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OPENSEQ.org
cIV_B_60_cI_M_60_1_human
Genes: A B A+B
Length: 227 459 683
Sequences: 2677 2643 2217
Seq/Len: 11.79 5.76 3.25
MirrorTree (Pazo et al. 2001) 0.85
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 0.33
10 0.00 0.00 3.12
20 0.00 0.00 3.14
100 0.00 0.00 3.18
∞ 0.00 0.00 3.23
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
76_I 336_R 1.80 0.99 0.95
95_L 164_L 1.51 0.96 0.87
52_N 388_W 1.31 0.91 0.75
160_L 72_L 1.24 0.87 0.69
38_V 140_P 1.19 0.84 0.64
83_I 377_G 1.16 0.82 0.61
144_L 388_W 1.15 0.81 0.60
32_F 402_V 1.12 0.79 0.57
9_L 243_M 1.12 0.79 0.57
160_L 263_V 1.09 0.76 0.54
175_I 120_I 1.09 0.76 0.54
156_S 362_A 1.08 0.75 0.53
192_Y 194_L 1.06 0.74 0.51
9_L 380_S 1.05 0.73 0.49
12_A 72_L 1.05 0.72 0.49
6_Q 318_A 1.04 0.72 0.48
156_S 95_Y 1.04 0.71 0.48
92_D 356_A 1.02 0.70 0.46
162_S 318_A 1.02 0.70 0.46
146_I 161_L 1.01 0.68 0.45
121_Y 138_S 1.00 0.68 0.44
174_A 398_L 1.00 0.68 0.44
58_A 210_Y 1.00 0.67 0.43
160_L 282_L 0.99 0.66 0.42
28_L 434_N 0.99 0.66 0.42
71_I 39_L 0.96 0.63 0.39
140_N 95_Y 0.95 0.61 0.37
63_T 406_Y 0.95 0.61 0.37
26_H 75_L 0.95 0.61 0.37
77_A 359_W 0.94 0.60 0.37
29_M 275_I 0.94 0.60 0.36
28_L 313_V 0.93 0.59 0.36
76_I 151_F 0.93 0.59 0.35
96_T 197_L 0.93 0.59 0.35
28_L 149_F 0.93 0.58 0.35
68_L 116_I 0.93 0.58 0.35
82_R 368_A 0.93 0.58 0.35
155_T 244_M 0.93 0.58 0.35
142_V 411_F 0.92 0.58 0.35
118_F 127_I 0.92 0.58 0.34
188_R 377_G 0.92 0.57 0.34
93_P 163_A 0.91 0.56 0.33
174_A 315_L 0.90 0.56 0.33
211_L 442_S 0.90 0.56 0.33
123_L 437_M 0.90 0.55 0.33
165_V 201_M 0.90 0.55 0.32
157_Q 95_Y 0.90 0.55 0.32
156_S 405_L 0.89 0.54 0.31
127_F 65_L 0.89 0.54 0.31
193_Y 453_I 0.89 0.53 0.31
13_T 286_I 0.88 0.52 0.29
82_R 330_A 0.87 0.52 0.29
120_S 372_T 0.87 0.51 0.29
215_P 446_L 0.87 0.51 0.29
156_S 173_S 0.87 0.51 0.29
13_T 278_R 0.87 0.51 0.29
138_V 457_F 0.87 0.51 0.29
132_D 147_T 0.86 0.50 0.28
55_I 410_M 0.86 0.50 0.28
215_P 212_L 0.86 0.50 0.28
121_Y 95_Y 0.86 0.50 0.28
37_L 149_F 0.85 0.49 0.27
153_M 198_A 0.85 0.49 0.27
199_I 324_S 0.85 0.49 0.27
42_L 308_S 0.85 0.49 0.27
144_L 181_L 0.85 0.48 0.27
160_L 333_N 0.85 0.48 0.27
67_I 158_L 0.84 0.48 0.26
96_T 315_L 0.84 0.48 0.26
184_F 278_R 0.84 0.47 0.26
140_N 51_S 0.84 0.47 0.26
38_V 297_V 0.84 0.47 0.26
97_I 2_L 0.84 0.47 0.26
174_A 291_I 0.83 0.47 0.25
182_T 317_I 0.83 0.46 0.25
193_Y 399_N 0.83 0.46 0.25
5_A 202_A 0.83 0.46 0.25
3_H 209_L 0.83 0.46 0.25
193_Y 205_V 0.82 0.46 0.24
129_E 164_L 0.82 0.45 0.24
95_L 101_S 0.82 0.45 0.24
153_M 207_M 0.82 0.45 0.24
11_D 251_N 0.81 0.44 0.23
50_L 107_I 0.81 0.43 0.23
12_A 358_W 0.81 0.43 0.23
49_K 56_F 0.81 0.43 0.23
202_A 325_L 0.81 0.43 0.23
95_L 143_L 0.81 0.43 0.23
68_L 301_I 0.81 0.43 0.23
60_E 420_T 0.80 0.42 0.22
214_I 61_L 0.80 0.42 0.22
110_Y 313_V 0.80 0.42 0.22
174_A 65_L 0.80 0.42 0.22
192_Y 95_Y 0.80 0.42 0.22
76_I 297_V 0.79 0.42 0.22
64_V 444_I 0.79 0.42 0.22
