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OPENSEQ.org
cIV_C_60_cI_N_40_1_human
Genes: A B A+B
Length: 261 347 606
Sequences: 2363 3322 1992
Seq/Len: 9.05 9.57 3.29
MirrorTree (Pazo et al. 2001) 0.90
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 0.08
5 0.00 0.00 3.09
10 0.00 0.00 3.28
20 0.00 0.00 3.28
100 0.00 0.00 3.28
∞ 0.00 0.00 3.28
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 168_G 1.53 0.97 0.80
21_A 298_Y 1.42 0.95 0.73
6_H 177_K 1.35 0.93 0.67
61_V 151_V 1.35 0.93 0.67
167_I 65_T 1.28 0.90 0.61
92_L 133_W 1.25 0.88 0.58
104_S 268_E 1.24 0.88 0.57
26_L 181_Y 1.19 0.84 0.52
6_H 295_R 1.16 0.82 0.49
104_S 170_L 1.16 0.82 0.49
25_L 122_T 1.16 0.82 0.49
199_V 74_I 1.16 0.82 0.48
70_H 64_A 1.14 0.81 0.47
120_G 118_V 1.12 0.80 0.45
112_L 15_A 1.12 0.80 0.45
13_P 27_F 1.12 0.79 0.44
144_I 119_T 1.12 0.79 0.44
80_R 58_K 1.11 0.78 0.43
147_A 136_L 1.10 0.78 0.42
199_V 285_I 1.10 0.78 0.42
96_G 174_Q 1.07 0.75 0.40
227_F 13_I 1.07 0.75 0.40
124_L 25_H 1.07 0.75 0.40
21_A 247_T 1.07 0.75 0.39
127_L 285_I 1.07 0.75 0.39
80_R 56_A 1.07 0.74 0.39
79_L 130_L 1.05 0.73 0.37
38_H 136_L 1.05 0.73 0.37
24_A 104_M 1.03 0.71 0.35
24_A 186_H 1.03 0.71 0.35
7_A 178_I 1.02 0.70 0.35
151_L 285_I 1.02 0.70 0.34
55_Y 20_T 1.01 0.69 0.34
21_A 193_V 1.01 0.69 0.33
168_L 92_Q 1.01 0.68 0.33
199_V 248_F 1.00 0.68 0.33
152_M 17_T 1.00 0.68 0.33
216_T 207_I 1.00 0.67 0.32
226_H 177_K 1.00 0.67 0.32
61_V 278_I 1.00 0.67 0.32
158_Q 267_I 0.99 0.67 0.32
254_V 118_V 0.99 0.66 0.31
159_M 68_M 0.99 0.66 0.31
96_G 120_Q 0.98 0.66 0.31
127_L 117_E 0.98 0.65 0.30
167_I 155_L 0.98 0.65 0.30
53_T 137_A 0.98 0.65 0.30
37_F 200_M 0.97 0.64 0.30
189_S 130_L 0.97 0.64 0.29
114_G 139_I 0.97 0.64 0.29
96_G 25_H 0.96 0.63 0.29
111_Q 106_L 0.96 0.63 0.29
209_I 178_I 0.96 0.63 0.29
91_V 68_M 0.95 0.62 0.28
29_S 77_N 0.95 0.62 0.28
151_L 309_N 0.95 0.62 0.28
47_L 16_G 0.95 0.62 0.28
212_S 104_M 0.94 0.60 0.26
2_T 61_L 0.94 0.60 0.26
50_N 24_S 0.94 0.60 0.26
92_L 106_L 0.93 0.59 0.26
233_F 172_Q 0.93 0.59 0.26
150_S 190_M 0.93 0.59 0.26
255_S 117_E 0.93 0.59 0.26
2_T 157_L 0.93 0.59 0.25
110_P 136_L 0.92 0.58 0.25
67_Y 275_S 0.92 0.58 0.25
223_L 102_M 0.92 0.57 0.25
27_M 8_V 0.92 0.57 0.24
189_S 9_I 0.91 0.57 0.24
124_L 201_T 0.91 0.57 0.24
52_L 113_F 0.90 0.56 0.23
103_H 139_I 0.90 0.55 0.23
80_R 121_G 0.90 0.55 0.23
26_L 296_L 0.90 0.55 0.23
55_Y 164_A 0.90 0.55 0.23
182_F 163_M 0.89 0.55 0.23
199_V 68_M 0.89 0.55 0.23
42_L 257_L 0.89 0.54 0.23
21_A 300_T 0.89 0.54 0.22
254_V 19_I 0.89 0.54 0.22
155_N 88_N 0.88 0.53 0.22
28_T 100_M 0.88 0.53 0.21
65_S 41_I 0.88 0.53 0.21
165_I 197_N 0.88 0.52 0.21
79_L 169_G 0.87 0.52 0.21
174_T 301_S 0.87 0.52 0.21
