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OPENSEQ.org
RL5_RL15
Genes: A B A+B
Length: 179 144 323
Sequences: 2042 3157 1730
Seq/Len: 11.41 21.92 5.36
MirrorTree (Pazo et al. 2001) 0.81
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 0.08 0.00
2 0.09 0.08 0.01
5 0.09 0.08 0.44
10 0.09 0.08 5.34
20 0.09 0.08 5.36
100 0.09 0.08 5.43
∞ 0.09 0.09 5.50
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
128_Y 90_V 0.95 0.76 0.01
36_L 96_K 0.91 0.71 0.01
173_F 4_N 0.86 0.66 0.01
79_I 100_I 0.85 0.64 0.01
61_S 128_T 0.84 0.63 0.01
38_M 29_K 0.84 0.62 0.01
97_W 75_A 0.82 0.60 0.01
50_L 42_S 0.81 0.58 0.01
173_F 79_L 0.79 0.56 0.01
85_I 40_S 0.78 0.54 0.01
93_G 33_R 0.74 0.49 0.01
173_F 48_R 0.73 0.46 0.01
102_R 92_L 0.72 0.46 0.01
85_I 79_L 0.72 0.45 0.01
143_Y 23_I 0.71 0.44 0.01
24_S 62_P 0.71 0.44 0.01
173_F 134_A 0.70 0.42 0.01
102_R 55_M 0.70 0.42 0.01
76_G 39_K 0.69 0.41 0.01
69_K 61_L 0.69 0.40 0.01
129_S 125_L 0.68 0.40 0.01
19_E 7_S 0.68 0.39 0.01
47_K 40_S 0.66 0.37 0.01
179_K 126_R 0.66 0.37 0.01
95_R 113_A 0.64 0.34 0.01
112_R 67_T 0.63 0.33 0.01
118_S 33_R 0.63 0.33 0.01
155_T 107_F 0.63 0.33 0.01
148_R 16_G 0.63 0.32 0.01
153_D 59_R 0.62 0.32 0.01
35_T 125_L 0.62 0.32 0.01
85_I 6_L 0.62 0.32 0.01
156_I 106_E 0.62 0.31 0.01
175_F 63_K 0.61 0.30 0.01
79_I 70_K 0.61 0.30 0.01
48_K 63_K 0.61 0.30 0.01
65_P 29_K 0.60 0.29 0.00
152_L 40_S 0.60 0.29 0.00
162_S 133_A 0.60 0.29 0.00
130_M 31_G 0.60 0.29 0.00
18_T 40_S 0.59 0.28 0.00
65_P 58_Y 0.59 0.28 0.00
132_V 81_D 0.59 0.28 0.00
39_G 33_R 0.59 0.28 0.00
71_R 74_T 0.59 0.28 0.00
10_D 101_I 0.58 0.27 0.00
75_A 50_F 0.58 0.27 0.00
55_A 6_L 0.58 0.27 0.00
68_T 49_G 0.58 0.27 0.00
134_E 63_K 0.58 0.26 0.00
156_I 76_E 0.57 0.26 0.00
28_V 13_K 0.57 0.26 0.00
179_K 58_Y 0.57 0.26 0.00
11_E 6_L 0.57 0.26 0.00
159_T 91_D 0.56 0.25 0.00
5_H 2_R 0.56 0.24 0.00
97_W 4_N 0.55 0.24 0.00
71_R 50_F 0.55 0.24 0.00
74_V 64_F 0.55 0.24 0.00
21_N 97_A 0.55 0.24 0.00
161_K 82_L 0.55 0.23 0.00
79_I 105_I 0.55 0.23 0.00
40_V 42_S 0.55 0.23 0.00
36_L 75_A 0.55 0.23 0.00
111_I 119_P 0.55 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
8944 5.36 RL5_RL15 Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.01 Done
1901 5.7 L5-L15 Δgene:(1, 20) A:(1E-06, 4) B:(1E-06, 4) msa: Jackhmmer (2015_03) 0.01 Done - Shared
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