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OPENSEQ.org
cIV_C_60_cI_M_60_1_human
Genes: A B A+B
Length: 261 459 718
Sequences: 2234 2643 2191
Seq/Len: 8.56 5.76 3.05
MirrorTree (Pazo et al. 2001) 0.84
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 0.08
2 0.00 0.00 0.23
5 0.00 0.00 2.77
10 0.00 0.00 2.96
20 0.00 0.00 3.00
100 0.00 0.00 3.00
∞ 0.00 0.00 3.04
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
61_V 32_L 1.46 0.95 0.66
222_Q 149_F 1.40 0.93 0.60
6_H 336_R 1.30 0.89 0.51
212_S 270_I 1.30 0.89 0.51
128_E 144_N 1.27 0.88 0.49
150_S 419_L 1.24 0.86 0.46
254_V 112_A 1.24 0.86 0.46
27_M 234_V 1.16 0.80 0.38
53_T 202_A 1.14 0.79 0.37
139_A 234_V 1.13 0.78 0.36
8_Y 445_L 1.13 0.78 0.35
168_L 201_M 1.09 0.74 0.32
91_V 163_A 1.07 0.73 0.30
196_T 355_M 1.06 0.71 0.29
78_G 278_R 1.05 0.70 0.28
230_K 339_S 1.05 0.70 0.28
61_V 257_M 1.04 0.70 0.28
184_S 234_V 1.04 0.69 0.27
213_T 52_C 1.03 0.69 0.27
23_S 149_F 1.02 0.68 0.26
185_P 408_L 1.02 0.67 0.26
45_L 450_N 1.01 0.66 0.25
25_L 154_L 1.00 0.65 0.24
199_V 301_I 1.00 0.65 0.24
192_I 257_M 0.99 0.64 0.23
142_V 318_A 0.98 0.63 0.23
168_L 411_F 0.97 0.62 0.22
139_A 149_F 0.95 0.60 0.21
260_G 240_G 0.95 0.59 0.21
8_Y 194_L 0.95 0.59 0.20
143_S 352_L 0.94 0.58 0.20
48_L 94_L 0.94 0.58 0.20
219_F 275_I 0.94 0.58 0.20
165_I 244_M 0.94 0.57 0.19
248_V 291_I 0.93 0.57 0.19
135_S 408_L 0.93 0.57 0.19
80_R 415_Q 0.92 0.56 0.19
101_F 404_A 0.92 0.56 0.18
112_L 403_T 0.92 0.56 0.18
120_G 278_R 0.92 0.55 0.18
8_Y 338_H 0.91 0.55 0.18
32_A 265_S 0.91 0.54 0.17
189_S 24_W 0.90 0.54 0.17
91_V 267_W 0.90 0.53 0.17
65_S 446_L 0.90 0.53 0.17
29_S 105_S 0.90 0.53 0.17
35_F 95_Y 0.90 0.53 0.17
138_L 151_F 0.90 0.53 0.17
212_S 57_S 0.89 0.52 0.17
81_Y 369_L 0.88 0.51 0.16
18_L 356_A 0.88 0.50 0.15
154_N 235_L 0.87 0.49 0.15
127_L 25_I 0.87 0.49 0.15
174_T 235_L 0.87 0.49 0.15
25_L 173_S 0.87 0.49 0.15
61_V 386_F 0.86 0.48 0.15
143_S 403_T 0.86 0.48 0.14
225_F 121_F 0.86 0.48 0.14
253_Y 394_L 0.86 0.48 0.14
8_Y 60_P 0.85 0.47 0.14
92_L 284_S 0.85 0.47 0.14
200_A 240_G 0.85 0.47 0.14
150_S 292_S 0.85 0.47 0.14
78_G 234_V 0.85 0.47 0.14
189_S 166_Y 0.85 0.47 0.14
144_I 175_N 0.85 0.47 0.14
149_H 226_A 0.85 0.47 0.14
162_A 425_N 0.85 0.47 0.14