49_K 197_L 0.79 0.42 0.22
142_V 394_L 0.79 0.41 0.21
123_L 86_S 0.79 0.41 0.21
130_P 143_L 0.79 0.41 0.21
96_T 380_S 0.79 0.41 0.21
8_G 64_P 0.79 0.41 0.21
40_Y 343_I 0.79 0.41 0.21
214_I 57_S 0.78 0.40 0.21
211_L 175_N 0.78 0.40 0.20
95_L 171_L 0.78 0.40 0.20
156_S 7_P 0.77 0.39 0.20
30_I 273_S 0.77 0.39 0.20
223_P 143_L 0.77 0.39 0.20
140_N 111_T 0.77 0.39 0.20
32_F 451_P 0.77 0.39 0.20
9_L 186_L 0.77 0.39 0.19
110_Y 59_D 0.77 0.38 0.19
87_T 125_T 0.76 0.38 0.19
84_L 161_L 0.76 0.38 0.19
179_L 377_G 0.76 0.37 0.19
72_I 451_P 0.76 0.37 0.18
156_S 352_L 0.76 0.37 0.18
193_Y 131_A 0.76 0.37 0.18
49_K 170_T 0.76 0.37 0.18
15_P 76_T 0.76 0.37 0.18
40_Y 388_W 0.75 0.37 0.18
6_Q 226_A 0.75 0.37 0.18
20_L 315_L 0.75 0.36 0.18
211_L 199_Y 0.75 0.36 0.18
153_M 270_I 0.75 0.36 0.18
13_T 199_Y 0.75 0.36 0.18
30_I 56_F 0.75 0.36 0.18
42_L 336_R 0.75 0.36 0.18
63_T 376_L 0.75 0.36 0.18
221_M 382_L 0.74 0.36 0.17
144_L 105_S 0.74 0.36 0.17
226_T 40_L 0.74 0.35 0.17
28_L 259_Y 0.74 0.35 0.17
12_A 285_L 0.74 0.35 0.17
152_M 251_N 0.74 0.35 0.17
27_A 240_G 0.74 0.35 0.17
89_E 207_M 0.74 0.35 0.17
124_P 330_A 0.74 0.35 0.17
143_V 197_L 0.74 0.35 0.17
100_I 391_I 0.74 0.35 0.17
220_E 81_Q 0.74 0.35 0.17
117_I 285_L 0.74 0.35 0.17
97_I 380_S 0.74 0.35 0.17
78_L 420_T 0.74 0.35 0.17
76_I 433_E 0.73 0.35 0.17
213_L 372_T 0.73 0.34 0.17
78_L 393_L 0.73 0.34 0.17
30_I 435_T 0.73 0.34 0.17
76_I 150_L 0.73 0.34 0.17
4_A 269_M 0.73 0.34 0.17
90_V 78_M 0.73 0.34 0.17
99_S 112_A 0.73 0.34 0.16
211_L 45_I 0.73 0.34 0.16
26_H 129_T 0.73 0.34 0.16
154_I 410_M 0.73 0.34 0.16
131_G 235_L 0.73 0.34 0.16
91_N 282_L 0.73 0.34 0.16
100_I 345_S 0.73 0.34 0.16
112_D 335_E 0.73 0.34 0.16
186_A 298_V 0.73 0.34 0.16
217_K 5_I 0.72 0.33 0.16
185_T 65_L 0.72 0.33 0.16
55_I 367_L 0.72 0.33 0.16
224_V 96_L 0.72 0.33 0.16
146_I 114_E 0.72 0.33 0.15
160_L 73_L 0.72 0.33 0.15
23_F 148_Y 0.72 0.33 0.15
93_P 383_V 0.72 0.33 0.15
34_I 162_I 0.72 0.33 0.15
156_S 380_S 0.72 0.32 0.15
71_I 338_H 0.72 0.32 0.15
192_Y 226_A 0.72 0.32 0.15
18_E 234_V 0.72 0.32 0.15
95_L 282_L 0.71 0.32 0.15
16_I 253_L 0.71 0.32 0.15
64_V 205_V 0.71 0.32 0.15
95_L 380_S 0.71 0.32 0.15
131_G 431_T 0.71 0.32 0.15
27_A 309_F 0.71 0.32 0.15
71_I 367_L 0.71 0.32 0.15
37_L 285_L 0.71 0.32 0.15
40_Y 344_L 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
4434 3.17 cIV_B_80_cI_M_60_1_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-60, 1) msa: Jackhmmer (2015_06) 0.94 Done - Shared
4433 2.51 cIV_B_60_cI_M_80_1_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.68 Done - Shared
4427 4.27 cIV_B_40_cI_M_40_1_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 1) msa: Jackhmmer (2015_06) 0.16 Done - Shared
4426 3.25 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
4425 2.51 cIV_B_80_cI_M_80_1_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.72 Done - Shared
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