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OPENSEQ.org
cI_4_40_cI_9_20_tt
Genes: A B A+B
Length: 409 182 559
Sequences: 1636 979 811
Seq/Len: 4 5.38 1.45
MirrorTree (Pazo et al. 2001) 0.85
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 0.06
2 0.00 0.01 0.25
5 0.00 0.01 1.04
10 0.01 0.02 1.18
20 0.01 0.02 1.23
100 0.01 0.03 1.28
∞ 0.05 0.07 1.37
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
203_E 19_S 2.09 0.98 0.94
174_R 106_E 1.41 0.80 0.59
206_A 12_I 1.37 0.77 0.55
381_L 22_V 1.12 0.56 0.30
212_P 5_A 1.11 0.55 0.29
171_N 103_L 1.11 0.55 0.29
73_R 67_A 1.08 0.51 0.26
332_T 61_A 1.08 0.51 0.26
166_Q 38_H 1.06 0.49 0.24
218_A 6_L 1.04 0.48 0.23
294_L 118_D 1.04 0.47 0.23
248_V 100_F 1.00 0.43 0.20
145_P 95_M 1.00 0.43 0.20
179_K 106_E 0.96 0.39 0.17
321_M 67_A 0.94 0.38 0.16
172_Y 70_V 0.94 0.37 0.15
369_K 60_A 0.92 0.35 0.14
83_P 113_I 0.92 0.35 0.14
394_V 103_L 0.91 0.34 0.14
28_L 30_P 0.91 0.34 0.13
225_P 14_L 0.90 0.34 0.13
114_E 35_P 0.90 0.34 0.13
394_V 29_A 0.90 0.33 0.13
144_T 7_A 0.89 0.33 0.13
401_D 86_R 0.87 0.31 0.12
73_R 113_I 0.86 0.30 0.11
80_T 96_L 0.86 0.30 0.11
54_E 78_E 0.85 0.29 0.11
241_A 72_P 0.85 0.29 0.11
138_L 54_I 0.85 0.29 0.10
192_K 47_P 0.85 0.29 0.10
201_I 5_A 0.85 0.29 0.10
207_L 13_T 0.84 0.29 0.10
21_L 29_A 0.84 0.28 0.10
391_P 30_P 0.84 0.28 0.10
178_V 125_E 0.83 0.28 0.10
79_I 131_Y 0.83 0.28 0.10
185_E 48_N 0.83 0.28 0.10
283_M 103_L 0.83 0.28 0.10
241_A 107_A 0.83 0.27 0.10
278_V 133_K 0.82 0.27 0.09
337_P 138_V 0.82 0.27 0.09
158_D 22_V 0.82 0.27 0.09
220_G 25_P 0.82 0.27 0.09
145_P 131_Y 0.82 0.26 0.09
123_L 13_T 0.82 0.26 0.09
52_V 112_A 0.81 0.26 0.09
371_R 126_Y 0.81 0.26 0.09
391_P 67_A 0.81 0.26 0.09
61_Y 103_L 0.81 0.26 0.09
128_S 96_L 0.81 0.26 0.09
126_L 130_V 0.80 0.25 0.08
79_I 96_L 0.80 0.25 0.08
211_S 9_S 0.80 0.25 0.08
400_L 40_R 0.80 0.25 0.08
30_V 6_L 0.80 0.25 0.08
320_S 116_G 0.80 0.25 0.08
360_D 137_L 0.79 0.24 0.08
376_V 74_E 0.79 0.24 0.08
97_Y 103_L 0.79 0.24 0.08
36_S 70_V 0.79 0.24 0.08
261_T 141_V 0.79 0.24 0.08
372_A 137_L 0.78 0.24 0.08
318_E 111_G 0.78 0.24 0.08
148_Y 28_D 0.78 0.24 0.08
29_N 36_R 0.78 0.24 0.08
148_Y 13_T 0.78 0.23 0.07
75_Y 112_A 0.78 0.23 0.07
64_T 82_S 0.78 0.23 0.07
329_K 65_A 0.78 0.23 0.07
142_A 9_S 0.77 0.23 0.07
144_T 66_Y 0.77 0.23 0.07
144_T 94_N 0.77 0.23 0.07
237_G 13_T 0.77 0.23 0.07
28_L 102_G 0.76 0.22 0.07
383_Y 132_G 0.76 0.22 0.07
