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OPENSEQ.org
cIp_9_60_cIV_III_40_human
Genes: A B A+B
Length: 210 261 419
Sequences: 586 3629 253
Seq/Len: 2.79 13.9 0.6
MirrorTree (Pazo et al. 2001) 0.81
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 0.00
2 0.00 0.00 0.00
5 0.00 0.00 0.00
10 0.00 0.00 0.01
20 0.00 0.00 0.02
100 0.00 0.00 0.06
∞ 0.00 0.00 0.54
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
64_L 97_F 1.88 0.85 0.13
71_T 97_F 1.56 0.66 0.06
130_A 58_W 1.37 0.52 0.03
131_E 78_G 1.35 0.50 0.03
67_G 97_F 1.33 0.49 0.03
58_T 62_T 1.32 0.48 0.03
208_L 120_G 1.32 0.47 0.03
155_F 10_M 1.31 0.47 0.03
202_N 144_I 1.27 0.43 0.02
83_N 234_G 1.26 0.43 0.02
147_M 251_F 1.25 0.42 0.02
78_E 129_V 1.24 0.41 0.02
137_S 78_G 1.23 0.40 0.02
129_E 60_D 1.21 0.39 0.02
129_E 166_T 1.20 0.38 0.02
129_E 143_S 1.18 0.36 0.02
137_S 183_E 1.17 0.35 0.02
191_N 237_A 1.16 0.35 0.02
208_L 155_N 1.16 0.35 0.02
63_E 77_K 1.16 0.35 0.02
84_Y 81_Y 1.15 0.34 0.02
63_E 109_T 1.13 0.33 0.01
187_K 107_A 1.12 0.32 0.01
77_R 223_L 1.11 0.32 0.01
60_L 20_G 1.09 0.30 0.01
68_L 191_G 1.08 0.29 0.01
73_S 151_L 1.08 0.29 0.01
120_I 230_K 1.07 0.29 0.01
174_S 50_N 1.07 0.29 0.01
159_A 88_T 1.06 0.28 0.01
186_E 23_S 1.06 0.28 0.01
58_T 233_F 1.05 0.28 0.01
182_L 152_M 1.05 0.27 0.01
129_E 83_M 1.03 0.26 0.01
106_S 170_G 1.01 0.25 0.01
186_E 172_Y 1.01 0.25 0.01
155_F 114_G 1.00 0.24 0.01
134_T 129_V 1.00 0.24 0.01
170_N 9_H 0.99 0.24 0.01
63_E 112_L 0.99 0.23 0.01
71_T 143_S 0.99 0.23 0.01
129_E 88_T 0.98 0.23 0.01
71_T 166_T 0.98 0.23 0.01
168_G 11_V 0.98 0.23 0.01
204_Q 231_H 0.98 0.23 0.01
206_D 225_F 0.98 0.23 0.01
206_D 129_V 0.97 0.23 0.01
186_E 219_F 0.97 0.23 0.01
182_L 47_L 0.97 0.22 0.01
206_D 170_G 0.97 0.22 0.01
204_Q 65_S 0.97 0.22 0.01
70_M 167_I 0.97 0.22 0.01
82_I 127_L 0.96 0.22 0.01
57_R 68_Q 0.96 0.22 0.01
71_T 191_G 0.96 0.22 0.01
159_A 146_W 0.96 0.22 0.01
168_G 9_H 0.96 0.22 0.01
120_I 171_L 0.95 0.22 0.01
147_M 214_F 0.95 0.21 0.01
68_L 26_L 0.94 0.21 0.01
182_L 29_S 0.94 0.21 0.01
201_A 255_S 0.94 0.21 0.01
120_I 2_T 0.94 0.21 0.01
63_E 166_T 0.94 0.21 0.01
51_V 40_M 0.94 0.21 0.01
63_E 143_S 0.93 0.20 0.01
178_H 225_F 0.93 0.20 0.01
73_S 100_A 0.93 0.20 0.01
180_E 16_W 0.93 0.20 0.01
182_L 53_T 0.93 0.20 0.01
105_P 54_M 0.93 0.20 0.01
187_K 10_M 0.93 0.20 0.01
171_F 32_T 0.93 0.20 0.01
182_L 28_T 0.92 0.20 0.01
91_L 18_L 0.91 0.20 0.01
202_N 126_P 0.91 0.20 0.01
203_I 15_P 0.91 0.19 0.01
60_L 27_M 0.91 0.19 0.01
67_G 78_G 0.90 0.19 0.01
67_G 191_G 0.90 0.19 0.01
157_Q 72_T 0.90 0.19 0.01
205_A 185_P 0.90 0.19 0.01
137_S 159_M 0.90 0.19 0.01
67_G 258_W 0.90 0.19 0.01
155_F 25_L 0.89 0.18 0.01
69_G 135_S 0.89 0.18 0.01
58_T 83_M 0.88 0.18 0.01
71_T 83_M 0.88 0.18 0.01
178_H 179_S 0.88 0.18 0.01
202_N 108_P 0.88 0.18 0.01
68_L 97_F 0.88 0.18 0.01
204_Q 39_S 0.88 0.18 0.01
202_N 238_A 0.88 0.18 0.01
72_L 195_S 0.87 0.17 0.01
132_P 27_M 0.87 0.17 0.01
194_K 155_N 0.87 0.17 0.01
68_L 153_E 0.87 0.17 0.01
177_T 72_T 0.87 0.17 0.01
201_A 128_E 0.86 0.17 0.01
202_N 150_S 0.86 0.17 0.01
131_E 139_A 0.86 0.17 0.01
59_L 196_T 0.86 0.17 0.01
83_N 259_W 0.86 0.17 0.01
