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OPENSEQ.org
cIV_B_40_cI_A_40_human
Genes: A B A+B
Length: 227 115 340
Sequences: 4037 1332 724
Seq/Len: 17.78 11.58 2.13
MirrorTree (Pazo et al. 2001) 0.64
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 2.14
10 0.00 0.00 2.12
20 0.00 0.00 2.12
100 0.01 0.00 2.12
∞ 0.01 0.00 2.12
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
140_N 13_L 1.76 0.97 0.87
53_T 78_A 1.76 0.97 0.87
58_A 78_A 1.69 0.96 0.85
214_I 102_L 1.63 0.95 0.82
155_T 18_M 1.51 0.92 0.74
172_T 78_A 1.47 0.91 0.71
57_D 22_F 1.42 0.89 0.67
23_F 80_Q 1.41 0.89 0.67
13_T 92_L 1.40 0.88 0.65
189_P 23_W 1.40 0.88 0.65
217_K 92_L 1.38 0.87 0.63
220_E 51_F 1.37 0.87 0.63
132_D 80_Q 1.36 0.86 0.62
191_V 80_Q 1.33 0.84 0.59
133_L 80_Q 1.28 0.81 0.54
213_L 100_L 1.26 0.79 0.52
170_L 80_Q 1.25 0.79 0.51
30_I 44_M 1.24 0.78 0.50
172_T 9_I 1.24 0.78 0.49
51_T 51_F 1.22 0.77 0.48
124_P 92_L 1.21 0.76 0.47
115_G 13_L 1.20 0.74 0.46
107_T 49_V 1.17 0.72 0.43
156_S 29_G 1.16 0.71 0.42
76_I 53_M 1.15 0.70 0.41
184_F 103_A 1.15 0.70 0.41
138_V 3_F 1.15 0.70 0.40
213_L 13_L 1.14 0.69 0.40
170_L 46_P 1.13 0.68 0.39
149_P 51_F 1.13 0.68 0.39
36_F 94_L 1.13 0.68 0.38
100_I 88_V 1.12 0.67 0.38
140_N 16_L 1.12 0.67 0.38
111_T 88_V 1.12 0.67 0.38
5_A 80_Q 1.11 0.66 0.36
9_L 21_T 1.11 0.66 0.36
220_E 102_L 1.10 0.65 0.35
155_T 97_I 1.09 0.64 0.35
213_L 35_T 1.09 0.64 0.34
37_L 87_M 1.08 0.63 0.34
221_M 95_I 1.08 0.63 0.33
67_I 58_V 1.07 0.62 0.32
210_V 85_P 1.07 0.61 0.32
107_T 21_T 1.06 0.61 0.32
99_S 107_L 1.06 0.60 0.31
146_I 28_N 1.05 0.60 0.31
138_V 78_A 1.05 0.60 0.30
175_I 78_A 1.04 0.59 0.30
57_D 45_S 1.04 0.59 0.30
40_Y 54_K 1.04 0.58 0.29
192_Y 53_M 1.03 0.58 0.29
89_E 61_T 1.03 0.58 0.29
156_S 44_M 1.02 0.56 0.28
218_I 75_L 1.02 0.56 0.28
10_Q 61_T 1.01 0.55 0.27
87_T 112_D 1.00 0.55 0.26
182_T 114_A 1.00 0.55 0.26
144_L 15_L 1.00 0.54 0.26
34_I 70_A 1.00 0.54 0.26
67_I 46_P 1.00 0.54 0.26
97_I 5_L 0.99 0.53 0.25
105_Y 64_L 0.98 0.52 0.24
138_V 88_V 0.98 0.52 0.24
32_F 5_L 0.98 0.52 0.24
164_A 82_T 0.97 0.51 0.23
156_S 97_I 0.97 0.51 0.23
32_F 14_A 0.97 0.50 0.23
27_A 7_L 0.96 0.50 0.23
30_I 51_F 0.96 0.49 0.23
90_V 2_N 0.96 0.49 0.22
214_I 51_F 0.96 0.49 0.22
28_L 3_F 0.95 0.48 0.22
70_A 54_K 0.95 0.48 0.22
37_L 58_V 0.94 0.47 0.21
202_A 80_Q 0.94 0.47 0.21
56_S 51_F 0.94 0.47 0.21
45_T 51_F 0.94 0.47 0.21
76_I 32_E 0.94 0.47 0.21
202_A 112_D 0.94 0.47 0.21
165_V 46_P 0.93 0.47 0.20
11_D 103_A 0.93 0.46 0.20
97_I 94_L 0.93 0.46 0.20
180_N 51_F 0.93 0.46 0.20
107_T 83_N 0.93 0.46 0.20
63_T 81_T 0.93 0.46 0.20
