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OPENSEQ.org
cIV_B_60_cI_N_80_1_human
Genes: A B A+B
Length: 227 347 572
Sequences: 2677 1991 1116
Seq/Len: 11.79 5.74 1.95
MirrorTree (Pazo et al. 2001) 0.74
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 0.02
2 0.00 0.00 1.94
5 0.00 0.00 1.94
10 0.00 0.00 1.95
20 0.00 0.00 1.94
100 0.00 0.00 1.94
∞ 0.00 0.00 1.94
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
110_Y 257_L 1.72 0.96 0.81
90_V 321_K 1.46 0.89 0.62
182_T 297_I 1.45 0.89 0.61
53_T 139_I 1.43 0.88 0.59
192_Y 214_T 1.41 0.87 0.58
61_M 62_T 1.41 0.86 0.57
149_P 33_L 1.35 0.83 0.52
99_S 304_L 1.28 0.79 0.45
111_T 170_L 1.25 0.77 0.43
220_E 117_E 1.24 0.76 0.42
58_A 104_M 1.23 0.75 0.41
64_V 147_P 1.23 0.74 0.40
192_Y 45_T 1.23 0.74 0.40
187_T 75_L 1.22 0.74 0.40
73_L 257_L 1.21 0.73 0.38
115_G 143_Y 1.21 0.73 0.38
73_L 304_L 1.19 0.71 0.36
155_T 70_L 1.17 0.69 0.35
32_F 285_I 1.15 0.68 0.33
140_N 45_T 1.15 0.67 0.33
192_Y 9_I 1.15 0.67 0.32
132_D 81_S 1.14 0.67 0.32
150_I 20_T 1.14 0.66 0.32
56_S 204_N 1.13 0.66 0.31
155_T 98_I 1.12 0.65 0.30
224_V 270_F 1.12 0.65 0.30
86_M 289_N 1.12 0.64 0.30
223_P 202_I 1.12 0.64 0.30
37_L 123_P 1.11 0.64 0.29
138_V 215_A 1.11 0.63 0.29
123_L 344_L 1.11 0.63 0.29
73_L 87_T 1.10 0.63 0.29
156_S 307_M 1.09 0.61 0.28
53_T 21_A 1.08 0.61 0.27
53_T 67_S 1.08 0.60 0.27
53_T 195_P 1.08 0.60 0.27
53_T 14_F 1.08 0.60 0.27
182_T 131_L 1.07 0.59 0.26
90_V 81_S 1.07 0.59 0.26
100_I 103_A 1.07 0.59 0.26
183_T 53_T 1.07 0.59 0.26
148_T 48_M 1.06 0.58 0.25
129_E 98_I 1.04 0.56 0.24
73_L 205_L 1.04 0.56 0.23
172_T 195_P 1.04 0.56 0.23
68_L 24_S 1.04 0.56 0.23
56_S 195_P 1.03 0.55 0.23
43_F 179_L 1.03 0.55 0.23
97_I 319_H 1.03 0.55 0.23
165_V 281_I 1.03 0.55 0.23
170_L 344_L 1.02 0.54 0.22
213_L 71_L 1.02 0.54 0.22
167_T 100_M 1.02 0.54 0.22
156_S 70_L 1.01 0.53 0.21
64_V 83_Q 1.01 0.53 0.21
220_E 229_L 1.01 0.53 0.21
192_Y 100_M 1.01 0.52 0.21
45_T 333_T 1.01 0.52 0.21
155_T 249_L 1.00 0.52 0.21
142_V 44_L 1.00 0.52 0.21
97_I 83_Q 1.00 0.51 0.20
30_I 83_Q 1.00 0.51 0.20
192_Y 153_L 0.99 0.51 0.20
168_L 117_E 0.99 0.50 0.20
2_A 40_F 0.99 0.50 0.20
44_L 122_T 0.99 0.50 0.20
150_I 191_M 0.98 0.50 0.19
46_L 274_N 0.98 0.50 0.19
36_F 285_I 0.98 0.50 0.19
155_T 283_A 0.98 0.50 0.19
167_T 6_Q 0.98 0.49 0.19
213_L 29_T 0.98 0.49 0.19
