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OPENSEQ.org
cIp_9_40_cIV_C_40
Genes: A B A+B
Length: 163 274 431
Sequences: 644 2529 247
Seq/Len: 3.95 9.23 0.57
MirrorTree (Pazo et al. 2001) 0.60
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 0.01
5 0.00 0.00 0.01
10 0.00 0.00 0.01
20 0.00 0.00 0.03
100 0.00 0.00 0.06
∞ 0.01 0.00 0.57
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
82_D 179_A 1.64 0.70 0.01
82_D 91_F 1.49 0.59 0.00
17_F 105_W 1.48 0.59 0.00
73_V 233_I 1.46 0.57 0.00
82_D 155_A 1.29 0.44 0.00
161_P 132_G 1.25 0.40 0.00
16_D 85_I 1.24 0.40 0.00
90_S 86_G 1.17 0.35 0.00
161_P 134_V 1.17 0.34 0.00
135_F 29_L 1.16 0.34 0.00
139_Q 229_F 1.15 0.33 0.00
87_E 268_V 1.15 0.33 0.00
24_G 105_W 1.13 0.32 0.00
159_D 238_G 1.09 0.29 0.00
124_F 132_G 1.08 0.28 0.00
22_G 26_F 1.06 0.27 0.00
157_Q 244_Q 1.06 0.27 0.00
127_A 59_V 1.05 0.27 0.00
131_R 9_Y 1.03 0.26 0.00
59_N 183_G 1.03 0.26 0.00
121_G 10_Q 1.03 0.25 0.00
12_F 241_T 1.03 0.25 0.00
84_E 86_G 1.03 0.25 0.00
20_G 105_W 1.02 0.24 0.00
133_E 122_P 1.01 0.24 0.00
82_D 69_D 1.01 0.24 0.00
21_F 204_T 1.01 0.24 0.00
108_F 181_I 1.01 0.24 0.00
127_A 181_I 1.00 0.24 0.00
100_M 264_F 1.00 0.24 0.00
31_P 141_L 1.00 0.24 0.00
83_A 67_W 1.00 0.23 0.00
159_D 141_L 1.00 0.23 0.00
28_F 126_G 0.98 0.23 0.00
35_L 3_H 0.98 0.22 0.00
33_P 9_Y 0.97 0.22 0.00
161_P 168_D 0.96 0.21 0.00
143_A 205_V 0.96 0.21 0.00
44_L 169_R 0.96 0.21 0.00
150_A 271_I 0.95 0.21 0.00
130_T 80_T 0.94 0.20 0.00
11_Y 86_G 0.94 0.20 0.00
97_D 219_A 0.94 0.20 0.00
157_Q 108_A 0.94 0.20 0.00
140_K 11_I 0.94 0.20 0.00
44_L 24_G 0.94 0.20 0.00
20_G 27_V 0.93 0.20 0.00
13_L 21_G 0.93 0.20 0.00
26_R 195_S 0.93 0.20 0.00
37_Y 89_Y 0.93 0.20 0.00
11_Y 111_K 0.92 0.19 0.00
39_H 12_L 0.92 0.19 0.00
85_R 96_M 0.92 0.19 0.00
58_P 196_H 0.92 0.19 0.00
121_G 199_F 0.92 0.19 0.00
155_N 156_V 0.91 0.19 0.00
139_Q 237_K 0.90 0.18 0.00
59_N 163_F 0.90 0.18 0.00
157_Q 177_I 0.90 0.18 0.00
40_E 110_I 0.90 0.18 0.00
5_F 271_I 0.89 0.18 0.00
20_G 22_A 0.89 0.18 0.00
11_Y 246_V 0.89 0.18 0.00
37_Y 92_I 0.89 0.18 0.00
33_P 223_I 0.89 0.17 0.00
58_P 172_T 0.88 0.17 0.00
4_D 147_L 0.88 0.17 0.00
16_D 240_M 0.88 0.17 0.00
154_R 268_V 0.88 0.17 0.00
90_S 151_L 0.87 0.17 0.00
150_A 168_D 0.87 0.17 0.00
135_F 229_F 0.87 0.17 0.00
58_P 50_W 0.87 0.17 0.00
22_G 267_V 0.86 0.17 0.00
155_N 125_D 0.86 0.16 0.00
15_W 184_V 0.86 0.16 0.00
21_F 205_V 0.86 0.16 0.00
20_G 205_V 0.85 0.16 0.00
108_F 185_C 0.85 0.16 0.00
41_K 54_I 0.85 0.16 0.00
58_P 126_G 0.84 0.16 0.00
90_S 196_H 0.84 0.16 0.00
36_N 247_G 0.84 0.16 0.00
140_K 74_G 0.84 0.15 0.00
21_F 3_H 0.83 0.15 0.00
24_G 179_A 0.83 0.15 0.00
151_E 3_H 0.83 0.15 0.00
31_P 5_K 0.83 0.15 0.00
156_L 119_P 0.83 0.15 0.00
35_L 211_Y 0.82 0.15 0.00
21_F 105_W 0.82 0.15 0.00
100_M 227_F 0.82 0.15 0.00
124_F 24_G 0.82 0.15 0.00
11_Y 6_N 0.82 0.15 0.00
8_A 180_V 0.82 0.15 0.00
22_G 202_A 0.82 0.15 0.00
35_L 58_G 0.82 0.15 0.00
110_Q 74_G 0.82 0.15 0.00
33_P 105_W 0.82 0.15 0.00
131_R 238_G 0.81 0.14 0.00
22_G 205_V 0.81 0.14 0.00
108_F 28_M 0.81 0.14 0.00
30_S 236_L 0.81 0.14 0.00
108_F 26_F 0.81 0.14 0.00
157_Q 181_I 0.81 0.14 0.00
82_D 80_T 0.81 0.14 0.00
16_D 235_L 0.81 0.14 0.00
39_H 111_K 0.80 0.14 0.00
140_K 133_I 0.80 0.14 0.00
23_L 35_W 0.80 0.14 0.00
13_L 112_N 0.80 0.14 0.00
117_A 165_L 0.80 0.14 0.00
11_Y 239_Q 0.80 0.14 0.00
158_L 54_I 0.80 0.14 0.00
143_A 180_V 0.80 0.14 0.00
37_Y 90_G 0.80 0.14 0.00
35_L 185_C 0.80 0.14 0.00
58_P 63_M 0.79 0.14 0.00
139_Q 53_L 0.79 0.14 0.00
144_N 132_G 0.79 0.14 0.00
6_A 63_M 0.79 0.14 0.00
141_L 257_F 0.79 0.14 0.00
131_R 183_G 0.79 0.14 0.00
139_Q 185_C 0.79 0.14 0.00
25_M 123_I 0.79 0.13 0.00
126_Y 22_A 0.79 0.13 0.00
135_F 82_V 0.79 0.13 0.00
12_F 124_K 0.78 0.13 0.00
90_S 181_I 0.78 0.13 0.00
110_Q 93_L 0.78 0.13 0.00
19_K 200_G 0.78 0.13 0.00
4_D 49_P 0.78 0.13 0.00
73_V 126_G 0.78 0.13 0.00
73_V 243_K 0.78 0.13 0.00
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
3871 0.41 cIp_9_40_1_cIV_C_40_1 Δgene:(1, ∞) A:(1E-40, 1) B:(1E-40, 1) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3687 1.02 cIp_9_4_cIV_C_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3686 0.57 cIp_9_40_cIV_C_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
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