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OPENSEQ.org
cIV_B_80_cI_A_40_2_human
Genes: A B A+B
Length: 227 115 339
Sequences: 1814 883 441
Seq/Len: 7.99 7.68 1.3
MirrorTree (Pazo et al. 2001) 0.54
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 1.29
10 0.00 0.00 1.29
20 0.00 0.00 1.29
100 0.00 0.00 1.29
∞ 0.00 0.00 1.29
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 1.98 0.97 0.87
172_T 78_A 1.79 0.94 0.78
170_L 53_M 1.78 0.94 0.78
192_Y 53_M 1.75 0.93 0.76
138_V 78_A 1.64 0.90 0.68
172_T 90_S 1.57 0.87 0.62
58_A 78_A 1.52 0.84 0.58
156_S 61_T 1.47 0.81 0.53
150_I 7_L 1.45 0.80 0.51
191_V 80_Q 1.43 0.79 0.49
27_A 21_T 1.42 0.78 0.48
170_L 46_P 1.39 0.76 0.46
86_M 30_Y 1.37 0.75 0.44
213_L 100_L 1.36 0.74 0.42
167_T 112_D 1.35 0.73 0.41
156_S 109_K 1.35 0.73 0.41
192_Y 27_L 1.34 0.73 0.41
156_S 54_K 1.29 0.68 0.36
23_F 80_Q 1.28 0.67 0.34
110_Y 87_M 1.25 0.64 0.32
28_L 80_Q 1.24 0.64 0.31
182_T 114_A 1.22 0.61 0.29
107_T 18_M 1.20 0.59 0.27
133_L 80_Q 1.17 0.57 0.26
218_I 86_L 1.17 0.57 0.25
187_T 19_I 1.16 0.56 0.25
192_Y 87_M 1.16 0.56 0.24
214_I 75_L 1.15 0.55 0.24
144_L 61_T 1.14 0.54 0.23
86_M 29_G 1.12 0.52 0.21
32_F 75_L 1.11 0.51 0.21
86_M 94_L 1.11 0.51 0.20
16_I 95_I 1.10 0.50 0.20
53_T 79_X 1.09 0.49 0.20
156_S 97_I 1.09 0.49 0.19
215_P 91_S 1.08 0.48 0.19
184_F 103_A 1.08 0.48 0.19
216_L 26_Q 1.08 0.48 0.19
63_T 26_Q 1.08 0.48 0.18
113_Y 7_L 1.07 0.47 0.18
53_T 88_V 1.06 0.47 0.18
170_L 80_Q 1.06 0.46 0.17
57_D 22_F 1.06 0.46 0.17
156_S 114_A 1.05 0.45 0.17
172_T 88_V 1.05 0.45 0.17
218_I 75_L 1.05 0.45 0.17
51_T 51_F 1.05 0.45 0.17
175_I 78_A 1.04 0.44 0.16
213_L 109_K 1.04 0.44 0.16
123_L 5_L 1.04 0.44 0.16
142_V 90_S 1.04 0.44 0.16
53_T 90_S 1.03 0.44 0.16
75_L 26_Q 1.02 0.42 0.15
132_D 81_T 1.01 0.42 0.15
113_Y 3_F 1.01 0.42 0.15
41_A 90_S 1.01 0.41 0.14
100_I 107_L 1.01 0.41 0.14
148_T 58_V 1.00 0.41 0.14
46_L 75_L 1.00 0.41 0.14
115_G 7_L 1.00 0.40 0.14
55_I 94_L 1.00 0.40 0.14
156_S 10_N 1.00 0.40 0.14
213_L 93_L 0.99 0.39 0.13
16_I 31_M 0.98 0.39 0.13
5_A 80_Q 0.98 0.39 0.13
60_E 80_Q 0.97 0.38 0.12
156_S 84_L 0.97 0.38 0.12
185_T 27_L 0.97 0.38 0.12
193_Y 19_I 0.97 0.38 0.12
220_E 51_F 0.97 0.37 0.12
111_T 12_L 0.96 0.36 0.12
123_L 97_I 0.96 0.36 0.12
213_L 35_T 0.95 0.36 0.11
13_T 21_T 0.95 0.36 0.11
63_T 75_L 0.95 0.35 0.11
72_I 11_T 0.95 0.35 0.11
156_S 30_Y 0.95 0.35 0.11
133_L 14_A 0.95 0.35 0.11
63_T 88_V 0.94 0.35 0.11
138_V 58_V 0.94 0.35 0.11
76_I 53_M 0.94 0.35 0.11
