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OPENSEQ.org
cIV_B_80_cI_N_80_1_human
Genes: A B A+B
Length: 227 347 570
Sequences: 1814 1991 1115
Seq/Len: 7.99 5.74 1.96
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 1.93
5 0.00 0.00 1.93
10 0.00 0.00 1.93
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 1.76 0.97 0.85
192_Y 214_T 1.58 0.93 0.74
192_Y 9_I 1.49 0.91 0.68
53_T 139_I 1.44 0.89 0.64
182_T 297_I 1.40 0.86 0.60
61_M 62_T 1.36 0.84 0.57
149_P 33_L 1.35 0.84 0.56
99_S 304_L 1.33 0.82 0.54
90_V 321_K 1.31 0.81 0.52
58_A 104_M 1.25 0.76 0.45
192_Y 45_T 1.24 0.76 0.45
220_E 117_E 1.24 0.75 0.44
73_L 257_L 1.23 0.75 0.44
64_V 147_P 1.22 0.74 0.43
73_L 304_L 1.22 0.74 0.43
155_T 98_I 1.20 0.72 0.40
187_T 75_L 1.20 0.72 0.40
111_T 170_L 1.16 0.68 0.36
156_S 307_M 1.15 0.68 0.36
115_G 143_Y 1.15 0.67 0.35
97_I 22_L 1.14 0.67 0.35
56_S 204_N 1.13 0.66 0.34
132_D 81_S 1.13 0.66 0.34
32_F 285_I 1.13 0.65 0.34
73_L 87_T 1.12 0.65 0.33
140_N 45_T 1.12 0.65 0.33
182_T 131_L 1.12 0.64 0.32
100_I 103_A 1.11 0.64 0.32
53_T 21_A 1.11 0.64 0.32
155_T 70_L 1.10 0.63 0.31
150_I 20_T 1.10 0.62 0.31
86_M 289_N 1.10 0.62 0.31
224_V 270_F 1.10 0.62 0.30
53_T 14_F 1.10 0.62 0.30
183_T 53_T 1.09 0.61 0.30
148_T 48_M 1.08 0.61 0.29
45_T 333_T 1.07 0.60 0.28
90_V 81_S 1.07 0.59 0.28
43_F 179_L 1.07 0.59 0.28
73_L 205_L 1.06 0.59 0.28
53_T 195_P 1.06 0.58 0.27
68_L 24_S 1.06 0.58 0.27
53_T 67_S 1.06 0.58 0.27
138_V 215_A 1.05 0.57 0.27
37_L 123_P 1.05 0.57 0.27
192_Y 153_L 1.05 0.57 0.26
56_S 195_P 1.04 0.56 0.25
223_P 202_I 1.04 0.56 0.25
142_V 44_L 1.03 0.55 0.25
172_T 195_P 1.03 0.55 0.25
213_L 71_L 1.02 0.54 0.24
220_E 229_L 1.02 0.54 0.24
97_I 83_Q 1.02 0.54 0.24
156_S 70_L 1.01 0.53 0.23
150_I 191_M 1.01 0.53 0.23
64_V 83_Q 1.01 0.53 0.23
97_I 201_T 1.01 0.53 0.23
44_L 122_T 1.01 0.52 0.23
168_L 117_E 1.00 0.52 0.22
30_I 83_Q 1.00 0.52 0.22
213_L 29_T 0.99 0.51 0.22
167_T 100_M 0.99 0.51 0.22
2_A 40_F 0.99 0.51 0.22
64_V 136_L 0.99 0.51 0.21
192_Y 100_M 0.98 0.50 0.21
113_Y 283_A 0.98 0.50 0.21
53_T 104_M 0.98 0.49 0.21
107_T 153_L 0.98 0.49 0.21
183_T 170_L 0.98 0.49 0.20
97_I 319_H 0.98 0.49 0.20
