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OPENSEQ.org
cI_4_10_cI_6_20_tt
Genes: A B A+B
Length: 409 181 557
Sequences: 3490 1141 1308
Seq/Len: 8.53 6.3 2.35
MirrorTree (Pazo et al. 2001) 0.77
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 0.01 0.01 0.52
2 0.01 0.01 1.84
5 0.03 0.01 1.93
10 0.04 0.02 1.94
20 0.05 0.02 1.97
100 0.06 0.03 2.05
∞ 0.13 0.08 2.22
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
66_F 118_F 1.87 0.99 0.94
158_D 57_R 1.82 0.98 0.93
69_T 120_N 1.65 0.96 0.88
64_T 83_R 1.52 0.94 0.82
81_Y 117_M 1.36 0.88 0.71
65_G 120_N 1.35 0.87 0.70
146_F 51_M 1.10 0.68 0.45
41_L 81_A 0.99 0.56 0.33
270_G 137_V 0.94 0.51 0.28
74_T 101_D 0.94 0.50 0.27
107_A 130_V 0.94 0.50 0.27
147_F 56_A 0.93 0.49 0.27
169_H 118_F 0.92 0.48 0.26
198_P 118_F 0.92 0.47 0.25
123_L 103_K 0.91 0.46 0.24
62_L 44_A 0.90 0.46 0.24
80_T 83_R 0.87 0.42 0.21
147_F 61_A 0.87 0.42 0.21
39_G 45_C 0.86 0.41 0.21
127_A 31_G 0.86 0.41 0.20
64_T 123_I 0.85 0.39 0.19
40_V 88_M 0.84 0.39 0.19
63_H 121_Y 0.84 0.39 0.19
86_D 88_M 0.83 0.38 0.18
192_K 130_V 0.82 0.37 0.17
69_T 110_A 0.82 0.37 0.17
161_E 143_R 0.82 0.37 0.17
33_Q 41_F 0.82 0.36 0.17
146_F 55_D 0.81 0.36 0.17
37_T 48_I 0.81 0.36 0.17
62_L 47_A 0.81 0.35 0.16
385_C 150_A 0.79 0.33 0.15
65_G 149_Y 0.79 0.33 0.15
399_S 27_L 0.78 0.33 0.15
88_L 48_I 0.78 0.33 0.15
342_V 84_L 0.78 0.33 0.15
202_D 153_Q 0.78 0.32 0.14
134_G 58_N 0.78 0.32 0.14
346_T 130_V 0.78 0.32 0.14
349_A 43_L 0.78 0.32 0.14
178_V 97_E 0.78 0.32 0.14
33_Q 39_A 0.78 0.32 0.14
407_V 70_A 0.77 0.32 0.14
40_V 41_F 0.77 0.31 0.14
276_M 55_D 0.77 0.31 0.14
405_G 47_A 0.76 0.30 0.13
349_A 84_L 0.75 0.29 0.13
403_V 43_L 0.75 0.29 0.12
64_T 110_A 0.74 0.29 0.12
350_R 92_M 0.74 0.29 0.12
144_T 104_W 0.74 0.28 0.12
194_L 60_L 0.73 0.28 0.12
87_Y 69_R 0.73 0.28 0.12
65_G 122_A 0.73 0.28 0.12
25_V 58_N 0.73 0.28 0.12
81_Y 118_F 0.73 0.27 0.11
52_V 159_R 0.72 0.27 0.11
138_L 68_F 0.72 0.27 0.11
147_F 54_T 0.72 0.27 0.11
33_Q 98_Q 0.72 0.27 0.11
370_V 122_A 0.71 0.26 0.11
341_E 99_M 0.71 0.26 0.11
29_N 45_C 0.71 0.26 0.11
58_H 86_K 0.71 0.26 0.10
64_T 85_S 0.71 0.26 0.10
377_N 110_A 0.71 0.25 0.10
139_D 108_M 0.71 0.25 0.10
150_F 68_F 0.71 0.25 0.10
403_V 47_A 0.70 0.25 0.10
150_F 51_M 0.70 0.25 0.10
405_G 44_A 0.70 0.25 0.10
261_T 103_K 0.70 0.25 0.10
83_P 126_N 0.70 0.25 0.10
235_T 154_L 0.69 0.24 0.10
77_Q 80_V 0.69 0.24 0.10
140_L 110_A 0.69 0.24 0.10
303_R 53_S 0.69 0.24 0.09
40_V 43_L 0.69 0.24 0.09
77_Q 148_I 0.69 0.24 0.09
69_T 146_A 0.69 0.24 0.09
266_L 21_F 0.69 0.24 0.09
220_G 131_V 0.69 0.24 0.09
73_R 118_F 0.68 0.23 0.09
24_E 65_S 0.68 0.23 0.09
295_E 147_L 0.68 0.23 0.09
112_R 136_Y 0.68 0.23 0.09
69_T 123_I 0.68 0.23 0.09
119_I 151_V 0.68 0.23 0.09
401_D 146_A 0.68 0.23 0.09
36_S 48_I 0.68 0.23 0.09
149_A 100_P 0.67 0.23 0.09
86_D 43_L 0.67 0.23 0.09
369_K 94_R 0.67 0.22 0.09
147_F 66_E 0.67 0.22 0.08
53_L 28_V 0.67 0.22 0.08
79_I 118_F 0.67 0.22 0.08
403_V 81_A 0.66 0.22 0.08
139_D 69_R 0.66 0.22 0.08
362_G 29_A 0.66 0.21 0.08
19_K 131_V 0.66 0.21 0.08
147_F 67_V 0.66 0.21 0.08
287_V 94_R 0.66 0.21 0.08
139_D 81_A 0.66 0.21 0.08
357_I 30_W 0.65 0.21 0.08
61_Y 94_R 0.65 0.21 0.08
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
6517 1.93 4 and 6 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.94 Done - Shared
4887 2.68 cI_4_20_cI_6_10_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.87 Done - Shared
4885 2.35 cI_4_10_cI_6_20_tt Δgene:(1, ∞) A:(1E-10, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.94 Done - Shared
4884 2.04 cI_4_40_cI_6_40_tt Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.87 Done - Shared
4883 2.31 cI_4_20_cI_6_20_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.95 Done - Shared
4882 2.93 cI_4_10_cI_6_10_tt Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.91 Done - Shared
4881 3.18 cI_4_6_cI_6_6_tt Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.88 Done - Shared
4866 3.43 cI_4_4_cI_6_4_tt Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.80 Done - Shared
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