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OPENSEQ.org
cIV_C_60_cI_H_40_human
Genes: A B A+B
Length: 261 318 576
Sequences: 2363 4127 2293
Seq/Len: 9.05 12.98 3.98
MirrorTree (Pazo et al. 2001) 0.79
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 0.09
2 0.00 0.00 0.26
5 0.00 0.00 0.60
10 0.00 0.00 3.42
20 0.00 0.01 3.56
100 0.00 0.01 3.59
∞ 0.00 0.02 3.96
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
135_S 187_I 1.10 0.82 0.06
127_L 126_N 1.09 0.82 0.06
172_Y 200_L 1.08 0.80 0.06
199_V 33_L 1.02 0.75 0.05
21_A 132_A 0.97 0.70 0.04
76_Q 105_I 0.95 0.67 0.04
143_S 172_F 0.94 0.66 0.04
78_G 151_L 0.92 0.64 0.04
21_A 229_T 0.90 0.61 0.03
12_K 52_A 0.88 0.59 0.03
142_V 270_F 0.88 0.59 0.03
52_L 106_L 0.88 0.59 0.03
178_A 296_L 0.87 0.58 0.03
25_L 168_T 0.87 0.57 0.03
101_F 213_I 0.87 0.57 0.03
128_E 33_L 0.85 0.55 0.03
138_L 158_G 0.85 0.54 0.03
83_M 45_L 0.84 0.54 0.03
40_M 305_V 0.84 0.53 0.03
255_S 280_F 0.83 0.53 0.03
172_Y 209_S 0.83 0.53 0.03
80_R 136_V 0.83 0.52 0.03
54_M 304_H 0.82 0.51 0.03
159_M 29_G 0.82 0.51 0.03
6_H 46_L 0.81 0.50 0.03
18_L 128_A 0.81 0.49 0.02
21_A 89_L 0.81 0.49 0.02
191_G 243_L 0.80 0.48 0.02
18_L 10_I 0.80 0.47 0.02
5_S 126_N 0.79 0.47 0.02
138_L 230_N 0.79 0.47 0.02
159_M 187_I 0.79 0.47 0.02
39_S 263_T 0.78 0.46 0.02
175_L 226_A 0.78 0.46 0.02
44_M 175_L 0.78 0.46 0.02
34_W 218_G 0.78 0.45 0.02
44_M 183_M 0.78 0.45 0.02
112_L 60_P 0.78 0.45 0.02
22_L 52_A 0.77 0.44 0.02
134_T 245_T 0.77 0.44 0.02
193_Y 155_L 0.77 0.43 0.02
100_A 12_P 0.77 0.43 0.02
48_L 8_L 0.77 0.43 0.02
129_V 277_Y 0.77 0.43 0.02
187_T 150_L 0.77 0.43 0.02
212_S 9_L 0.76 0.43 0.02
8_Y 239_T 0.76 0.43 0.02
129_V 203_G 0.76 0.43 0.02
213_T 89_L 0.76 0.42 0.02
179_S 91_M 0.76 0.42 0.02
112_L 151_L 0.76 0.42 0.02
47_L 246_T 0.75 0.42 0.02
150_S 135_A 0.75 0.42 0.02
91_V 10_I 0.75 0.41 0.02
149_H 52_A 0.75 0.41 0.02
209_I 265_L 0.75 0.41 0.02
38_H 213_I 0.75 0.41 0.02
142_V 240_T 0.74 0.41 0.02
35_F 29_G 0.74 0.41 0.02
8_Y 65_T 0.74 0.41 0.02
193_Y 302_M 0.74 0.41 0.02
157_N 11_V 0.74 0.41 0.02
13_P 109_S 0.74 0.40 0.02
27_M 107_A 0.74 0.40 0.02
135_S 150_L 0.74 0.40 0.02
256_I 22_L 0.74 0.40 0.02
96_G 196_T 0.74 0.40 0.02
92_L 89_L 0.74 0.40 0.02
135_S 232_I 0.74 0.40 0.02
48_L 83_L 0.74 0.40 0.02
31_L 309_I 0.73 0.39 0.02
67_Y 4_A 0.73 0.39 0.02
217_I 73_T 0.73 0.39 0.02
104_S 238_T 0.73 0.39 0.02
28_T 238_T 0.73 0.39 0.02
8_Y 184_M 0.73 0.39 0.02
61_V 15_I 0.73 0.39 0.02
34_W 42_P 0.73 0.39 0.02
217_I 177_P 0.73 0.39 0.02
175_L 159_S 0.73 0.38 0.02
32_A 27_I 0.72 0.38 0.02
23_S 61_L 0.72 0.38 0.02
6_H 213_I 0.72 0.38 0.02
113_G 209_S 0.72 0.37 0.02
68_Q 20_L 0.72 0.37 0.02
212_S 82_A 0.72 0.37 0.02
179_S 225_M 0.72 0.37 0.02
96_G 223_F 0.71 0.37 0.02
119_T 154_L 0.71 0.37 0.02
33_M 232_I 0.71 0.37 0.02
165_I 265_L 0.71 0.36 0.02
101_F 111_L 0.71 0.36 0.02
84_I 155_L 0.71 0.36 0.02
42_L 230_N 0.71 0.36 0.02
101_F 185_W 0.71 0.36 0.02
193_Y 41_G 0.71 0.36 0.02
158_Q 128_A 0.71 0.36 0.02
95_A 64_A 0.71 0.36 0.02
240_W 35_K 0.70 0.35 0.02
172_Y 32_Q 0.70 0.35 0.02
170_G 203_G 0.70 0.35 0.02
23_S 63_P 0.70 0.35 0.02
230_K 102_L 0.70 0.35 0.02
6_H 49_F 0.70 0.35 0.02
213_T 4_A 0.70 0.35 0.02
46_G 153_T 0.70 0.35 0.02
10_M 268_S 0.70 0.35 0.02
139_A 119_S 0.69 0.34 0.02
167_I 257_T 0.69 0.34 0.02
259_W 127_Y 0.69 0.34 0.02
114_G 293_F 0.69 0.34 0.02
176_L 28_L 0.69 0.34 0.02
209_I 288_L 0.69 0.34 0.02
214_F 294_L 0.69 0.34 0.02
38_H 230_N 0.69 0.34 0.02
80_R 219_P 0.69 0.34 0.02
215_L 185_W 0.69 0.34 0.02
240_W 144_V 0.69 0.34 0.02
70_H 184_M 0.69 0.34 0.01
255_S 125_S 0.69 0.33 0.01
109_T 280_F 0.69 0.33 0.01
95_A 310_T 0.68 0.33 0.01
250_L 17_M 0.68 0.33 0.01
138_L 268_S 0.68 0.33 0.01
121_I 112_A 0.68 0.33 0.01
124_L 196_T 0.68 0.32 0.01
95_A 261_T 0.68 0.32 0.01
226_H 43_Y 0.68 0.32 0.01
175_L 162_L 0.68 0.32 0.01
38_H 110_S 0.68 0.32 0.01
50_N 190_L 0.68 0.32 0.01
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
4586 3.98 cIV_C_60_cI_H_40_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.06 Done - Shared
4584 3.93 cIV_C_60_cI_H_60_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.12 Done - Shared
4582 3.67 cIV_C_80_cI_H_80_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 8) msa: Jackhmmer (2015_06) 0.08 Done - Shared
4581 3.95 cIV_C_60_cI_H_20_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.08 Done - Shared
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