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OPENSEQ.org
cIV_B_80_cI_A_40_human
Genes: A B A+B
Length: 227 115 339
Sequences: 1814 1332 728
Seq/Len: 7.99 11.58 2.15
MirrorTree (Pazo et al. 2001) 0.63
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 0.00 0.00 2.13
10 0.00 0.00 2.13
20 0.00 0.00 2.13
100 0.00 0.00 2.13
∞ 0.00 0.00 2.13
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
53_T 78_A 1.92 0.99 0.95
140_N 13_L 1.76 0.97 0.91
58_A 78_A 1.66 0.96 0.88
155_T 18_M 1.57 0.94 0.83
172_T 78_A 1.51 0.92 0.80
214_I 102_L 1.50 0.92 0.79
57_D 22_F 1.47 0.91 0.78
23_F 80_Q 1.41 0.89 0.73
132_D 80_Q 1.41 0.89 0.73
220_E 51_F 1.36 0.86 0.69
191_V 80_Q 1.34 0.85 0.68
189_P 23_W 1.34 0.85 0.67
115_G 13_L 1.32 0.84 0.65
13_T 92_L 1.31 0.83 0.65
133_L 80_Q 1.29 0.82 0.62
30_I 44_M 1.27 0.81 0.61
37_L 87_M 1.24 0.78 0.58
217_K 92_L 1.22 0.77 0.55
107_T 49_V 1.22 0.76 0.55
170_L 80_Q 1.21 0.75 0.54
138_V 3_F 1.17 0.72 0.50
149_P 51_F 1.17 0.72 0.50
175_I 78_A 1.17 0.72 0.50
155_T 97_I 1.17 0.72 0.50
218_I 75_L 1.17 0.72 0.49
172_T 9_I 1.17 0.72 0.49
36_F 94_L 1.14 0.69 0.46
9_L 21_T 1.12 0.67 0.44
182_T 114_A 1.10 0.66 0.43
220_E 102_L 1.10 0.65 0.42
213_L 100_L 1.09 0.64 0.41
111_T 88_V 1.08 0.64 0.40
76_I 53_M 1.07 0.62 0.39
184_F 103_A 1.06 0.61 0.38
51_T 51_F 1.05 0.60 0.37
2_A 103_A 1.04 0.59 0.36
105_Y 64_L 1.04 0.59 0.36
192_Y 53_M 1.04 0.59 0.36
5_A 80_Q 1.04 0.59 0.36
100_I 88_V 1.04 0.59 0.36
99_S 107_L 1.04 0.59 0.36
40_Y 54_K 1.03 0.58 0.35
155_T 63_L 1.03 0.58 0.35
124_P 92_L 1.03 0.58 0.34
213_L 13_L 1.03 0.57 0.34
115_G 11_T 1.02 0.57 0.34
67_I 46_P 1.02 0.57 0.34
89_E 61_T 1.02 0.57 0.34
172_T 3_F 1.02 0.57 0.34
74_V 87_M 1.02 0.56 0.33
68_L 6_I 1.01 0.56 0.33
34_I 70_A 1.01 0.56 0.33
156_S 44_M 1.01 0.55 0.32
202_A 80_Q 1.00 0.55 0.32
10_Q 61_T 1.00 0.54 0.31
58_A 53_M 0.99 0.54 0.31
107_T 21_T 0.99 0.53 0.31
52_N 91_S 0.99 0.53 0.30
175_I 6_I 0.98 0.53 0.30
164_A 95_I 0.98 0.53 0.30
133_L 97_I 0.98 0.52 0.30
70_A 54_K 0.98 0.52 0.29
138_V 88_V 0.98 0.52 0.29
76_I 32_E 0.98 0.52 0.29
95_L 102_L 0.97 0.51 0.29
28_L 3_F 0.97 0.51 0.28
138_V 78_A 0.96 0.50 0.28
32_F 14_A 0.96 0.50 0.28
56_S 75_L 0.96 0.50 0.28
67_I 58_V 0.95 0.49 0.27
57_D 45_S 0.95 0.49 0.26
45_T 51_F 0.95 0.48 0.26
29_M 80_Q 0.95 0.48 0.26
42_L 90_S 0.94 0.48 0.26
63_T 81_T 0.94 0.48 0.26
42_L 54_K 0.94 0.47 0.25
99_S 6_I 0.93 0.47 0.25
13_T 5_L 0.93 0.47 0.25
30_I 51_F 0.93 0.47 0.25
137_D 80_Q 0.93 0.47 0.25
113_Y 51_F 0.93 0.47 0.25
213_L 35_T 0.93 0.46 0.24
156_S 97_I 0.93 0.46 0.24
27_A 7_L 0.92 0.46 0.24
165_V 46_P 0.92 0.45 0.24
64_V 53_M 0.92 0.45 0.24
214_I 51_F 0.92 0.45 0.23
123_L 88_V 0.91 0.45 0.23
211_L 92_L 0.91 0.45 0.23
97_I 5_L 0.91 0.44 0.23
32_F 5_L 0.90 0.43 0.22
92_D 58_V 0.90 0.43 0.22
56_S 51_F 0.90 0.43 0.22
157_Q 103_A 0.90 0.43 0.22
210_V 21_T 0.89 0.42 0.22
55_I 26_Q 0.89 0.42 0.22
164_A 82_T 0.89 0.42 0.21
