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OPENSEQ.org
cIp_9_4_cIV_I_4_human
Genes: A B A+B
Length: 210 378 536
Sequences: 638 4484 252
Seq/Len: 3.04 11.86 0.47
MirrorTree (Pazo et al. 2001) 0.78
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 0.05
∞ 0.00 0.00 0.43
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
203_I 49_L 1.77 0.73 0.01
201_A 75_Y 1.48 0.53 0.01
67_G 50_F 1.42 0.48 0.01
67_G 12_K 1.39 0.46 0.01
57_R 108_L 1.32 0.41 0.00
72_L 8_N 1.29 0.38 0.00
157_Q 252_D 1.24 0.35 0.00
186_E 354_A 1.18 0.31 0.00
193_D 156_I 1.18 0.31 0.00
206_D 193_A 1.16 0.30 0.00
180_E 108_L 1.14 0.29 0.00
65_F 155_Y 1.14 0.29 0.00
82_I 354_A 1.14 0.29 0.00
147_M 172_S 1.13 0.28 0.00
59_L 168_Y 1.13 0.28 0.00
73_S 241_T 1.12 0.27 0.00
53_D 197_L 1.11 0.27 0.00
163_D 134_P 1.10 0.26 0.00
89_G 123_T 1.09 0.26 0.00
181_L 319_P 1.08 0.25 0.00
204_Q 326_W 1.08 0.25 0.00
84_Y 185_L 1.07 0.24 0.00
199_I 44_Q 1.07 0.24 0.00
71_T 205_S 1.06 0.24 0.00
180_E 254_D 1.05 0.23 0.00
199_I 176_T 1.05 0.23 0.00
52_T 320_L 1.04 0.23 0.00
60_L 226_I 1.04 0.23 0.00
201_A 10_L 1.03 0.22 0.00
155_F 352_Q 1.03 0.22 0.00
71_T 50_F 1.03 0.22 0.00
54_R 117_I 1.02 0.22 0.00
72_L 132_V 1.02 0.22 0.00
83_N 364_I 1.02 0.22 0.00
72_L 156_I 1.01 0.21 0.00
181_L 117_I 1.01 0.21 0.00
152_Y 108_L 1.01 0.21 0.00
148_T 286_N 1.00 0.21 0.00
168_G 275_L 1.00 0.21 0.00
130_A 126_T 1.00 0.21 0.00
183_Y 227_K 1.00 0.21 0.00
68_L 373_E 1.00 0.21 0.00
80_A 37_L 1.00 0.21 0.00
202_N 252_D 1.00 0.21 0.00
199_I 204_G 0.99 0.20 0.00
147_M 56_S 0.99 0.20 0.00
90_P 236_I 0.99 0.20 0.00
82_I 30_W 0.99 0.20 0.00
68_L 112_T 0.99 0.20 0.00
72_L 93_C 0.99 0.20 0.00
203_I 328_L 0.99 0.20 0.00
63_E 205_S 0.98 0.20 0.00
147_M 164_I 0.98 0.20 0.00
62_T 190_A 0.98 0.20 0.00
199_I 54_H 0.98 0.20 0.00
75_L 18_L 0.97 0.20 0.00
194_K 115_I 0.97 0.20 0.00
167_E 176_T 0.97 0.19 0.00
181_L 191_A 0.96 0.19 0.00
193_D 233_L 0.96 0.19 0.00
186_E 293_A 0.96 0.19 0.00
204_Q 109_Y 0.96 0.19 0.00
164_A 103_Y 0.95 0.18 0.00
106_S 199_F 0.95 0.18 0.00
187_K 102_L 0.95 0.18 0.00
80_A 50_F 0.95 0.18 0.00
159_A 249_L 0.95 0.18 0.00
73_S 61_T 0.95 0.18 0.00
68_L 245_F 0.95 0.18 0.00
59_L 181_F 0.95 0.18 0.00
90_P 262_L 0.95 0.18 0.00
148_T 50_F 0.94 0.18 0.00
72_L 18_L 0.94 0.18 0.00
155_F 234_L 0.94 0.18 0.00
91_L 161_V 0.94 0.18 0.00
199_I 79_I 0.94 0.18 0.00
168_G 271_E 0.94 0.18 0.00
194_K 369_I 0.93 0.17 0.00
208_L 341_Q 0.93 0.17 0.00
155_F 30_W 0.93 0.17 0.00
194_K 158_T 0.93 0.17 0.00
71_T 37_L 0.93 0.17 0.00
194_K 215_S 0.92 0.17 0.00
190_N 258_L 0.92 0.17 0.00
181_L 367_P 0.92 0.17 0.00
169_P 373_E 0.92 0.17 0.00
67_G 35_S 0.92 0.17 0.00
204_Q 245_F 0.92 0.17 0.00
168_G 31_W 0.91 0.17 0.00
183_Y 117_I 0.91 0.17 0.00
57_R 330_A 0.91 0.17 0.00
62_T 333_L 0.91 0.17 0.00
83_N 369_I 0.91 0.16 0.00
155_F 211_I 0.90 0.16 0.00
82_I 334_I 0.90 0.16 0.00
181_L 181_F 0.90 0.16 0.00
68_L 342_P 0.90 0.16 0.00
74_Y 92_I 0.90 0.16 0.00
130_A 59_A 0.90 0.16 0.00
68_L 50_F 0.90 0.16 0.00
60_L 47_T 0.89 0.16 0.00
187_K 298_I 0.89 0.16 0.00
67_G 229_A 0.89 0.16 0.00
65_F 215_S 0.89 0.16 0.00
77_R 356_V 0.89 0.16 0.00
180_E 298_I 0.89 0.16 0.00
208_L 253_P 0.89 0.16 0.00
131_E 224_Y 0.88 0.15 0.00
60_L 327_L 0.88 0.15 0.00
129_E 237_L 0.88 0.15 0.00