167_I 211_L 0.87 0.52 0.21
110_P 98_I 0.87 0.52 0.21
53_T 165_G 0.87 0.52 0.21
185_P 55_A 0.87 0.52 0.21
109_T 194_L 0.87 0.52 0.21
76_Q 62_T 0.87 0.51 0.20
21_A 66_A 0.87 0.51 0.20
189_S 236_K 0.86 0.51 0.20
103_H 5_A 0.86 0.51 0.20
142_V 298_Y 0.86 0.51 0.20
185_P 92_Q 0.86 0.51 0.20
128_E 104_M 0.86 0.50 0.20
8_Y 333_T 0.86 0.50 0.20
23_S 70_L 0.86 0.50 0.20
209_I 254_L 0.86 0.50 0.20
3_H 186_H 0.85 0.50 0.20
135_S 117_E 0.85 0.49 0.19
158_Q 31_V 0.85 0.49 0.19
212_S 142_M 0.85 0.49 0.19
128_E 198_P 0.85 0.49 0.19
21_A 211_L 0.85 0.49 0.19
178_A 55_A 0.85 0.49 0.19
213_T 98_I 0.85 0.49 0.19
162_A 11_S 0.85 0.49 0.19
61_V 231_S 0.85 0.49 0.19
213_T 103_A 0.85 0.49 0.19
162_A 113_F 0.85 0.49 0.19
103_H 104_M 0.85 0.49 0.19
124_L 174_Q 0.85 0.48 0.19
184_S 56_A 0.84 0.48 0.19
195_S 74_I 0.84 0.48 0.19
96_G 289_N 0.84 0.48 0.19
112_L 271_T 0.84 0.48 0.18
48_L 270_F 0.84 0.48 0.18
158_Q 296_L 0.84 0.48 0.18
143_S 254_L 0.84 0.48 0.18
55_Y 297_I 0.84 0.48 0.18
21_A 53_T 0.84 0.48 0.18
220_I 211_L 0.84 0.47 0.18
230_K 24_S 0.84 0.47 0.18
168_L 210_I 0.84 0.47 0.18
212_S 148_S 0.83 0.47 0.18
167_I 181_Y 0.83 0.47 0.18
193_Y 154_L 0.83 0.47 0.18
135_S 29_T 0.83 0.47 0.18
54_M 192_A 0.83 0.46 0.18
104_S 342_F 0.83 0.46 0.17
109_T 68_M 0.83 0.46 0.17
103_H 204_N 0.83 0.46 0.17
37_F 157_L 0.83 0.46 0.17
125_N 103_A 0.83 0.46 0.17
138_L 161_S 0.83 0.46 0.17
22_L 99_M 0.82 0.46 0.17
139_A 291_Y 0.82 0.46 0.17
31_L 56_A 0.82 0.46 0.17
37_F 289_N 0.82 0.46 0.17
229_S 19_I 0.82 0.46 0.17
210_I 66_A 0.82 0.45 0.17
195_S 111_F 0.82 0.45 0.17
7_A 269_E 0.82 0.45 0.17
27_M 16_G 0.82 0.45 0.17
125_N 4_L 0.82 0.45 0.17
175_L 97_M 0.82 0.45 0.17
136_V 316_Q 0.82 0.45 0.17
128_E 117_E 0.81 0.45 0.17
216_T 67_S 0.81 0.45 0.17
151_L 80_L 0.81 0.44 0.17
10_M 298_Y 0.81 0.44 0.16
45_L 65_T 0.81 0.44 0.16
12_K 128_L 0.81 0.44 0.16
36_H 176_R 0.81 0.44 0.16
29_S 252_G 0.81 0.44 0.16
178_A 141_I 0.81 0.43 0.16
114_G 117_E 0.81 0.43 0.16
48_L 159_I 0.81 0.43 0.16
48_L 332_L 0.81 0.43 0.16
4_Q 104_M 0.81 0.43 0.16
136_V 174_Q 0.81 0.43 0.16
96_G 201_T 0.80 0.43 0.16
61_V 4_L 0.80 0.42 0.15
20_G 262_P 0.80 0.42 0.15
101_F 52_S 0.80 0.42 0.15
178_A 14_F 0.80 0.42 0.15
178_A 202_I 0.80 0.42 0.15
20_G 264_W 0.79 0.42 0.15
10_M 257_L 0.79 0.42 0.15
43_L 246_S 0.79 0.42 0.15
128_E 174_Q 0.79 0.42 0.15
216_T 314_K 0.79 0.41 0.15
185_P 180_A 0.79 0.41 0.15
27_M 43_V 0.79 0.41 0.15
8_Y 206_T 0.79 0.41 0.15
27_M 85_T 0.79 0.41 0.15
25_L 219_L 0.79 0.41 0.15
135_S 58_K 0.79 0.41 0.15
70_H 198_P 0.79 0.41 0.15
160_I 49_N 0.79 0.41 0.15
103_H 83_Q 0.79 0.41 0.15
151_L 232_R 0.79 0.41 0.15
22_L 199_N 0.79 0.41 0.15
13_P 120_Q 0.79 0.41 0.15
217_I 45_T 0.78 0.41 0.14
