0.90 0.21 0.04
413_H 52_G 0.90 0.21 0.04
281_G 31_V 0.89 0.21 0.04
448_T 8_L 0.89 0.21 0.04
134_G 146_Y 0.89 0.21 0.04
279_S 35_S 0.89 0.21 0.04
399_L 138_D 0.89 0.20 0.04
266_E 157_G 0.88 0.20 0.04
391_G 156_T 0.88 0.20 0.04
275_W 20_S 0.88 0.20 0.03
282_F 161_F 0.88 0.20 0.03
63_F 158_W 0.88 0.20 0.03
262_S 134_L 0.88 0.20 0.03
36_L 170_I 0.88 0.20 0.03
330_S 20_S 0.88 0.20 0.03
467_L 163_G 0.88 0.20 0.03
120_A 18_G 0.88 0.20 0.03
63_F 74_A 0.87 0.20 0.03
403_Y 157_G 0.87 0.20 0.03
434_S 70_T 0.87 0.20 0.03
258_V 154_V 0.87 0.20 0.03
468_M 157_G 0.87 0.20 0.03
128_V 36_G 0.87 0.20 0.03
35_L 43_I 0.86 0.19 0.03
434_S 29_G 0.86 0.19 0.03
467_L 72_A 0.86 0.19 0.03
327_L 31_V 0.86 0.19 0.03
120_A 156_T 0.85 0.19 0.03
122_A 27_Y 0.85 0.19 0.03
481_K 159_T 0.85 0.19 0.03
272_G 31_V 0.85 0.19 0.03
170_N 57_L 0.85 0.19 0.03
299_V 31_V 0.85 0.19 0.03
218_T 153_V 0.85 0.19 0.03
120_A 76_E 0.85 0.19 0.03
136_Y 51_M 0.85 0.19 0.03
73_I 138_D 0.85 0.19 0.03
350_V 138_D 0.85 0.19 0.03
350_V 142_A 0.85 0.19 0.03
297_M 150_R 0.85 0.19 0.03
204_A 23_P 0.85 0.18 0.03
464_A 166_I 0.84 0.18 0.03
46_N 26_I 0.84 0.18 0.03
274_V 154_V 0.84 0.18 0.03
480_R 43_I 0.84 0.18 0.03
136_Y 20_S 0.84 0.18 0.03
465_V 28_G 0.84 0.18 0.03
482_V 159_T 0.84 0.18 0.03
20_L 13_V 0.84 0.18 0.03
506_E 96_L 0.84 0.18 0.03
24_A 34_V 0.84 0.18 0.03
458_S 153_V 0.84 0.18 0.03
172_K 165_Y 0.84 0.18 0.03
39_A 39_G 0.83 0.18 0.03
175_A 168_I 0.83 0.18 0.03
223_A 80_E 0.83 0.18 0.03
333_K 97_A 0.83 0.18 0.03
434_S 43_I 0.83 0.18 0.03
327_L 74_A 0.83 0.18 0.03
417_M 36_G 0.83 0.18 0.03
410_A 68_G 0.83 0.18 0.03
56_V 155_V 0.83 0.18 0.03
469_I 75_I 0.83 0.18 0.03
108_S 24_S 0.83 0.18 0.03
197_L 57_L 0.83 0.18 0.03
155_V 24_S 0.83 0.17 0.03
489_S 51_M 0.83 0.17 0.03
359_A 172_R 0.83 0.17 0.03
327_L 1_M 0.83 0.17 0.03
356_I 92_V 0.83 0.17 0.03
57_I 156_T 0.82 0.17 0.03
338_V 12_L 0.82 0.17 0.03
482_V 28_G 0.82 0.17 0.03
109_L 37_V 0.82 0.17 0.03
459_F 7_L 0.82 0.17 0.03
413_H 38_V 0.82 0.17 0.03
257_I 173_G 0.82 0.17 0.03
204_A 21_S 0.82 0.17 0.03
135_N 170_I 0.82 0.17 0.03
495_L 158_W 0.82 0.17 0.03
108_S 74_A 0.82 0.17 0.03
318_V 77_E 0.82 0.17 0.03
21_L 132_S 0.81 0.17 0.03
509_V 157_G 0.81 0.17 0.03
39_A 151_W 0.81 0.17 0.03
401_S 98_M 0.81 0.17 0.03
395_H 156_T 0.81 0.17 0.03
481_K 143_G 0.81 0.17 0.03
391_G 173_G 0.81 0.17 0.03
28_V 57_L 0.81 0.17 0.03
3_A 132_S 0.81 0.17 0.03
464_A 171_A 0.81 0.17 0.02
187_S 171_A 0.81 0.17 0.02
330_S 165_Y 0.81 0.17 0.02
403_Y 43_I 0.81 0.17 0.02
253_M 54_M 0.81 0.17 0.02
28_V 31_V 0.81 0.17 0.02
109_L 84_S 0.81 0.17 0.02
443_Y 51_M 0.81 0.17 0.02
327_L 107_K 0.81 0.16 0.02
506_E 142_A 0.80 0.16 0.02
20_L 64_M 0.80 0.16 0.02
327_L 75_I 0.80 0.16 0.02
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)
ID Seq/Len Name Options I_Prob Status
4528 1.73 cIV_A_60_cI_J_10_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.59 Done - Shared
4527 0.73 cIV_A_80_cI_J_20_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.86 Done - Shared
4526 0.72 cIV_A_60_cI_J_20_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.88 Done - Shared
4525 0.71 cIV_A_40_cI_J_20_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.86 Done - Shared
4523 0.09 cIV_A_40_cI_J_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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