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OPENSEQ.org
cI_1_20_cI_5_20_tt
Genes: A B A+B
Length: 438 207 607
Sequences: 2608 1089 606
Seq/Len: 5.95 5.26 1
MirrorTree (Pazo et al. 2001) 0.84
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 0.00 0.01
2 0.01 0.00 0.21
5 0.01 0.00 0.78
10 0.02 0.01 0.83
20 0.03 0.01 0.84
100 0.05 0.02 0.86
∞ 0.14 0.04 0.94
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
429_R 88_F 1.20 0.52 0.00
138_Y 114_L 1.16 0.48 0.00
429_R 23_G 1.13 0.46 0.00
227_V 127_E 1.12 0.45 0.00
313_Y 108_W 1.04 0.37 0.00
84_G 52_I 1.02 0.35 0.00
175_R 73_E 1.01 0.35 0.00
392_P 23_G 1.01 0.35 0.00
361_E 151_P 1.00 0.34 0.00
218_I 88_F 0.99 0.34 0.00
107_L 9_E 0.99 0.33 0.00
158_L 27_V 0.98 0.32 0.00
399_F 138_P 0.98 0.32 0.00
277_Y 175_T 0.94 0.29 0.00
276_I 38_M 0.94 0.29 0.00
379_G 124_I 0.93 0.28 0.00
370_L 128_G 0.92 0.28 0.00
208_Q 121_L 0.92 0.28 0.00
132_I 31_R 0.91 0.27 0.00
223_T 125_V 0.91 0.27 0.00
195_L 140_D 0.91 0.27 0.00
348_Y 152_L 0.90 0.26 0.00
240_Q 105_T 0.90 0.26 0.00
122_G 144_H 0.90 0.26 0.00
36_G 53_V 0.89 0.26 0.00
154_A 92_V 0.89 0.25 0.00
135_R 34_F 0.88 0.25 0.00
139_R 73_E 0.87 0.24 0.00
135_R 72_Y 0.87 0.24 0.00
272_F 73_E 0.87 0.24 0.00
290_I 140_D 0.86 0.24 0.00
165_T 77_L 0.86 0.23 0.00
34_R 32_E 0.86 0.23 0.00
251_L 40_H 0.85 0.23 0.00
31_Y 12_A 0.85 0.23 0.00
157_Y 103_T 0.85 0.23 0.00
250_K 56_D 0.85 0.23 0.00
311_M 51_D 0.84 0.22 0.00
171_L 14_G 0.84 0.22 0.00
212_W 121_L 0.84 0.22 0.00
123_Y 88_F 0.84 0.22 0.00
196_R 138_P 0.83 0.22 0.00
115_I 121_L 0.83 0.22 0.00
173_V 72_Y 0.83 0.22 0.00
51_D 54_G 0.83 0.21 0.00
42_K 39_A 0.83 0.21 0.00
268_M 162_G 0.83 0.21 0.00
59_R 88_F 0.82 0.21 0.00
153_R 136_L 0.82 0.21 0.00
74_L 135_I 0.82 0.21 0.00
323_L 137_T 0.82 0.21 0.00
300_L 32_E 0.82 0.21 0.00
57_V 8_E 0.82 0.21 0.00
152_A 149_D 0.81 0.21 0.00
106_I 138_P 0.81 0.21 0.00
41_A 46_F 0.81 0.20 0.00
135_R 166_I 0.81 0.20 0.00
189_M 157_T 0.81 0.20 0.00
378_Q 90_V 0.81 0.20 0.00
93_A 92_V 0.81 0.20 0.00
378_Q 121_L 0.81 0.20 0.00
150_K 32_E 0.81 0.20 0.00
332_P 109_G 0.80 0.20 0.00
154_A 105_T 0.80 0.20 0.00
120_L 108_W 0.80 0.20 0.00
126_R 59_T 0.80 0.20 0.00
138_Y 166_I 0.80 0.20 0.00
79_M 150_Y 0.80 0.20 0.00
307_L 124_I 0.80 0.20 0.00
29_L 92_V 0.80 0.19 0.00
383_D 124_I 0.79 0.19 0.00
34_R 105_T 0.79 0.19 0.00
232_E 27_V 0.79 0.19 0.00
173_V 122_F 0.79 0.19 0.00
53_V 125_V 0.79 0.19 0.00
93_A 124_I 0.78 0.18 0.00
223_T 36_E 0.78 0.18 0.00
338_V 39_A 0.78 0.18 0.00
196_R 141_L 0.78 0.18 0.00
314_E 46_F 0.77 0.18 0.00
49_T 97_E 0.77 0.18 0.00
158_L 176_G 0.77 0.18 0.00
371_F 60_Y 0.77 0.18 0.00
319_K 121_L 0.77 0.18 0.00
330_L 121_L 0.77 0.18 0.00
163_F 118_V 0.77 0.18 0.00
270_T 102_P 0.77 0.18 0.00
91_C 104_V 0.77 0.18 0.00
115_I 32_E 0.77 0.18 0.00
260_R 106_D 0.76 0.18 0.00
173_V 88_F 0.76 0.18 0.00
164_G 36_E 0.76 0.17 0.00
84_G 88_F 0.76 0.17 0.00
169_F 137_T 0.76 0.17 0.00
114_L 38_M 0.76 0.17 0.00
155_R 15_Y 0.76 0.17 0.00
283_P 152_L 0.75 0.17 0.00
243_T 112_N 0.75 0.17 0.00
169_F 147_R 0.75 0.17 0.00
46_K 36_E 0.75 0.17 0.00
161_N 16_P 0.75 0.17 0.00
52_E 122_F 0.75 0.17 0.00
89_L 64_R 0.75 0.17 0.00
146_E 103_T 0.75 0.17 0.00
171_L 121_L 0.75 0.17 0.00
108_E 138_P 0.75 0.17 0.00
143_D 118_V 0.75 0.17 0.00
211_L 71_V 0.75 0.17 0.00
179_A 153_G 0.74 0.17 0.00
290_I 131_D 0.74 0.17 0.00
161_N 35_K 0.74 0.17 0.00
259_K 55_L 0.74 0.17 0.00
318_A 106_D 0.74 0.17 0.00
260_R 45_G 0.74 0.17 0.00
158_L 171_R 0.74 0.17 0.00
167_F 174_L 0.74 0.16 0.00
46_K 23_G 0.74 0.16 0.00
198_N 99_P 0.74 0.16 0.00
115_I 52_I 0.74 0.16 0.00
132_I 149_D 0.74 0.16 0.00
236_D 128_G 0.73 0.16 0.00
189_M 4_E 0.73 0.16 0.00
315_H 127_E 0.73 0.16 0.00
399_F 141_L 0.73 0.16 0.00
60_S 151_P 0.73 0.16 0.00
149_I 45_G 0.73 0.16 0.00
136_G 149_D 0.73 0.16 0.00
243_T 7_L 0.73 0.16 0.00
399_F 150_Y 0.73 0.16 0.00
34_R 30_P 0.73 0.16 0.00
289_A 135_I 0.73 0.16 0.00
364_A 153_G 0.73 0.16 0.00
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
4923 1 cI_1_20_cI_5_20_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4839 0.97 cI_1_4_cI_5_4_tt Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4838 0.02 cI_1_40_cI_5_40_tt Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) Killed - Shared
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