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OPENSEQ.org
cIV_B_60_cI_M_60_1_human
Genes: A B A+B
Length: 252 459 681
Sequences: 2518 2643 2223
Seq/Len: 9.99 5.76 3.26
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 0.01
2 0.00 0.00 0.05
5 0.00 0.00 0.32
10 0.00 0.00 3.05
20 0.00 0.00 3.07
100 0.00 0.00 3.08
∞ 0.00 0.00 3.13
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
92_I 336_R 1.80 0.99 0.95
112_L 164_L 1.50 0.96 0.87
68_P 388_W 1.32 0.91 0.77
180_I 72_L 1.26 0.89 0.72
49_V 140_P 1.20 0.85 0.66
99_I 377_G 1.14 0.81 0.60
195_V 120_I 1.14 0.80 0.59
43_T 402_V 1.13 0.80 0.59
180_I 263_V 1.12 0.79 0.58
20_F 243_M 1.10 0.77 0.55
176_A 95_Y 1.08 0.76 0.53
17_G 318_A 1.06 0.73 0.51
164_V 388_W 1.05 0.73 0.50
182_A 318_A 1.04 0.71 0.48
20_F 380_S 1.04 0.71 0.48
212_Y 194_L 1.03 0.71 0.47
185_I 201_M 1.01 0.69 0.45
176_A 362_A 1.01 0.69 0.45
87_L 39_L 1.01 0.68 0.45
39_L 149_F 1.01 0.68 0.45
23_A 72_L 1.00 0.67 0.44
137_L 138_S 0.97 0.64 0.41
166_V 161_L 0.97 0.64 0.41
74_N 210_Y 0.97 0.64 0.41
143_A 65_L 0.97 0.64 0.40
39_L 434_N 0.97 0.63 0.40
37_F 75_L 0.96 0.62 0.39
194_A 398_L 0.96 0.62 0.39
160_N 95_Y 0.96 0.62 0.39
92_I 151_F 0.95 0.62 0.39
108_N 356_A 0.95 0.62 0.39
39_L 313_V 0.95 0.61 0.38
79_V 406_Y 0.94 0.61 0.38
84_V 116_I 0.94 0.60 0.36
194_A 315_L 0.93 0.58 0.35
48_F 149_F 0.93 0.58 0.35
177_T 95_Y 0.92 0.58 0.35
113_V 197_L 0.92 0.58 0.35
164_V 181_L 0.92 0.57 0.34
208_Q 377_G 0.92 0.57 0.34
134_F 127_I 0.92 0.57 0.34
235_S 212_L 0.91 0.57 0.34
40_Y 275_I 0.91 0.56 0.33
162_V 411_F 0.91 0.56 0.33
175_T 244_M 0.91 0.56 0.33
180_I 282_L 0.90 0.55 0.33
98_P 368_A 0.90 0.55 0.33
80_I 444_I 0.90 0.55 0.33
137_L 95_Y 0.90 0.55 0.32
136_A 372_T 0.90 0.55 0.32
93_G 359_W 0.89 0.54 0.31
110_P 163_A 0.89 0.54 0.31
98_P 330_A 0.88 0.53 0.31
212_Y 95_Y 0.88 0.53 0.30
152_D 147_T 0.87 0.52 0.29
139_L 437_M 0.87 0.52 0.29
231_V 442_S 0.87 0.51 0.29
180_I 333_N 0.86 0.51 0.29
176_A 173_S 0.86 0.50 0.28
213_F 399_N 0.86 0.50 0.28
49_V 297_V 0.85 0.49 0.28
53_L 308_S 0.85 0.48 0.27
16_G 202_A 0.85 0.48 0.27
24_S 278_R 0.84 0.48 0.27
71_F 410_M 0.84 0.48 0.26
173_Q 198_A 0.84 0.47 0.26
164_V 105_S 0.83 0.47 0.26
204_F 278_R 0.83 0.47 0.25
106_M 78_M 0.83 0.47 0.25
219_L 324_S 0.83 0.46 0.25
235_S 446_L 0.83 0.46 0.25
113_V 315_L 0.83 0.46 0.25
112_L 171_L 0.83 0.46 0.25
213_F 453_I 0.83 0.46 0.25
231_V 175_N 0.83 0.46 0.25
112_L 143_L 0.82 0.45 0.24
176_A 380_S 0.82 0.45 0.24
222_I 325_L 0.82 0.45 0.24
202_L 317_I 0.81 0.44 0.23
194_A 291_I 0.81 0.44 0.23
112_L 101_S 0.81 0.44 0.23
114_I 2_L 0.81 0.44 0.23
24_S 286_I 0.81 0.44 0.23
176_A 405_L 0.81 0.44 0.23
147_A 235_L 0.81 0.44 0.23
173_Q 207_M 0.81 0.43 0.23
23_A 358_W 0.81 0.43 0.23
43_T 451_P 0.81 0.43 0.23
127_Y 313_V 0.80 0.43 0.23
22_P 251_N 0.80 0.43 0.23
92_I 297_V 0.80 0.42 0.22
76_P 420_T 0.80 0.42 0.22