72_I 82_T 0.94 0.35 0.11
115_G 13_L 0.94 0.34 0.11
53_T 75_L 0.94 0.34 0.11
202_A 80_Q 0.93 0.34 0.11
110_Y 26_Q 0.93 0.33 0.10
211_L 109_K 0.93 0.33 0.10
142_V 30_Y 0.93 0.33 0.10
110_Y 75_L 0.93 0.33 0.10
144_L 114_A 0.93 0.33 0.10
138_V 88_V 0.92 0.33 0.10
211_L 61_T 0.92 0.33 0.10
123_L 103_A 0.92 0.33 0.10
132_D 80_Q 0.92 0.33 0.10
192_Y 102_L 0.92 0.33 0.10
157_Q 35_T 0.91 0.32 0.09
37_L 78_A 0.91 0.32 0.09
57_D 91_S 0.90 0.31 0.09
100_I 89_M 0.90 0.31 0.09
46_L 54_K 0.90 0.31 0.09
32_F 103_A 0.89 0.31 0.09
143_V 19_I 0.89 0.30 0.09
97_I 44_M 0.89 0.30 0.09
36_F 34_S 0.89 0.30 0.09
58_A 88_V 0.88 0.30 0.09
126_L 19_I 0.88 0.30 0.09
21_I 78_A 0.88 0.30 0.09
86_M 99_A 0.88 0.30 0.08
213_L 19_I 0.88 0.29 0.08
86_M 61_T 0.88 0.29 0.08
107_T 21_T 0.88 0.29 0.08
42_L 58_V 0.87 0.29 0.08
61_M 90_S 0.87 0.28 0.08
71_I 95_I 0.86 0.28 0.08
16_I 87_M 0.86 0.28 0.08
214_I 51_F 0.86 0.28 0.08
58_A 79_X 0.86 0.28 0.08
28_L 22_F 0.86 0.28 0.08
115_G 5_L 0.86 0.28 0.07
30_I 11_T 0.86 0.28 0.07
124_P 22_F 0.85 0.28 0.07
44_L 14_A 0.85 0.28 0.07
149_P 51_F 0.85 0.28 0.07
92_D 31_M 0.85 0.27 0.07
56_S 75_L 0.85 0.27 0.07
90_V 11_T 0.85 0.27 0.07
68_L 92_L 0.85 0.27 0.07
13_T 92_L 0.85 0.27 0.07
97_I 100_L 0.85 0.27 0.07
60_E 103_A 0.85 0.27 0.07
52_N 31_M 0.85 0.27 0.07
5_A 26_Q 0.84 0.26 0.07
13_T 54_K 0.83 0.26 0.07
58_A 94_L 0.83 0.26 0.07
36_F 99_A 0.83 0.26 0.07
55_I 80_Q 0.83 0.26 0.07
41_A 12_L 0.82 0.25 0.07
7_V 6_I 0.82 0.25 0.07
28_L 79_X 0.82 0.25 0.06
124_P 92_L 0.82 0.25 0.06
52_N 91_S 0.82 0.25 0.06
107_T 49_V 0.82 0.25 0.06
7_V 89_M 0.82 0.25 0.06
217_K 92_L 0.82 0.25 0.06
117_I 90_S 0.82 0.25 0.06
55_I 78_A 0.82 0.25 0.06
155_T 26_Q 0.82 0.25 0.06
100_I 12_L 0.81 0.24 0.06
202_A 13_L 0.81 0.24 0.06
146_I 20_I 0.81 0.24 0.06
182_T 61_T 0.81 0.24 0.06
192_Y 91_S 0.81 0.24 0.06
73_L 87_M 0.81 0.24 0.06
124_P 80_Q 0.81 0.24 0.06
184_F 109_K 0.80 0.24 0.06
110_Y 79_X 0.80 0.24 0.06
192_Y 80_Q 0.80 0.23 0.06
186_A 4_A 0.80 0.23 0.06
144_L 109_K 0.80 0.23 0.06
97_I 8_M 0.79 0.23 0.06
58_A 53_M 0.79 0.23 0.06
218_I 10_N 0.79 0.23 0.05
191_V 27_L 0.79 0.23 0.05
156_S 29_G 0.79 0.23 0.05
32_F 88_V 0.79 0.23 0.05
23_F 2_N 0.78 0.22 0.05
13_T 16_L 0.78 0.22 0.05
140_N 13_L 0.78 0.22 0.05
126_L 97_I 0.78 0.22 0.05
221_M 26_Q 0.78 0.22 0.05
5_A 14_A 0.78 0.22 0.05
52_N 80_Q 0.78 0.22 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
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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