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OPENSEQ.org
cIp_2_40_cIV_3_40
Genes: A B A+B
Length: 249 261 465
Sequences: 654 2465 103
Seq/Len: 2.63 9.44 0.22
MirrorTree (Pazo et al. 2001) 0.56
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 0.00
20 0.00 0.00 0.01
100 0.00 0.00 0.01
∞ 0.00 0.00 0.20
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
208_L 47_L 1.51 0.35 0.00
226_E 32_T 1.43 0.30 0.00
192_Y 78_G 1.43 0.30 0.00
101_V 198_F 1.41 0.29 0.00
106_Q 19_T 1.37 0.27 0.00
51_T 176_L 1.35 0.27 0.00
76_A 209_I 1.31 0.25 0.00
169_F 50_N 1.30 0.24 0.00
162_E 160_I 1.30 0.24 0.00
106_Q 2_T 1.18 0.19 0.00
218_P 50_N 1.17 0.19 0.00
193_Y 23_S 1.17 0.18 0.00
214_P 70_H 1.16 0.18 0.00
156_L 194_G 1.16 0.18 0.00
143_R 233_F 1.16 0.18 0.00
80_L 198_F 1.15 0.18 0.00
101_V 190_D 1.14 0.18 0.00
204_I 175_L 1.14 0.17 0.00
219_R 259_W 1.13 0.17 0.00
94_P 76_Q 1.13 0.17 0.00
149_L 258_W 1.13 0.17 0.00
120_T 28_T 1.11 0.16 0.00
50_D 96_G 1.09 0.16 0.00
97_A 96_G 1.09 0.16 0.00
120_T 15_P 1.09 0.16 0.00
136_T 258_W 1.09 0.16 0.00
120_T 166_T 1.09 0.16 0.00
170_T 97_F 1.08 0.15 0.00
191_N 259_W 1.07 0.15 0.00
113_Y 27_M 1.06 0.15 0.00
112_V 189_S 1.06 0.15 0.00
68_K 65_S 1.06 0.15 0.00
221_G 61_V 1.06 0.15 0.00
108_P 122_T 1.06 0.15 0.00
220_S 20_G 1.05 0.15 0.00
164_T 124_L 1.05 0.15 0.00
145_S 220_I 1.05 0.15 0.00
76_A 206_L 1.05 0.15 0.00
205_I 157_N 1.05 0.15 0.00
233_S 48_L 1.05 0.14 0.00
136_T 7_A 1.05 0.14 0.00
181_V 49_T 1.04 0.14 0.00
79_V 15_P 1.04 0.14 0.00
155_K 10_M 1.03 0.14 0.00
143_R 166_T 1.03 0.14 0.00
147_S 127_L 1.03 0.14 0.00
58_E 183_E 1.02 0.14 0.00
168_L 77_K 1.02 0.14 0.00
145_S 185_P 1.02 0.14 0.00
166_D 213_T 1.02 0.14 0.00
67_V 154_N 1.02 0.14 0.00
216_P 79_L 1.01 0.14 0.00
94_P 105_S 1.01 0.13 0.00
120_T 167_I 1.00 0.13 0.00
214_P 73_P 1.00 0.13 0.00
88_R 152_M 1.00 0.13 0.00
156_L 97_F 1.00 0.13 0.00
233_S 61_V 0.99 0.13 0.00
141_M 256_I 0.99 0.13 0.00
210_A 154_N 0.99 0.13 0.00
218_P 54_M 0.99 0.13 0.00
202_E 196_T 0.98 0.13 0.00
165_P 79_L 0.98 0.13 0.00
204_I 139_A 0.98 0.12 0.00
120_T 143_S 0.98 0.12 0.00
143_R 15_P 0.98 0.12 0.00
229_G 120_G 0.97 0.12 0.00
