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OPENSEQ.org
cIV_C_40_cI_A_40_4_human
Genes: A B A+B
Length: 261 115 376
Sequences: 2457 1332 691
Seq/Len: 9.41 11.58 1.84
MirrorTree (Pazo et al. 2001) 0.59
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 1.84
2 0.00 0.00 1.83
5 0.00 0.00 1.84
10 0.00 0.00 1.84
20 0.00 0.00 1.84
100 0.00 0.00 1.84
∞ 0.00 0.00 1.84
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
92_L 58_V 2.09 0.99 0.97
229_S 80_Q 2.07 0.99 0.96
212_S 80_Q 1.68 0.95 0.87
129_V 19_I 1.65 0.94 0.86
103_H 75_L 1.61 0.93 0.84
23_S 97_I 1.58 0.93 0.82
104_S 75_L 1.54 0.91 0.80
35_F 61_T 1.53 0.91 0.79
35_F 110_G 1.51 0.90 0.78
101_F 32_E 1.44 0.87 0.73
189_S 54_K 1.43 0.87 0.72
250_L 61_T 1.41 0.86 0.71
127_L 34_S 1.39 0.84 0.69
135_S 54_K 1.37 0.83 0.67
114_G 75_L 1.36 0.83 0.66
7_A 53_M 1.35 0.82 0.65
199_V 109_K 1.32 0.80 0.62
212_S 81_T 1.32 0.80 0.62
150_S 2_N 1.32 0.80 0.62
103_H 51_F 1.31 0.80 0.62
135_S 61_T 1.31 0.79 0.61
150_S 80_Q 1.29 0.78 0.59
107_A 61_T 1.28 0.78 0.59
150_S 75_L 1.28 0.77 0.58
184_S 64_L 1.26 0.76 0.57
8_Y 100_L 1.25 0.75 0.56
156_R 64_L 1.25 0.75 0.55
5_S 75_L 1.24 0.74 0.54
228_T 77_W 1.20 0.71 0.50
61_V 86_L 1.20 0.71 0.50
28_T 78_A 1.20 0.70 0.49
209_I 114_A 1.19 0.69 0.48
73_P 81_T 1.17 0.68 0.47
79_L 49_V 1.17 0.67 0.46
103_H 61_T 1.16 0.67 0.46
191_G 80_Q 1.16 0.67 0.46
104_S 51_F 1.14 0.64 0.43
88_T 11_T 1.13 0.64 0.42
151_L 84_L 1.13 0.63 0.42
88_T 95_I 1.12 0.62 0.41
261_S 19_I 1.12 0.62 0.41
127_L 95_I 1.11 0.62 0.41
7_A 22_F 1.11 0.62 0.40
143_S 51_F 1.11 0.62 0.40
248_V 25_P 1.11 0.61 0.40
151_L 24_L 1.11 0.61 0.40
51_T 30_Y 1.10 0.61 0.40
127_L 54_K 1.09 0.60 0.38
184_S 112_D 1.09 0.59 0.38
129_V 28_N 1.09 0.59 0.38
96_G 77_W 1.09 0.59 0.38
73_P 2_N 1.09 0.59 0.38
150_S 92_L 1.09 0.59 0.38
199_V 103_A 1.09 0.59 0.38
212_S 14_A 1.08 0.58 0.37
20_G 110_G 1.07 0.58 0.36
199_V 61_T 1.07 0.57 0.35
42_L 2_N 1.06 0.56 0.34
212_S 90_S 1.05 0.56 0.34
119_T 80_Q 1.04 0.55 0.33
158_Q 75_L 1.04 0.55 0.33
26_L 58_V 1.04 0.55 0.33
158_Q 2_N 1.04 0.54 0.33
78_G 49_V 1.04 0.54 0.33
196_T 32_E 1.04 0.54 0.32
8_Y 87_M 1.03 0.54 0.32
61_V 97_I 1.03 0.53 0.32
220_I 91_S 1.03 0.53 0.31
18_L 60_I 1.02 0.52 0.31
192_I 53_M 1.02 0.52 0.30
32_A 45_S 1.02 0.52 0.30
115_H 9_I 1.01 0.52 0.30
189_S 114_A 1.01 0.52 0.30
27_M 10_N 1.01 0.51 0.30
143_S 110_G 1.01 0.51 0.30
209_I 46_P 1.01 0.51 0.30
111_Q 110_G 1.01 0.51 0.30
91_V 17_L 1.01 0.51 0.29
121_I 81_T 1.01 0.51 0.29
88_T 30_Y 1.01 0.51 0.29
253_Y 34_S 1.01 0.51 0.29
189_S 46_P 1.00 0.50 0.29
76_Q 77_W 1.00 0.49 0.28
151_L 2_N 0.99 0.49 0.28
27_M 13_L 0.99 0.49 0.28
127_L 30_Y 0.99 0.49 0.28
88_T 21_T 0.99 0.49 0.28
213_T 75_L 0.97 0.47 0.26
150_S 95_I 0.97 0.47 0.26
217_I 75_L 0.97 0.46 0.26
25_L 13_L 0.96 0.46 0.25
8_Y 2_N 0.96 0.46 0.25
8_Y 42_D 0.96 0.45 0.25
68_Q 57_L 0.96 0.45 0.24
112_L 51_F 0.95 0.45 0.24
156_R 49_V 0.95 0.45 0.24
103_H 1_M 0.95 0.45 0.24
100_A 114_A 0.95 0.45 0.24
91_V 91_S 0.95 0.44 0.24
42_L 30_Y 0.95 0.44 0.24
102_Y 16_L 0.94 0.43 0.23
23_S 84_L 0.93 0.43 0.23
229_S 84_L 0.93 0.42 0.22
250_L 110_G 0.93 0.42 0.22
62_T 6_I 0.93 0.42 0.22
119_T 110_G 0.92 0.42 0.22
