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OPENSEQ.org
cI_1_40_cI_6_40_tt
Genes: A B A+B
Length: 438 181 581
Sequences: 2218 1163 813
Seq/Len: 5.06 6.43 1.4
MirrorTree (Pazo et al. 2001) 0.60
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 0.00
2 0.01 0.01 0.04
5 0.01 0.01 0.93
10 0.02 0.02 0.98
20 0.02 0.02 0.99
100 0.04 0.03 1.01
∞ 0.12 0.08 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
355_K 119_N 0.92 0.34 0.00
29_L 34_N 0.86 0.29 0.00
316_L 99_M 0.83 0.27 0.00
224_L 56_A 0.83 0.27 0.00
129_V 60_L 0.82 0.26 0.00
254_I 77_V 0.82 0.26 0.00
57_V 13_E 0.81 0.25 0.00
314_E 120_N 0.80 0.24 0.00
325_T 56_A 0.79 0.24 0.00
415_R 60_L 0.79 0.24 0.00
385_E 97_E 0.79 0.24 0.00
118_M 28_V 0.78 0.23 0.00
275_L 148_I 0.78 0.23 0.00
315_H 22_T 0.77 0.23 0.00
319_K 68_F 0.77 0.22 0.00
369_N 150_A 0.76 0.22 0.00
238_F 161_Q 0.76 0.21 0.00
126_R 156_K 0.76 0.21 0.00
30_D 27_L 0.75 0.21 0.00
212_W 131_V 0.75 0.21 0.00
275_L 78_M 0.75 0.21 0.00
410_V 145_E 0.73 0.20 0.00
336_S 19_I 0.73 0.20 0.00
292_P 118_F 0.73 0.20 0.00
79_M 84_L 0.72 0.19 0.00
93_A 96_W 0.72 0.19 0.00
295_S 95_V 0.72 0.19 0.00
133_Y 47_A 0.72 0.19 0.00
161_N 34_N 0.72 0.19 0.00
410_V 27_L 0.71 0.18 0.00
115_I 161_Q 0.71 0.18 0.00
276_I 56_A 0.71 0.18 0.00
53_V 18_G 0.71 0.18 0.00
172_H 137_V 0.70 0.18 0.00
343_N 119_N 0.70 0.18 0.00
61_G 95_V 0.70 0.17 0.00
249_M 96_W 0.69 0.17 0.00
196_R 118_F 0.69 0.17 0.00
238_F 107_S 0.69 0.17 0.00
110_V 71_S 0.68 0.17 0.00
171_L 34_N 0.68 0.17 0.00
34_R 152_M 0.68 0.17 0.00
230_I 137_V 0.68 0.17 0.00
224_L 55_D 0.68 0.16 0.00
127_A 95_V 0.68 0.16 0.00
243_T 19_I 0.67 0.16 0.00
214_K 24_L 0.67 0.16 0.00
207_A 51_M 0.67 0.16 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
4926 1.42 cI_1_20_cI_6_20_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4922 1.57 cI_1_4_cI_6_4_tt Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4921 1.4 cI_1_40_cI_6_40_tt Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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