45_T 285_I 0.98 0.49 0.19
27_A 282_M 0.98 0.49 0.19
187_T 214_T 0.98 0.49 0.19
115_G 175_L 0.96 0.48 0.18
53_T 104_M 0.96 0.47 0.18
9_L 123_P 0.96 0.47 0.18
97_I 201_T 0.96 0.47 0.18
183_T 170_L 0.96 0.47 0.18
97_I 22_L 0.96 0.47 0.17
73_L 144_Q 0.95 0.46 0.17
132_D 28_F 0.95 0.46 0.17
64_V 136_L 0.95 0.46 0.17
3_H 339_I 0.94 0.45 0.17
155_T 21_A 0.94 0.45 0.17
113_Y 283_A 0.94 0.45 0.16
64_V 245_P 0.93 0.44 0.16
110_Y 219_L 0.93 0.44 0.16
58_A 99_M 0.93 0.44 0.16
52_N 213_T 0.93 0.44 0.15
192_Y 195_P 0.93 0.44 0.15
64_V 229_L 0.93 0.43 0.15
202_A 108_M 0.92 0.43 0.15
156_S 79_M 0.92 0.43 0.15
115_G 218_L 0.92 0.43 0.15
86_M 128_L 0.92 0.42 0.15
182_T 25_H 0.92 0.42 0.15
27_A 17_T 0.91 0.42 0.14
187_T 187_M 0.91 0.42 0.14
214_I 283_A 0.91 0.41 0.14
123_L 87_T 0.91 0.41 0.14
140_N 2_N 0.91 0.41 0.14
32_F 265_A 0.91 0.41 0.14
27_A 130_L 0.90 0.41 0.14
144_L 49_N 0.90 0.41 0.14
156_S 305_L 0.90 0.41 0.14
67_I 210_I 0.90 0.40 0.14
94_S 267_I 0.89 0.40 0.14
140_N 88_N 0.89 0.40 0.14
211_L 164_A 0.89 0.40 0.14
150_I 337_L 0.89 0.40 0.13
107_T 153_L 0.89 0.40 0.13
43_F 244_I 0.89 0.39 0.13
157_Q 328_T 0.89 0.39 0.13
73_L 96_L 0.89 0.39 0.13
140_N 215_A 0.89 0.39 0.13
150_I 21_A 0.89 0.39 0.13
64_V 218_L 0.88 0.39 0.13
97_I 296_L 0.88 0.39 0.13
202_A 130_L 0.88 0.39 0.13
52_N 93_Y 0.88 0.39 0.13
184_F 187_M 0.88 0.39 0.13
167_T 222_N 0.88 0.38 0.13
53_T 103_A 0.88 0.38 0.13
133_L 68_M 0.88 0.38 0.13
165_V 64_A 0.88 0.38 0.12
215_P 174_Q 0.88 0.38 0.12
27_A 41_I 0.88 0.38 0.12
111_T 70_L 0.87 0.38 0.12
5_A 187_M 0.87 0.38 0.12
168_L 45_T 0.87 0.38 0.12
167_T 302_I 0.87 0.38 0.12
191_V 81_S 0.87 0.37 0.12
115_G 277_I 0.87 0.37 0.12
64_V 146_S 0.87 0.37 0.12
184_F 14_F 0.86 0.37 0.12
192_Y 223_S 0.86 0.37 0.12
175_I 5_A 0.86 0.37 0.12
64_V 222_N 0.86 0.36 0.12
143_V 271_T 0.86 0.36 0.12
152_M 233_T 0.86 0.36 0.12
100_I 196_Y 0.86 0.36 0.12
213_L 289_N 0.86 0.36 0.12
4_A 53_T 0.85 0.36 0.12
90_V 240_L 0.85 0.36 0.11
112_D 107_G 0.85 0.35 0.11
120_S 41_I 0.85 0.35 0.11
107_T 217_L 0.85 0.35 0.11
218_I 194_L 0.85 0.35 0.11
75_L 214_T 0.85 0.35 0.11
138_V 21_A 0.85 0.35 0.11
45_T 56_A 0.85 0.35 0.11
142_V 137_A 0.84 0.35 0.11
154_I 9_I 0.84 0.34 0.11
64_V 323_T 0.84 0.34 0.11
113_Y 326_L 0.84 0.34 0.11
71_I 152_S 0.84 0.34 0.11
9_L 122_T 0.83 0.34 0.10
