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OPENSEQ.org
cIV_B_60_cI_H_20_human
Genes: A B A+B
Length: 227 318 541
Sequences: 2677 4631 2265
Seq/Len: 11.79 14.56 4.19
MirrorTree (Pazo et al. 2001) 0.80
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 0.13
2 0.00 0.00 0.30
5 0.00 0.00 1.89
10 0.00 0.01 3.59
20 0.00 0.01 3.72
100 0.00 0.02 3.79
∞ 0.00 0.04 4.16
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
144_L 237_L 1.20 0.90 0.21
99_S 79_L 1.15 0.87 0.18
33_L 118_W 1.15 0.87 0.18
127_F 87_T 1.13 0.85 0.17
162_S 217_A 1.04 0.78 0.13
192_Y 78_A 1.01 0.76 0.12
11_D 231_I 1.00 0.74 0.12
203_N 212_N 0.98 0.72 0.11
155_T 128_A 0.98 0.72 0.11
76_I 97_N 0.95 0.69 0.10
223_P 222_L 0.95 0.69 0.10
160_L 109_S 0.94 0.68 0.10
121_Y 82_A 0.94 0.67 0.09
184_F 115_S 0.91 0.64 0.08
95_L 11_V 0.90 0.63 0.08
186_A 302_M 0.90 0.62 0.08
61_M 144_V 0.89 0.62 0.08
77_A 48_P 0.89 0.62 0.08
168_L 89_L 0.89 0.61 0.08
143_V 257_T 0.88 0.61 0.08
155_T 158_G 0.88 0.61 0.08
205_S 203_G 0.88 0.60 0.08
34_I 46_L 0.88 0.60 0.07
90_V 132_A 0.88 0.60 0.07
12_A 116_I 0.88 0.60 0.07
121_Y 32_Q 0.88 0.60 0.07
34_I 17_M 0.88 0.60 0.07
206_F 144_V 0.87 0.59 0.07
160_L 132_A 0.87 0.59 0.07
24_H 114_Y 0.87 0.59 0.07
116_L 172_F 0.86 0.58 0.07
32_F 266_L 0.86 0.58 0.07
188_R 269_L 0.86 0.57 0.07
105_Y 81_I 0.85 0.57 0.07
23_F 209_S 0.85 0.56 0.07
127_F 309_I 0.84 0.55 0.07
9_L 97_N 0.84 0.55 0.07
83_I 67_T 0.84 0.55 0.06
38_V 193_T 0.84 0.55 0.06
156_S 293_F 0.83 0.54 0.06
8_G 11_V 0.83 0.54 0.06
142_V 157_S 0.83 0.53 0.06
12_A 52_A 0.82 0.53 0.06
88_D 225_M 0.82 0.53 0.06
29_M 165_L 0.82 0.52 0.06
148_T 307_M 0.82 0.52 0.06
170_L 45_L 0.81 0.51 0.06
95_L 150_L 0.81 0.50 0.06
192_Y 263_T 0.81 0.50 0.06
59_Q 113_V 0.80 0.49 0.06
215_P 160_F 0.80 0.49 0.06
86_M 101_G 0.79 0.48 0.05
144_L 103_L 0.78 0.47 0.05
9_L 135_A 0.78 0.47 0.05
83_I 7_L 0.78 0.47 0.05
76_I 9_L 0.78 0.47 0.05
157_Q 193_T 0.78 0.47 0.05
175_I 118_W 0.77 0.45 0.05
4_A 39_V 0.77 0.45 0.05
25_D 205_S 0.77 0.45 0.05
105_Y 273_I 0.76 0.44 0.05
205_S 209_S 0.76 0.43 0.05
83_I 297_T 0.76 0.43 0.05
178_R 121_W 0.76 0.43 0.05
191_V 229_T 0.75 0.43 0.05
164_A 108_T 0.75 0.43 0.05
74_V 29_G 0.75 0.43 0.05
61_M 104_F 0.75 0.43 0.05
205_S 201_A 0.75 0.43 0.04
16_I 307_M 0.75 0.43 0.04
34_I 64_A 0.75 0.43 0.04
37_L 232_I 0.75 0.42 0.04
139_D 148_I 0.75 0.42 0.04
51_T 119_S 0.75 0.42 0.04
175_I 126_N 0.75 0.42 0.04