66_P 107_I 0.80 0.42 0.22
51_L 343_I 0.80 0.42 0.22
234_V 61_L 0.80 0.42 0.22
213_F 205_V 0.79 0.41 0.22
162_V 394_L 0.79 0.41 0.21
245_G 394_L 0.79 0.41 0.21
31_Q 315_L 0.78 0.41 0.21
117_I 105_S 0.78 0.40 0.21
160_N 51_S 0.78 0.40 0.21
187_A 393_L 0.78 0.40 0.21
41_I 273_S 0.78 0.40 0.21
176_A 7_P 0.78 0.40 0.21
19_N 64_P 0.78 0.39 0.20
145_A 274_S 0.77 0.39 0.20
172_V 251_N 0.77 0.39 0.20
84_V 301_I 0.77 0.39 0.20
65_N 170_T 0.77 0.39 0.20
144_L 243_M 0.77 0.39 0.20
199_I 377_G 0.77 0.38 0.19
92_I 150_L 0.77 0.38 0.19
65_N 56_F 0.77 0.38 0.19
147_A 278_R 0.76 0.38 0.19
234_V 44_Q 0.76 0.38 0.19
100_L 161_L 0.76 0.38 0.19
51_L 388_W 0.76 0.38 0.19
244_A 96_L 0.76 0.38 0.19
176_A 352_L 0.76 0.37 0.19
140_E 330_A 0.76 0.37 0.19
212_Y 173_S 0.76 0.37 0.18
139_L 86_S 0.76 0.37 0.18
127_Y 59_D 0.76 0.37 0.18
103_S 125_T 0.76 0.37 0.18
88_I 451_P 0.75 0.37 0.18
113_V 380_S 0.75 0.37 0.18
53_L 336_R 0.75 0.37 0.18
24_S 199_Y 0.75 0.36 0.18
163_V 56_F 0.75 0.36 0.18
26_P 76_T 0.75 0.36 0.18
194_A 65_L 0.75 0.36 0.18
129_N 335_E 0.75 0.36 0.18
17_G 226_A 0.74 0.36 0.18
67_V 389_S 0.74 0.36 0.17
23_A 285_L 0.74 0.35 0.17
57_I 164_L 0.74 0.35 0.17
139_L 358_W 0.74 0.35 0.17
27_L 253_L 0.74 0.35 0.17
94_A 420_T 0.74 0.35 0.17
51_L 344_L 0.74 0.35 0.17
39_L 259_Y 0.73 0.35 0.17
83_L 158_L 0.73 0.35 0.17
69_A 411_F 0.73 0.34 0.17
234_V 57_S 0.73 0.34 0.17
212_Y 164_L 0.73 0.34 0.17
71_F 367_L 0.73 0.34 0.17
79_V 376_L 0.73 0.34 0.17
176_A 149_F 0.73 0.34 0.17
205_S 65_L 0.73 0.34 0.17
116_A 112_A 0.73 0.34 0.16
20_F 186_L 0.73 0.34 0.16
99_I 210_Y 0.73 0.34 0.16
233_A 372_T 0.73 0.34 0.16
114_I 380_S 0.73 0.34 0.16
92_I 433_E 0.73 0.34 0.16
180_I 73_L 0.72 0.34 0.16
211_V 150_L 0.72 0.33 0.16
173_Q 270_I 0.72 0.33 0.16
38_V 309_F 0.72 0.33 0.16
158_T 457_F 0.72 0.33 0.16
213_F 210_Y 0.72 0.33 0.16
240_E 81_Q 0.72 0.33 0.16
38_V 240_G 0.72 0.33 0.16
112_L 282_L 0.72 0.33 0.16
69_A 360_L 0.72 0.33 0.16
16_G 204_M 0.72 0.33 0.16
213_F 131_A 0.72 0.33 0.16
56_C 144_N 0.72 0.33 0.16
41_I 435_T 0.71 0.32 0.15
117_I 345_S 0.71 0.32 0.15
243_L 143_L 0.71 0.32 0.15
231_V 45_I 0.71 0.32 0.15
94_A 393_L 0.71 0.32 0.15
188_F 234_V 0.71 0.32 0.15
127_Y 149_F 0.71 0.32 0.15
110_P 383_V 0.71 0.32 0.15
69_A 367_L 0.71 0.32 0.15
110_P 91_R 0.71 0.32 0.15
83_L 333_N 0.71 0.32 0.15
157_A 42_F 0.71 0.32 0.15
77_I 452_D 0.71 0.32 0.15
145_A 164_L 0.71 0.32 0.15
231_V 77_I 0.71 0.32 0.15
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
4424 3.26 cIV_B_60_cI_M_60_1_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 1) msa: Jackhmmer (2015_06) 0.95 Done - Shared
4423 2.55 cIV_B_60_cI_M_80_1_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.69 Done - Shared
4422 2.51 cIV_B_80_cI_M_80_1_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.69 Done - Shared
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