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OPENSEQ.org
cI_4_10_cI_9_10_tt
Genes: A B A+B
Length: 409 182 562
Sequences: 3490 961 777
Seq/Len: 8.53 5.28 1.38
MirrorTree (Pazo et al. 2001) 0.78
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 0.09
2 0.01 0.05 0.29
5 0.03 0.05 0.97
10 0.04 0.06 1.11
20 0.05 0.06 1.17
100 0.06 0.07 1.22
∞ 0.13 0.11 1.31
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 1.56 0.87 0.21
174_R 106_E 1.35 0.74 0.12
206_A 12_I 1.30 0.71 0.10
212_P 5_A 1.20 0.62 0.07
207_L 13_T 1.10 0.52 0.05
28_L 30_P 1.05 0.47 0.04
145_P 131_Y 1.00 0.42 0.04
79_I 96_L 0.99 0.41 0.04
321_M 67_A 0.99 0.41 0.04
300_G 113_I 0.97 0.39 0.03
332_T 61_A 0.96 0.38 0.03
73_R 67_A 0.95 0.37 0.03
401_D 86_R 0.95 0.37 0.03
261_T 141_V 0.95 0.37 0.03
144_T 7_A 0.94 0.36 0.03
318_E 111_G 0.94 0.36 0.03
391_P 67_A 0.93 0.35 0.03
208_F 119_F 0.92 0.34 0.03
156_I 141_V 0.91 0.33 0.03
126_L 130_V 0.91 0.33 0.03
69_T 37_F 0.90 0.33 0.03
65_G 99_I 0.90 0.32 0.03
106_G 14_L 0.88 0.30 0.02
225_P 14_L 0.88 0.30 0.02
320_S 116_G 0.87 0.29 0.02
206_A 8_Q 0.86 0.29 0.02
61_Y 103_L 0.86 0.29 0.02
138_L 54_I 0.86 0.29 0.02
166_Q 38_H 0.86 0.29 0.02
327_H 45_R 0.85 0.28 0.02
218_A 6_L 0.85 0.28 0.02
376_V 74_E 0.85 0.28 0.02
86_D 120_E 0.85 0.28 0.02
355_Y 54_I 0.84 0.27 0.02
369_K 60_A 0.84 0.27 0.02
105_L 13_T 0.84 0.27 0.02
384_A 113_I 0.84 0.27 0.02
397_I 6_L 0.84 0.27 0.02
201_I 5_A 0.84 0.27 0.02
97_Y 103_L 0.83 0.27 0.02
80_T 96_L 0.83 0.27 0.02
179_K 106_E 0.83 0.26 0.02
148_Y 28_D 0.82 0.26 0.02
369_K 52_K 0.82 0.26 0.02
297_L 60_A 0.82 0.26 0.02
156_I 121_M 0.81 0.25 0.02
171_N 103_L 0.81 0.25 0.02
394_V 103_L 0.81 0.25 0.02
85_M 17_L 0.80 0.24 0.02
114_E 35_P 0.80 0.24 0.02
69_T 88_A 0.80 0.24 0.02
248_V 100_F 0.79 0.24 0.02
192_K 47_P 0.79 0.24 0.02
79_I 11_G 0.79 0.23 0.02
190_L 62_A 0.79 0.23 0.02
290_I 47_P 0.78 0.23 0.02
119_I 22_V 0.78 0.23 0.02
232_L 138_V 0.78 0.23 0.02
220_G 7_A 0.77 0.22 0.01
194_L 37_F 0.77 0.22 0.01
324_V 45_R 0.77 0.22 0.01
404_M 37_F 0.77 0.22 0.01
358_V 106_E 0.76 0.22 0.01
145_P 95_M 0.76 0.22 0.01
36_S 70_V 0.75 0.21 0.01
128_S 52_K 0.75 0.21 0.01
234_L 14_L 0.75 0.20 0.01
278_V 133_K 0.74 0.20 0.01
147_F 70_V 0.74 0.20 0.01
20_E 127_S 0.74 0.20 0.01
80_T 115_L 0.74 0.20 0.01
313_P 24_V 0.74 0.20 0.01
131_V 62_A 0.74 0.20 0.01
176_G 53_C 0.74 0.20 0.01
176_G 56_C 0.74 0.20 0.01
176_G 59_C 0.74 0.20 0.01
176_G 63_C 0.74 0.20 0.01
176_G 98_C 0.74 0.20 0.01
176_G 101_C 0.74 0.20 0.01
176_G 104_C 0.74 0.20 0.01
176_G 108_C 0.74 0.20 0.01
351_G 53_C 0.74 0.20 0.01
351_G 56_C 0.74 0.20 0.01
351_G 59_C 0.74 0.20 0.01
351_G 63_C 0.74 0.20 0.01
351_G 98_C 0.74 0.20 0.01
351_G 101_C 0.74 0.20 0.01
351_G 104_C 0.74 0.20 0.01
351_G 108_C 0.74 0.20 0.01
202_D 32_A 0.74 0.20 0.01
51_E 125_E 0.73 0.20 0.01
123_L 13_T 0.73 0.19 0.01
266_L 35_P 0.73 0.19 0.01
180_E 35_P 0.73 0.19 0.01
212_P 110_T 0.72 0.19 0.01
109_V 156_P 0.72 0.19 0.01
64_T 75_N 0.72 0.19 0.01
151_R 118_D 0.72 0.19 0.01
211_S 9_S 0.72 0.19 0.01
317_L 111_G 0.72 0.19 0.01
274_D 105_E 0.72 0.19 0.01
203_E 12_I 0.72 0.19 0.01
273_F 112_A 0.72 0.19 0.01
283_M 25_P 0.72 0.19 0.01
371_R 126_Y 0.72 0.19 0.01
250_K 121_M 0.71 0.18 0.01
179_K 6_L 0.71 0.18 0.01
144_T 66_Y 0.71 0.18 0.01
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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