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OPENSEQ.org
cI_4_6_cI_9_6_tt
Genes: A B A+B
Length: 409 182 560
Sequences: 3489 855 690
Seq/Len: 8.53 4.7 1.23
MirrorTree (Pazo et al. 2001) 0.79
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 0.07
2 0.01 0.00 0.24
5 0.03 0.01 0.84
10 0.04 0.01 0.96
20 0.05 0.01 1.02
100 0.06 0.01 1.08
∞ 0.13 0.03 1.17
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
174_R 106_E 1.44 0.78 0.03
203_E 19_S 1.42 0.77 0.03
85_M 17_L 1.24 0.61 0.02
166_Q 38_H 1.13 0.52 0.01
145_P 95_M 1.13 0.51 0.01
171_N 103_L 1.12 0.50 0.01
401_D 86_R 1.09 0.48 0.01
114_E 35_P 1.03 0.42 0.01
116_I 103_L 1.02 0.41 0.01
261_T 141_V 1.01 0.40 0.01
321_M 67_A 1.01 0.40 0.01
211_S 112_A 1.00 0.39 0.01
288_K 122_A 0.99 0.38 0.01
397_I 6_L 0.97 0.36 0.01
381_L 149_E 0.97 0.36 0.01
337_P 138_V 0.97 0.36 0.01
149_A 149_E 0.96 0.35 0.01
214_F 72_P 0.96 0.35 0.01
28_L 30_P 0.96 0.35 0.01
73_R 67_A 0.95 0.35 0.01
151_R 13_T 0.94 0.33 0.01
212_P 5_A 0.94 0.33 0.01
108_V 148_R 0.93 0.33 0.01
320_S 116_G 0.93 0.33 0.01
394_V 103_L 0.93 0.33 0.01
206_A 12_I 0.93 0.32 0.01
218_A 6_L 0.92 0.32 0.01
184_E 128_D 0.92 0.32 0.01
381_L 22_V 0.91 0.31 0.01
106_G 10_L 0.90 0.30 0.01
144_T 7_A 0.90 0.30 0.01
69_T 37_F 0.90 0.30 0.01
226_P 20_K 0.88 0.29 0.01
194_L 107_A 0.88 0.29 0.01
346_T 15_K 0.88 0.29 0.01
52_V 7_A 0.88 0.28 0.01
203_E 28_D 0.87 0.28 0.01
29_N 36_R 0.86 0.27 0.01
390_V 30_P 0.86 0.27 0.01
37_T 13_T 0.86 0.27 0.01
80_T 96_L 0.86 0.27 0.01
283_M 103_L 0.85 0.26 0.01
79_I 11_G 0.85 0.26 0.01
385_C 8_Q 0.85 0.26 0.01
145_P 131_Y 0.84 0.26 0.01
138_L 54_I 0.84 0.25 0.01
241_A 72_P 0.84 0.25 0.01
144_T 12_I 0.83 0.25 0.01
107_A 126_Y 0.83 0.24 0.01
148_Y 28_D 0.82 0.24 0.01
332_T 61_A 0.82 0.24 0.01
232_L 95_M 0.82 0.24 0.01
36_S 70_V 0.81 0.23 0.01
371_R 126_Y 0.81 0.23 0.01
250_K 15_K 0.81 0.23 0.01
59_I 93_I 0.81 0.23 0.00
386_K 30_P 0.81 0.23 0.00
48_S 7_A 0.81 0.23 0.00
159_L 22_V 0.81 0.23 0.00
64_T 75_N 0.81 0.23 0.00
305_P 47_P 0.81 0.23 0.00
355_Y 36_R 0.81 0.23 0.00
179_K 106_E 0.81 0.23 0.00
399_S 115_L 0.81 0.23 0.00
324_V 45_R 0.80 0.23 0.00
296_R 122_A 0.80 0.22 0.00
369_K 54_I 0.80 0.22 0.00
41_L 57_S 0.79 0.22 0.00
393_M 127_S 0.79 0.22 0.00
144_T 123_D 0.79 0.22 0.00
261_T 82_S 0.79 0.22 0.00
276_M 113_I 0.79 0.22 0.00
55_V 88_A 0.79 0.22 0.00
259_T 22_V 0.79 0.22 0.00
131_V 62_A 0.79 0.22 0.00
327_H 45_R 0.79 0.21 0.00
109_V 20_K 0.78 0.21 0.00
86_D 120_E 0.78 0.21 0.00
220_G 7_A 0.78 0.21 0.00
212_P 110_T 0.78 0.21 0.00
223_V 8_Q 0.78 0.21 0.00
148_Y 95_M 0.77 0.20 0.00
218_A 10_L 0.77 0.20 0.00
376_V 74_E 0.77 0.20 0.00
314_R 54_I 0.77 0.20 0.00
307_P 28_D 0.77 0.20 0.00
127_A 110_T 0.76 0.20 0.00
119_I 22_V 0.76 0.20 0.00
206_A 8_Q 0.76 0.20 0.00
303_R 33_L 0.76 0.20 0.00
225_P 14_L 0.76 0.20 0.00
65_G 99_I 0.75 0.19 0.00
208_F 119_F 0.75 0.19 0.00
369_K 60_A 0.75 0.19 0.00
337_P 111_G 0.75 0.19 0.00
134_G 124_Y 0.75 0.19 0.00
278_V 146_Q 0.75 0.19 0.00
329_K 65_A 0.75 0.19 0.00
128_S 55_G 0.75 0.19 0.00
176_G 53_C 0.75 0.19 0.00
176_G 56_C 0.75 0.19 0.00
176_G 59_C 0.75 0.19 0.00
176_G 63_C 0.75 0.19 0.00
176_G 98_C 0.75 0.19 0.00
176_G 101_C 0.75 0.19 0.00
176_G 104_C 0.75 0.19 0.00
176_G 108_C 0.75 0.19 0.00
351_G 53_C 0.75 0.19 0.00
351_G 56_C 0.75 0.19 0.00
351_G 59_C 0.75 0.19 0.00
351_G 63_C 0.75 0.19 0.00
351_G 98_C 0.75 0.19 0.00
351_G 101_C 0.75 0.19 0.00
351_G 104_C 0.75 0.19 0.00
351_G 108_C 0.75 0.19 0.00
36_S 91_Y 0.74 0.19 0.00
174_R 39_G 0.74 0.19 0.00
179_K 6_L 0.74 0.19 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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