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OPENSEQ.org
cIV_B_40_cI_K_20_human
Genes: A B A+B
Length: 227 98 323
Sequences: 4037 1088 676
Seq/Len: 17.78 11.1 2.09
MirrorTree (Pazo et al. 2001) 0.69
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 0.05
2 0.00 0.00 0.06
5 0.00 0.00 2.05
10 0.00 0.00 2.08
20 0.00 0.00 2.08
100 0.01 0.00 2.08
∞ 0.01 0.00 2.08
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
73_L 77_L 1.99 0.99 0.96
68_L 78_L 1.70 0.96 0.89
68_L 76_A 1.63 0.95 0.87
11_D 33_L 1.53 0.93 0.82
73_L 31_L 1.52 0.92 0.81
183_T 78_L 1.51 0.92 0.81
156_S 22_Y 1.51 0.92 0.81
170_L 39_S 1.50 0.92 0.80
30_I 78_L 1.42 0.89 0.74
41_A 35_G 1.29 0.81 0.63
31_I 35_G 1.28 0.81 0.62
140_N 88_D 1.26 0.79 0.60
150_I 66_F 1.26 0.79 0.60
214_I 91_H 1.23 0.77 0.57
110_Y 77_L 1.22 0.76 0.56
157_Q 20_L 1.20 0.74 0.54
57_D 37_M 1.19 0.73 0.53
144_L 29_S 1.18 0.72 0.51
144_L 19_M 1.17 0.72 0.51
141_R 86_G 1.17 0.71 0.50
183_T 90_V 1.15 0.70 0.48
140_N 43_M 1.14 0.69 0.47
115_G 5_Y 1.13 0.68 0.46
110_Y 31_L 1.13 0.67 0.46
47_S 6_M 1.12 0.67 0.45
23_F 27_M 1.11 0.66 0.44
39_L 60_P 1.11 0.66 0.44
13_T 81_I 1.11 0.65 0.43
167_T 42_I 1.11 0.65 0.43
37_L 72_A 1.10 0.65 0.43
67_I 72_A 1.10 0.64 0.42
182_T 87_L 1.09 0.63 0.41
123_L 50_N 1.08 0.63 0.41
27_A 17_L 1.08 0.63 0.41
110_Y 90_V 1.08 0.62 0.41
71_I 17_L 1.08 0.62 0.40
52_N 27_M 1.08 0.62 0.40
52_N 47_M 1.07 0.62 0.40
192_Y 46_F 1.07 0.61 0.39
157_Q 38_L 1.05 0.59 0.38
185_T 72_A 1.05 0.59 0.37
224_V 56_A 1.05 0.59 0.37
141_R 49_L 1.04 0.58 0.36
10_Q 83_N 1.04 0.58 0.36
216_L 79_V 1.04 0.58 0.36
35_C 60_P 1.04 0.58 0.36
37_L 55_L 1.03 0.57 0.35
107_T 23_R 1.03 0.57 0.35
167_T 89_Y 1.03 0.57 0.35
61_M 72_A 1.03 0.57 0.35
92_D 51_T 1.02 0.56 0.34
175_I 78_L 1.02 0.55 0.34
99_S 40_L 1.01 0.55 0.33
32_F 6_M 1.00 0.53 0.32
202_A 33_L 0.99 0.53 0.31
46_L 7_N 0.99 0.53 0.31
30_I 87_L 0.98 0.52 0.30
184_F 63_M 0.98 0.52 0.30
95_L 41_F 0.98 0.52 0.30
99_S 84_T 0.98 0.52 0.30
29_M 37_M 0.98 0.51 0.30
28_L 97_Q 0.98 0.51 0.30
155_T 11_A 0.97 0.50 0.29
73_L 90_V 0.97 0.50 0.29
115_G 39_S 0.97 0.50 0.29
37_L 51_T 0.97 0.50 0.28
210_V 97_Q 0.96 0.49 0.28
26_H 60_P 0.96 0.49 0.28
143_V 63_M 0.96 0.49 0.28
82_R 60_P 0.95 0.48 0.27
148_T 7_N 0.95 0.48 0.27
57_D 76_A 0.95 0.48 0.27
116_L 10_L 0.95 0.47 0.27
170_L 47_M 0.95 0.47 0.27
192_Y 20_L 0.94 0.47 0.26
58_A 23_R 0.94 0.47 0.26
37_L 73_V 0.94 0.47 0.26
202_A 47_M 0.94 0.47 0.26
220_E 78_L 0.94 0.47 0.26
202_A 27_M 0.94 0.47 0.26
23_F 49_L 0.94 0.47 0.26
30_I 76_A 0.94 0.46 0.26
193_Y 35_G 0.93 0.46 0.25
170_L 87_L 0.93 0.46 0.25
137_D 95_L 0.93 0.46 0.25
73_L 89_Y 0.93 0.45 0.25
3_H 91_H 0.92 0.45 0.24
154_I 46_F 0.92 0.45 0.24
