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OPENSEQ.org
cIV_B_80_cI_N_60_1_human
Genes: A B A+B
Length: 227 347 570
Sequences: 1814 2495 1317
Seq/Len: 7.99 7.19 2.31
MirrorTree (Pazo et al. 2001) 0.75
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 0.02
2 0.00 0.00 2.25
5 0.00 0.00 2.26
10 0.00 0.00 2.29
20 0.00 0.00 2.29
100 0.00 0.00 2.29
∞ 0.00 0.00 2.29
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
110_Y 257_L 1.56 0.95 0.68
111_T 170_L 1.33 0.86 0.48
49_K 175_L 1.26 0.82 0.42
165_V 64_A 1.25 0.81 0.41
192_Y 9_I 1.23 0.79 0.38
138_V 215_A 1.22 0.79 0.38
115_G 277_I 1.22 0.78 0.37
170_L 148_S 1.20 0.77 0.36
97_I 83_Q 1.19 0.76 0.35
150_I 252_G 1.19 0.76 0.35
90_V 321_K 1.17 0.75 0.34
156_S 307_M 1.17 0.74 0.33
67_I 210_I 1.16 0.73 0.32
64_V 223_S 1.15 0.73 0.32
172_T 104_M 1.15 0.73 0.32
183_T 53_T 1.14 0.71 0.30
91_N 330_I 1.14 0.71 0.30
192_Y 214_T 1.13 0.70 0.30
182_T 297_I 1.12 0.70 0.29
211_L 141_I 1.12 0.70 0.29
113_Y 326_L 1.12 0.69 0.29
116_L 131_L 1.12 0.69 0.28
156_S 305_L 1.11 0.69 0.28
73_L 304_L 1.10 0.68 0.27
183_T 207_I 1.10 0.68 0.27
149_P 33_L 1.09 0.67 0.27
75_L 67_S 1.09 0.66 0.26
58_A 104_M 1.09 0.66 0.26
27_A 130_L 1.08 0.66 0.26
27_A 41_I 1.08 0.66 0.26
123_L 344_L 1.07 0.65 0.25
146_I 201_T 1.07 0.64 0.25
97_I 319_H 1.06 0.64 0.24
140_N 204_N 1.06 0.63 0.24
220_E 229_L 1.05 0.63 0.23
211_L 164_A 1.05 0.62 0.23
73_L 257_L 1.04 0.61 0.23
143_V 283_A 1.03 0.60 0.21
192_Y 104_M 1.02 0.59 0.21
51_T 252_G 1.01 0.58 0.20
99_S 191_M 1.01 0.57 0.20
47_S 164_A 1.01 0.57 0.20
155_T 98_I 1.00 0.57 0.20
99_S 304_L 1.00 0.57 0.20
152_M 332_L 1.00 0.57 0.20
192_Y 45_T 0.99 0.56 0.19
86_M 289_N 0.99 0.56 0.19
120_S 41_I 0.98 0.55 0.18
54_N 67_S 0.98 0.55 0.18
73_L 87_T 0.97 0.53 0.18
30_I 83_Q 0.97 0.53 0.17
63_T 41_I 0.97 0.53 0.17
33_L 2_N 0.96 0.53 0.17
150_I 191_M 0.96 0.53 0.17
130_P 219_L 0.96 0.52 0.17
68_L 24_S 0.96 0.52 0.17
150_I 284_T 0.96 0.52 0.17
142_V 44_L 0.96 0.52 0.17
53_T 139_I 0.96 0.52 0.17
167_T 100_M 0.96 0.52 0.17
213_L 29_T 0.96 0.52 0.17
115_G 143_Y 0.95 0.52 0.17
187_T 75_L 0.95 0.51 0.17
144_L 49_N 0.95 0.51 0.17
107_T 153_L 0.95 0.51 0.17
64_V 83_Q 0.95 0.51 0.17
75_L 219_L 0.95 0.51 0.16
