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OPENSEQ.org
DJ_1_C6
Genes: A B A+B
Length: 293 189 434
Sequences: 1446 12329 105
Seq/Len: 4.94 65.23 0.24
MirrorTree (Pazo et al. 2001) 0.28
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 0.08 0.05 0.00
2 0.09 0.07 0.00
5 0.09 0.07 0.01
10 0.10 0.09 0.01
20 0.10 0.10 0.01
100 0.10 0.14 0.06
∞ 0.14 0.22 0.22
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
249_L 168_I 1.45 0.33 0.00
159_I 125_T 1.39 0.30 0.00
52_H 148_K 1.29 0.25 0.00
234_E 128_L 1.24 0.22 0.00
162_A 157_G 1.21 0.21 0.00
48_L 149_D 1.18 0.20 0.00
211_S 97_N 1.18 0.20 0.00
131_D 122_K 1.17 0.20 0.00
234_E 56_A 1.16 0.19 0.00
159_I 37_G 1.14 0.19 0.00
252_V 149_D 1.14 0.18 0.00
122_G 149_D 1.13 0.18 0.00
159_I 9_I 1.11 0.17 0.00
96_L 112_L 1.10 0.17 0.00
185_L 60_D 1.09 0.17 0.00
248_L 105_I 1.05 0.15 0.00
109_A 25_V 1.05 0.15 0.00
122_G 75_G 1.04 0.15 0.00
54_R 70_V 1.02 0.14 0.00
274_Q 124_T 1.02 0.14 0.00
67_T 124_T 1.02 0.14 0.00
122_G 155_S 1.01 0.14 0.00
230_Q 172_L 1.01 0.14 0.00
228_Y 108_G 1.01 0.14 0.00
162_A 181_V 1.01 0.14 0.00
96_L 63_K 1.01 0.14 0.00
157_I 164_F 1.00 0.14 0.00
256_V 146_V 1.00 0.14 0.00
282_L 29_A 1.00 0.14 0.00
230_Q 73_P 1.00 0.14 0.00
280_S 181_V 1.00 0.14 0.00
95_E 9_I 0.99 0.14 0.00
124_G 30_G 0.99 0.14 0.00
129_A 122_K 0.98 0.13 0.00
85_V 36_A 0.98 0.13 0.00
134_I 36_A 0.98 0.13 0.00
100_I 53_C 0.98 0.13 0.00
50_F 78_G 0.97 0.13 0.00
159_I 7_L 0.97 0.13 0.00
93_A 121_S 0.97 0.13 0.00
131_D 149_D 0.96 0.13 0.00
96_L 134_M 0.96 0.13 0.00
273_K 36_A 0.96 0.12 0.00
116_C 111_A 0.95 0.12 0.00
50_F 99_K 0.95 0.12 0.00
134_I 93_K 0.94 0.12 0.00
237_G 67_Y 0.94 0.12 0.00
78_F 121_S 0.94 0.12 0.00
141_G 52_I 0.94 0.12 0.00
118_F 159_G 0.93 0.12 0.00
50_F 48_R 0.93 0.12 0.00
48_L 108_G 0.91 0.11 0.00
280_S 147_E 0.91 0.11 0.00
62_P 168_I 0.91 0.11 0.00
76_R 26_M 0.91 0.11 0.00
70_D 124_T 0.90 0.11 0.00
240_G 32_K 0.89 0.11 0.00
229_I 6_A 0.89 0.11 0.00
84_E 144_N 0.89 0.11 0.00
210_Y 168_I 0.89 0.11 0.00
143_F 156_R 0.88 0.10 0.00
211_S 12_K 0.88 0.10 0.00
80_D 112_L 0.88 0.10 0.00
208_M 52_I 0.87 0.10 0.00
228_Y 155_S 0.87 0.10 0.00
160_I 90_E 0.87 0.10 0.00
156_K 107_A 0.87 0.10 0.00
73_N 167_A 0.86 0.10 0.00
102_E 117_I 0.86 0.10 0.00
51_N 115_H 0.86 0.10 0.00
127_I 14_A 0.86 0.10 0.00
281_M 147_E 0.85 0.10 0.00
240_G 102_I 0.85 0.10 0.00
139_L 36_A 0.85 0.10 0.00
279_A 85_S 0.85 0.10 0.00
77_R 92_L 0.85 0.10 0.00
118_F 91_I 0.85 0.10 0.00
216_Y 125_T 0.85 0.10 0.00
218_S 14_A 0.85 0.10 0.00
256_V 43_P 0.84 0.10 0.00
83_F 149_D 0.84 0.10 0.00
165_G 54_P 0.84 0.10 0.00
230_Q 167_A 0.84 0.10 0.00
164_R 12_K 0.84 0.10 0.00
156_K 102_I 0.84 0.10 0.00
251_L 116_E 0.84 0.10 0.00
220_R 57_S 0.84 0.10 0.00
179_D 6_A 0.84 0.10 0.00
207_L 102_I 0.83 0.09 0.00
71_R 7_L 0.83 0.09 0.00
133_K 85_S 0.83 0.09 0.00
154_K 103_A 0.83 0.09 0.00
212_V 90_E 0.83 0.09 0.00
229_I 187_L 0.83 0.09 0.00
116_C 150_G 0.83 0.09 0.00
218_S 52_I 0.82 0.09 0.00
105_T 5_R 0.82 0.09 0.00
159_I 108_G 0.82 0.09 0.00
216_Y 14_A 0.82 0.09 0.00
101_H 20_V 0.82 0.09 0.00
75_T 50_V 0.82 0.09 0.00
218_S 153_L 0.82 0.09 0.00
115_V 170_E 0.82 0.09 0.00
131_D 10_L 0.81 0.09 0.00
232_L 104_A 0.81 0.09 0.00
94_E 169_V 0.81 0.09 0.00
236_L 42_D 0.81 0.09 0.00
131_D 172_L 0.81 0.09 0.00
91_L 32_K 0.80 0.09 0.00
287_H 19_T 0.80 0.09 0.00
159_I 123_V 0.80 0.09 0.00
230_Q 125_T 0.80 0.09 0.00
97_L 24_D 0.80 0.09 0.00
215_G 59_E 0.80 0.09 0.00
108_H 69_V 0.79 0.09 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
6518 0.01 DJ_1_C6 Δgene:(1, 100) A:(1E-60, 8) B:(1E-60, 8) msa: HHblits (2015_06) Killed - Shared
6487 0.24 DJ_1_C6 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) 0.00 Done
6486 0.06 DJ_1_C6 Δgene:(1, 100) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) Killed
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