60_Y 185_P 0.97 0.12 0.00
99_N 185_P 0.97 0.12 0.00
186_V 159_M 0.97 0.12 0.00
139_P 166_T 0.97 0.12 0.00
235_T 154_N 0.97 0.12 0.00
204_I 176_L 0.97 0.12 0.00
90_N 78_G 0.96 0.12 0.00
109_P 41_A 0.96 0.12 0.00
139_P 83_M 0.96 0.12 0.00
106_Q 224_M 0.96 0.12 0.00
93_L 190_D 0.96 0.12 0.00
171_L 194_G 0.95 0.12 0.00
205_I 135_S 0.95 0.12 0.00
52_P 78_G 0.95 0.12 0.00
94_P 68_Q 0.95 0.12 0.00
59_N 259_W 0.94 0.11 0.00
214_P 209_I 0.94 0.11 0.00
59_N 260_G 0.94 0.11 0.00
218_P 128_E 0.93 0.11 0.00
58_E 15_P 0.93 0.11 0.00
158_I 97_F 0.93 0.11 0.00
130_Y 40_M 0.93 0.11 0.00
54_D 25_L 0.92 0.11 0.00
69_N 132_L 0.92 0.11 0.00
143_R 143_S 0.92 0.11 0.00
106_Q 125_N 0.92 0.11 0.00
60_Y 182_F 0.92 0.11 0.00
201_I 193_Y 0.92 0.11 0.00
231_L 261_S 0.92 0.11 0.00
170_T 195_S 0.91 0.11 0.00
86_A 100_A 0.91 0.11 0.00
181_V 39_S 0.91 0.11 0.00
165_P 174_T 0.91 0.11 0.00
136_T 97_F 0.90 0.10 0.00
68_K 88_T 0.90 0.10 0.00
171_L 7_A 0.90 0.10 0.00
122_Y 58_W 0.90 0.10 0.00
214_P 112_L 0.90 0.10 0.00
49_P 96_G 0.90 0.10 0.00
214_P 110_P 0.90 0.10 0.00
147_S 210_I 0.90 0.10 0.00
72_E 65_S 0.90 0.10 0.00
202_E 105_S 0.89 0.10 0.00
74_H 10_M 0.89 0.10 0.00
205_I 216_T 0.89 0.10 0.00
141_M 84_I 0.89 0.10 0.00
76_A 139_A 0.89 0.10 0.00
121_M 132_L 0.89 0.10 0.00
100_K 198_F 0.88 0.10 0.00
209_K 258_W 0.88 0.10 0.00
65_A 18_L 0.88 0.10 0.00
221_G 33_M 0.88 0.10 0.00
213_I 209_I 0.88 0.10 0.00
139_P 143_S 0.88 0.10 0.00
61_K 23_S 0.88 0.10 0.00
216_P 223_L 0.88 0.10 0.00
187_Q 76_Q 0.88 0.10 0.00
186_V 105_S 0.87 0.10 0.00
208_L 36_H 0.87 0.10 0.00
215_K 216_T 0.87 0.10 0.00
47_N 48_L 0.87 0.10 0.00
161_G 18_L 0.87 0.10 0.00
169_F 27_M 0.87 0.10 0.00
199_K 51_T 0.87 0.10 0.00
205_I 160_I 0.86 0.10 0.00
66_I 36_H 0.86 0.10 0.00
162_E 168_L 0.86 0.10 0.00
164_T 153_E 0.86 0.10 0.00
209_K 121_I 0.86 0.10 0.00
55_F 174_T 0.86 0.10 0.00
80_L 195_S 0.86 0.10 0.00
123_N 43_L 0.85 0.09 0.00
159_K 183_E 0.84 0.09 0.00
164_T 123_P 0.84 0.09 0.00
60_Y 123_P 0.84 0.09 0.00
170_T 209_I 0.84 0.09 0.00
230_G 63_R 0.84 0.09 0.00
51_T 123_P 0.84 0.09 0.00
99_N 59_R 0.84 0.09 0.00
66_I 103_H 0.84 0.09 0.00
64_E 53_T 0.84 0.09 0.00
152_I 167_I 0.84 0.09 0.00
