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OPENSEQ.org
RL5_RL18
Genes: A B A+B
Length: 179 117 288
Sequences: 2042 2981 1759
Seq/Len: 11.41 25.48 6.11
MirrorTree (Pazo et al. 2001) 0.78
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.09 0.09 0.00
2 0.09 0.09 0.03
5 0.09 0.09 5.76
10 0.09 0.09 5.91
20 0.09 0.09 5.94
100 0.09 0.09 5.97
∞ 0.09 0.09 6.10
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
41_G 38_Q 0.83 0.66 0.00
174_D 24_T 0.75 0.54 0.00
28_V 104_Q 0.74 0.52 0.00
34_I 41_A 0.72 0.48 0.00
38_M 10_R 0.71 0.48 0.00
81_Q 83_L 0.71 0.48 0.00
24_S 27_V 0.71 0.47 0.00
87_C 27_V 0.71 0.47 0.00
111_I 112_E 0.70 0.46 0.00
26_M 7_R 0.69 0.44 0.00
28_V 98_Q 0.69 0.44 0.00
35_T 47_V 0.68 0.42 0.00
159_T 59_A 0.67 0.41 0.00
139_P 36_Y 0.67 0.41 0.00
46_D 10_R 0.66 0.39 0.00
129_S 81_R 0.65 0.39 0.00
46_D 29_H 0.65 0.39 0.00
130_M 104_Q 0.63 0.35 0.00
163_D 86_G 0.62 0.35 0.00
171_A 23_A 0.62 0.34 0.00
74_V 8_I 0.60 0.33 0.00
174_D 18_L 0.60 0.31 0.00
58_A 33_R 0.59 0.31 0.00
152_L 27_V 0.59 0.31 0.00
134_E 30_R 0.59 0.30 0.00
165_E 37_A 0.58 0.30 0.00
179_K 32_P 0.58 0.29 0.00
38_M 34_H 0.57 0.29 0.00
34_I 81_R 0.57 0.28 0.00
157_T 91_S 0.57 0.28 0.00
143_Y 29_H 0.57 0.28 0.00
137_I 37_A 0.57 0.28 0.00
104_I 78_V 0.56 0.27 0.00
136_I 14_A 0.56 0.27 0.00
173_F 8_I 0.56 0.27 0.00
81_Q 105_A 0.56 0.27 0.00
152_L 70_A 0.55 0.26 0.00
173_F 29_H 0.55 0.26 0.00
174_D 42_P 0.55 0.26 0.00
75_A 96_G 0.55 0.25 0.00
5_H 50_A 0.55 0.25 0.00
59_A 19_Q 0.54 0.25 0.00
71_R 27_V 0.54 0.24 0.00
21_N 113_A 0.53 0.24 0.00
47_K 11_A 0.53 0.23 0.00
146_V 64_Y 0.53 0.23 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
8943 6.11 RL5_RL18 Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.00 Done - Shared
1902 6.38 L5-L18 Δgene:(1, 20) A:(1E-06, 4) B:(1E-06, 4) msa: Jackhmmer (2015_03) 0.01 Done - Shared
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