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OPENSEQ.org
cIV_B_80_cI_A_40_4_human
Genes: A B A+B
Length: 227 115 339
Sequences: 1814 1302 721
Seq/Len: 7.99 11.32 2.13
MirrorTree (Pazo et al. 2001) 0.62
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 0.00
2 0.00 0.00 0.01
5 0.00 0.00 2.13
10 0.00 0.00 2.11
20 0.00 0.00 2.11
100 0.00 0.00 2.11
∞ 0.00 0.00 2.11
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
53_T 78_A 1.84 0.98 0.92
140_N 13_L 1.81 0.98 0.91
58_A 78_A 1.76 0.97 0.89
214_I 102_L 1.55 0.94 0.80
155_T 18_M 1.51 0.92 0.78
115_G 13_L 1.51 0.92 0.77
37_L 87_M 1.47 0.91 0.75
57_D 22_F 1.47 0.91 0.74
172_T 78_A 1.44 0.90 0.73
23_F 80_Q 1.43 0.89 0.71
220_E 51_F 1.38 0.87 0.67
132_D 80_Q 1.37 0.86 0.67
213_L 100_L 1.37 0.86 0.66
191_V 80_Q 1.34 0.85 0.64
189_P 23_W 1.30 0.82 0.61
36_F 94_L 1.26 0.80 0.56
155_T 97_I 1.25 0.78 0.55
107_T 49_V 1.22 0.76 0.52
13_T 92_L 1.21 0.76 0.51
170_L 80_Q 1.19 0.74 0.49
133_L 80_Q 1.18 0.73 0.48
156_S 44_M 1.17 0.72 0.47
30_I 44_M 1.17 0.72 0.47
149_P 51_F 1.17 0.71 0.46
138_V 78_A 1.16 0.71 0.45
5_A 80_Q 1.15 0.70 0.44
28_L 3_F 1.14 0.69 0.44
172_T 9_I 1.14 0.69 0.44
9_L 21_T 1.14 0.69 0.43
175_I 78_A 1.13 0.68 0.42
67_I 46_P 1.13 0.68 0.42
184_F 103_A 1.12 0.67 0.41
217_K 92_L 1.12 0.67 0.41
107_T 21_T 1.12 0.67 0.41
57_D 45_S 1.12 0.67 0.41
76_I 53_M 1.10 0.66 0.40
182_T 114_A 1.09 0.65 0.39
220_E 102_L 1.09 0.64 0.38
218_I 75_L 1.08 0.63 0.37
111_T 88_V 1.07 0.62 0.36
157_Q 11_T 1.07 0.62 0.36
51_T 51_F 1.05 0.60 0.34
105_Y 64_L 1.04 0.59 0.33
23_F 2_N 1.03 0.57 0.32
156_S 97_I 1.02 0.57 0.31
156_S 29_G 1.01 0.56 0.30
40_Y 54_K 1.01 0.56 0.30
2_A 103_A 1.01 0.55 0.30
100_I 88_V 1.01 0.55 0.29
89_E 61_T 1.00 0.55 0.29
27_A 7_L 1.00 0.54 0.29
32_F 14_A 1.00 0.54 0.29
124_P 92_L 0.99 0.53 0.28
133_L 97_I 0.99 0.53 0.28
155_T 63_L 0.98 0.53 0.28
10_Q 61_T 0.98 0.52 0.27
34_I 70_A 0.98 0.52 0.27
63_T 81_T 0.98 0.52 0.27
214_I 51_F 0.97 0.51 0.27
70_A 54_K 0.97 0.51 0.26
76_I 32_E 0.97 0.51 0.26
123_L 91_S 0.97 0.51 0.26
68_L 6_I 0.97 0.51 0.26
192_Y 53_M 0.96 0.50 0.26
30_I 51_F 0.96 0.50 0.25
72_I 12_L 0.95 0.49 0.25
170_L 46_P 0.95 0.49 0.25
116_L 95_I 0.95 0.49 0.24
138_V 88_V 0.95 0.48 0.24
138_V 3_F 0.94 0.48 0.24
45_T 51_F 0.94 0.48 0.24
37_L 95_I 0.94 0.47 0.23
180_N 51_F 0.94 0.47 0.23
8_G 94_L 0.94 0.47 0.23
56_S 51_F 0.94 0.47 0.23
213_L 35_T 0.93 0.47 0.23
47_S 58_V 0.93 0.47 0.23
113_Y 51_F 0.93 0.46 0.23
202_A 112_D 0.93 0.46 0.23
183_T 25_P 0.93 0.46 0.22
64_V 86_L 0.93 0.46 0.22
175_I 6_I 0.92 0.46 0.22
41_A 13_L 0.92 0.45 0.22
11_D 103_A 0.92 0.45 0.21
42_L 90_S 0.92 0.45 0.21
52_N 91_S 0.91 0.44 0.21
150_I 31_M 0.91 0.44 0.21
137_D 80_Q 0.91 0.44 0.21
202_A 80_Q 0.91 0.44 0.21
13_T 21_T 0.91 0.44 0.21
99_S 107_L 0.90 0.43 0.20
95_L 15_L 0.90 0.43 0.20
56_S 75_L 0.90 0.43 0.20