143_S 53_M 0.92 0.41 0.21
165_I 114_A 0.92 0.41 0.21
142_V 54_K 0.91 0.41 0.21
224_M 25_P 0.91 0.40 0.20
250_L 14_A 0.91 0.40 0.20
159_M 95_I 0.90 0.39 0.20
65_S 90_S 0.90 0.39 0.20
101_F 70_A 0.90 0.39 0.20
215_L 17_L 0.89 0.38 0.19
135_S 103_A 0.89 0.38 0.19
114_G 51_F 0.89 0.38 0.19
183_E 22_F 0.89 0.38 0.19
209_I 24_L 0.89 0.38 0.19
223_L 78_A 0.89 0.38 0.19
81_Y 44_M 0.88 0.37 0.18
220_I 5_L 0.88 0.37 0.18
49_T 89_M 0.88 0.37 0.18
154_N 96_I 0.88 0.37 0.18
119_T 46_P 0.87 0.36 0.18
26_L 16_L 0.87 0.36 0.18
179_S 54_K 0.87 0.36 0.18
248_V 85_P 0.87 0.36 0.18
79_L 32_E 0.87 0.36 0.18
192_I 80_Q 0.87 0.36 0.17
61_V 7_L 0.87 0.36 0.17
154_N 53_M 0.86 0.35 0.17
139_A 81_T 0.86 0.35 0.17
25_L 102_L 0.86 0.35 0.17
23_S 30_Y 0.86 0.35 0.17
88_T 103_A 0.86 0.35 0.17
224_M 53_M 0.86 0.35 0.17
49_T 114_A 0.86 0.35 0.17
220_I 112_D 0.86 0.35 0.17
248_V 91_S 0.86 0.35 0.16
143_S 109_K 0.85 0.34 0.16
68_Q 20_I 0.85 0.34 0.16
101_F 49_V 0.85 0.34 0.16
224_M 12_L 0.85 0.34 0.16
158_Q 80_Q 0.85 0.34 0.16
27_M 54_K 0.85 0.34 0.16
92_L 53_M 0.85 0.34 0.16
61_V 13_L 0.85 0.34 0.16
224_M 19_I 0.85 0.34 0.16
35_F 115_E 0.84 0.33 0.15
103_H 102_L 0.84 0.33 0.15
187_T 114_A 0.84 0.33 0.15
171_L 3_F 0.84 0.33 0.15
35_F 14_A 0.83 0.33 0.15
107_A 54_K 0.83 0.32 0.15
103_H 110_G 0.83 0.32 0.15
5_S 22_F 0.83 0.32 0.15
209_I 13_L 0.83 0.32 0.15
157_N 21_T 0.83 0.32 0.15
19_T 110_G 0.83 0.32 0.15
251_F 3_F 0.83 0.32 0.14
135_S 34_S 0.83 0.32 0.14
50_N 25_P 0.82 0.32 0.14
224_M 4_A 0.82 0.31 0.14
143_S 58_V 0.82 0.31 0.14
167_I 91_S 0.82 0.31 0.14
112_L 26_Q 0.82 0.31 0.14
153_E 75_L 0.82 0.31 0.14
18_L 54_K 0.82 0.31 0.14
25_L 88_V 0.81 0.30 0.14
254_V 12_L 0.81 0.30 0.13
88_T 44_M 0.81 0.30 0.13
23_S 108_Q 0.81 0.30 0.13
254_V 80_Q 0.81 0.30 0.13
125_N 13_L 0.81 0.30 0.13
79_L 51_F 0.80 0.30 0.13
95_A 22_F 0.80 0.30 0.13
62_T 11_T 0.80 0.30 0.13
188_I 9_I 0.80 0.30 0.13
192_I 14_A 0.80 0.29 0.13
54_M 110_G 0.80 0.29 0.13
13_P 77_W 0.80 0.29 0.13
121_I 8_M 0.80 0.29 0.13
164_L 8_M 0.80 0.29 0.12
112_L 6_I 0.79 0.29 0.12
171_L 31_M 0.79 0.29 0.12
159_M 109_K 0.79 0.28 0.12
54_M 91_S 0.79 0.28 0.12
183_E 77_W 0.79 0.28 0.12
114_G 1_M 0.79 0.28 0.12
182_F 81_T 0.79 0.28 0.12
49_T 53_M 0.79 0.28 0.12
62_T 25_P 0.79 0.28 0.12
179_S 34_S 0.79 0.28 0.12
223_L 91_S 0.79 0.28 0.12
8_Y 102_L 0.78 0.28 0.12
151_L 114_A 0.78 0.28 0.12
104_S 54_K 0.78 0.28 0.12
29_S 58_V 0.78 0.28 0.12
45_L 9_I 0.78 0.28 0.12
100_A 63_L 0.78 0.28 0.12
25_L 51_F 0.78 0.28 0.12
67_Y 88_V 0.78 0.28 0.12
250_L 46_P 0.78 0.27 0.12
22_L 6_I 0.78 0.27 0.12
22_L 90_S 0.78 0.27 0.12
212_S 102_L 0.78 0.27 0.11
184_S 108_Q 0.78 0.27 0.11
19_T 61_T 0.77 0.27 0.11
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
4500 6.13 cIV_C_40_cI_A_20_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.96 Done - Shared
4499 1.84 cIV_C_60_cI_A_40_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.95 Done - Shared
4497 0.01 cIV_C_40_cI_A_60_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) Killed - Shared
4494 1.84 cIV_C_40_cI_A_40_4_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.97 Done - Shared
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