202_N 50_F 0.88 0.15 0.00
84_Y 271_E 0.88 0.15 0.00
78_E 8_N 0.88 0.15 0.00
168_G 103_Y 0.88 0.15 0.00
64_L 50_F 0.87 0.15 0.00
206_D 225_T 0.87 0.15 0.00
200_A 302_A 0.87 0.15 0.00
182_L 236_I 0.87 0.15 0.00
68_L 231_G 0.86 0.15 0.00
194_K 293_A 0.86 0.15 0.00
155_F 18_L 0.86 0.15 0.00
66_R 171_D 0.86 0.15 0.00
207_Y 245_F 0.86 0.15 0.00
202_N 122_A 0.86 0.14 0.00
84_Y 331_D 0.86 0.14 0.00
159_A 293_A 0.86 0.14 0.00
78_E 43_L 0.86 0.14 0.00
207_Y 54_H 0.86 0.14 0.00
130_A 183_F 0.86 0.14 0.00
202_N 204_G 0.85 0.14 0.00
106_S 306_I 0.85 0.14 0.00
183_Y 165_W 0.85 0.14 0.00
84_Y 369_I 0.85 0.14 0.00
176_E 274_F 0.85 0.14 0.00
178_H 308_H 0.85 0.14 0.00
78_E 193_A 0.84 0.14 0.00
183_Y 29_A 0.84 0.14 0.00
183_Y 191_A 0.84 0.14 0.00
54_R 13_L 0.84 0.14 0.00
201_A 30_W 0.84 0.14 0.00
63_E 285_P 0.84 0.14 0.00
75_L 170_V 0.84 0.14 0.00
208_L 232_L 0.84 0.14 0.00
68_L 360_T 0.83 0.14 0.00
56_A 140_F 0.83 0.14 0.00
71_T 221_H 0.83 0.14 0.00
104_Y 208_P 0.83 0.14 0.00
204_Q 232_L 0.83 0.14 0.00
87_E 101_G 0.83 0.14 0.00
120_I 218_I 0.83 0.14 0.00
80_A 8_N 0.83 0.14 0.00
141_T 284_V 0.83 0.14 0.00
75_L 349_I 0.83 0.14 0.00
67_G 15_N 0.83 0.13 0.00
198_E 114_N 0.83 0.13 0.00
159_A 180_T 0.82 0.13 0.00
152_Y 185_L 0.82 0.13 0.00
178_H 3_P 0.82 0.13 0.00
55_A 50_F 0.82 0.13 0.00
80_A 21_L 0.82 0.13 0.00
183_Y 320_L 0.82 0.13 0.00
75_L 16_H 0.82 0.13 0.00
164_A 126_T 0.82 0.13 0.00
186_E 155_Y 0.82 0.13 0.00
64_L 319_P 0.81 0.13 0.00
66_R 334_I 0.81 0.13 0.00
91_L 373_E 0.81 0.13 0.00
82_I 327_L 0.81 0.13 0.00
134_T 360_T 0.81 0.13 0.00
99_H 176_T 0.81 0.13 0.00
152_Y 286_N 0.81 0.13 0.00
131_E 241_T 0.81 0.13 0.00
76_F 188_I 0.81 0.13 0.00
173_F 192_L 0.81 0.13 0.00
204_Q 6_K 0.81 0.13 0.00
74_Y 260_N 0.81 0.13 0.00
60_L 119_L 0.81 0.13 0.00
71_T 218_I 0.81 0.13 0.00
69_G 330_A 0.80 0.13 0.00
159_A 364_I 0.80 0.13 0.00
194_K 257_T 0.80 0.12 0.00
152_Y 289_G 0.80 0.12 0.00
168_G 84_A 0.80 0.12 0.00
171_F 364_I 0.80 0.12 0.00
164_A 275_L 0.80 0.12 0.00
183_Y 103_Y 0.80 0.12 0.00
59_L 300_I 0.80 0.12 0.00
71_T 231_G 0.80 0.12 0.00
194_K 287_K 0.79 0.12 0.00
202_N 319_P 0.79 0.12 0.00
194_K 162_Q 0.79 0.12 0.00
184_N 109_Y 0.79 0.12 0.00
63_E 141_W 0.79 0.12 0.00
175_T 298_I 0.79 0.12 0.00
70_M 114_N 0.79 0.12 0.00
169_P 74_N 0.79 0.12 0.00
184_N 12_K 0.79 0.12 0.00
171_F 108_L 0.79 0.12 0.00
182_L 369_I 0.79 0.12 0.00
181_L 343_V 0.79 0.12 0.00
54_R 350_I 0.79 0.12 0.00
137_S 224_Y 0.79 0.12 0.00
76_F 286_N 0.79 0.12 0.00
202_N 40_C 0.79 0.12 0.00
195_W 147_T 0.79 0.12 0.00
187_K 343_V 0.79 0.12 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
5835 0.27 cIp_9_4_cytb_40_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-40, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5645 0.47 cIp_9_40_cIV_I_20_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5624 0.36 cIp_9_10_cIV_I_40_human Δgene:(1, ∞) A:(1E-10, 8) B:(1E-40, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5623 0.46 cIp_9_40_cIV_I_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2016_06b) 0.01 Done - Shared
5622 0.47 cIp_9_4_cIV_I_4_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-10, 8) msa: Jackhmmer (2016_06b) 0.01 Done - Shared
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