130_A 151_L 0.86 0.17 0.01
157_Q 31_L 0.85 0.17 0.01
130_A 214_F 0.85 0.17 0.01
164_A 146_W 0.85 0.17 0.01
73_S 229_S 0.85 0.17 0.01
144_D 206_L 0.85 0.17 0.01
203_I 9_H 0.85 0.17 0.01
124_Q 6_H 0.85 0.17 0.01
60_L 104_S 0.85 0.16 0.01
58_T 159_M 0.84 0.16 0.01
105_P 161_Q 0.84 0.16 0.01
194_K 123_P 0.84 0.16 0.01
67_G 192_I 0.84 0.16 0.01
86_F 83_M 0.84 0.16 0.01
197_A 158_Q 0.84 0.16 0.01
152_Y 176_L 0.84 0.16 0.01
55_A 167_I 0.84 0.16 0.01
91_L 156_R 0.83 0.16 0.01
182_L 132_L 0.83 0.16 0.01
105_P 82_G 0.83 0.16 0.01
70_M 19_T 0.83 0.16 0.01
80_A 36_H 0.83 0.15 0.01
91_L 104_S 0.83 0.15 0.01
58_T 143_S 0.82 0.15 0.01
194_K 84_I 0.82 0.15 0.01
172_E 60_D 0.82 0.15 0.01
208_L 128_E 0.82 0.15 0.01
67_G 254_V 0.82 0.15 0.01
168_G 85_L 0.82 0.15 0.01
171_F 113_G 0.82 0.15 0.01
75_L 108_P 0.81 0.15 0.00
52_T 65_S 0.81 0.15 0.00
194_K 150_S 0.81 0.15 0.00
57_R 213_T 0.81 0.15 0.00
59_L 189_S 0.81 0.15 0.00
180_E 131_L 0.81 0.15 0.00
101_L 195_S 0.81 0.15 0.00
51_V 212_S 0.81 0.15 0.00
207_Y 92_F 0.81 0.15 0.00
68_L 195_S 0.81 0.15 0.00
155_F 65_S 0.81 0.15 0.00
72_L 127_L 0.81 0.15 0.00
59_L 194_G 0.81 0.15 0.00
89_G 9_H 0.80 0.14 0.00
168_G 200_A 0.80 0.14 0.00
178_H 159_M 0.80 0.14 0.00
159_A 163_L 0.80 0.14 0.00
190_N 164_L 0.80 0.14 0.00
155_F 18_L 0.80 0.14 0.00
187_K 75_V 0.80 0.14 0.00
181_L 206_L 0.80 0.14 0.00
82_I 175_L 0.80 0.14 0.00
202_N 149_H 0.80 0.14 0.00
134_T 256_I 0.80 0.14 0.00
75_L 231_H 0.80 0.14 0.00
170_N 11_V 0.79 0.14 0.00
64_L 7_A 0.79 0.14 0.00
56_A 165_I 0.79 0.14 0.00
202_N 255_S 0.79 0.14 0.00
186_E 20_G 0.79 0.14 0.00
204_Q 18_L 0.79 0.14 0.00
148_T 155_N 0.79 0.14 0.00
181_L 77_K 0.79 0.14 0.00
124_Q 179_S 0.79 0.14 0.00
53_D 54_M 0.79 0.14 0.00
59_L 255_S 0.78 0.14 0.00
186_E 237_A 0.78 0.14 0.00
63_E 152_M 0.78 0.14 0.00
58_T 166_T 0.78 0.14 0.00
209_Y 56_Q 0.78 0.14 0.00
204_Q 100_A 0.78 0.14 0.00
80_A 8_Y 0.78 0.14 0.00
70_M 216_T 0.78 0.13 0.00
71_T 59_R 0.78 0.13 0.00
197_A 142_V 0.77 0.13 0.00
72_L 125_N 0.77 0.13 0.00
164_A 13_P 0.77 0.13 0.00
69_G 23_S 0.77 0.13 0.00
86_F 233_F 0.77 0.13 0.00
148_T 77_K 0.77 0.13 0.00
133_R 129_V 0.77 0.13 0.00
86_F 11_V 0.77 0.13 0.00
203_I 79_L 0.77 0.13 0.00
195_W 118_P 0.76 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
6073 0.6 cIp_9_60_cIV_III_40_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-40, 8) msa: Jackhmmer (2016_06b) 0.13 Done - Shared
6070 0.14 cIp_9_40_cIV_III_60_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-60, 8) msa: HHblits (2015_06) 0.00 Done - Shared
5699 0.58 cIp_9_40_cIV_III_60_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-60, 8) msa: Jackhmmer (2016_06b) 0.10 Done - Shared
5696 0.62 cIp_9_40_cIV_III_20_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2016_06b) 0.01 Done - Shared
5693 0.58 cIp_9_20_cIV_III_40_human Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: Jackhmmer (2016_06b) 0.09 Done - Shared
5692 0.6 cIp_9_40_cIV_III_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2016_06b) 0.14 Done - Shared
5691 0.17 cIp_9_4_cIV_III_4_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
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