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OPENSEQ.org
cIp_9_40_cIV_III_20_human
Genes: A B A+B
Length: 210 261 418
Sequences: 638 3818 258
Seq/Len: 3.04 14.63 0.62
MirrorTree (Pazo et al. 2001) 0.58
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 0.05
∞ 0.00 0.00 0.55
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 1.64 0.73 0.01
84_Y 81_Y 1.54 0.66 0.01
155_F 10_M 1.44 0.58 0.01
130_A 58_W 1.41 0.56 0.01
71_T 97_F 1.30 0.47 0.00
131_E 78_G 1.29 0.46 0.00
182_L 29_S 1.26 0.43 0.00
58_T 62_T 1.24 0.42 0.00
83_N 234_G 1.20 0.39 0.00
182_L 28_T 1.17 0.37 0.00
68_L 26_L 1.16 0.36 0.00
64_L 193_Y 1.12 0.33 0.00
63_E 109_T 1.11 0.32 0.00
202_N 144_I 1.09 0.31 0.00
67_G 97_F 1.09 0.31 0.00
65_F 37_F 1.09 0.31 0.00
187_K 107_A 1.09 0.31 0.00
168_G 11_V 1.09 0.31 0.00
63_E 152_M 1.07 0.29 0.00
191_N 237_A 1.07 0.29 0.00
203_I 10_M 1.06 0.29 0.00
186_E 172_Y 1.05 0.28 0.00
186_E 23_S 1.05 0.28 0.00
147_M 251_F 1.05 0.28 0.00
60_L 20_G 1.04 0.27 0.00
62_T 59_R 1.03 0.27 0.00
202_N 150_S 1.02 0.26 0.00
59_L 255_S 1.02 0.26 0.00
129_E 88_T 1.01 0.25 0.00
171_F 32_T 1.00 0.25 0.00
70_M 37_F 1.00 0.25 0.00
180_E 16_W 1.00 0.25 0.00
86_F 11_V 1.00 0.25 0.00
63_E 77_K 1.00 0.25 0.00
137_S 251_F 1.00 0.25 0.00
129_E 60_D 0.99 0.24 0.00
137_S 78_G 0.99 0.24 0.00
159_A 146_W 0.98 0.23 0.00
71_T 83_M 0.98 0.23 0.00
82_I 121_I 0.98 0.23 0.00
68_L 191_G 0.97 0.23 0.00
77_R 223_L 0.97 0.23 0.00
204_Q 18_L 0.96 0.23 0.00
170_N 9_H 0.96 0.23 0.00
82_I 127_L 0.96 0.23 0.00
134_T 129_V 0.96 0.23 0.00
203_I 9_H 0.96 0.23 0.00
78_E 129_V 0.96 0.23 0.00
51_V 118_P 0.96 0.22 0.00
73_S 151_L 0.95 0.22 0.00
168_G 9_H 0.95 0.22 0.00
170_N 11_V 0.95 0.22 0.00
205_A 185_P 0.95 0.22 0.00
174_S 50_N 0.95 0.22 0.00
129_E 83_M 0.95 0.22 0.00
201_A 128_E 0.94 0.21 0.00
182_L 47_L 0.94 0.21 0.00
55_A 167_I 0.94 0.21 0.00
86_F 83_M 0.93 0.21 0.00
180_E 131_L 0.93 0.21 0.00
186_E 219_F 0.92 0.20 0.00
58_T 233_F 0.92 0.20 0.00
132_P 27_M 0.92 0.20 0.00
86_F 143_S 0.92 0.20 0.00
71_T 143_S 0.92 0.20 0.00
91_L 18_L 0.92 0.20 0.00
71_T 166_T 0.91 0.20 0.00
155_F 25_L 0.91 0.20 0.00
67_G 254_V 0.91 0.20 0.00
82_I 39_S 0.91 0.20 0.00
187_K 65_S 0.91 0.20 0.00
177_T 115_H 0.90 0.19 0.00
204_Q 49_T 0.90 0.19 0.00
57_R 68_Q 0.90 0.19 0.00
202_N 238_A 0.89 0.19 0.00