28_L 14_L 0.76 0.22 0.07
180_E 105_E 0.76 0.22 0.07
127_A 100_F 0.76 0.22 0.07
109_V 129_L 0.76 0.22 0.07
221_V 14_L 0.76 0.22 0.07
62_L 70_V 0.76 0.22 0.07
290_I 102_G 0.75 0.22 0.07
144_T 102_G 0.75 0.21 0.07
209_A 35_P 0.75 0.21 0.07
119_I 47_P 0.75 0.21 0.07
202_D 30_P 0.75 0.21 0.07
131_V 62_A 0.75 0.21 0.06
44_M 103_L 0.75 0.21 0.06
307_P 15_K 0.75 0.21 0.06
109_V 11_G 0.74 0.21 0.06
135_T 94_N 0.74 0.21 0.06
65_G 39_G 0.74 0.21 0.06
143_L 9_S 0.74 0.21 0.06
106_G 152_R 0.74 0.21 0.06
233_G 116_G 0.74 0.21 0.06
128_S 55_G 0.74 0.21 0.06
328_F 58_L 0.74 0.21 0.06
250_K 35_P 0.74 0.21 0.06
65_G 99_I 0.73 0.20 0.06
311_P 115_L 0.73 0.20 0.06
203_E 12_I 0.73 0.20 0.06
36_S 55_G 0.73 0.20 0.06
174_R 99_I 0.73 0.20 0.06
404_M 37_F 0.73 0.20 0.06
164_T 124_Y 0.73 0.20 0.06
99_L 86_R 0.73 0.20 0.06
369_K 54_I 0.72 0.20 0.06
58_H 97_R 0.72 0.20 0.06
193_L 22_V 0.72 0.20 0.06
288_K 11_G 0.72 0.20 0.06
192_K 14_L 0.72 0.19 0.06
300_G 113_I 0.72 0.19 0.06
173_I 61_A 0.72 0.19 0.05
83_P 38_H 0.72 0.19 0.05
261_T 121_M 0.72 0.19 0.05
65_G 112_A 0.71 0.19 0.05
148_Y 95_M 0.71 0.19 0.05
324_V 51_E 0.71 0.19 0.05
185_E 35_P 0.71 0.19 0.05
313_P 11_G 0.71 0.19 0.05
73_R 37_F 0.71 0.19 0.05
304_D 35_P 0.71 0.19 0.05
386_K 113_I 0.71 0.19 0.05
86_D 120_E 0.71 0.19 0.05
356_Y 148_R 0.71 0.18 0.05
309_I 70_V 0.71 0.18 0.05
40_V 91_Y 0.70 0.18 0.05
306_N 48_N 0.70 0.18 0.05
211_S 112_A 0.70 0.18 0.05
144_T 113_I 0.70 0.18 0.05
40_V 70_V 0.70 0.18 0.05
215_Y 119_F 0.70 0.18 0.05
288_K 122_A 0.70 0.18 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
4903 1.14 cI_4_20_cI_9_40_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.95 Done - Shared
4896 1.45 cI_4_40_cI_9_20_tt Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.94 Done - Shared
4895 0.51 cI_4_60_cI_9_60_tt Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.06 Done - Shared
4894 1.13 cI_4_40_cI_9_40_tt Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.97 Done - Shared
4893 1.53 cI_4_20_cI_9_20_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.74 Done - Shared
4892 1.38 cI_4_10_cI_9_10_tt Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.21 Done - Shared
4889 1.23 cI_4_6_cI_9_6_tt Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.03 Done - Shared
4888 1.07 cI_4_4_cI_9_4_tt Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
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