154_I 10_N 0.93 0.46 0.20
211_L 92_L 0.92 0.45 0.19
95_L 102_L 0.92 0.45 0.19
137_D 80_Q 0.91 0.44 0.19
86_M 30_Y 0.91 0.44 0.19
58_A 31_M 0.91 0.43 0.18
175_I 109_K 0.90 0.43 0.18
115_G 11_T 0.90 0.43 0.18
175_I 6_I 0.90 0.43 0.18
51_T 102_L 0.90 0.42 0.18
42_L 90_S 0.90 0.42 0.18
211_L 61_T 0.90 0.42 0.18
68_L 6_I 0.89 0.42 0.17
47_S 30_Y 0.89 0.42 0.17
133_L 97_I 0.89 0.42 0.17
184_F 84_L 0.89 0.42 0.17
183_T 25_P 0.89 0.41 0.17
2_A 103_A 0.89 0.41 0.17
175_I 14_A 0.89 0.41 0.17
113_Y 51_F 0.88 0.41 0.17
72_I 53_M 0.88 0.41 0.17
58_A 53_M 0.88 0.41 0.17
143_V 11_T 0.88 0.41 0.16
61_M 99_A 0.88 0.40 0.16
30_I 75_L 0.88 0.40 0.16
7_V 1_M 0.87 0.40 0.16
210_V 21_T 0.87 0.40 0.16
72_I 8_M 0.87 0.40 0.16
64_V 53_M 0.87 0.40 0.16
183_T 78_A 0.87 0.39 0.16
123_L 97_I 0.86 0.39 0.15
113_Y 53_M 0.86 0.39 0.15
164_A 95_I 0.86 0.39 0.15
56_S 75_L 0.86 0.38 0.15
172_T 3_F 0.86 0.38 0.15
41_A 90_S 0.86 0.38 0.15
164_A 94_L 0.85 0.38 0.15
52_N 31_M 0.84 0.37 0.14
29_M 80_Q 0.84 0.37 0.14
28_L 58_V 0.84 0.37 0.14
154_I 100_L 0.84 0.37 0.14
18_E 23_W 0.84 0.36 0.14
186_A 26_Q 0.84 0.36 0.14
72_I 12_L 0.84 0.36 0.14
88_D 54_K 0.84 0.36 0.14
99_S 6_I 0.84 0.36 0.14
153_M 51_F 0.84 0.36 0.14
123_L 88_V 0.84 0.36 0.14
6_Q 71_L 0.83 0.36 0.14
21_I 86_L 0.83 0.36 0.14
10_Q 110_G 0.83 0.36 0.14
214_I 75_L 0.83 0.35 0.14
52_N 78_A 0.83 0.35 0.14
8_G 110_G 0.83 0.35 0.13
111_T 15_L 0.83 0.35 0.13
53_T 2_N 0.82 0.35 0.13
8_G 94_L 0.82 0.34 0.13
74_V 26_Q 0.82 0.34 0.13
23_F 2_N 0.82 0.34 0.13
183_T 53_M 0.82 0.34 0.13
120_S 37_Y 0.82 0.34 0.13
13_T 21_T 0.82 0.34 0.13
55_I 94_L 0.81 0.34 0.12
7_V 20_I 0.81 0.34 0.12
74_V 87_M 0.81 0.33 0.12
211_L 112_D 0.81 0.33 0.12
41_A 9_I 0.81 0.33 0.12
57_D 91_S 0.81 0.33 0.12
46_L 78_A 0.81 0.33 0.12
23_F 81_T 0.81 0.33 0.12
191_V 88_V 0.80 0.33 0.12
36_F 83_N 0.80 0.33 0.12
140_N 27_L 0.80 0.33 0.12
152_M 37_Y 0.80 0.32 0.12
146_I 14_A 0.80 0.32 0.12
9_L 112_D 0.80 0.32 0.12
30_I 30_Y 0.80 0.32 0.12
11_D 99_A 0.80 0.32 0.12
45_T 97_I 0.80 0.32 0.12
42_L 24_L 0.79 0.32 0.11
100_I 92_L 0.79 0.32 0.11
13_T 5_L 0.79 0.31 0.11
36_F 96_I 0.79 0.31 0.11
154_I 95_I 0.78 0.31 0.11
55_I 26_Q 0.78 0.31 0.11
127_F 99_A 0.78 0.30 0.11
30_I 102_L 0.78 0.30 0.11
218_I 1_M 0.78 0.30 0.11
52_N 85_P 0.78 0.30 0.11
167_T 86_L 0.78 0.30 0.11
75_L 75_L 0.78 0.30 0.11
144_L 45_S 0.78 0.30 0.11
41_A 16_L 0.78 0.30 0.11
86_M 61_T 0.78 0.30 0.11
192_Y 22_F 0.78 0.30 0.10
183_T 90_S 0.78 0.30 0.10
27_A 21_T 0.77 0.30 0.10
192_Y 95_I 0.77 0.30 0.10
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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