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OPENSEQ.org
cIp_2_4_cyt1_2_human
Genes: A B A+B
Length: 249 325 473
Sequences: 861 747 151
Seq/Len: 3.46 2.3 0.32
MirrorTree (Pazo et al. 2001) 0.74
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 0.01 0.02 0.00
2 0.01 0.02 0.00
5 0.01 0.02 0.00
10 0.01 0.02 0.00
20 0.01 0.02 0.00
100 0.01 0.02 0.02
∞ 0.01 0.02 0.26
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
132_I 148_L 1.65 0.54 0.00
129_K 174_Y 1.45 0.40 0.00
106_Q 271_C 1.45 0.40 0.00
226_E 293_L 1.44 0.39 0.00
74_H 295_M 1.31 0.31 0.00
131_H 237_F 1.28 0.30 0.00
207_E 172_F 1.28 0.29 0.00
84_D 138_V 1.27 0.29 0.00
164_T 98_H 1.25 0.28 0.00
61_K 215_L 1.21 0.26 0.00
55_F 307_K 1.21 0.26 0.00
149_L 232_Y 1.21 0.26 0.00
164_T 114_F 1.21 0.26 0.00
136_T 109_S 1.20 0.25 0.00
136_T 132_Y 1.20 0.25 0.00
142_L 292_M 1.18 0.24 0.00
212_K 216_T 1.17 0.23 0.00
163_T 137_G 1.17 0.23 0.00
236_E 69_A 1.16 0.23 0.00
165_P 151_E 1.15 0.23 0.00
204_I 131_A 1.14 0.22 0.00
188_I 110_I 1.13 0.22 0.00
69_N 186_R 1.12 0.21 0.00
97_A 157_G 1.11 0.21 0.00
197_T 286_K 1.11 0.21 0.00
99_N 138_V 1.10 0.20 0.00
204_I 129_F 1.09 0.20 0.00
145_S 238_P 1.09 0.20 0.00
169_F 182_S 1.09 0.20 0.00
54_D 310_K 1.08 0.20 0.00
155_K 153_E 1.08 0.19 0.00
198_A 238_P 1.07 0.19 0.00
82_V 142_E 1.07 0.19 0.00
108_P 232_Y 1.06 0.19 0.00
97_A 127_M 1.06 0.19 0.00
69_N 134_H 1.05 0.18 0.00
169_F 242_I 1.05 0.18 0.00
98_M 205_H 1.05 0.18 0.00
116_A 215_L 1.05 0.18 0.00
189_N 245_A 1.04 0.18 0.00
65_A 114_F 1.04 0.18 0.00
167_K 201_V 1.04 0.18 0.00
60_Y 312_S 1.03 0.18 0.00
216_P 232_Y 1.03 0.18 0.00
94_P 312_S 1.03 0.18 0.00
185_M 202_R 1.03 0.18 0.00
170_T 164_M 1.03 0.17 0.00
198_A 189_N 1.01 0.17 0.00
101_V 283_D 1.00 0.17 0.00
147_S 180_P 1.00 0.17 0.00
122_Y 213_S 1.00 0.17 0.00
162_E 75_A 1.00 0.16 0.00
232_T 199_Y 1.00 0.16 0.00
171_L 138_V 0.99 0.16 0.00
165_P 85_S 0.99 0.16 0.00
108_P 245_A 0.98 0.16 0.00
95_I 138_V 0.98 0.15 0.00
136_T 272_T 0.98 0.15 0.00
218_P 287_R 0.98 0.15 0.00
129_K 74_L 0.97 0.15 0.00
122_Y 145_A 0.97 0.15 0.00
235_T 169_G 0.97 0.15 0.00
205_I 235_P 0.97 0.15 0.00
68_K 172_F 0.96 0.15 0.00
143_R 100_G 0.96 0.15 0.00
205_I 186_R 0.95 0.15 0.00
109_P 151_E 0.95 0.14 0.00
181_V 257_D 0.95 0.14 0.00
232_T 237_F 0.95 0.14 0.00
72_E 297_A 0.94 0.14 0.00
82_V 209_D 0.94 0.14 0.00
104_V 172_F 0.94 0.14 0.00
130_Y 206_G 0.94 0.14 0.00
88_R 144_E 0.93 0.14 0.00
76_A 288_M 0.93 0.14 0.00
97_A 165_F 0.93 0.14 0.00
212_K 312_S 0.93 0.14 0.00
139_P 140_Y 0.93 0.14 0.00
169_F 165_F 0.93 0.14 0.00
214_P 209_D 0.93 0.14 0.00
93_L 299_L 0.92 0.14 0.00
82_V 307_K 0.92 0.14 0.00
221_G 287_R 0.92 0.13 0.00
219_R 278_S 0.92 0.13 0.00
74_H 139_C 0.92 0.13 0.00
109_P 168_P 0.91 0.13 0.00
84_D 137_G 0.91 0.13 0.00
95_I 186_R 0.91 0.13 0.00
58_E 227_L 0.91 0.13 0.00
228_A 310_K 0.91 0.13 0.00
108_P 199_Y 0.91 0.13 0.00
226_E 233_F 0.91 0.13 0.00
48_N 111_R 0.91 0.13 0.00
122_Y 74_L 0.91 0.13 0.00
179_A 290_L 0.91 0.13 0.00
199_K 298_L 0.90 0.13 0.00
165_P 292_M 0.90 0.13 0.00
73_G 142_E 0.90 0.13 0.00
110_M 308_R 0.90 0.13 0.00
139_P 230_G 0.90 0.13 0.00
205_I 291_K 0.90 0.13 0.00
163_T 138_V 0.89 0.13 0.00
112_V 123_S 0.89 0.13 0.00
169_F 267_A 0.89 0.13 0.00
