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OPENSEQ.org
cI_4_4_cI_9_4_tt
Genes: A B A+B
Length: 409 182 560
Sequences: 3475 870 599
Seq/Len: 8.5 4.78 1.07
MirrorTree (Pazo et al. 2001) 0.77
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 0.06
2 0.01 0.00 0.21
5 0.03 0.01 0.66
10 0.04 0.01 0.79
20 0.05 0.01 0.83
100 0.06 0.01 0.91
∞ 0.13 0.02 1.01
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
171_N 103_L 1.45 0.75 0.01
174_R 106_E 1.43 0.73 0.01
203_E 19_S 1.34 0.67 0.01
114_E 35_P 1.32 0.65 0.01
184_E 128_D 1.27 0.60 0.01
357_I 113_I 1.20 0.54 0.01
321_M 67_A 1.10 0.45 0.01
85_M 17_L 1.09 0.44 0.01
48_S 24_V 1.08 0.43 0.01
106_G 14_L 1.07 0.42 0.01
272_V 128_D 1.06 0.41 0.01
288_K 122_A 1.05 0.40 0.01
332_T 61_A 1.01 0.36 0.00
384_A 113_I 0.99 0.35 0.00
97_Y 103_L 0.99 0.35 0.00
296_R 122_A 0.97 0.33 0.00
64_T 75_N 0.97 0.33 0.00
218_A 6_L 0.96 0.33 0.00
107_A 126_Y 0.96 0.32 0.00
144_T 94_N 0.95 0.32 0.00
305_P 47_P 0.94 0.31 0.00
37_T 9_S 0.94 0.30 0.00
116_I 103_L 0.94 0.30 0.00
166_Q 38_H 0.94 0.30 0.00
320_S 116_G 0.91 0.28 0.00
145_P 95_M 0.90 0.27 0.00
159_L 22_V 0.89 0.27 0.00
313_P 24_V 0.89 0.27 0.00
237_G 13_T 0.89 0.27 0.00
396_I 17_L 0.89 0.27 0.00
134_G 25_P 0.89 0.27 0.00
176_G 53_C 0.89 0.27 0.00
176_G 56_C 0.89 0.27 0.00
176_G 59_C 0.89 0.27 0.00
176_G 98_C 0.89 0.27 0.00
176_G 108_C 0.89 0.27 0.00
351_G 53_C 0.89 0.27 0.00
351_G 56_C 0.89 0.27 0.00
351_G 59_C 0.89 0.27 0.00
351_G 98_C 0.89 0.27 0.00
351_G 108_C 0.89 0.27 0.00
106_G 11_G 0.89 0.26 0.00
36_S 55_G 0.88 0.26 0.00
276_M 113_I 0.88 0.26 0.00
37_T 13_T 0.87 0.25 0.00
371_R 126_Y 0.87 0.25 0.00
128_S 96_L 0.87 0.25 0.00
316_L 66_Y 0.86 0.25 0.00
69_T 37_F 0.86 0.25 0.00
131_V 62_A 0.86 0.24 0.00
261_T 141_V 0.84 0.23 0.00
296_R 7_A 0.84 0.23 0.00
179_K 6_L 0.84 0.23 0.00
176_G 63_C 0.83 0.23 0.00
176_G 101_C 0.83 0.23 0.00
176_G 104_C 0.83 0.23 0.00
351_G 63_C 0.83 0.23 0.00
351_G 101_C 0.83 0.23 0.00
351_G 104_C 0.83 0.23 0.00
80_T 96_L 0.83 0.23 0.00
337_P 138_V 0.83 0.23 0.00
207_L 22_V 0.83 0.23 0.00
194_L 8_Q 0.83 0.23 0.00
36_S 70_V 0.82 0.22 0.00
106_G 10_L 0.82 0.22 0.00
112_R 93_I 0.82 0.22 0.00
349_A 100_F 0.82 0.22 0.00
261_T 7_A 0.82 0.22 0.00
327_H 45_R 0.82 0.22 0.00
295_E 141_V 0.82 0.22 0.00
355_Y 36_R 0.81 0.21 0.00
325_I 133_K 0.81 0.21 0.00
287_V 130_V 0.81 0.21 0.00
106_G 119_F 0.80 0.21 0.00
55_V 6_L 0.80 0.21 0.00
79_I 9_S 0.80 0.20 0.00
29_N 36_R 0.79 0.20 0.00
290_I 153_T 0.79 0.20 0.00
212_P 5_A 0.79 0.20 0.00
138_L 54_I 0.78 0.20 0.00
314_R 54_I 0.78 0.19 0.00
394_V 9_S 0.78 0.19 0.00
358_V 113_I 0.78 0.19 0.00
382_P 14_L 0.78 0.19 0.00
349_A 136_M 0.78 0.19 0.00
123_L 13_T 0.77 0.19 0.00
235_T 145_P 0.77 0.19 0.00
178_V 69_Y 0.77 0.18 0.00
394_V 13_T 0.77 0.18 0.00
145_P 131_Y 0.77 0.18 0.00
294_L 118_D 0.76 0.18 0.00
147_F 70_V 0.76 0.18 0.00
291_K 145_P 0.76 0.18 0.00
134_G 91_Y 0.76 0.18 0.00
108_V 135_D 0.76 0.18 0.00
262_F 41_H 0.76 0.18 0.00
194_L 107_A 0.76 0.18 0.00
177_G 53_C 0.75 0.18 0.00
177_G 56_C 0.75 0.18 0.00
177_G 59_C 0.75 0.18 0.00
177_G 98_C 0.75 0.18 0.00
177_G 108_C 0.75 0.18 0.00
221_V 131_Y 0.75 0.18 0.00
151_R 118_D 0.75 0.18 0.00
313_P 7_A 0.75 0.18 0.00
166_Q 24_V 0.75 0.17 0.00
48_S 12_I 0.75 0.17 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
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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