152_M 137_A 0.78 0.41 0.14
162_A 304_L 0.78 0.40 0.14
8_Y 177_K 0.78 0.40 0.14
103_H 24_S 0.78 0.40 0.14
160_I 194_L 0.78 0.40 0.14
230_K 131_L 0.78 0.40 0.14
22_L 289_N 0.78 0.40 0.14
191_G 190_M 0.78 0.40 0.14
62_T 73_A 0.78 0.40 0.14
67_Y 292_F 0.78 0.40 0.14
217_I 61_L 0.78 0.40 0.14
49_T 72_M 0.78 0.40 0.14
213_T 312_K 0.78 0.40 0.14
125_N 247_T 0.77 0.40 0.14
127_L 58_K 0.77 0.40 0.14
112_L 170_L 0.77 0.40 0.14
174_T 248_F 0.77 0.39 0.14
143_S 123_P 0.77 0.39 0.14
27_M 285_I 0.77 0.39 0.14
26_L 50_P 0.77 0.39 0.14
217_I 294_L 0.77 0.39 0.14
195_S 95_S 0.77 0.39 0.14
127_L 270_F 0.77 0.39 0.14
8_Y 81_S 0.77 0.39 0.14
127_L 294_L 0.77 0.39 0.14
121_I 278_I 0.77 0.39 0.14
219_F 218_L 0.77 0.39 0.14
8_Y 61_L 0.77 0.39 0.14
21_A 51_R 0.77 0.39 0.14
104_S 8_V 0.77 0.39 0.14
26_L 39_A 0.77 0.39 0.14
157_N 179_L 0.77 0.39 0.14
217_I 222_N 0.77 0.39 0.14
84_I 332_L 0.77 0.39 0.14
80_R 166_S 0.76 0.38 0.13
128_E 72_M 0.76 0.38 0.13
10_M 10_Y 0.76 0.38 0.13
73_P 187_M 0.76 0.38 0.13
155_N 67_S 0.76 0.38 0.13
184_S 291_Y 0.76 0.38 0.13
171_L 16_G 0.76 0.38 0.13
109_T 159_I 0.76 0.38 0.13
129_V 118_V 0.76 0.38 0.13
107_A 25_H 0.76 0.38 0.13
219_F 136_L 0.76 0.38 0.13
135_S 24_S 0.76 0.38 0.13
158_Q 41_I 0.76 0.37 0.13
209_I 190_M 0.76 0.37 0.13
103_H 311_V 0.76 0.37 0.13
28_T 66_A 0.75 0.37 0.13
61_V 315_W 0.75 0.37 0.13
32_A 277_I 0.75 0.37 0.13
192_I 339_I 0.75 0.37 0.13
147_A 130_L 0.75 0.37 0.13
175_L 247_T 0.75 0.37 0.13
22_L 4_L 0.75 0.37 0.13
136_V 185_T 0.75 0.36 0.12
32_A 177_K 0.75 0.36 0.12
112_L 251_L 0.75 0.36 0.12
226_H 120_Q 0.75 0.36 0.12
70_H 44_L 0.74 0.36 0.12
127_L 74_I 0.74 0.36 0.12
178_A 109_A 0.74 0.36 0.12
81_Y 20_T 0.74 0.36 0.12
26_L 197_N 0.74 0.36 0.12
33_M 201_T 0.74 0.36 0.12
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
4561 3.97 cIV_C_40_cI_N_20_1_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 1) msa: Jackhmmer (2015_06) 0.89 Done - Shared
4560 4.43 cIV_C_60_cI_N_20_8_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.03 Done - Shared
4559 3.96 cIV_C_60_cI_N_40_1_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-20, 1) msa: Jackhmmer (2015_06) 0.89 Done - Shared
4558 3.29 cIV_C_60_cI_N_40_1_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-40, 1) msa: Jackhmmer (2015_06) 0.80 Done - Shared
4557 2.14 cIV_C_60_cI_N_60_1_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 1) msa: Jackhmmer (2015_06) 0.69 Done - Shared
4555 1.79 cIV_C_80_cI_N_80_1_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.36 Done - Shared
4554 1.79 cIV_C_80_cI_N_80_1_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.23 Done - Shared
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