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OPENSEQ.org
cI_1_4_cI_5_4_tt
Genes: A B A+B
Length: 438 207 609
Sequences: 2611 1052 589
Seq/Len: 5.96 5.08 0.97
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 0.01 0.77
10 0.02 0.01 0.83
20 0.03 0.01 0.84
100 0.05 0.01 0.85
∞ 0.14 0.03 0.91
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
158_L 27_V 1.41 0.69 0.00
348_Y 152_L 1.21 0.52 0.00
115_I 52_I 1.14 0.46 0.00
429_R 23_G 1.11 0.43 0.00
138_Y 114_L 1.07 0.39 0.00
107_L 27_V 1.06 0.39 0.00
429_R 88_F 1.00 0.33 0.00
120_L 108_W 0.99 0.33 0.00
188_L 147_R 0.98 0.32 0.00
376_T 121_L 0.98 0.32 0.00
121_A 88_F 0.97 0.31 0.00
311_M 51_D 0.97 0.31 0.00
93_A 92_V 0.96 0.30 0.00
81_K 107_L 0.96 0.30 0.00
223_T 125_V 0.94 0.29 0.00
195_L 140_D 0.94 0.29 0.00
115_I 32_E 0.93 0.28 0.00
241_M 121_L 0.93 0.28 0.00
275_L 131_D 0.92 0.27 0.00
150_K 8_E 0.92 0.27 0.00
135_R 178_D 0.92 0.27 0.00
51_D 27_V 0.91 0.27 0.00
212_W 121_L 0.91 0.27 0.00
392_P 23_G 0.91 0.26 0.00
108_E 138_P 0.91 0.26 0.00
189_M 8_E 0.90 0.26 0.00
134_V 178_D 0.89 0.25 0.00
115_I 121_L 0.89 0.25 0.00
268_M 47_N 0.88 0.24 0.00
135_R 179_P 0.88 0.24 0.00
122_G 55_L 0.87 0.24 0.00
425_A 104_V 0.87 0.24 0.00
290_I 131_D 0.87 0.23 0.00
74_L 135_I 0.87 0.23 0.00
399_F 138_P 0.87 0.23 0.00
161_N 21_G 0.86 0.23 0.00
218_I 88_F 0.86 0.23 0.00
398_S 68_F 0.86 0.23 0.00
276_I 70_V 0.86 0.23 0.00
151_E 33_R 0.86 0.23 0.00
122_G 17_I 0.86 0.23 0.00
295_S 152_L 0.85 0.23 0.00
55_E 122_F 0.85 0.22 0.00
161_N 35_K 0.84 0.22 0.00
122_G 144_H 0.84 0.22 0.00
302_F 10_A 0.84 0.22 0.00
133_Y 24_N 0.84 0.21 0.00
154_A 92_V 0.84 0.21 0.00
276_I 125_V 0.83 0.21 0.00
420_Q 171_R 0.83 0.21 0.00
399_F 150_Y 0.83 0.21 0.00
139_R 73_E 0.83 0.21 0.00
378_Q 121_L 0.82 0.20 0.00
374_I 108_W 0.82 0.20 0.00
323_L 149_D 0.81 0.20 0.00
175_R 73_E 0.81 0.20 0.00
192_L 29_L 0.80 0.20 0.00
349_A 122_F 0.80 0.19 0.00
152_A 149_D 0.80 0.19 0.00
173_V 88_F 0.80 0.19 0.00
80_P 105_T 0.79 0.19 0.00
307_L 124_I 0.79 0.19 0.00
231_M 33_R 0.79 0.19 0.00
88_Y 157_T 0.79 0.19 0.00
371_F 60_Y 0.78 0.18 0.00
371_F 52_I 0.78 0.18 0.00
140_R 73_E 0.78 0.18 0.00
179_A 153_G 0.78 0.18 0.00
34_R 12_A 0.78 0.18 0.00
396_G 76_S 0.78 0.18 0.00
238_F 130_P 0.78 0.18 0.00
140_R 26_W 0.78 0.18 0.00
254_I 164_Y 0.78 0.18 0.00
227_V 127_E 0.77 0.18 0.00
364_A 67_R 0.77 0.18 0.00
167_F 178_D 0.77 0.18 0.00
399_F 141_L 0.77 0.17 0.00
379_G 124_I 0.77 0.17 0.00
135_R 72_Y 0.76 0.17 0.00
150_K 32_E 0.76 0.17 0.00
223_T 171_R 0.76 0.17 0.00
173_V 11_R 0.76 0.17 0.00
227_V 102_P 0.76 0.17 0.00
87_H 146_L 0.76 0.17 0.00
387_L 124_I 0.76 0.17 0.00
107_L 8_E 0.76 0.17 0.00
313_Y 108_W 0.76 0.17 0.00
131_Y 104_V 0.76 0.17 0.00
177_A 178_D 0.75 0.17 0.00
138_Y 178_D 0.75 0.17 0.00
374_I 110_S 0.75 0.17 0.00
165_T 77_L 0.75 0.17 0.00
319_K 35_K 0.75 0.17 0.00
361_E 151_P 0.75 0.17 0.00
318_A 106_D 0.75 0.17 0.00
46_K 36_E 0.75 0.17 0.00
243_T 112_N 0.75 0.17 0.00
175_R 50_A 0.75 0.17 0.00
34_R 105_T 0.75 0.17 0.00
259_K 77_L 0.75 0.16 0.00
168_S 55_L 0.75 0.16 0.00
106_I 138_P 0.74 0.16 0.00
192_L 39_A 0.74 0.16 0.00
228_V 103_T 0.74 0.16 0.00
132_I 149_D 0.74 0.16 0.00
114_L 38_M 0.74 0.16 0.00
34_R 77_L 0.74 0.16 0.00
344_L 180_G 0.74 0.16 0.00
338_V 39_A 0.74 0.16 0.00
272_F 171_R 0.74 0.16 0.00
163_F 73_E 0.74 0.16 0.00
304_E 101_L 0.74 0.16 0.00
149_I 10_A 0.73 0.16 0.00
107_L 11_R 0.73 0.16 0.00
289_A 135_I 0.73 0.16 0.00
157_Y 103_T 0.73 0.16 0.00
36_G 53_V 0.73 0.16 0.00
217_T 133_R 0.73 0.16 0.00
157_Y 11_R 0.73 0.16 0.00
40_T 69_A 0.73 0.15 0.00
403_A 171_R 0.73 0.15 0.00
129_V 127_E 0.72 0.15 0.00
82_D 34_F 0.72 0.15 0.00
224_L 111_A 0.72 0.15 0.00
275_L 136_L 0.72 0.15 0.00
53_V 125_V 0.72 0.15 0.00
392_P 52_I 0.72 0.15 0.00
237_W 178_D 0.72 0.15 0.00
426_R 91_R 0.72 0.15 0.00
235_A 135_I 0.72 0.15 0.00
300_L 32_E 0.72 0.15 0.00
91_C 104_V 0.72 0.15 0.00
135_R 34_F 0.72 0.15 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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