164_A 153_L 0.83 0.33 0.10
72_I 68_M 0.83 0.33 0.10
112_D 270_F 0.83 0.33 0.10
55_I 304_L 0.83 0.33 0.10
97_I 240_L 0.83 0.33 0.10
73_L 136_L 0.82 0.33 0.10
187_T 201_T 0.82 0.33 0.10
123_L 336_L 0.82 0.33 0.10
53_T 106_L 0.82 0.33 0.10
187_T 156_T 0.82 0.33 0.10
42_L 153_L 0.82 0.33 0.10
3_H 19_I 0.82 0.33 0.10
164_A 340_S 0.82 0.33 0.10
192_Y 226_T 0.82 0.33 0.10
43_F 227_T 0.82 0.32 0.10
100_I 139_I 0.82 0.32 0.10
175_I 22_L 0.82 0.32 0.10
183_T 317_F 0.82 0.32 0.10
51_T 280_T 0.81 0.32 0.10
13_T 65_T 0.81 0.32 0.10
22_T 334_T 0.81 0.32 0.10
63_T 106_L 0.81 0.32 0.10
3_H 257_L 0.81 0.32 0.10
95_L 170_L 0.81 0.32 0.10
44_L 209_I 0.81 0.32 0.10
155_T 7_P 0.81 0.31 0.09
192_Y 74_I 0.81 0.31 0.09
20_L 248_F 0.81 0.31 0.09
41_A 191_M 0.81 0.31 0.09
123_L 215_A 0.81 0.31 0.09
46_L 291_Y 0.81 0.31 0.09
27_A 91_N 0.81 0.31 0.09
113_Y 264_W 0.80 0.31 0.09
22_T 237_L 0.80 0.31 0.09
140_N 204_N 0.80 0.31 0.09
47_S 151_V 0.80 0.30 0.09
147_E 160_L 0.80 0.30 0.09
172_T 67_S 0.80 0.30 0.09
32_F 252_G 0.80 0.30 0.09
51_T 283_A 0.80 0.30 0.09
220_E 323_T 0.80 0.30 0.09
97_I 225_T 0.80 0.30 0.09
3_H 344_L 0.80 0.30 0.09
61_M 53_T 0.80 0.30 0.09
132_D 62_T 0.80 0.30 0.09
167_T 5_A 0.79 0.30 0.09
67_I 296_L 0.79 0.30 0.09
191_V 86_M 0.79 0.30 0.09
221_M 33_L 0.79 0.30 0.09
94_S 74_I 0.79 0.30 0.09
184_F 72_M 0.79 0.30 0.09
3_H 62_T 0.79 0.30 0.09
107_T 18_L 0.79 0.30 0.09
51_T 267_I 0.79 0.29 0.09
9_L 151_V 0.79 0.29 0.09
123_L 140_S 0.79 0.29 0.09
92_D 241_T 0.79 0.29 0.09
43_F 321_K 0.79 0.29 0.09
155_T 73_A 0.79 0.29 0.09
148_T 12_T 0.79 0.29 0.09
144_L 285_I 0.79 0.29 0.08
156_S 299_S 0.78 0.29 0.08
67_I 148_S 0.78 0.29 0.08
133_L 140_S 0.78 0.29 0.08
46_L 67_S 0.78 0.29 0.08
170_L 227_T 0.78 0.29 0.08
144_L 72_M 0.78 0.29 0.08
114_G 191_M 0.78 0.29 0.08
223_P 218_L 0.78 0.28 0.08
58_A 67_S 0.78 0.28 0.08
111_T 283_A 0.78 0.28 0.08
168_L 127_G 0.78 0.28 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
4562 2.31 cIV_B_80_cI_N_60_1_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-60, 1) msa: Jackhmmer (2015_06) 0.68 Done - Shared
4553 1.95 cIV_B_60_cI_N_80_1_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.81 Done - Shared
4551 1.96 cIV_B_80_cI_N_80_1_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.85 Done - Shared
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