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OPENSEQ.org
cIV_B_80_cI_M_60_1_human
Genes: A B A+B
Length: 227 459 681
Sequences: 1814 2643 2156
Seq/Len: 7.99 5.76 3.17
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 0.04
5 0.00 0.00 0.31
10 0.00 0.00 3.08
20 0.00 0.00 3.10
100 0.00 0.00 3.14
∞ 0.00 0.00 3.14
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 1.76 0.99 0.94
95_L 164_L 1.53 0.97 0.87
144_L 388_W 1.35 0.92 0.76
52_N 388_W 1.31 0.91 0.73
160_L 72_L 1.29 0.89 0.71
156_S 362_A 1.21 0.85 0.64
162_S 318_A 1.20 0.84 0.63
155_T 244_M 1.18 0.83 0.61
83_I 377_G 1.16 0.81 0.59
32_F 402_V 1.14 0.80 0.57
71_I 39_L 1.10 0.76 0.53
58_A 210_Y 1.09 0.75 0.51
192_Y 194_L 1.08 0.75 0.51
156_S 95_Y 1.08 0.74 0.50
92_D 356_A 1.08 0.74 0.50
160_L 263_V 1.06 0.73 0.49
28_L 149_F 1.06 0.73 0.48
82_R 368_A 1.06 0.72 0.48
9_L 243_M 1.05 0.72 0.47
6_Q 318_A 1.05 0.72 0.47
37_L 149_F 1.03 0.70 0.46
121_Y 138_S 1.02 0.69 0.44
28_L 434_N 1.02 0.69 0.44
175_I 120_I 1.01 0.68 0.43
26_H 75_L 1.01 0.68 0.43
76_I 151_F 1.01 0.67 0.43
156_S 405_L 1.01 0.67 0.43
38_V 140_P 0.99 0.65 0.41
12_A 72_L 0.99 0.65 0.40
63_T 406_Y 0.98 0.65 0.40
67_I 158_L 0.98 0.64 0.40
174_A 315_L 0.98 0.64 0.39
174_A 398_L 0.97 0.63 0.39
160_L 282_L 0.96 0.62 0.37
68_L 116_I 0.96 0.62 0.37
182_T 317_I 0.95 0.61 0.36
211_L 442_S 0.94 0.59 0.35
199_I 324_S 0.92 0.56 0.32
193_Y 453_I 0.92 0.56 0.32
146_I 161_L 0.91 0.56 0.32
64_V 444_I 0.91 0.56 0.32
144_L 181_L 0.91 0.56 0.32
120_S 372_T 0.91 0.55 0.31
9_L 380_S 0.91 0.55 0.31
5_A 202_A 0.90 0.55 0.31
13_T 286_I 0.90 0.54 0.31
82_R 330_A 0.90 0.54 0.31
193_Y 399_N 0.90 0.54 0.30
157_Q 95_Y 0.90 0.54 0.30
215_P 446_L 0.89 0.53 0.29
95_L 143_L 0.89 0.53 0.29
130_P 143_L 0.89 0.52 0.29
96_T 315_L 0.88 0.52 0.29
96_T 197_L 0.88 0.52 0.28
12_A 358_W 0.88 0.52 0.28
55_I 367_L 0.88 0.51 0.28
138_V 457_F 0.88 0.51 0.28
55_I 410_M 0.87 0.51 0.28
29_M 275_I 0.87 0.51 0.28
188_R 377_G 0.87 0.50 0.27
153_M 198_A 0.86 0.50 0.27
154_I 291_I 0.86 0.50 0.27
40_Y 343_I 0.86 0.50 0.27
64_V 205_V 0.86 0.49 0.27
123_L 437_M 0.86 0.49 0.26
121_Y 95_Y 0.86 0.49 0.26
95_L 101_S 0.86 0.49 0.26
215_P 212_L 0.85 0.48 0.26
179_L 377_G 0.85 0.48 0.26
93_P 163_A 0.85 0.48 0.26
46_L 164_L 0.85 0.48 0.26
8_G 64_P 0.85 0.48 0.25
165_V 201_M 0.84 0.47 0.25
9_L 407_S 0.83 0.46 0.24
132_D 147_T 0.83 0.46 0.24
28_L 313_V 0.83 0.46 0.24
156_S 173_S 0.83 0.46 0.24
160_L 333_N 0.83 0.46 0.24
77_A 359_W 0.83 0.45 0.23
140_N 95_Y 0.83 0.45 0.23
184_F 278_R 0.82 0.45 0.23
38_V 297_V 0.82 0.45 0.23
97_I 2_L 0.82 0.44 0.23
160_L 298_V 0.82 0.44 0.23
214_I 57_S 0.82 0.44 0.22
40_Y 388_W 0.81 0.43 0.22
132_D 69_T 0.81 0.43 0.22
49_K 56_F 0.81 0.43 0.22
144_L 105_S 0.81 0.43 0.21
97_I 261_F 0.81 0.42 0.21
142_V 411_F 0.81 0.42 0.21
3_H 209_L 0.80 0.42 0.21
211_L 175_N 0.80 0.42 0.21
100_I 345_S 0.80 0.42 0.21
220_E 81_Q 0.80 0.42 0.21
167_T 277_L 0.80 0.42 0.21
76_I 297_V 0.80 0.41 0.21