82_I 175_L 0.89 0.19 0.00
130_A 151_L 0.89 0.19 0.00
186_E 237_A 0.89 0.18 0.00
201_A 28_T 0.89 0.18 0.00
105_P 54_M 0.88 0.18 0.00
120_I 222_Q 0.88 0.18 0.00
204_Q 164_L 0.88 0.18 0.00
67_G 78_G 0.88 0.18 0.00
65_F 198_F 0.88 0.18 0.00
201_A 255_S 0.88 0.18 0.00
182_L 152_M 0.88 0.18 0.00
204_Q 60_D 0.88 0.18 0.00
82_I 49_T 0.88 0.18 0.00
63_E 227_F 0.88 0.18 0.00
206_D 225_F 0.87 0.18 0.00
206_D 129_V 0.87 0.18 0.00
51_V 40_M 0.87 0.18 0.00
174_S 58_W 0.87 0.18 0.00
157_Q 72_T 0.87 0.18 0.00
63_E 143_S 0.87 0.18 0.00
75_L 5_S 0.86 0.17 0.00
63_E 112_L 0.86 0.17 0.00
164_A 146_W 0.86 0.17 0.00
155_F 114_G 0.85 0.17 0.00
71_T 191_G 0.85 0.17 0.00
209_Y 167_I 0.85 0.17 0.00
78_E 26_L 0.85 0.17 0.00
80_A 36_H 0.85 0.17 0.00
72_L 195_S 0.85 0.17 0.00
91_L 156_R 0.85 0.17 0.00
204_Q 168_L 0.84 0.17 0.00
130_A 214_F 0.84 0.17 0.00
91_L 175_L 0.84 0.16 0.00
194_K 84_I 0.84 0.16 0.00
186_E 209_I 0.84 0.16 0.00
203_I 15_P 0.83 0.16 0.00
191_N 81_Y 0.83 0.16 0.00
101_L 195_S 0.83 0.16 0.00
134_T 62_T 0.83 0.16 0.00
86_F 166_T 0.83 0.16 0.00
105_P 40_M 0.83 0.16 0.00
51_V 45_L 0.83 0.16 0.00
182_L 53_T 0.83 0.16 0.00
66_R 10_M 0.83 0.16 0.00
68_L 153_E 0.83 0.16 0.00
62_T 55_Y 0.82 0.16 0.00
208_L 155_N 0.82 0.15 0.00
57_R 213_T 0.82 0.15 0.00
83_N 259_W 0.82 0.15 0.00
164_A 13_P 0.82 0.15 0.00
159_A 47_L 0.82 0.15 0.00
194_K 123_P 0.81 0.15 0.00
194_K 155_N 0.81 0.15 0.00
60_L 27_M 0.81 0.15 0.00
148_T 155_N 0.81 0.15 0.00
56_A 165_I 0.81 0.15 0.00
58_T 83_M 0.81 0.15 0.00
89_G 9_H 0.81 0.15 0.00
129_E 143_S 0.81 0.15 0.00
202_N 108_P 0.80 0.15 0.00
157_Q 31_L 0.80 0.15 0.00
73_S 100_A 0.80 0.15 0.00
144_D 206_L 0.80 0.15 0.00
187_K 75_V 0.80 0.15 0.00
67_G 21_A 0.80 0.14 0.00
53_D 54_M 0.80 0.14 0.00
65_F 31_L 0.79 0.14 0.00
91_L 104_S 0.79 0.14 0.00
169_P 34_W 0.79 0.14 0.00
137_S 195_S 0.79 0.14 0.00
148_T 114_G 0.79 0.14 0.00
91_L 157_N 0.79 0.14 0.00
58_T 103_H 0.79 0.14 0.00
168_G 85_L 0.79 0.14 0.00
77_R 84_I 0.78 0.14 0.00
182_L 8_Y 0.78 0.14 0.00
67_G 258_W 0.78 0.14 0.00
124_Q 179_S 0.78 0.14 0.00
194_K 150_S 0.78 0.14 0.00
201_A 48_L 0.78 0.14 0.00
178_H 225_F 0.78 0.14 0.00
101_L 15_P 0.78 0.14 0.00
152_Y 176_L 0.78 0.14 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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