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OPENSEQ.org
cIV_B_60_cI_H_60_human
Genes: A B A+B
Length: 227 318 541
Sequences: 2677 3920 2271
Seq/Len: 11.79 12.33 4.2
MirrorTree (Pazo et al. 2001) 0.80
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 0.13
2 0.00 0.00 0.29
5 0.00 0.00 1.90
10 0.00 0.00 3.58
20 0.00 0.00 3.70
100 0.00 0.01 3.77
∞ 0.00 0.02 4.17
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
33_L 118_W 1.15 0.87 0.12
99_S 79_L 1.14 0.86 0.12
162_S 217_A 1.08 0.82 0.10
170_L 45_L 1.05 0.80 0.09
144_L 237_L 1.05 0.79 0.09
11_D 231_I 1.02 0.77 0.09
127_F 87_T 1.02 0.77 0.08
34_I 17_M 1.01 0.76 0.08
90_V 132_A 0.99 0.73 0.08
76_I 97_N 0.98 0.73 0.07
95_L 11_V 0.97 0.71 0.07
24_H 114_Y 0.95 0.69 0.07
192_Y 78_A 0.94 0.68 0.07
155_T 128_A 0.93 0.67 0.06
206_F 144_V 0.93 0.67 0.06
61_M 144_V 0.93 0.67 0.06
168_L 89_L 0.93 0.66 0.06
203_N 35_K 0.92 0.65 0.06
92_D 266_L 0.91 0.65 0.06
34_I 46_L 0.91 0.64 0.06
105_Y 81_I 0.91 0.64 0.06
116_L 172_F 0.89 0.62 0.05
203_N 212_N 0.89 0.61 0.05
23_F 209_S 0.89 0.61 0.05
160_L 109_S 0.87 0.59 0.05
184_F 115_S 0.87 0.59 0.05
29_M 165_L 0.87 0.59 0.05
99_S 95_L 0.87 0.59 0.05
61_M 104_F 0.87 0.59 0.05
155_T 158_G 0.87 0.59 0.05
205_S 203_G 0.86 0.58 0.05
160_L 132_A 0.85 0.57 0.05
77_A 48_P 0.85 0.56 0.05
12_A 116_I 0.85 0.56 0.05
37_L 232_I 0.84 0.55 0.05
12_A 52_A 0.83 0.54 0.04
152_M 157_S 0.83 0.54 0.04
170_L 311_I 0.83 0.54 0.04
148_T 307_M 0.83 0.53 0.04
76_I 9_L 0.82 0.53 0.04
83_I 67_T 0.82 0.52 0.04
142_V 157_S 0.82 0.52 0.04
164_A 248_D 0.81 0.52 0.04
95_L 150_L 0.81 0.51 0.04
9_L 135_A 0.81 0.51 0.04
86_M 232_I 0.81 0.51 0.04
223_P 222_L 0.81 0.51 0.04
99_S 257_T 0.81 0.50 0.04
38_V 193_T 0.80 0.50 0.04
215_P 160_F 0.80 0.50 0.04
88_D 225_M 0.80 0.49 0.04
192_Y 263_T 0.80 0.49 0.04
63_T 217_A 0.80 0.49 0.04
178_R 121_W 0.80 0.49 0.04
188_R 269_L 0.80 0.49 0.04
121_Y 82_A 0.80 0.49 0.04
190_G 151_L 0.79 0.48 0.04
205_S 209_S 0.79 0.48 0.04
186_A 302_M 0.79 0.48 0.04
59_Q 200_L 0.79 0.48 0.04
59_Q 113_V 0.79 0.48 0.04
46_L 4_A 0.79 0.47 0.04
156_S 293_F 0.79 0.47 0.04
175_I 118_W 0.78 0.47 0.04
143_V 257_T 0.78 0.47 0.04
175_I 126_N 0.78 0.47 0.04
223_P 237_L 0.78 0.47 0.04
83_I 297_T 0.78 0.46 0.04
127_F 77_L 0.77 0.46 0.04
217_K 15_I 0.77 0.46 0.04
193_Y 135_A 0.77 0.46 0.04
35_C 271_L 0.77 0.46 0.04
51_T 71_Y 0.77 0.45 0.04
87_T 303_W 0.77 0.45 0.03
105_Y 273_I 0.77 0.45 0.03
19_E 203_G 0.76 0.45 0.03
110_Y 162_L 0.76 0.45 0.03
78_L 154_L 0.76 0.45 0.03
64_V 15_I 0.76 0.45 0.03
131_G 88_P 0.76 0.44 0.03
162_S 271_L 0.76 0.44 0.03
34_I 302_M 0.76 0.44 0.03
25_D 205_S 0.76 0.44 0.03
216_L 102_L 0.76 0.44 0.03
139_D 79_L 0.76 0.44 0.03
