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OPENSEQ.org
cIV_B_40_cI_J_10_4_human
Genes: A B A+B
Length: 227 174 394
Sequences: 4037 1710 1103
Seq/Len: 17.78 9.83 2.8
MirrorTree (Pazo et al. 2001) 0.76
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 0.07
10 0.00 0.00 2.74
20 0.00 0.00 2.75
100 0.01 0.00 2.75
∞ 0.01 0.00 2.75
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
213_L 154_V 1.44 0.94 0.57
53_T 157_G 1.36 0.91 0.50
73_L 8_L 1.33 0.89 0.47
73_L 73_M 1.29 0.88 0.44
115_G 145_L 1.25 0.85 0.40
68_L 64_M 1.25 0.85 0.40
67_I 125_M 1.23 0.84 0.38
57_D 29_G 1.22 0.83 0.37
149_P 138_D 1.21 0.83 0.37
188_R 131_G 1.21 0.82 0.37
16_I 24_S 1.19 0.81 0.34
154_I 132_S 1.17 0.80 0.33
9_L 33_I 1.16 0.79 0.32
133_L 52_G 1.16 0.78 0.32
94_S 27_Y 1.14 0.77 0.31
154_I 13_V 1.12 0.75 0.28
129_E 93_L 1.08 0.71 0.26
220_E 72_A 1.08 0.71 0.26
9_L 52_G 1.05 0.69 0.24
64_V 85_G 1.05 0.68 0.23
16_I 128_E 1.04 0.67 0.23
64_V 7_L 1.03 0.66 0.22
112_D 145_L 1.01 0.64 0.21
150_I 92_V 1.01 0.64 0.21
110_Y 48_G 1.01 0.64 0.20
63_T 52_G 1.01 0.63 0.20
127_F 34_V 1.00 0.63 0.20
61_M 17_V 1.00 0.63 0.20
54_N 11_G 1.00 0.62 0.20
123_L 154_V 0.99 0.62 0.19
97_I 51_M 0.99 0.61 0.19
184_F 55_V 0.98 0.61 0.19
123_L 108_E 0.98 0.61 0.19
186_A 74_A 0.98 0.61 0.19
124_P 104_L 0.97 0.59 0.18
116_L 137_E 0.97 0.59 0.18
52_N 28_G 0.96 0.58 0.17
52_N 29_G 0.96 0.58 0.17
23_F 52_G 0.96 0.57 0.17
116_L 134_L 0.96 0.57 0.17
67_I 92_V 0.95 0.57 0.17
11_D 30_L 0.95 0.57 0.17
220_E 170_I 0.95 0.57 0.17
23_F 64_M 0.94 0.56 0.16
43_F 11_G 0.94 0.56 0.16
30_I 75_I 0.94 0.56 0.16
141_R 52_G 0.94 0.55 0.16
148_T 170_I 0.94 0.55 0.16
59_Q 77_E 0.93 0.55 0.16
64_V 24_S 0.93 0.54 0.15
154_I 7_L 0.93 0.54 0.15
132_D 51_M 0.92 0.53 0.15
202_A 9_S 0.92 0.53 0.15
192_Y 3_Y 0.91 0.52 0.14
184_F 2_M 0.91 0.52 0.14
52_N 128_E 0.90 0.51 0.14
57_D 66_V 0.90 0.51 0.14
54_N 58_I 0.89 0.50 0.13
150_I 151_W 0.89 0.50 0.13
61_M 145_L 0.89 0.49 0.13
211_L 58_I 0.89 0.49 0.13
112_D 41_V 0.88 0.48 0.13
57_D 20_S 0.88 0.47 0.12
217_K 7_L 0.88 0.47 0.12
27_A 73_M 0.87 0.47 0.12
32_F 17_V 0.87 0.47 0.12
124_P 92_V 0.87 0.47 0.12
183_T 52_G 0.86 0.46 0.12
187_T 76_E 0.86 0.46 0.12
95_L 28_G 0.86 0.46 0.12
186_A 3_Y 0.86 0.45 0.12
221_M 159_T 0.85 0.45 0.11
147_E 135_I 0.85 0.45 0.11
29_M 158_W 0.85 0.45 0.11