75_K 188_I 0.84 0.09 0.00
58_E 65_S 0.84 0.09 0.00
189_N 107_A 0.83 0.09 0.00
70_Y 118_P 0.83 0.09 0.00
56_T 38_H 0.83 0.09 0.00
157_G 166_T 0.83 0.09 0.00
139_P 15_P 0.83 0.09 0.00
214_P 61_V 0.83 0.09 0.00
112_V 111_Q 0.83 0.09 0.00
63_I 172_Y 0.83 0.09 0.00
197_T 124_L 0.83 0.09 0.00
146_D 40_M 0.83 0.09 0.00
203_E 111_Q 0.83 0.09 0.00
221_G 256_I 0.83 0.09 0.00
131_H 23_S 0.83 0.09 0.00
156_L 162_A 0.83 0.09 0.00
139_P 233_F 0.82 0.09 0.00
108_P 18_L 0.82 0.09 0.00
155_K 175_L 0.82 0.09 0.00
80_L 194_G 0.82 0.09 0.00
68_K 76_Q 0.82 0.09 0.00
93_L 76_Q 0.82 0.09 0.00
181_V 237_A 0.82 0.09 0.00
122_Y 198_F 0.82 0.09 0.00
73_G 259_W 0.82 0.09 0.00
197_T 84_I 0.82 0.09 0.00
143_R 103_H 0.82 0.09 0.00
218_P 153_E 0.82 0.09 0.00
218_P 165_I 0.82 0.09 0.00
187_Q 176_L 0.82 0.09 0.00
229_G 3_H 0.81 0.09 0.00
143_R 88_T 0.81 0.09 0.00
143_R 83_M 0.81 0.09 0.00
79_V 189_S 0.81 0.09 0.00
57_P 135_S 0.81 0.09 0.00
115_V 144_I 0.81 0.09 0.00
91_G 34_W 0.81 0.09 0.00
192_Y 77_K 0.81 0.09 0.00
207_E 36_H 0.81 0.09 0.00
197_T 34_W 0.81 0.09 0.00
208_L 20_G 0.80 0.08 0.00
98_M 195_S 0.80 0.08 0.00
186_V 100_A 0.80 0.08 0.00
171_L 97_F 0.80 0.08 0.00
189_N 49_T 0.80 0.08 0.00
143_R 107_A 0.80 0.08 0.00
169_F 58_W 0.80 0.08 0.00
142_L 168_L 0.80 0.08 0.00
236_E 62_T 0.80 0.08 0.00
62_R 190_D 0.80 0.08 0.00
49_P 69_G 0.80 0.08 0.00
125_K 124_L 0.80 0.08 0.00
108_P 66_T 0.80 0.08 0.00
63_I 227_F 0.80 0.08 0.00
185_M 179_S 0.80 0.08 0.00
63_I 53_T 0.79 0.08 0.00
191_N 4_Q 0.79 0.08 0.00
167_K 129_V 0.79 0.08 0.00
132_I 122_T 0.79 0.08 0.00
132_I 55_Y 0.79 0.08 0.00
56_T 153_E 0.79 0.08 0.00
187_Q 135_S 0.79 0.08 0.00
137_T 81_Y 0.79 0.08 0.00
139_P 88_T 0.79 0.08 0.00
165_P 224_M 0.79 0.08 0.00
193_Y 119_T 0.79 0.08 0.00
61_K 220_I 0.79 0.08 0.00
182_N 14_S 0.79 0.08 0.00
228_A 105_S 0.79 0.08 0.00
156_L 69_G 0.79 0.08 0.00
150_E 47_L 0.78 0.08 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
4187 0.22 cIp_2_40_cIV_3_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4184 0.25 cIp_2_4_cIV_3_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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