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OPENSEQ.org
cIV_B_60_cI_A_40_human
Genes: A B A+B
Length: 227 115 341
Sequences: 2677 1332 715
Seq/Len: 11.79 11.58 2.1
MirrorTree (Pazo et al. 2001) 0.64
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 2.09
10 0.00 0.00 2.09
20 0.00 0.00 2.09
100 0.00 0.00 2.09
∞ 0.00 0.00 2.09
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 1.86 0.98 0.93
58_A 78_A 1.78 0.98 0.90
140_N 13_L 1.69 0.96 0.87
13_T 92_L 1.61 0.95 0.83
172_T 78_A 1.51 0.92 0.78
57_D 22_F 1.48 0.91 0.76
155_T 18_M 1.47 0.91 0.75
214_I 102_L 1.47 0.91 0.75
23_F 80_Q 1.43 0.89 0.72
132_D 80_Q 1.43 0.89 0.71
217_K 92_L 1.39 0.87 0.68
191_V 80_Q 1.34 0.84 0.64
189_P 23_W 1.30 0.82 0.61
220_E 51_F 1.29 0.81 0.59
115_G 13_L 1.27 0.80 0.57
36_F 94_L 1.26 0.79 0.56
170_L 80_Q 1.23 0.76 0.53
9_L 21_T 1.19 0.73 0.48
133_L 80_Q 1.18 0.72 0.48
192_Y 53_M 1.17 0.71 0.47
138_V 78_A 1.17 0.71 0.46
210_V 85_P 1.16 0.70 0.45
218_I 75_L 1.15 0.70 0.45
30_I 44_M 1.15 0.70 0.45
107_T 49_V 1.15 0.69 0.44
149_P 51_F 1.15 0.69 0.44
213_L 13_L 1.14 0.69 0.43
138_V 3_F 1.14 0.69 0.43
184_F 103_A 1.10 0.65 0.39
76_I 53_M 1.10 0.65 0.39
67_I 58_V 1.09 0.63 0.38
51_T 51_F 1.08 0.62 0.37
37_L 87_M 1.08 0.62 0.37
111_T 88_V 1.07 0.62 0.36
172_T 3_F 1.07 0.62 0.36
68_L 6_I 1.07 0.61 0.36
5_A 80_Q 1.07 0.61 0.36
40_Y 54_K 1.06 0.61 0.35
67_I 46_P 1.06 0.61 0.35
182_T 114_A 1.06 0.61 0.35
220_E 102_L 1.06 0.60 0.35
2_A 103_A 1.05 0.59 0.34
105_Y 64_L 1.04 0.58 0.33
116_L 95_I 1.04 0.58 0.33
100_I 88_V 1.04 0.58 0.33
213_L 100_L 1.04 0.58 0.33
89_E 61_T 1.03 0.58 0.32
124_P 92_L 1.03 0.57 0.32
34_I 70_A 1.03 0.57 0.32
107_T 21_T 1.02 0.56 0.31
10_Q 61_T 1.01 0.55 0.30
99_S 107_L 1.01 0.55 0.30
97_I 5_L 1.01 0.54 0.29
156_S 44_M 1.00 0.54 0.29
202_A 80_Q 1.00 0.54 0.29
37_L 95_I 0.98 0.52 0.27
74_V 87_M 0.98 0.52 0.27
30_I 51_F 0.98 0.51 0.27
70_A 54_K 0.98 0.51 0.27
180_N 51_F 0.97 0.51 0.27
213_L 35_T 0.97 0.51 0.27
76_I 32_E 0.97 0.50 0.26
57_D 45_S 0.96 0.50 0.26
32_F 14_A 0.96 0.50 0.26
153_M 51_F 0.96 0.49 0.25
42_L 90_S 0.96 0.49 0.25
170_L 46_P 0.96 0.49 0.25
211_L 92_L 0.96 0.49 0.25
137_D 80_Q 0.96 0.49 0.25
29_M 80_Q 0.95 0.49 0.25
42_L 54_K 0.95 0.48 0.24
155_T 63_L 0.95 0.48 0.24
140_N 16_L 0.95 0.48 0.24
11_D 103_A 0.95 0.48 0.24
175_I 14_A 0.95 0.48 0.24
58_A 53_M 0.94 0.47 0.24
175_I 78_A 0.94 0.47 0.23
138_V 88_V 0.94 0.47 0.23
56_S 75_L 0.94 0.47 0.23
133_L 97_I 0.93 0.46 0.23
90_V 2_N 0.93 0.46 0.23
28_L 3_F 0.93 0.46 0.22
113_Y 51_F 0.93 0.46 0.22
95_L 102_L 0.93 0.46 0.22
74_V 16_L 0.93 0.45 0.22
111_T 87_M 0.93 0.45 0.22