90_V 41_F 0.91 0.44 0.24
58_A 82_S 0.91 0.43 0.23
142_V 36_M 0.91 0.43 0.23
156_S 90_V 0.91 0.43 0.23
186_A 15_S 0.91 0.43 0.23
23_F 47_M 0.91 0.43 0.23
138_V 5_Y 0.90 0.43 0.23
146_I 55_L 0.90 0.42 0.22
170_L 91_H 0.90 0.42 0.22
186_A 65_V 0.90 0.42 0.22
23_F 66_F 0.89 0.42 0.22
68_L 79_V 0.89 0.41 0.22
111_T 66_F 0.89 0.41 0.21
53_T 65_V 0.89 0.41 0.21
89_E 83_N 0.89 0.41 0.21
36_F 94_N 0.89 0.41 0.21
78_L 15_S 0.89 0.41 0.21
76_I 23_R 0.88 0.40 0.21
149_P 63_M 0.88 0.40 0.20
50_L 35_G 0.88 0.40 0.20
224_V 97_Q 0.88 0.40 0.20
215_P 29_S 0.87 0.39 0.20
184_F 48_T 0.87 0.39 0.20
141_R 27_M 0.87 0.39 0.20
191_V 50_N 0.87 0.39 0.20
40_Y 33_L 0.87 0.39 0.20
86_M 65_V 0.86 0.38 0.19
99_S 16_L 0.86 0.38 0.19
23_F 24_S 0.86 0.38 0.19
61_M 73_V 0.86 0.38 0.19
167_T 76_A 0.86 0.38 0.19
154_I 38_L 0.85 0.37 0.18
74_V 42_I 0.85 0.37 0.18
57_D 61_I 0.85 0.37 0.18
67_I 82_S 0.85 0.37 0.18
75_L 76_A 0.85 0.37 0.18
210_V 92_N 0.85 0.37 0.18
9_L 10_L 0.84 0.36 0.18
23_F 97_Q 0.84 0.36 0.17
37_L 5_Y 0.84 0.36 0.17
13_T 46_F 0.84 0.36 0.17
188_R 12_F 0.83 0.35 0.17
26_H 38_L 0.83 0.35 0.17
27_A 54_L 0.83 0.35 0.17
48_T 61_I 0.83 0.34 0.17
186_A 33_L 0.83 0.34 0.17
155_T 79_V 0.83 0.34 0.17
99_S 17_L 0.82 0.34 0.16
187_T 54_L 0.82 0.34 0.16
81_L 82_S 0.82 0.34 0.16
146_I 10_L 0.82 0.34 0.16
30_I 82_S 0.82 0.34 0.16
191_V 3_L 0.82 0.34 0.16
13_T 89_Y 0.82 0.34 0.16
51_T 15_S 0.81 0.33 0.16
156_S 81_I 0.81 0.33 0.16
123_L 92_N 0.81 0.33 0.15
49_K 36_M 0.81 0.33 0.15
123_L 48_T 0.81 0.33 0.15
129_E 14_I 0.81 0.33 0.15
32_F 39_S 0.81 0.33 0.15
114_G 65_V 0.81 0.33 0.15
223_P 16_L 0.81 0.33 0.15
61_M 48_T 0.81 0.32 0.15
9_L 16_L 0.80 0.32 0.15
7_V 21_V 0.80 0.32 0.15
155_T 17_L 0.80 0.32 0.14
127_F 97_Q 0.79 0.31 0.14
47_S 8_I 0.79 0.31 0.14
225_F 97_Q 0.79 0.31 0.14
170_L 7_N 0.78 0.30 0.14
44_L 82_S 0.78 0.30 0.14
49_K 98_C 0.78 0.30 0.14
47_S 31_L 0.78 0.30 0.14
120_S 77_L 0.78 0.30 0.13
107_T 70_E 0.78 0.30 0.13
155_T 49_L 0.78 0.30 0.13
211_L 90_V 0.78 0.30 0.13
111_T 35_G 0.78 0.30 0.13
156_S 29_S 0.78 0.30 0.13
56_S 45_T 0.78 0.30 0.13
185_T 56_A 0.78 0.30 0.13
220_E 62_A 0.78 0.30 0.13
154_I 10_L 0.77 0.29 0.13
185_T 22_Y 0.77 0.29 0.13
215_P 86_G 0.77 0.29 0.13
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
4514 5.9 cIV_B_60_cI_K_10_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.76 Done - Shared
4513 2.12 cIV_B_60_cI_K_20_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.97 Done - Shared
4510 2.09 cIV_B_40_cI_K_20_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.96 Done - Shared
4509 0.18 cIV_B_40_cI_K_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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