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OPENSEQ.org
cI_4_20_cI_9_20_tt
Genes: A B A+B
Length: 409 182 562
Sequences: 2519 979 859
Seq/Len: 6.16 5.38 1.53
MirrorTree (Pazo et al. 2001) 0.80
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 0.13
2 0.00 0.01 0.33
5 0.01 0.01 1.12
10 0.02 0.02 1.25
20 0.02 0.02 1.32
100 0.04 0.03 1.35
∞ 0.10 0.07 1.45
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 1.78 0.95 0.74
174_R 106_E 1.49 0.86 0.52
381_L 22_V 1.20 0.65 0.26
206_A 12_I 1.15 0.60 0.22
212_P 5_A 1.12 0.57 0.21
332_T 61_A 1.10 0.55 0.19
294_L 118_D 1.05 0.50 0.16
166_Q 38_H 1.05 0.49 0.16
401_D 86_R 1.04 0.49 0.16
73_R 67_A 1.04 0.49 0.16
218_A 6_L 1.04 0.49 0.15
28_L 30_P 1.04 0.48 0.15
171_N 103_L 1.03 0.48 0.15
404_M 37_F 1.02 0.46 0.14
55_V 106_E 1.01 0.46 0.14
145_P 95_M 0.96 0.40 0.11
61_Y 103_L 0.95 0.40 0.11
369_K 60_A 0.95 0.39 0.11
144_T 7_A 0.94 0.39 0.11
321_M 67_A 0.94 0.38 0.10
83_P 113_I 0.92 0.36 0.10
52_V 112_A 0.90 0.35 0.09
337_P 138_V 0.90 0.34 0.09
391_P 67_A 0.89 0.33 0.08
192_K 47_P 0.88 0.33 0.08
65_G 99_I 0.88 0.33 0.08
59_I 136_M 0.88 0.33 0.08
178_V 125_E 0.86 0.31 0.07
80_T 96_L 0.86 0.31 0.07
128_S 96_L 0.85 0.31 0.07
288_K 122_A 0.85 0.30 0.07
148_Y 13_T 0.85 0.30 0.07
73_R 37_F 0.85 0.30 0.07
394_V 103_L 0.84 0.29 0.07
138_L 54_I 0.84 0.29 0.07
21_L 29_A 0.84 0.29 0.07
278_V 133_K 0.84 0.29 0.07
36_S 70_V 0.83 0.29 0.07
307_P 15_K 0.83 0.28 0.07
299_P 35_P 0.83 0.28 0.07
241_A 107_A 0.83 0.28 0.07
207_L 13_T 0.83 0.28 0.07
225_P 14_L 0.82 0.28 0.06
54_E 78_E 0.82 0.28 0.06
179_K 106_E 0.82 0.27 0.06
164_T 124_Y 0.82 0.27 0.06
73_R 39_G 0.81 0.27 0.06
127_A 100_F 0.81 0.27 0.06
318_E 111_G 0.81 0.27 0.06
142_A 9_S 0.81 0.27 0.06
79_I 96_L 0.81 0.26 0.06
144_T 102_G 0.81 0.26 0.06
250_K 35_P 0.80 0.26 0.06
391_P 30_P 0.80 0.26 0.06
145_P 131_Y 0.79 0.26 0.06
79_I 131_Y 0.79 0.25 0.06
64_T 82_S 0.79 0.25 0.06
109_V 11_G 0.79 0.25 0.05
123_L 13_T 0.79 0.25 0.05
320_S 47_P 0.79 0.25 0.05
101_V 15_K 0.79 0.25 0.05
61_Y 106_E 0.79 0.25 0.05
59_I 93_I 0.79 0.25 0.05
283_M 103_L 0.79 0.25 0.05
224_I 14_L 0.79 0.25 0.05
201_I 5_A 0.78 0.25 0.05
261_T 141_V 0.78 0.24 0.05
128_S 55_G 0.78 0.24 0.05
211_S 9_S 0.78 0.24 0.05
386_K 113_I 0.77 0.24 0.05
371_R 126_Y 0.76 0.23 0.05
320_S 116_G 0.76 0.23 0.05
158_D 22_V 0.76 0.23 0.05
309_I 70_V 0.76 0.23 0.05
180_E 105_E 0.76 0.23 0.05
393_M 127_S 0.76 0.23 0.05
172_Y 70_V 0.75 0.22 0.04
86_D 120_E 0.75 0.22 0.04
28_L 102_G 0.75 0.22 0.04
144_T 66_Y 0.75 0.22 0.04
131_V 62_A 0.75 0.22 0.04
376_V 74_E 0.75 0.22 0.04
106_G 32_A 0.74 0.22 0.04
295_E 35_P 0.74 0.22 0.04
192_K 14_L 0.74 0.21 0.04
317_L 111_G 0.74 0.21 0.04
29_N 36_R 0.74 0.21 0.04
97_Y 103_L 0.74 0.21 0.04
291_K 128_D 0.73 0.21 0.04
185_E 48_N 0.73 0.21 0.04
230_I 19_S 0.73 0.21 0.04
114_E 35_P 0.73 0.21 0.04
28_L 54_I 0.73 0.21 0.04
311_P 115_L 0.73 0.20 0.04
134_G 91_Y 0.72 0.20 0.04
155_T 149_E 0.72 0.20 0.04
241_A 72_P 0.72 0.20 0.04
235_T 145_P 0.72 0.20 0.04
315_H 48_N 0.72 0.20 0.04
131_V 10_L 0.72 0.20 0.04
144_T 94_N 0.71 0.20 0.04
106_G 11_G 0.71 0.20 0.04
279_R 64_P 0.71 0.20 0.04
180_E 67_A 0.71 0.20 0.04
37_T 13_T 0.71 0.20 0.04
61_Y 67_A 0.71 0.20 0.04
183_P 36_R 0.71 0.20 0.04
166_Q 52_K 0.71 0.20 0.04
299_P 113_I 0.71 0.20 0.04
73_R 113_I 0.70 0.19 0.04
290_I 47_P 0.70 0.19 0.04
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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