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cIV_B_60_cI_H_40_human

Genes: A B A+B
Length: 227 318 541
Sequences: 2677 4127 2277
Seq/Len: 11.79 12.98 4.21
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 0.29
5 0.00 0.00 1.90
10 0.00 0.00 3.61
20 0.00 0.01 3.77
100 0.00 0.01 3.81
0.00 0.02 4.18
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
99_S 79_L 1.27 0.93 0.36
144_L 237_L 1.20 0.90 0.31
33_L 118_W 1.12 0.85 0.25
95_L 11_V 1.04 0.79 0.20
162_S 217_A 1.04 0.78 0.20
127_F 87_T 1.03 0.77 0.19
11_D 231_I 1.02 0.77 0.18
90_V 132_A 1.01 0.76 0.18
203_N 212_N 1.00 0.75 0.18
170_L 45_L 1.00 0.74 0.17
192_Y 78_A 0.98 0.72 0.16
76_I 97_N 0.94 0.68 0.14
34_I 46_L 0.93 0.67 0.14
184_F 115_S 0.92 0.66 0.13
160_L 109_S 0.92 0.66 0.13
168_L 89_L 0.92 0.65 0.13
105_Y 81_I 0.91 0.64 0.13
29_M 165_L 0.90 0.64 0.12
155_T 158_G 0.90 0.64 0.12
143_V 257_T 0.90 0.63 0.12
61_M 144_V 0.90 0.63 0.12
205_S 203_G 0.89 0.62 0.12
155_T 128_A 0.89 0.61 0.12
206_F 144_V 0.89 0.61 0.12
34_I 17_M 0.88 0.61 0.12
77_A 48_P 0.88 0.61 0.12
12_A 52_A 0.88 0.60 0.12
12_A 116_I 0.88 0.60 0.11
121_Y 82_A 0.87 0.60 0.11
160_L 132_A 0.86 0.58 0.11
152_M 157_S 0.85 0.57 0.10
148_T 307_M 0.85 0.57 0.10
24_H 114_Y 0.85 0.56 0.10
88_D 225_M 0.84 0.55 0.10
223_P 222_L 0.84 0.55 0.10
8_G 11_V 0.84 0.55 0.10
23_F 209_S 0.83 0.54 0.10
213_L 74_A 0.83 0.53 0.09
186_A 302_M 0.83 0.53 0.09
97_I 260_V 0.83 0.53 0.09
32_F 266_L 0.83 0.53 0.09
142_V 157_S 0.83 0.53 0.09
9_L 135_A 0.82 0.53 0.09
9_L 97_N 0.82 0.52 0.09
61_M 104_F 0.81 0.52 0.09
192_Y 263_T 0.81 0.51 0.09
63_T 217_A 0.81 0.51 0.09
83_I 67_T 0.81 0.51 0.09
105_Y 273_I 0.81 0.51 0.09
76_I 9_L 0.80 0.50 0.09
188_R 269_L 0.80 0.49 0.08
178_R 121_W 0.79 0.49 0.08
156_S 293_F 0.79 0.49 0.08
100_I 7_L 0.79 0.48 0.08
59_Q 113_V 0.78 0.47 0.08
203_N 35_K 0.78 0.47 0.08
38_V 193_T 0.78 0.47 0.08
64_V 15_I 0.78 0.47 0.08
86_M 232_I 0.78 0.47 0.08
127_F 77_L 0.78 0.47 0.08
92_D 266_L 0.78 0.47 0.08
175_I 126_N 0.78 0.47 0.08
59_Q 200_L 0.78 0.47 0.08
121_Y 32_Q 0.78 0.46 0.08
223_P 237_L 0.76 0.45 0.07
35_C 271_L 0.76 0.44 0.07
205_S 209_S 0.76 0.44 0.07
110_Y 162_L 0.76 0.44 0.07
83_I 297_T 0.76 0.44 0.07
116_L 172_F 0.76 0.44 0.07
119_N 114_Y 0.76 0.43 0.07
25_D 205_S 0.75 0.43 0.07
215_P 160_F 0.75 0.43 0.07
138_V 25_R 0.75 0.43 0.07
175_I 118_W 0.75 0.43 0.07
162_S 271_L 0.75 0.43 0.07
86_M 101_G 0.75 0.43 0.07
77_A 133_L 0.74 0.42 0.07
23_F 84_L 0.74 0.42 0.07
127_F 309_I 0.74 0.42 0.07
74_V 29_G 0.74 0.42 0.07
116_L 132_A 0.74 0.41 0.07
61_M 8_L 0.74 0.41 0.07
217_K 15_I 0.74 0.41 0.06
15_P 211_F 0.74 0.41 0.06
4_A 39_V 0.73 0.41 0.06
42_L 223_F 0.73 0.41 0.06
163_W 181_L 0.73 0.40 0.06
81_L 33_L 0.72 0.40 0.06
164_A 108_T 0.72 0.39 0.06
225_F 77_L 0.72 0.39 0.06
95_L 150_L 0.72 0.39 0.06
99_S 95_L 0.72 0.39 0.06
150_I 65_T 0.72 0.39 0.06
34_I 64_A 0.72 0.39 0.06
20_L 239_T 0.72 0.39 0.06
190_G 151_L 0.72 0.39 0.06
97_I 85_L 0.72 0.39 0.06
143_V 269_L 0.72 0.39 0.06
123_L 225_M 0.71 0.38 0.06
193_Y 135_A 0.71 0.38 0.06
139_D 148_I 0.71 0.38 0.06
168_L 147_A 0.71 0.38 0.06
59_Q 185_W 0.71 0.38 0.06
154_I 84_L 0.71 0.38 0.06
78_L 154_L 0.71 0.38 0.06
87_T 303_W 0.71 0.38 0.06
51_T 119_S 0.71 0.37 0.06
55_I 154_L 0.71 0.37 0.06
70_A 241_I 0.71 0.37 0.06
111_T 271_L 0.71 0.37 0.06
51_T 71_Y 0.71 0.37 0.06
205_S 201_A 0.70 0.37 0.06
87_T 182_A 0.70 0.37 0.06
170_L 185_W 0.70 0.37 0.06
222_G 219_P 0.70 0.36 0.05
139_D 79_L 0.70 0.36 0.05
12_A 111_L 0.70 0.36 0.05
220_E 162_L 0.70 0.36 0.05
164_A 248_D 0.70 0.36 0.05
87_T 52_A 0.70 0.36 0.05
102_H 100_L 0.70 0.36 0.05
205_S 205_S 0.69 0.36 0.05
215_P 16_A 0.69 0.35 0.05
122_M 22_L 0.69 0.35 0.05
89_E 221_A 0.69 0.35 0.05
141_R 90_P 0.69 0.35 0.05
65_W 121_W 0.69 0.35 0.05
6_Q 117_L 0.69 0.35 0.05
152_M 179_W 0.69 0.35 0.05
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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