61_M 270_F 0.95 0.51 0.16
71_I 99_M 0.95 0.51 0.16
157_Q 145_I 0.95 0.50 0.16
175_I 285_I 0.94 0.50 0.16
9_L 123_P 0.94 0.50 0.16
164_A 153_L 0.93 0.49 0.15
187_T 187_M 0.93 0.49 0.15
155_T 194_L 0.93 0.49 0.15
123_L 219_L 0.93 0.49 0.15
120_S 233_T 0.93 0.49 0.15
97_I 200_M 0.93 0.48 0.15
54_N 104_M 0.93 0.48 0.15
67_I 167_W 0.92 0.48 0.15
184_F 11_S 0.92 0.47 0.15
115_G 175_L 0.92 0.47 0.15
156_S 235_N 0.92 0.47 0.14
191_V 27_F 0.91 0.47 0.14
213_L 267_I 0.91 0.47 0.14
53_T 195_P 0.91 0.47 0.14
95_L 170_L 0.91 0.47 0.14
9_L 86_M 0.91 0.47 0.14
120_S 100_M 0.91 0.46 0.14
56_S 195_P 0.91 0.46 0.14
155_T 203_L 0.91 0.46 0.14
213_L 289_N 0.91 0.46 0.14
99_S 62_T 0.90 0.45 0.14
214_I 245_P 0.90 0.45 0.13
150_I 103_A 0.90 0.45 0.13
13_T 65_T 0.90 0.45 0.13
90_V 240_L 0.89 0.44 0.13
170_L 332_L 0.89 0.44 0.13
45_T 283_A 0.89 0.44 0.13
71_I 221_L 0.89 0.44 0.13
192_Y 139_I 0.88 0.43 0.13
9_L 164_A 0.88 0.43 0.13
41_A 224_S 0.88 0.43 0.12
52_N 37_M 0.88 0.43 0.12
154_I 233_T 0.88 0.43 0.12
164_A 340_S 0.88 0.43 0.12
223_P 252_G 0.88 0.42 0.12
154_I 237_L 0.88 0.42 0.12
99_S 97_M 0.88 0.42 0.12
143_V 1_M 0.87 0.42 0.12
47_S 155_L 0.87 0.42 0.12
64_V 226_T 0.87 0.41 0.12
56_S 204_N 0.87 0.41 0.12
115_G 218_L 0.86 0.41 0.12
107_T 217_L 0.86 0.41 0.12
213_L 316_Q 0.86 0.41 0.12
215_P 67_S 0.86 0.41 0.12
27_A 17_T 0.86 0.40 0.11
52_N 213_T 0.86 0.40 0.11
132_D 81_S 0.86 0.40 0.11
168_L 127_G 0.86 0.40 0.11
100_I 103_A 0.85 0.40 0.11
94_S 267_I 0.85 0.40 0.11
47_S 282_M 0.85 0.40 0.11
27_A 65_T 0.85 0.40 0.11
97_I 201_T 0.85 0.40 0.11
152_M 233_T 0.85 0.40 0.11
45_T 285_I 0.85 0.40 0.11
192_Y 130_L 0.85 0.40 0.11
191_V 237_L 0.85 0.40 0.11
224_V 270_F 0.85 0.40 0.11
167_T 222_N 0.85 0.39 0.11
184_F 294_L 0.85 0.39 0.11
154_I 286_T 0.84 0.39 0.11
97_I 296_L 0.84 0.38 0.11
9_L 318_E 0.84 0.38 0.10
30_I 294_L 0.84 0.38 0.10
20_L 248_F 0.84 0.38 0.10
111_T 267_I 0.84 0.38 0.10
184_F 14_F 0.83 0.38 0.10
167_T 104_M 0.83 0.38 0.10
210_V 277_I 0.83 0.38 0.10
49_K 236_K 0.83 0.38 0.10
146_I 53_T 0.83 0.37 0.10
170_L 130_L 0.83 0.37 0.10
90_V 5_A 0.83 0.37 0.10
213_L 65_T 0.83 0.37 0.10
53_T 21_A 0.82 0.37 0.10
123_L 336_L 0.82 0.37 0.10
213_L 71_L 0.82 0.37 0.10
156_S 273_N 0.82 0.37 0.10