21_A 382_L 0.85 0.47 0.14
4_Q 280_T 0.84 0.46 0.14
28_T 202_A 0.84 0.46 0.14
189_S 418_S 0.84 0.46 0.14
109_T 131_A 0.84 0.45 0.13
142_V 204_M 0.83 0.45 0.13
129_V 298_V 0.83 0.45 0.13
36_H 396_T 0.83 0.44 0.13
164_L 181_L 0.83 0.44 0.13
109_T 235_L 0.82 0.44 0.13
227_F 238_L 0.82 0.43 0.12
139_A 167_T 0.82 0.43 0.12
104_S 106_L 0.82 0.43 0.12
152_M 346_Q 0.82 0.43 0.12
217_I 250_L 0.82 0.43 0.12
147_A 291_I 0.81 0.42 0.12
128_E 307_W 0.81 0.42 0.12
4_Q 202_A 0.81 0.42 0.12
219_F 282_L 0.81 0.42 0.12
34_W 225_I 0.81 0.42 0.12
29_S 385_T 0.81 0.42 0.12
143_S 130_L 0.81 0.41 0.12
171_L 387_S 0.80 0.41 0.12
44_M 449_L 0.80 0.41 0.11
120_G 271_M 0.80 0.41 0.11
8_Y 50_F 0.80 0.41 0.11
36_H 408_L 0.80 0.41 0.11
104_S 400_M 0.80 0.40 0.11
175_L 262_L 0.79 0.39 0.11
159_M 226_A 0.79 0.39 0.11
168_L 173_S 0.79 0.39 0.11
136_V 273_S 0.79 0.39 0.11
13_P 207_M 0.79 0.39 0.11
135_S 280_T 0.78 0.39 0.11
91_V 375_L 0.78 0.39 0.11
217_I 147_T 0.78 0.39 0.10
12_K 380_S 0.78 0.38 0.10
80_R 196_W 0.78 0.38 0.10
51_T 37_I 0.78 0.38 0.10
172_Y 129_T 0.78 0.38 0.10
161_Q 307_W 0.78 0.38 0.10
199_V 377_G 0.78 0.38 0.10
21_A 388_W 0.78 0.38 0.10
91_V 18_S 0.77 0.38 0.10
22_L 351_L 0.77 0.38 0.10
107_A 70_T 0.77 0.38 0.10
18_L 325_L 0.77 0.37 0.10
31_L 338_H 0.77 0.37 0.10
48_L 169_N 0.77 0.37 0.10
61_V 82_R 0.77 0.37 0.10
104_S 141_E 0.77 0.37 0.10
109_T 132_I 0.77 0.37 0.10
167_I 78_M 0.77 0.37 0.10
144_I 450_N 0.77 0.37 0.10
139_A 160_L 0.77 0.37 0.10
6_H 326_L 0.77 0.37 0.10
165_I 315_L 0.77 0.37 0.10
229_S 179_L 0.77 0.37 0.10
127_L 210_Y 0.77 0.37 0.10
184_S 349_Q 0.77 0.37 0.10
5_S 413_T 0.77 0.37 0.10
31_L 37_I 0.77 0.37 0.10
67_Y 410_M 0.76 0.36 0.10
8_Y 362_A 0.76 0.36 0.10
139_A 65_L 0.76 0.36 0.10
155_N 380_S 0.76 0.36 0.10
8_Y 121_F 0.76 0.36 0.10
44_M 70_T 0.76 0.36 0.09
155_N 358_W 0.75 0.35 0.09
55_Y 166_Y 0.75 0.35 0.09
73_P 116_I 0.75 0.35 0.09
34_W 125_T 0.75 0.35 0.09
171_L 41_F 0.75 0.35 0.09
151_L 361_L 0.75 0.35 0.09
225_F 344_L 0.75 0.35 0.09
37_F 338_H 0.75 0.35 0.09
212_S 262_L 0.75 0.34 0.09
136_V 112_A 0.75 0.34 0.09
107_A 280_T 0.74 0.34 0.09
38_H 405_L 0.74 0.34 0.09
3_H 368_A 0.74 0.34 0.09
62_T 338_H 0.74 0.34 0.09
28_T 274_S 0.74 0.34 0.09
80_R 369_L 0.74 0.34 0.09