27_A 282_M 0.97 0.49 0.20
155_T 249_L 0.97 0.48 0.20
73_L 144_Q 0.97 0.48 0.20
132_D 28_F 0.96 0.48 0.20
187_T 214_T 0.96 0.48 0.20
155_T 21_A 0.96 0.47 0.19
3_H 339_I 0.95 0.47 0.19
115_G 277_I 0.95 0.46 0.18
123_L 344_L 0.95 0.46 0.18
58_A 99_M 0.95 0.46 0.18
202_A 108_M 0.95 0.46 0.18
123_L 336_L 0.95 0.46 0.18
155_T 283_A 0.95 0.46 0.18
115_G 218_L 0.95 0.46 0.18
156_S 79_M 0.94 0.46 0.18
46_L 274_N 0.94 0.45 0.18
156_S 305_L 0.94 0.45 0.18
115_G 175_L 0.94 0.45 0.18
45_T 285_I 0.93 0.44 0.17
168_L 45_T 0.93 0.44 0.17
9_L 123_P 0.93 0.43 0.17
22_T 237_L 0.93 0.43 0.17
36_F 285_I 0.92 0.43 0.17
86_M 128_L 0.92 0.43 0.17
170_L 344_L 0.92 0.42 0.16
214_I 283_A 0.92 0.42 0.16
94_S 267_I 0.92 0.42 0.16
97_I 225_T 0.91 0.42 0.16
64_V 146_S 0.91 0.42 0.16
140_N 88_N 0.91 0.42 0.16
150_I 21_A 0.91 0.41 0.16
52_N 213_T 0.90 0.41 0.15
73_L 96_L 0.90 0.41 0.15
138_V 21_A 0.90 0.41 0.15
129_E 98_I 0.90 0.41 0.15
192_Y 195_P 0.90 0.41 0.15
3_H 19_I 0.90 0.41 0.15
191_V 27_F 0.90 0.41 0.15
111_T 70_L 0.90 0.40 0.15
110_Y 219_L 0.90 0.40 0.15
202_A 130_L 0.89 0.40 0.15
53_T 103_A 0.89 0.40 0.15
167_T 6_Q 0.89 0.40 0.15
183_T 317_F 0.89 0.40 0.15
123_L 87_T 0.89 0.40 0.15
64_V 245_P 0.89 0.40 0.15
97_I 296_L 0.89 0.40 0.15
164_A 153_L 0.89 0.39 0.14
187_T 187_M 0.88 0.39 0.14
4_A 53_T 0.88 0.39 0.14
140_N 2_N 0.88 0.39 0.14
165_V 156_T 0.88 0.38 0.14
120_S 41_I 0.88 0.38 0.14
164_A 340_S 0.88 0.38 0.14
140_N 204_N 0.87 0.38 0.14
184_F 14_F 0.87 0.38 0.14
51_T 280_T 0.87 0.38 0.14
165_V 320_T 0.87 0.38 0.13
133_L 68_M 0.87 0.37 0.13
184_F 187_M 0.87 0.37 0.13
27_A 130_L 0.87 0.37 0.13
113_Y 326_L 0.86 0.37 0.13
192_Y 74_I 0.86 0.37 0.13
64_V 222_N 0.86 0.37 0.13
45_T 56_A 0.86 0.37 0.13
27_A 17_T 0.86 0.37 0.13
192_Y 223_S 0.86 0.36 0.13
46_L 291_Y 0.86 0.36 0.13
213_L 289_N 0.86 0.36 0.13
112_D 270_F 0.86 0.36 0.13
182_T 25_H 0.86 0.36 0.13
3_H 344_L 0.86 0.36 0.13
175_I 5_A 0.85 0.36 0.13
150_I 337_L 0.85 0.36 0.12
92_D 202_I 0.85 0.36 0.12
143_V 271_T 0.85 0.36 0.12
51_T 283_A 0.85 0.35 0.12
215_P 174_Q 0.85 0.35 0.12
112_D 107_G 0.85 0.35 0.12
67_I 210_I 0.85 0.35 0.12
140_N 215_A 0.85 0.35 0.12
144_L 49_N 0.85 0.35 0.12