11_D 103_A 0.89 0.42 0.21
183_T 78_A 0.89 0.42 0.21
170_L 46_P 0.88 0.41 0.21
180_N 51_F 0.88 0.41 0.21
95_L 15_L 0.88 0.41 0.21
46_L 78_A 0.88 0.41 0.21
53_T 2_N 0.88 0.41 0.21
47_S 30_Y 0.88 0.41 0.20
140_N 16_L 0.88 0.41 0.20
45_T 97_I 0.88 0.41 0.20
156_S 29_G 0.88 0.41 0.20
30_I 75_L 0.88 0.40 0.20
37_L 58_V 0.87 0.40 0.20
184_F 84_L 0.87 0.40 0.20
116_L 95_I 0.86 0.39 0.19
164_A 53_M 0.86 0.39 0.19
74_V 26_Q 0.86 0.39 0.19
97_I 94_L 0.86 0.38 0.18
13_T 21_T 0.85 0.38 0.18
28_L 58_V 0.85 0.38 0.18
6_Q 71_L 0.85 0.38 0.18
7_V 1_M 0.85 0.38 0.18
64_V 86_L 0.85 0.37 0.18
140_N 27_L 0.85 0.37 0.18
8_G 94_L 0.84 0.37 0.18
10_Q 110_G 0.84 0.37 0.18
140_N 25_P 0.84 0.37 0.18
210_V 85_P 0.84 0.37 0.17
90_V 2_N 0.83 0.36 0.17
74_V 16_L 0.83 0.36 0.17
152_M 6_I 0.83 0.36 0.17
72_I 12_L 0.83 0.36 0.17
88_D 54_K 0.83 0.36 0.17
58_A 31_M 0.83 0.36 0.17
27_A 21_T 0.83 0.35 0.17
7_V 19_I 0.83 0.35 0.16
146_I 28_N 0.82 0.35 0.16
132_D 25_P 0.82 0.35 0.16
170_L 8_M 0.82 0.35 0.16
154_I 11_T 0.82 0.34 0.16
23_F 2_N 0.82 0.34 0.16
175_I 109_K 0.82 0.34 0.16
153_M 51_F 0.81 0.34 0.15
154_I 95_I 0.81 0.34 0.15
202_A 112_D 0.81 0.34 0.15
8_G 110_G 0.81 0.33 0.15
183_T 53_M 0.81 0.33 0.15
73_L 1_M 0.81 0.33 0.15
55_I 94_L 0.81 0.33 0.15
51_T 102_L 0.81 0.33 0.15
99_S 51_F 0.81 0.33 0.15
3_H 46_P 0.80 0.33 0.15
192_Y 22_F 0.80 0.33 0.15
68_L 51_F 0.80 0.32 0.14
41_A 90_S 0.80 0.32 0.14
217_K 4_A 0.79 0.32 0.14
210_V 86_L 0.79 0.32 0.14
7_V 20_I 0.79 0.32 0.14
41_A 9_I 0.79 0.32 0.14
44_L 78_A 0.79 0.32 0.14
192_Y 95_I 0.79 0.32 0.14
132_D 21_T 0.79 0.32 0.14
41_A 16_L 0.79 0.32 0.14
211_L 61_T 0.79 0.32 0.14
125_P 14_A 0.79 0.32 0.14
143_V 11_T 0.79 0.32 0.14
213_L 109_K 0.79 0.31 0.14
164_A 94_L 0.79 0.31 0.14
74_V 58_V 0.79 0.31 0.14
175_I 14_A 0.79 0.31 0.14
156_S 61_T 0.78 0.31 0.14
23_F 81_T 0.78 0.31 0.13
86_M 30_Y 0.78 0.30 0.13
89_E 110_G 0.78 0.30 0.13
146_I 58_V 0.78 0.30 0.13
154_I 100_L 0.78 0.30 0.13
146_I 96_I 0.77 0.30 0.13
99_S 114_A 0.77 0.30 0.13
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
4484 2.13 cIV_B_80_cI_A_40_4_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-40, 4) msa: Jackhmmer (2015_06) 0.92 Done - Shared
4481 1.3 cIV_B_80_cI_A_40_2_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-40, 2) msa: Jackhmmer (2015_06) 0.87 Done - Shared
4479 0.24 cIV_B_80_cI_A_40_1_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-40, 1) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4478 2.15 cIV_B_80_cI_A_40_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.95 Done - Shared
4477 2.1 cIV_B_60_cI_A_40_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.93 Done - Shared
4476 0.01 cIV_B_40_cI_A_60_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) Killed - Shared
4475 2.13 cIV_B_40_cI_A_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.87 Done - Shared
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