225_F 77_L 0.75 0.43 0.03
219_F 146_L 0.75 0.43 0.03
15_P 211_F 0.75 0.43 0.03
82_R 225_M 0.75 0.43 0.03
163_W 181_L 0.75 0.43 0.03
77_A 133_L 0.75 0.43 0.03
122_M 22_L 0.75 0.42 0.03
215_P 237_L 0.75 0.42 0.03
138_V 25_R 0.74 0.42 0.03
93_P 272_W 0.74 0.42 0.03
97_I 176_L 0.74 0.42 0.03
222_G 219_P 0.74 0.42 0.03
59_Q 185_W 0.74 0.42 0.03
116_L 132_A 0.74 0.42 0.03
92_D 53_M 0.74 0.42 0.03
8_G 11_V 0.74 0.41 0.03
111_T 271_L 0.74 0.41 0.03
29_M 91_M 0.73 0.41 0.03
119_N 114_Y 0.73 0.41 0.03
34_I 148_I 0.73 0.40 0.03
121_Y 32_Q 0.73 0.40 0.03
61_M 8_L 0.73 0.40 0.03
61_M 266_L 0.73 0.40 0.03
215_P 217_A 0.73 0.40 0.03
12_A 111_L 0.73 0.40 0.03
117_I 175_L 0.73 0.40 0.03
157_Q 193_T 0.73 0.40 0.03
168_L 147_A 0.73 0.40 0.03
165_V 43_Y 0.72 0.40 0.03
141_R 90_P 0.72 0.40 0.03
97_I 85_L 0.72 0.39 0.03
225_F 307_M 0.72 0.39 0.03
51_T 119_S 0.72 0.39 0.03
2_A 29_G 0.72 0.39 0.03
86_M 211_F 0.72 0.39 0.03
170_L 185_W 0.72 0.39 0.03
11_D 111_L 0.72 0.39 0.03
100_I 7_L 0.72 0.39 0.03
219_F 174_L 0.72 0.39 0.03
20_L 239_T 0.72 0.39 0.03
128_L 116_I 0.72 0.39 0.03
42_L 223_F 0.71 0.38 0.03
97_I 260_V 0.71 0.38 0.03
214_I 292_N 0.71 0.38 0.03
99_S 66_S 0.71 0.38 0.03
213_L 74_A 0.71 0.38 0.03
102_H 100_L 0.71 0.38 0.03
223_P 151_L 0.71 0.38 0.03
199_I 203_G 0.71 0.38 0.03
87_T 182_A 0.71 0.38 0.03
87_T 177_P 0.71 0.38 0.03
154_I 84_L 0.71 0.37 0.03
32_F 266_L 0.70 0.36 0.03
205_S 201_A 0.70 0.36 0.03
102_H 212_N 0.70 0.36 0.03
154_I 140_I 0.70 0.36 0.03
65_W 121_W 0.70 0.36 0.03
139_D 148_I 0.70 0.36 0.03
72_I 243_L 0.70 0.36 0.03
39_L 188_S 0.70 0.36 0.03
72_I 3_M 0.70 0.36 0.03
70_A 241_I 0.70 0.36 0.03
7_V 90_P 0.70 0.36 0.03
167_T 182_A 0.69 0.36 0.03
123_L 225_M 0.69 0.35 0.03
89_E 221_A 0.69 0.35 0.03
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
4579 4.19 cIV_B_60_cI_H_20_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.21 Done - Shared
4574 4.21 cIV_B_60_cI_H_40_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.36 Done - Shared
4573 3.59 cIV_B_80_cI_H_60_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.33 Done - Shared
4568 3.98 cIV_B_60_cI_H_80_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-80, 8) msa: Jackhmmer (2015_06) 0.28 Done - Shared
4567 3.6 cIV_B_80_cI_H_60_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.21 Done - Shared
4565 4.2 cIV_B_60_cI_H_60_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.12 Done - Shared
4564 5.01 cIV_B_40_cI_H_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
4563 3.53 cIV_B_80_cI_H_80_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 8) msa: Jackhmmer (2015_06) 0.19 Done - Shared
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