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OPENSEQ.org
cI_4_40_cI_6_40_tt
Genes: A B A+B
Length: 409 181 556
Sequences: 1636 1163 1137
Seq/Len: 4 6.43 2.04
MirrorTree (Pazo et al. 2001) 0.88
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 0.01 0.45
2 0.00 0.01 1.63
5 0.00 0.01 1.68
10 0.01 0.02 1.69
20 0.01 0.02 1.71
100 0.01 0.03 1.79
∞ 0.05 0.08 1.93
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 1.77 0.97 0.87
64_T 83_R 1.77 0.97 0.87
69_T 120_N 1.56 0.93 0.77
65_G 120_N 1.45 0.89 0.68
158_D 57_R 1.40 0.87 0.64
81_Y 117_M 1.39 0.86 0.63
146_F 51_M 1.08 0.61 0.32
41_L 81_A 1.07 0.61 0.32
80_T 83_R 1.03 0.56 0.27
40_V 41_F 1.00 0.53 0.25
169_H 118_F 0.99 0.52 0.24
221_V 118_F 0.98 0.51 0.23
123_L 103_K 0.97 0.50 0.22
40_V 88_M 0.97 0.49 0.22
74_T 101_D 0.96 0.48 0.21
198_P 118_F 0.94 0.46 0.20
147_F 54_T 0.93 0.45 0.19
349_A 84_L 0.92 0.43 0.18
33_Q 41_F 0.92 0.43 0.18
285_E 58_N 0.91 0.43 0.18
87_Y 69_R 0.90 0.42 0.17
65_G 122_A 0.89 0.41 0.17
107_A 130_V 0.88 0.40 0.16
401_D 146_A 0.88 0.40 0.16
399_S 27_L 0.88 0.40 0.16
147_F 61_A 0.87 0.39 0.15
62_L 47_A 0.85 0.36 0.14
144_T 95_V 0.85 0.36 0.14
37_T 48_I 0.85 0.36 0.14
64_T 123_I 0.85 0.36 0.14
147_F 56_A 0.84 0.35 0.13
266_L 21_F 0.84 0.35 0.13
68_K 121_Y 0.84 0.35 0.13
235_T 154_L 0.84 0.35 0.13
86_D 88_M 0.83 0.35 0.13
157_L 70_A 0.82 0.33 0.12
161_E 154_L 0.81 0.33 0.12
219_R 122_A 0.81 0.32 0.12
404_M 117_M 0.81 0.32 0.12
146_F 55_D 0.81 0.32 0.12
369_K 94_R 0.81 0.32 0.12
62_L 44_A 0.81 0.32 0.11
313_P 135_V 0.80 0.32 0.11
329_K 92_M 0.80 0.32 0.11
41_L 48_I 0.79 0.30 0.11
140_L 110_A 0.79 0.30 0.10
120_L 107_S 0.78 0.29 0.10
404_M 107_S 0.78 0.29 0.10
79_I 118_F 0.77 0.28 0.10
64_T 85_S 0.77 0.28 0.10
385_C 150_A 0.76 0.28 0.09
405_G 47_A 0.76 0.28 0.09
188_P 36_L 0.76 0.28 0.09
25_V 103_K 0.76 0.28 0.09
370_V 122_A 0.76 0.27 0.09
147_F 67_V 0.76 0.27 0.09
343_Y 44_A 0.76 0.27 0.09
261_T 103_K 0.76 0.27 0.09
403_V 43_L 0.75 0.27 0.09
197_L 25_E 0.75 0.27 0.09
69_T 110_A 0.75 0.27 0.09
80_T 85_S 0.75 0.27 0.09
77_Q 148_I 0.75 0.26 0.09
61_Y 94_R 0.74 0.26 0.09
33_Q 39_A 0.74 0.26 0.08
403_V 42_G 0.74 0.26 0.08
137_L 110_A 0.74 0.26 0.08
64_T 120_N 0.73 0.26 0.08
223_V 106_I 0.73 0.25 0.08
220_G 131_V 0.73 0.25 0.08
248_V 158_V 0.73 0.25 0.08
373_P 112_A 0.73 0.25 0.08
402_P 56_A 0.73 0.25 0.08
61_Y 144_P 0.73 0.25 0.08
291_K 150_A 0.73 0.25 0.08
325_I 117_M 0.72 0.25 0.08
407_V 70_A 0.72 0.24 0.08
81_Y 120_N 0.72 0.24 0.08
41_L 20_L 0.72 0.24 0.08
350_R 92_M 0.72 0.24 0.07
220_G 84_L 0.72 0.24 0.07
144_T 104_W 0.72 0.24 0.07
78_N 131_V 0.72 0.24 0.07
399_S 78_M 0.72 0.24 0.07
57_P 108_M 0.72 0.24 0.07
150_F 68_F 0.72 0.24 0.07
369_K 56_A 0.72 0.24 0.07
299_P 148_I 0.71 0.24 0.07
184_E 148_I 0.71 0.23 0.07
321_M 93_R 0.71 0.23 0.07
64_T 122_A 0.71 0.23 0.07
96_A 153_Q 0.70 0.23 0.07
139_D 108_M 0.70 0.23 0.07
86_D 42_G 0.70 0.23 0.07
146_F 61_A 0.70 0.23 0.07
160_F 88_M 0.70 0.23 0.07
106_G 56_A 0.70 0.23 0.07
325_I 41_F 0.70 0.23 0.07
166_Q 118_F 0.70 0.23 0.07
83_P 126_N 0.70 0.23 0.07
202_D 152_M 0.70 0.23 0.07
19_K 131_V 0.70 0.22 0.07
138_L 44_A 0.70 0.22 0.07
194_L 60_L 0.69 0.22 0.07
50_E 76_D 0.69 0.22 0.07
72_H 146_A 0.69 0.22 0.07
147_F 66_E 0.69 0.22 0.07
269_R 25_E 0.69 0.22 0.07
385_C 103_K 0.69 0.22 0.07
75_Y 149_Y 0.68 0.21 0.06
69_T 83_R 0.68 0.21 0.06
141_G 158_V 0.68 0.21 0.06
128_S 118_F 0.68 0.21 0.06
160_F 117_M 0.68 0.21 0.06
287_V 20_L 0.68 0.21 0.06
342_V 84_L 0.68 0.21 0.06
95_L 149_Y 0.68 0.21 0.06
382_P 84_L 0.67 0.21 0.06
328_F 104_W 0.67 0.21 0.06
183_P 151_V 0.67 0.20 0.06
201_I 161_Q 0.67 0.20 0.06
276_M 157_K 0.67 0.20 0.06
138_L 68_F 0.67 0.20 0.06
33_Q 98_Q 0.67 0.20 0.06
260_Y 129_S 0.67 0.20 0.06
193_L 127_V 0.66 0.20 0.06
142_A 74_Q 0.66 0.20 0.06
129_H 46_C 0.66 0.20 0.06
270_G 137_V 0.66 0.20 0.06
38_H 126_N 0.66 0.20 0.06
235_T 101_D 0.66 0.20 0.06
147_F 60_L 0.66 0.20 0.06
287_V 26_K 0.66 0.19 0.06
295_E 75_A 0.65 0.19 0.05
149_A 100_P 0.65 0.19 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
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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