203_N 35_K 0.74 0.42 0.04
60_E 155_L 0.74 0.42 0.04
43_F 151_L 0.74 0.42 0.04
152_M 179_W 0.74 0.42 0.04
116_L 132_A 0.74 0.42 0.04
122_M 22_L 0.74 0.41 0.04
77_A 21_M 0.74 0.41 0.04
215_P 16_A 0.74 0.41 0.04
59_Q 200_L 0.73 0.41 0.04
182_T 20_L 0.73 0.41 0.04
123_L 225_M 0.73 0.41 0.04
97_I 85_L 0.73 0.40 0.04
100_I 7_L 0.73 0.40 0.04
42_L 223_F 0.73 0.40 0.04
32_F 161_N 0.73 0.40 0.04
127_F 77_L 0.73 0.40 0.04
51_T 71_Y 0.72 0.39 0.04
55_I 154_L 0.72 0.39 0.04
141_R 90_P 0.72 0.39 0.04
59_Q 185_W 0.72 0.39 0.04
46_L 43_Y 0.72 0.39 0.04
63_T 217_A 0.72 0.39 0.04
87_T 182_A 0.72 0.39 0.04
61_M 266_L 0.72 0.39 0.04
190_G 151_L 0.72 0.39 0.04
139_D 79_L 0.72 0.38 0.04
217_K 15_I 0.71 0.38 0.04
152_M 157_S 0.71 0.38 0.04
92_D 266_L 0.71 0.38 0.04
87_T 177_P 0.71 0.38 0.04
191_V 167_T 0.71 0.38 0.04
110_Y 162_L 0.71 0.38 0.04
89_E 221_A 0.71 0.38 0.04
205_S 205_S 0.71 0.37 0.04
223_P 7_L 0.71 0.37 0.04
19_E 203_G 0.71 0.37 0.04
154_I 84_L 0.71 0.37 0.04
163_W 181_L 0.71 0.37 0.04
83_I 130_I 0.71 0.37 0.04
162_S 271_L 0.70 0.37 0.04
215_P 237_L 0.70 0.37 0.04
64_V 15_I 0.70 0.37 0.04
193_Y 135_A 0.70 0.37 0.04
147_E 13_I 0.70 0.37 0.04
168_L 147_A 0.70 0.36 0.04
214_I 91_M 0.70 0.36 0.04
21_I 247_Y 0.70 0.36 0.04
118_F 273_I 0.70 0.36 0.04
131_G 88_P 0.70 0.36 0.04
99_S 95_L 0.70 0.36 0.04
46_L 4_A 0.70 0.36 0.04
111_T 271_L 0.70 0.36 0.04
7_V 90_P 0.69 0.36 0.04
86_M 232_I 0.69 0.35 0.04
12_A 111_L 0.69 0.35 0.04
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
4579 4.19 cIV_B_60_cI_H_20_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.21 Done - Shared
4574 4.21 cIV_B_60_cI_H_40_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.36 Done - Shared
4573 3.59 cIV_B_80_cI_H_60_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.33 Done - Shared
4568 3.98 cIV_B_60_cI_H_80_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-80, 8) msa: Jackhmmer (2015_06) 0.28 Done - Shared
4567 3.6 cIV_B_80_cI_H_60_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.21 Done - Shared
4565 4.2 cIV_B_60_cI_H_60_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.12 Done - Shared
4564 5.01 cIV_B_40_cI_H_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
4563 3.53 cIV_B_80_cI_H_80_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 8) msa: Jackhmmer (2015_06) 0.19 Done - Shared
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