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OPENSEQ.org
x250-s1
Genes: A B A+B
Length: 250 239 486
Sequences: 269 56493 95
Seq/Len: 1.08 236.37 0.2
MirrorTree (Pazo et al. 2001) 0.37
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 0.00 0.03 0.00
2 0.00 0.04 0.04
5 0.00 0.07 0.05
10 0.00 0.10 0.06
20 0.00 0.14 0.09
100 0.00 0.23 0.19
∞ 0.03 0.28 0.30
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
212_F 144_A 1.52 0.33 0.00
173_V 207_V 1.39 0.26 0.00
202_I 223_T 1.18 0.18 0.00
106_V 186_R 1.16 0.17 0.00
55_Y 36_D 1.16 0.17 0.00
69_V 155_I 1.16 0.17 0.00
113_P 141_L 1.15 0.17 0.00
210_A 30_I 1.12 0.16 0.00
146_V 48_I 1.11 0.16 0.00
16_K 100_D 1.10 0.15 0.00
212_F 122_V 1.08 0.15 0.00
5_V 186_R 1.07 0.14 0.00
4_K 30_I 1.06 0.14 0.00
69_V 60_L 1.05 0.14 0.00
110_I 149_E 1.04 0.14 0.00
247_I 156_G 1.03 0.13 0.00
62_M 80_L 1.03 0.13 0.00
64_Q 145_L 1.01 0.12 0.00
94_A 144_A 0.99 0.12 0.00
94_A 215_G 0.99 0.12 0.00
56_E 82_S 0.99 0.12 0.00
171_K 177_K 0.99 0.12 0.00
64_Q 100_D 0.98 0.12 0.00
14_I 153_I 0.97 0.12 0.00
110_I 192_A 0.97 0.12 0.00
10_G 225_G 0.97 0.12 0.00
237_V 69_S 0.96 0.11 0.00
9_G 35_H 0.96 0.11 0.00
9_G 143_N 0.96 0.11 0.00
9_G 203_G 0.96 0.11 0.00
16_K 228_T 0.95 0.11 0.00
134_T 12_H 0.95 0.11 0.00
233_K 141_L 0.94 0.11 0.00
97_F 140_I 0.94 0.11 0.00
112_I 67_I 0.94 0.11 0.00
125_L 168_I 0.94 0.11 0.00
189_V 229_T 0.93 0.11 0.00
189_V 28_Q 0.93 0.11 0.00
96_N 63_E 0.93 0.11 0.00
99_R 118_V 0.93 0.11 0.00
141_R 39_T 0.92 0.10 0.00
64_Q 115_G 0.92 0.10 0.00
94_A 200_S 0.92 0.10 0.00
109_V 98_V 0.92 0.10 0.00
69_V 171_Y 0.92 0.10 0.00
15_G 204_L 0.91 0.10 0.00
145_N 132_W 0.91 0.10 0.00
110_I 126_V 0.91 0.10 0.00
62_M 140_I 0.91 0.10 0.00
132_V 235_P 0.90 0.10 0.00
15_G 70_M 0.90 0.10 0.00
126_G 121_K 0.90 0.10 0.00
110_I 94_L 0.90 0.10 0.00
8_A 148_S 0.90 0.10 0.00
245_R 186_R 0.90 0.10 0.00
93_A 60_L 0.89 0.10 0.00
144_V 14_E 0.89 0.10 0.00
128_Y 63_E 0.89 0.10 0.00
60_A 97_M 0.89 0.10 0.00
101_A 225_G 0.88 0.10 0.00
140_K 186_R 0.88 0.10 0.00
210_A 202_M 0.88 0.10 0.00
56_E 141_L 0.88 0.10 0.00
90_T 153_I 0.88 0.10 0.00
249_E 130_I 0.88 0.09 0.00
67_I 155_I 0.87 0.09 0.00
206_V 165_S 0.87 0.09 0.00
227_L 171_Y 0.87 0.09 0.00
31_I 144_A 0.86 0.09 0.00
50_C 17_V 0.86 0.09 0.00
173_V 217_H 0.86 0.09 0.00
67_I 183_I 0.86 0.09 0.00
16_K 142_S 0.86 0.09 0.00
110_I 122_V 0.86 0.09 0.00
190_K 177_K 0.86 0.09 0.00
68_A 206_L 0.85 0.09 0.00
173_V 183_I 0.85 0.09 0.00
8_A 145_L 0.85 0.09 0.00
206_V 11_A 0.85 0.09 0.00
14_I 232_L 0.85 0.09 0.00
9_G 40_P 0.85 0.09 0.00
7_L 92_V 0.85 0.09 0.00
173_V 87_M 0.85 0.09 0.00
124_R 33_F 0.84 0.09 0.00
20_E 155_I 0.84 0.09 0.00
100_A 170_D 0.84 0.09 0.00
22_I 195_N 0.84 0.09 0.00
82_T 39_T 0.84 0.09 0.00
62_M 187_G 0.84 0.09 0.00
5_V 103_Q 0.84 0.09 0.00
140_K 226_K 0.84 0.09 0.00
110_I 129_D 0.84 0.09 0.00
53_F 200_S 0.84 0.09 0.00
63_N 236_L 0.83 0.09 0.00
72_I 137_I 0.83 0.09 0.00
96_N 38_K 0.83 0.09 0.00
7_L 145_L 0.83 0.09 0.00
63_N 49_D 0.83 0.09 0.00
7_L 51_E 0.83 0.09 0.00
57_Q 77_I 0.83 0.09 0.00
35_P 98_V 0.83 0.09 0.00
233_K 155_I 0.83 0.09 0.00
24_N 183_I 0.82 0.08 0.00
18_L 160_N 0.82 0.08 0.00
94_A 70_M 0.82 0.08 0.00
9_G 201_G 0.82 0.08 0.00
67_I 228_T 0.82 0.08 0.00
60_A 217_H 0.82 0.08 0.00
46_T 42_T 0.82 0.08 0.00
27_E 212_D 0.82 0.08 0.00
85_S 167_Y 0.82 0.08 0.00
165_P 39_T 0.82 0.08 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
11250 0.04 x250-s2 Δgene:(1, 100) A:(1E-80, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
11249 0.2 x250-s1 Δgene:(1, 100) A:(1E-04, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.00 Done - Shared
11222 4.88 x250-s Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
11221 1.73 x250-s Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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