256_I 291_I 0.74 0.34 0.09
18_L 358_W 0.74 0.34 0.09
112_L 218_K 0.74 0.34 0.09
185_P 74_P 0.74 0.34 0.09
135_S 160_L 0.73 0.33 0.09
20_G 335_E 0.73 0.33 0.09
43_L 86_S 0.73 0.33 0.08
192_I 187_S 0.73 0.33 0.08
13_P 297_V 0.73 0.33 0.08
28_T 438_F 0.73 0.33 0.08
13_P 98_M 0.73 0.33 0.08
33_M 285_L 0.73 0.33 0.08
209_I 57_S 0.73 0.33 0.08
129_V 102_L 0.73 0.33 0.08
37_F 271_M 0.73 0.33 0.08
121_I 333_N 0.73 0.32 0.08
187_T 132_I 0.73 0.32 0.08
195_S 78_M 0.73 0.32 0.08
32_A 304_Q 0.73 0.32 0.08
195_S 354_L 0.72 0.32 0.08
209_I 385_T 0.72 0.32 0.08
236_E 245_R 0.72 0.32 0.08
45_L 55_T 0.72 0.32 0.08
101_F 291_I 0.72 0.32 0.08
21_A 346_Q 0.72 0.32 0.08
62_T 116_I 0.72 0.32 0.08
212_S 408_L 0.72 0.32 0.08
236_E 59_D 0.72 0.32 0.08
31_L 69_T 0.72 0.32 0.08
139_A 411_F 0.72 0.32 0.08
20_G 382_L 0.72 0.32 0.08
27_M 5_I 0.72 0.32 0.08
107_A 61_L 0.72 0.31 0.08
250_L 358_W 0.72 0.31 0.08
61_V 258_A 0.72 0.31 0.08
176_L 240_G 0.72 0.31 0.08
229_S 453_I 0.72 0.31 0.08
185_P 270_I 0.72 0.31 0.08
79_L 418_S 0.71 0.31 0.08
158_Q 360_L 0.71 0.31 0.08
54_M 372_T 0.71 0.31 0.08
139_A 235_L 0.71 0.31 0.08
162_A 391_I 0.71 0.31 0.08
2_T 380_S 0.71 0.31 0.08
135_S 134_T 0.71 0.31 0.08
19_T 344_L 0.71 0.31 0.08
56_Q 415_Q 0.71 0.31 0.08
161_Q 158_L 0.71 0.31 0.08
129_V 143_L 0.71 0.30 0.08
136_V 205_V 0.71 0.30 0.08
250_L 328_C 0.71 0.30 0.08
24_A 330_A 0.71 0.30 0.08
10_M 410_M 0.71 0.30 0.07
152_M 74_P 0.71 0.30 0.07
128_E 243_M 0.71 0.30 0.07
36_H 150_L 0.71 0.30 0.07
175_L 49_L 0.71 0.30 0.07
92_L 436_L 0.71 0.30 0.07
213_T 417_G 0.70 0.30 0.07
25_L 45_I 0.70 0.30 0.07
192_I 438_F 0.70 0.30 0.07
144_I 308_S 0.70 0.30 0.07
160_I 37_I 0.70 0.29 0.07
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
4673 3.07 cIV_C_60_cI_M_60_1_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 1) msa: Jackhmmer (2015_06) 0.57 Done - Shared
4438 2.36 cIV_C_60_cI_M_80_1_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.80 Done - Shared
4437 2.38 cIV_C_80_cI_M_80_1_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.83 Done - Shared
4435 3.05 cIV_C_60_cI_M_60_1_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-60, 1) msa: Jackhmmer (2015_06) 0.66 Done - Shared
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