52_P 190_N 0.89 0.13 0.00
63_I 109_S 0.89 0.13 0.00
208_L 108_T 0.89 0.12 0.00
61_K 200_I 0.89 0.12 0.00
82_V 93_S 0.89 0.12 0.00
73_G 253_L 0.88 0.12 0.00
64_E 304_Y 0.88 0.12 0.00
233_S 128_D 0.88 0.12 0.00
153_Q 262_T 0.87 0.12 0.00
56_T 213_S 0.87 0.12 0.00
225_C 254_E 0.87 0.12 0.00
147_S 131_A 0.87 0.12 0.00
93_L 300_V 0.87 0.12 0.00
110_M 154_V 0.87 0.12 0.00
199_K 292_M 0.87 0.12 0.00
93_L 238_P 0.86 0.12 0.00
69_N 182_S 0.86 0.12 0.00
170_T 303_V 0.86 0.12 0.00
150_E 67_L 0.86 0.12 0.00
153_Q 127_M 0.86 0.12 0.00
201_I 286_K 0.86 0.12 0.00
208_L 98_H 0.86 0.12 0.00
101_V 246_P 0.86 0.12 0.00
99_N 305_T 0.85 0.12 0.00
205_I 127_M 0.85 0.12 0.00
113_Y 118_K 0.85 0.12 0.00
131_H 302_L 0.85 0.12 0.00
145_S 261_A 0.84 0.11 0.00
58_E 310_K 0.84 0.11 0.00
113_Y 104_S 0.84 0.11 0.00
181_V 172_F 0.84 0.11 0.00
42_R 91_P 0.84 0.11 0.00
101_V 312_S 0.84 0.11 0.00
215_K 182_S 0.84 0.11 0.00
204_I 140_Y 0.84 0.11 0.00
56_T 290_L 0.84 0.11 0.00
202_E 79_H 0.84 0.11 0.00
212_K 73_G 0.84 0.11 0.00
101_V 68_A 0.84 0.11 0.00
99_N 130_V 0.84 0.11 0.00
150_E 73_G 0.83 0.11 0.00
93_L 142_E 0.83 0.11 0.00
187_Q 140_Y 0.83 0.11 0.00
61_K 292_M 0.83 0.11 0.00
121_M 311_W 0.83 0.11 0.00
163_T 267_A 0.83 0.11 0.00
203_E 186_R 0.83 0.11 0.00
58_E 267_A 0.83 0.11 0.00
74_H 247_P 0.83 0.11 0.00
109_P 108_T 0.83 0.11 0.00
237_P 126_S 0.82 0.11 0.00
162_E 68_A 0.82 0.11 0.00
132_I 300_V 0.82 0.11 0.00
212_K 235_P 0.82 0.11 0.00
57_P 148_L 0.82 0.11 0.00
55_F 114_F 0.82 0.11 0.00
129_K 93_S 0.82 0.11 0.00
81_P 298_L 0.82 0.11 0.00
230_G 237_F 0.82 0.10 0.00
226_E 122_A 0.82 0.10 0.00
232_T 164_M 0.82 0.10 0.00
99_N 171_L 0.81 0.10 0.00
136_T 249_Y 0.81 0.10 0.00
175_E 289_G 0.81 0.10 0.00
198_A 85_S 0.81 0.10 0.00
98_M 179_Y 0.81 0.10 0.00
143_R 292_M 0.81 0.10 0.00
79_V 123_S 0.81 0.10 0.00
211_G 272_T 0.81 0.10 0.00
132_I 97_S 0.81 0.10 0.00
101_V 176_P 0.81 0.10 0.00
120_T 233_F 0.81 0.10 0.00
103_E 154_V 0.81 0.10 0.00
210_A 122_A 0.81 0.10 0.00
105_L 304_Y 0.80 0.10 0.00
192_Y 291_K 0.80 0.10 0.00
82_V 255_F 0.80 0.10 0.00
106_Q 316_S 0.80 0.10 0.00
196_L 210_Y 0.80 0.10 0.00
129_K 108_T 0.80 0.10 0.00
159_K 212_F 0.80 0.10 0.00
205_I 160_E 0.80 0.10 0.00
145_S 68_A 0.80 0.10 0.00
88_R 114_F 0.80 0.10 0.00
56_T 238_P 0.80 0.10 0.00
153_Q 302_L 0.80 0.10 0.00
165_P 224_G 0.80 0.10 0.00
164_T 309_H 0.80 0.10 0.00
218_P 260_P 0.80 0.10 0.00
221_G 188_A 0.80 0.10 0.00
206_D 119_Q 0.80 0.10 0.00
226_E 118_K 0.79 0.10 0.00
144_N 296_M 0.79 0.10 0.00
214_P 101_L 0.79 0.10 0.00
156_L 98_H 0.79 0.10 0.00
125_K 148_L 0.79 0.10 0.00
177_L 170_K 0.79 0.10 0.00
112_V 189_N 0.78 0.10 0.00
88_R 307_K 0.78 0.10 0.00
145_S 147_E 0.78 0.10 0.00
90_N 308_R 0.78 0.10 0.00
236_E 294_M 0.78 0.10 0.00
221_G 283_D 0.78 0.10 0.00
115_V 145_A 0.78 0.10 0.00
94_P 142_E 0.78 0.10 0.00
215_K 312_S 0.78 0.10 0.00
179_A 299_L 0.78 0.10 0.00
235_T 171_L 0.78 0.10 0.00
235_T 130_V 0.78 0.10 0.00
216_P 277_A 0.78 0.10 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
5867 0.32 cIp_2_40_cyt1_2_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5866 0.32 cIp_2_4_cyt1_2_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
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