154_I 11_T 0.92 0.45 0.22
56_S 51_F 0.92 0.44 0.21
172_T 9_I 0.91 0.44 0.21
214_I 51_F 0.91 0.44 0.21
52_N 91_S 0.91 0.44 0.21
45_T 51_F 0.91 0.44 0.21
46_L 78_A 0.91 0.44 0.21
156_S 97_I 0.91 0.43 0.21
27_A 7_L 0.90 0.43 0.20
156_S 29_G 0.90 0.42 0.20
202_A 112_D 0.90 0.42 0.20
28_L 58_V 0.90 0.42 0.20
116_L 9_I 0.90 0.42 0.20
55_I 94_L 0.90 0.42 0.20
184_F 84_L 0.89 0.42 0.20
92_D 20_I 0.89 0.41 0.19
165_V 46_P 0.89 0.41 0.19
64_V 53_M 0.89 0.41 0.19
226_T 100_L 0.89 0.41 0.19
87_T 112_D 0.88 0.40 0.19
155_T 97_I 0.88 0.40 0.18
74_V 58_V 0.88 0.40 0.18
7_V 1_M 0.88 0.40 0.18
175_I 6_I 0.88 0.40 0.18
27_A 96_I 0.87 0.40 0.18
53_T 2_N 0.87 0.40 0.18
213_L 92_L 0.87 0.39 0.18
13_T 21_T 0.86 0.39 0.17
164_A 95_I 0.86 0.39 0.17
8_G 94_L 0.86 0.38 0.17
7_V 19_I 0.86 0.38 0.17
63_T 81_T 0.85 0.37 0.17
10_Q 110_G 0.85 0.37 0.17
187_T 20_I 0.85 0.37 0.17
217_K 4_A 0.85 0.37 0.16
45_T 97_I 0.85 0.37 0.16
41_A 90_S 0.85 0.37 0.16
75_L 20_I 0.85 0.37 0.16
154_I 100_L 0.84 0.37 0.16
154_I 95_I 0.84 0.36 0.16
187_T 32_E 0.84 0.36 0.16
88_D 54_K 0.84 0.36 0.16
120_S 37_Y 0.84 0.36 0.16
183_T 53_M 0.84 0.36 0.16
143_V 11_T 0.84 0.36 0.16
138_V 58_V 0.84 0.36 0.16
157_Q 103_A 0.83 0.35 0.15
164_A 82_T 0.83 0.35 0.15
120_S 89_M 0.83 0.35 0.15
6_Q 71_L 0.83 0.35 0.15
99_S 6_I 0.83 0.35 0.15
30_I 75_L 0.83 0.35 0.15
47_S 30_Y 0.83 0.35 0.15
73_L 1_M 0.83 0.35 0.15
167_T 88_V 0.82 0.34 0.15
140_N 25_P 0.82 0.34 0.15
192_Y 87_M 0.82 0.34 0.15
8_G 110_G 0.82 0.34 0.15
95_L 15_L 0.82 0.34 0.14
175_I 109_K 0.82 0.34 0.14
72_I 85_P 0.82 0.34 0.14
41_A 9_I 0.82 0.34 0.14
72_I 8_M 0.82 0.34 0.14
123_L 91_S 0.82 0.34 0.14
87_T 8_M 0.81 0.34 0.14
97_I 94_L 0.81 0.33 0.14
32_F 5_L 0.81 0.33 0.14
58_A 31_M 0.81 0.33 0.14
175_I 27_L 0.81 0.33 0.14
86_M 95_I 0.81 0.33 0.14
52_N 78_A 0.81 0.33 0.14
86_M 30_Y 0.80 0.32 0.13
23_F 81_T 0.80 0.32 0.13
125_P 14_A 0.80 0.32 0.13
107_T 18_M 0.80 0.32 0.13
183_T 25_P 0.80 0.32 0.13
35_C 61_T 0.79 0.31 0.13
35_C 22_F 0.79 0.31 0.13
86_M 61_T 0.79 0.31 0.13
213_L 109_K 0.79 0.31 0.13
23_F 2_N 0.79 0.31 0.12
165_V 14_A 0.79 0.31 0.12
144_L 15_L 0.78 0.30 0.12
156_S 61_T 0.78 0.30 0.12
127_F 13_L 0.78 0.30 0.12
51_T 6_I 0.78 0.30 0.12
192_Y 27_L 0.78 0.30 0.12
64_V 86_L 0.78 0.30 0.12
111_T 10_N 0.78 0.30 0.12
86_M 13_L 0.78 0.30 0.12
154_I 10_N 0.78 0.30 0.12
95_L 64_L 0.78 0.30 0.12
127_F 95_I 0.78 0.30 0.12
89_E 110_G 0.78 0.30 0.12
57_D 91_S 0.78 0.30 0.12
52_N 85_P 0.78 0.30 0.12
7_V 20_I 0.78 0.30 0.12
127_F 27_L 0.78 0.30 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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