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OPENSEQ.org
cIV_C_60_cI_H_60_human
Genes: A B A+B
Length: 261 318 576
Sequences: 2363 3920 2266
Seq/Len: 9.05 12.33 3.93
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 0.25
5 0.00 0.00 0.58
10 0.00 0.00 3.42
20 0.00 0.00 3.51
100 0.00 0.01 3.60
∞ 0.00 0.02 3.91
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 1.16 0.86 0.12
172_Y 200_L 1.14 0.84 0.12
127_L 126_N 1.11 0.83 0.11
199_V 33_L 1.01 0.74 0.08
78_G 151_L 0.97 0.69 0.07
143_S 172_F 0.94 0.66 0.06
101_F 213_I 0.93 0.65 0.06
12_K 52_A 0.92 0.63 0.06
21_A 132_A 0.91 0.63 0.06
142_V 270_F 0.91 0.62 0.06
21_A 229_T 0.90 0.61 0.05
193_Y 302_M 0.89 0.60 0.05
129_V 277_Y 0.88 0.58 0.05
255_S 280_F 0.86 0.56 0.05
138_L 158_G 0.86 0.55 0.05
25_L 168_T 0.85 0.55 0.05
76_Q 105_I 0.84 0.54 0.04
40_M 305_V 0.84 0.53 0.04
8_Y 184_M 0.84 0.53 0.04
6_H 46_L 0.84 0.53 0.04
5_S 126_N 0.83 0.52 0.04
44_M 183_M 0.83 0.52 0.04
80_R 136_V 0.83 0.52 0.04
150_S 135_A 0.83 0.51 0.04
52_L 106_L 0.83 0.51 0.04
54_M 304_H 0.82 0.51 0.04
129_V 203_G 0.82 0.50 0.04
104_S 238_T 0.81 0.48 0.04
134_T 245_T 0.80 0.48 0.04
212_S 82_A 0.80 0.48 0.04
100_A 12_P 0.80 0.47 0.04
83_M 45_L 0.80 0.47 0.04
34_W 218_G 0.80 0.47 0.04
22_L 52_A 0.80 0.47 0.04
84_I 155_L 0.78 0.46 0.04
38_H 213_I 0.78 0.45 0.04
128_E 33_L 0.78 0.45 0.04
178_A 296_L 0.78 0.45 0.04
18_L 10_I 0.78 0.45 0.04
172_Y 209_S 0.78 0.45 0.04
191_G 243_L 0.78 0.45 0.03
13_P 109_S 0.77 0.44 0.03
193_Y 41_G 0.77 0.43 0.03
212_S 9_L 0.77 0.43 0.03
112_L 60_P 0.77 0.43 0.03
39_S 263_T 0.76 0.43 0.03
48_L 8_L 0.76 0.43 0.03
76_Q 200_L 0.76 0.43 0.03
23_S 63_P 0.76 0.42 0.03
114_G 293_F 0.76 0.42 0.03
170_G 203_G 0.75 0.41 0.03
139_A 119_S 0.75 0.41 0.03
8_Y 239_T 0.75 0.41 0.03
96_G 196_T 0.75 0.41 0.03
157_N 11_V 0.74 0.40 0.03
28_T 238_T 0.74 0.40 0.03
21_A 89_L 0.74 0.40 0.03
230_K 102_L 0.74 0.40 0.03
176_L 28_L 0.74 0.40 0.03
172_Y 32_Q 0.74 0.40 0.03
215_L 94_P 0.74 0.40 0.03
149_H 52_A 0.74 0.39 0.03
33_M 232_I 0.74 0.39 0.03
256_I 22_L 0.74 0.39 0.03
217_I 177_P 0.73 0.39 0.03
45_L 175_L 0.73 0.39 0.03
44_M 175_L 0.73 0.39 0.03
159_M 29_G 0.73 0.39 0.03
138_L 230_N 0.73 0.39 0.03
165_I 6_L 0.73 0.39 0.03
235_F 114_Y 0.73 0.39 0.03
175_L 226_A 0.73 0.39 0.03
119_T 154_L 0.73 0.39 0.03
47_L 246_T 0.73 0.39 0.03
61_V 272_W 0.73 0.39 0.03
34_W 42_P 0.73 0.38 0.03
149_H 133_L 0.72 0.38 0.03
163_L 123_S 0.72 0.38 0.03
27_M 107_A 0.72 0.38 0.03
113_G 209_S 0.72 0.37 0.03
115_H 3_M 0.72 0.37 0.03
253_Y 79_L 0.72 0.37 0.03
179_S 91_M 0.72 0.37 0.03
142_V 240_T 0.72 0.37 0.03
96_G 223_F 0.71 0.37 0.03
240_W 35_K 0.71 0.37 0.03
223_L 73_T 0.71 0.36 0.03
250_L 17_M 0.71 0.36 0.03
209_I 288_L 0.71 0.36 0.03
6_H 213_I 0.71 0.36 0.03
12_K 211_F 0.71 0.36 0.03
70_H 184_M 0.71 0.36 0.03
92_L 89_L 0.71 0.36 0.03
229_S 266_L 0.70 0.35 0.03
187_T 150_L 0.70 0.35 0.03
73_P 15_I 0.70 0.35 0.03
135_S 150_L 0.70 0.35 0.03
32_A 27_I 0.70 0.35 0.03
159_M 187_I 0.70 0.35 0.03
217_I 73_T 0.70 0.35 0.03
88_T 96_V 0.70 0.35 0.03
215_L 185_W 0.70 0.35 0.03
68_Q 20_L 0.70 0.35 0.03
193_Y 155_L 0.70 0.35 0.03
6_H 49_F 0.70 0.35 0.03
150_S 102_L 0.70 0.35 0.03
8_Y 268_S 0.70 0.35 0.03
214_F 294_L 0.70 0.35 0.03
209_I 265_L 0.70 0.34 0.03
120_G 280_F 0.70 0.34 0.03
35_F 29_G 0.70 0.34 0.03
138_L 268_S 0.70 0.34 0.03
61_V 15_I 0.69 0.34 0.03
183_E 278_P 0.69 0.34 0.03
134_T 79_L 0.69 0.34 0.03
18_L 128_A 0.69 0.34 0.03
261_S 79_L 0.69 0.34 0.03
220_I 152_S 0.69 0.34 0.03
80_R 232_I 0.69 0.34 0.03
162_A 91_M 0.69 0.34 0.02
179_S 225_M 0.69 0.34 0.02
46_G 153_T 0.69 0.33 0.02
112_L 151_L 0.69 0.33 0.02
253_Y 126_N 0.69 0.33 0.02
128_E 238_T 0.69 0.33 0.02
80_R 219_P 0.69 0.33 0.02
10_M 177_P 0.69 0.33 0.02
195_S 93_N 0.69 0.33 0.02
77_K 84_L 0.68 0.33 0.02
136_V 131_G 0.68 0.33 0.02
38_H 230_N 0.68 0.32 0.02
127_L 164_T 0.68 0.32 0.02
250_L 13_I 0.68 0.32 0.02
95_A 261_T 0.68 0.32 0.02
194_G 22_L 0.68 0.32 0.02
124_L 196_T 0.68 0.32 0.02
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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