154_I 148_Y 0.85 0.44 0.11
75_L 48_G 0.85 0.44 0.11
58_A 157_G 0.85 0.44 0.11
40_Y 57_L 0.84 0.44 0.11
72_I 4_A 0.84 0.44 0.11
155_T 97_A 0.84 0.44 0.11
46_L 157_G 0.84 0.44 0.11
47_S 21_S 0.84 0.43 0.11
143_V 18_G 0.84 0.43 0.11
68_L 48_G 0.84 0.43 0.11
133_L 43_I 0.84 0.43 0.11
175_I 122_G 0.84 0.43 0.11
111_T 124_W 0.84 0.43 0.11
218_I 105_W 0.84 0.43 0.11
157_Q 96_L 0.84 0.43 0.11
92_D 11_G 0.83 0.43 0.11
133_L 161_F 0.83 0.43 0.11
191_V 6_F 0.83 0.42 0.10
147_E 10_V 0.83 0.42 0.10
92_D 165_Y 0.83 0.42 0.10
3_H 167_V 0.83 0.42 0.10
140_N 73_M 0.82 0.41 0.10
53_T 145_L 0.82 0.41 0.10
167_T 139_P 0.82 0.41 0.10
90_V 107_K 0.82 0.41 0.10
127_F 14_M 0.82 0.41 0.10
126_L 90_V 0.82 0.40 0.10
110_Y 41_V 0.82 0.40 0.10
45_T 148_Y 0.81 0.40 0.10
168_L 58_I 0.81 0.40 0.10
42_L 165_Y 0.81 0.40 0.10
47_S 10_V 0.81 0.40 0.10
32_F 82_W 0.81 0.40 0.10
16_I 3_Y 0.81 0.40 0.10
57_D 74_A 0.81 0.39 0.09
138_V 40_C 0.80 0.39 0.09
142_V 171_A 0.80 0.39 0.09
138_V 3_Y 0.80 0.39 0.09
155_T 103_V 0.80 0.39 0.09
94_S 64_M 0.80 0.39 0.09
221_M 58_I 0.80 0.39 0.09
154_I 35_S 0.80 0.38 0.09
19_E 66_V 0.80 0.38 0.09
110_Y 8_L 0.80 0.38 0.09
110_Y 56_F 0.80 0.38 0.09
94_S 153_V 0.79 0.38 0.09
127_F 103_V 0.79 0.37 0.09
130_P 139_P 0.79 0.37 0.09
187_T 81_A 0.79 0.37 0.09
48_T 167_V 0.79 0.37 0.09
67_I 100_V 0.78 0.36 0.08
82_R 23_P 0.78 0.36 0.08
140_N 170_I 0.78 0.36 0.08
165_V 90_V 0.78 0.36 0.08
202_A 5_L 0.78 0.36 0.08
9_L 162_V 0.78 0.36 0.08
156_S 22_K 0.78 0.36 0.08
167_T 73_M 0.77 0.36 0.08
214_I 96_L 0.77 0.36 0.08
45_T 64_M 0.77 0.35 0.08
156_S 85_G 0.77 0.35 0.08
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
4649 7.41 cIV_B_40_cI_J_6_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.47 Done - Shared
4648 2.8 cIV_B_40_cI_J_10_4_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-10, 4) msa: Jackhmmer (2015_06) 0.57 Done - Shared
4647 5.35 cIV_B_40_cI_J_10_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.85 Done - Shared
4646 2.7 cIV_B_60_cI_J_20_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.31 Done - Shared
4645 0.29 cIV_B_60_cI_J_60_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4644 2.71 cIV_B_40_cI_J_20_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.47 Done - Shared
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