107_T 207_I 0.82 0.36 0.10
192_Y 226_T 0.82 0.36 0.10
86_M 68_M 0.82 0.36 0.10
11_D 291_Y 0.82 0.36 0.10
170_L 304_L 0.82 0.36 0.10
97_I 118_V 0.81 0.35 0.09
37_L 123_P 0.81 0.35 0.09
76_I 178_I 0.81 0.35 0.09
5_A 257_L 0.81 0.35 0.09
28_L 67_S 0.81 0.35 0.09
146_I 73_A 0.81 0.35 0.09
63_T 302_I 0.80 0.34 0.09
170_L 344_L 0.80 0.34 0.09
43_F 244_I 0.80 0.34 0.09
220_E 117_E 0.80 0.34 0.09
133_L 273_N 0.80 0.34 0.09
156_S 275_S 0.80 0.34 0.09
49_K 210_I 0.80 0.34 0.09
130_P 300_T 0.80 0.34 0.09
164_A 156_T 0.80 0.34 0.09
170_L 318_E 0.80 0.34 0.09
164_A 148_S 0.79 0.33 0.09
116_L 20_T 0.79 0.33 0.09
36_F 285_I 0.79 0.33 0.09
53_T 104_M 0.79 0.33 0.09
73_L 96_L 0.79 0.33 0.09
3_H 64_A 0.79 0.33 0.09
39_L 212_T 0.79 0.33 0.09
82_R 298_Y 0.79 0.33 0.08
133_L 39_A 0.79 0.33 0.08
41_A 191_M 0.79 0.33 0.08
23_F 16_G 0.79 0.33 0.08
124_P 230_L 0.79 0.33 0.08
187_T 214_T 0.78 0.32 0.08
140_N 45_T 0.78 0.32 0.08
143_V 271_T 0.78 0.32 0.08
132_D 181_Y 0.78 0.32 0.08
175_I 267_I 0.78 0.32 0.08
27_A 317_F 0.78 0.32 0.08
133_L 44_L 0.78 0.32 0.08
71_I 145_I 0.78 0.32 0.08
9_L 245_P 0.77 0.31 0.08
150_I 337_L 0.77 0.31 0.08
47_S 223_S 0.77 0.31 0.08
55_I 194_L 0.77 0.31 0.08
192_Y 312_K 0.77 0.31 0.08
30_I 170_L 0.77 0.31 0.08
215_P 288_L 0.77 0.31 0.08
73_L 205_L 0.77 0.31 0.08
112_D 270_F 0.77 0.31 0.08
155_T 249_L 0.77 0.31 0.08
100_I 74_I 0.77 0.30 0.08
113_Y 283_A 0.76 0.30 0.07
223_P 202_I 0.76 0.30 0.07
155_T 226_T 0.76 0.30 0.07
182_T 323_T 0.76 0.30 0.07
191_V 73_A 0.76 0.30 0.07
193_Y 327_P 0.76 0.30 0.07
141_R 288_L 0.76 0.30 0.07
97_I 305_L 0.76 0.30 0.07
165_V 119_T 0.76 0.30 0.07
107_T 154_L 0.76 0.30 0.07
5_A 187_M 0.76 0.30 0.07
9_L 142_M 0.76 0.30 0.07
126_L 31_V 0.76 0.30 0.07
157_Q 81_S 0.76 0.30 0.07
141_R 168_G 0.76 0.30 0.07
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
4562 2.31 cIV_B_80_cI_N_60_1_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-60, 1) msa: Jackhmmer (2015_06) 0.68 Done - Shared
4553 1.95 cIV_B_60_cI_N_80_1_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.81 Done - Shared
4551 1.96 cIV_B_80_cI_N_80_1_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.85 Done - Shared
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