107_T 18_M 0.89 0.42 0.20
58_A 53_M 0.89 0.42 0.19
127_F 27_L 0.89 0.41 0.19
210_V 85_P 0.89 0.41 0.19
99_S 6_I 0.88 0.41 0.19
157_Q 103_A 0.88 0.41 0.19
140_N 16_L 0.88 0.41 0.19
146_I 28_N 0.88 0.41 0.19
183_T 53_M 0.88 0.41 0.19
92_D 58_V 0.88 0.41 0.18
186_A 83_N 0.88 0.40 0.18
86_M 61_T 0.87 0.40 0.18
46_L 78_A 0.87 0.40 0.18
192_Y 22_F 0.87 0.40 0.18
154_I 10_N 0.87 0.39 0.18
165_V 46_P 0.87 0.39 0.18
146_I 96_I 0.86 0.39 0.17
123_L 88_V 0.86 0.39 0.17
99_S 114_A 0.86 0.39 0.17
140_N 25_P 0.86 0.39 0.17
30_I 75_L 0.86 0.38 0.17
211_L 92_L 0.86 0.38 0.17
42_L 54_K 0.85 0.38 0.17
41_A 90_S 0.85 0.38 0.17
45_T 97_I 0.85 0.37 0.16
8_G 110_G 0.85 0.37 0.16
95_L 102_L 0.85 0.37 0.16
29_M 80_Q 0.84 0.37 0.16
140_N 27_L 0.84 0.36 0.16
51_T 3_F 0.84 0.36 0.16
120_S 37_Y 0.84 0.36 0.16
107_T 25_P 0.84 0.36 0.16
64_V 53_M 0.84 0.36 0.16
154_I 95_I 0.84 0.36 0.15
164_A 82_T 0.83 0.36 0.15
86_M 30_Y 0.83 0.36 0.15
210_V 93_L 0.83 0.35 0.15
115_G 11_T 0.83 0.35 0.15
213_L 109_K 0.83 0.35 0.15
175_I 109_K 0.83 0.35 0.15
55_I 94_L 0.83 0.35 0.15
6_Q 71_L 0.83 0.35 0.15
47_S 30_Y 0.82 0.35 0.15
153_M 51_F 0.82 0.35 0.15
211_L 61_T 0.82 0.34 0.14
68_L 51_F 0.82 0.34 0.14
41_A 9_I 0.82 0.34 0.14
5_A 102_L 0.82 0.34 0.14
74_V 16_L 0.82 0.34 0.14
47_S 87_M 0.82 0.34 0.14
170_L 8_M 0.81 0.33 0.14
126_L 3_F 0.81 0.33 0.14
51_T 102_L 0.81 0.33 0.14
175_I 14_A 0.81 0.33 0.14
116_L 11_T 0.81 0.33 0.14
74_V 8_M 0.81 0.33 0.14
154_I 11_T 0.80 0.33 0.14
55_I 26_Q 0.80 0.33 0.13
187_T 20_I 0.80 0.32 0.13
61_M 19_I 0.80 0.32 0.13
58_A 31_M 0.79 0.32 0.13
23_F 81_T 0.79 0.32 0.13
152_M 37_Y 0.79 0.31 0.13
209_I 25_P 0.79 0.31 0.13
88_D 54_K 0.79 0.31 0.13
10_Q 110_G 0.79 0.31 0.13
27_A 103_A 0.79 0.31 0.13
2_A 25_P 0.79 0.31 0.12
44_L 78_A 0.78 0.30 0.12
99_S 3_F 0.78 0.30 0.12
97_I 94_L 0.78 0.30 0.12
53_T 2_N 0.78 0.30 0.12
172_T 3_F 0.77 0.30 0.12
192_Y 95_I 0.77 0.30 0.12
52_N 85_P 0.77 0.29 0.12
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
4484 2.13 cIV_B_80_cI_A_40_4_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-40, 4) msa: Jackhmmer (2015_06) 0.92 Done - Shared
4481 1.3 cIV_B_80_cI_A_40_2_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-40, 2) msa: Jackhmmer (2015_06) 0.87 Done - Shared
4479 0.24 cIV_B_80_cI_A_40_1_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-40, 1) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4478 2.15 cIV_B_80_cI_A_40_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.95 Done - Shared
4477 2.1 cIV_B_60_cI_A_40_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.93 Done - Shared
4476 0.01 cIV_B_40_cI_A_60_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) Killed - Shared
4475 2.13 cIV_B_40_cI_A_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.87 Done - Shared
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