142_V 394_L 0.80 0.41 0.21
50_L 389_S 0.80 0.41 0.21
67_I 333_N 0.80 0.41 0.21
53_T 367_L 0.80 0.41 0.20
131_G 235_L 0.80 0.41 0.20
174_A 291_I 0.80 0.41 0.20
185_T 65_L 0.79 0.41 0.20
49_K 197_L 0.79 0.41 0.20
27_A 309_F 0.79 0.41 0.20
6_Q 226_A 0.79 0.40 0.20
156_S 7_P 0.79 0.40 0.20
28_L 259_Y 0.79 0.40 0.20
127_F 332_S 0.79 0.40 0.20
110_Y 149_F 0.79 0.40 0.20
123_L 86_S 0.79 0.40 0.20
13_T 199_Y 0.78 0.40 0.19
77_A 279_Q 0.78 0.40 0.19
224_V 302_L 0.78 0.40 0.19
76_I 433_E 0.78 0.40 0.19
211_L 199_Y 0.78 0.40 0.19
117_I 95_Y 0.78 0.39 0.19
127_F 65_L 0.78 0.39 0.19
37_L 151_F 0.78 0.39 0.19
61_M 452_D 0.78 0.39 0.19
43_F 77_I 0.78 0.39 0.19
83_I 210_Y 0.78 0.39 0.19
153_M 207_M 0.77 0.39 0.19
187_T 176_I 0.77 0.39 0.19
90_V 78_M 0.77 0.38 0.18
152_M 251_N 0.77 0.38 0.18
118_F 127_I 0.77 0.38 0.18
31_I 132_I 0.77 0.38 0.18
6_Q 235_L 0.77 0.38 0.18
42_L 308_S 0.77 0.38 0.18
214_I 61_L 0.76 0.37 0.18
78_L 420_T 0.76 0.37 0.18
191_V 150_L 0.76 0.37 0.18
60_E 420_T 0.76 0.37 0.18
71_I 226_A 0.76 0.37 0.18
215_P 415_Q 0.76 0.37 0.18
217_K 5_I 0.76 0.37 0.18
174_A 65_L 0.76 0.37 0.18
23_F 164_L 0.76 0.37 0.18
23_F 148_Y 0.76 0.37 0.17
84_L 161_L 0.76 0.37 0.17
154_I 410_M 0.76 0.36 0.17
156_S 149_F 0.75 0.36 0.17
51_T 389_S 0.75 0.36 0.17
186_A 233_A 0.75 0.36 0.17
11_D 251_N 0.75 0.36 0.17
153_M 104_I 0.75 0.36 0.17
213_L 372_T 0.75 0.36 0.17
63_T 376_L 0.75 0.36 0.17
143_V 197_L 0.75 0.36 0.17
52_N 234_V 0.75 0.36 0.17
72_I 282_L 0.75 0.36 0.17
129_E 164_L 0.75 0.36 0.17
192_Y 95_Y 0.75 0.36 0.17
140_N 265_S 0.75 0.35 0.17
72_I 451_P 0.75 0.35 0.17
140_N 51_S 0.74 0.35 0.16
193_Y 205_V 0.74 0.35 0.16
12_A 113_T 0.74 0.35 0.16
78_L 393_L 0.74 0.35 0.16
110_Y 87_E 0.74 0.35 0.16
32_F 451_P 0.74 0.35 0.16
96_T 380_S 0.74 0.35 0.16
224_V 96_L 0.74 0.35 0.16
160_L 149_F 0.74 0.35 0.16
13_T 278_R 0.74 0.34 0.16
49_K 170_T 0.74 0.34 0.16
30_I 273_S 0.73 0.34 0.16
11_D 56_F 0.73 0.34 0.16
42_L 87_E 0.73 0.34 0.16
124_P 330_A 0.73 0.34 0.15
143_V 56_F 0.73 0.34 0.15
156_S 380_S 0.73 0.34 0.15
53_T 360_L 0.73 0.34 0.15
18_E 234_V 0.73 0.33 0.15
151_R 245_R 0.73 0.33 0.15
86_M 307_W 0.73 0.33 0.15
68_L 301_I 0.73 0.33 0.15
55_I 106_L 0.73 0.33 0.15
220_E 230_V 0.72 0.33 0.15
140_N 111_T 0.72 0.33 0.15
202_A 325_L 0.72 0.33 0.15
128_L 19_K 0.72 0.33 0.15
35_C 317_I 0.72 0.32 0.15
154_I 47_N 0.72 0.32 0.15
167_T 30_H 0.72 0.32 0.14
37_L 285_L 0.72 0.32 0.14
94_S 210_Y 0.72 0.32 0.14
12_A 285_L 0.72 0.32 0.14
5_A 243_M 0.72 0.32 0.14
167_T 393_L 0.72 0.32 0.14
75_L 95_Y 0.71 0.32 0.14
15_P 408_L 0.71 0.32 0.14
26_H 129_T 0.71 0.32 0.14
147_E 326_L 0.71 0.32 0.14
26_H 367_L 0.71 0.32 0.14
15_P 76_T 0.71 0.32 0.14
42_L 336_R 0.71 0.32 0.14
183_T 278_R 0.71 0.32 0.14
4_A 269_M 0.71 0.32 0.14
50_L 393_L 0.71 0.32 0.14
131_G 431_T 0.71 0.32 0.14
95_L 171_L 0.71 0.31 0.14
155_T 127_I 0.71 0.31 0.14
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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