3_H 62_T 0.84 0.35 0.12
218_I 194_L 0.84 0.35 0.12
167_T 302_I 0.84 0.35 0.12
55_I 304_L 0.84 0.35 0.12
142_V 137_A 0.84 0.35 0.12
154_I 9_I 0.84 0.34 0.12
165_V 64_A 0.84 0.34 0.12
175_I 22_L 0.84 0.34 0.12
192_Y 226_T 0.84 0.34 0.12
107_T 217_L 0.83 0.34 0.12
27_A 41_I 0.83 0.34 0.12
133_L 140_S 0.83 0.34 0.11
211_L 164_A 0.83 0.34 0.11
60_E 286_T 0.83 0.34 0.11
192_Y 139_I 0.83 0.34 0.11
64_V 229_L 0.83 0.34 0.11
144_L 285_I 0.83 0.34 0.11
157_Q 328_T 0.83 0.33 0.11
53_T 106_L 0.83 0.33 0.11
5_A 257_L 0.83 0.33 0.11
73_L 136_L 0.83 0.33 0.11
46_L 69_I 0.82 0.33 0.11
165_V 281_I 0.82 0.33 0.11
43_F 227_T 0.82 0.33 0.11
51_T 267_I 0.82 0.33 0.11
52_N 93_Y 0.82 0.32 0.11
27_A 91_N 0.82 0.32 0.11
63_T 106_L 0.82 0.32 0.11
117_I 53_T 0.81 0.32 0.11
186_A 85_T 0.81 0.32 0.11
9_L 86_M 0.81 0.32 0.10
114_G 191_M 0.81 0.32 0.10
67_I 296_L 0.81 0.32 0.10
9_L 122_T 0.81 0.32 0.10
47_S 10_Y 0.81 0.32 0.10
75_L 214_T 0.81 0.31 0.10
113_Y 264_W 0.81 0.31 0.10
72_I 68_M 0.81 0.31 0.10
155_T 7_P 0.80 0.31 0.10
92_D 156_T 0.80 0.31 0.10
20_L 248_F 0.80 0.31 0.10
74_V 278_I 0.80 0.31 0.10
49_K 175_L 0.80 0.31 0.10
22_T 334_T 0.80 0.31 0.10
223_P 218_L 0.80 0.31 0.10
3_H 213_T 0.80 0.31 0.10
44_L 209_I 0.80 0.31 0.10
157_Q 145_I 0.80 0.30 0.10
156_S 299_S 0.80 0.30 0.10
221_M 33_L 0.80 0.30 0.10
67_I 28_F 0.80 0.30 0.10
41_A 191_M 0.80 0.30 0.10
154_I 233_T 0.80 0.30 0.10
107_T 18_L 0.80 0.30 0.10
61_M 270_F 0.79 0.30 0.10
3_H 257_L 0.79 0.30 0.10
147_E 310_N 0.79 0.30 0.10
64_V 323_T 0.79 0.30 0.10
111_T 283_A 0.79 0.30 0.10
147_E 160_L 0.79 0.29 0.09
51_T 154_L 0.79 0.29 0.09
168_L 127_G 0.79 0.29 0.09
110_Y 209_I 0.79 0.29 0.09
11_D 127_G 0.79 0.29 0.09
157_Q 18_L 0.79 0.29 0.09
13_T 89_T 0.79 0.29 0.09
75_L 219_L 0.79 0.29 0.09
167_T 5_A 0.79 0.29 0.09
64_V 327_P 0.79 0.29 0.09
217_K 333_T 0.79 0.29 0.09
223_P 310_N 0.78 0.29 0.09
155_T 73_A 0.78 0.29 0.09
43_F 321_K 0.78 0.29 0.09
164_A 148_S 0.78 0.29 0.09
54_N 104_M 0.78 0.29 0.09
100_I 139_I 0.78 0.29 0.09
175_I 111_F 0.78 0.29 0.09
83_I 296_L 0.78 0.28 0.09
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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