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OPENSEQ.org
test
Genes: A B A+B
Length: 139 287 423
Sequences: 1826 2360 1353
Seq/Len: 13.14 8.22 3.2
MirrorTree (Pazo et al. 2001) 0.77
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 0.00 0.00 0.04
2 0.00 0.00 3.04
5 0.00 0.00 3.13
10 0.00 0.00 3.14
20 0.00 0.00 3.18
100 0.00 0.00 3.22
∞ 0.00 0.01 3.37
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
43_L 56_L 1.38 0.93 0.51
40_A 207_L 1.27 0.89 0.41
69_I 221_R 1.11 0.78 0.28
12_A 146_L 1.04 0.71 0.22
30_E 209_E 1.00 0.67 0.20
9_V 215_L 0.99 0.65 0.19
71_E 206_Y 0.98 0.64 0.18
28_G 209_E 0.97 0.63 0.18
82_D 222_R 0.96 0.62 0.17
49_G 5_K 0.96 0.61 0.17
124_K 285_A 0.94 0.59 0.16
82_D 168_L 0.93 0.59 0.15
71_E 48_T 0.92 0.57 0.15
73_Q 55_H 0.92 0.57 0.15
26_V 282_S 0.91 0.56 0.14
79_V 228_V 0.90 0.55 0.14
17_F 177_N 0.90 0.54 0.14
36_Y 277_L 0.89 0.53 0.13
41_P 65_H 0.89 0.53 0.13
11_S 258_I 0.88 0.52 0.13
8_D 48_T 0.88 0.52 0.12
78_T 146_L 0.86 0.50 0.12
27_T 1_M 0.85 0.49 0.11
30_E 215_L 0.85 0.48 0.11
45_A 215_L 0.85 0.48 0.11
49_G 31_K 0.84 0.47 0.11
131_V 172_S 0.84 0.47 0.11
71_E 244_M 0.83 0.46 0.10
12_A 6_E 0.82 0.45 0.10
49_G 1_M 0.82 0.45 0.10
95_A 189_L 0.82 0.44 0.10
52_R 90_G 0.81 0.44 0.10
24_I 2_A 0.81 0.43 0.09
86_R 26_M 0.81 0.43 0.09
88_Q 10_K 0.81 0.43 0.09
102_A 83_T 0.81 0.43 0.09
101_K 136_Q 0.80 0.42 0.09
34_G 223_Y 0.80 0.42 0.09
77_V 35_S 0.80 0.42 0.09
41_P 204_W 0.80 0.42 0.09
32_E 224_V 0.80 0.41 0.09
129_L 53_I 0.80 0.41 0.09
84_A 144_P 0.79 0.41 0.09
38_G 55_H 0.78 0.39 0.08
22_E 103_M 0.78 0.39 0.08
60_E 162_E 0.77 0.39 0.08
53_I 12_A 0.76 0.37 0.08
23_K 16_N 0.76 0.37 0.08
43_L 52_V 0.76 0.37 0.08
25_Q 242_A 0.76 0.37 0.08
64_Y 268_A 0.76 0.37 0.08
70_L 249_A 0.75 0.36 0.07
79_V 264_V 0.75 0.36 0.07
46_I 277_L 0.75 0.36 0.07
21_V 165_L 0.75 0.36 0.07
49_G 92_N 0.74 0.35 0.07
100_R 135_A 0.74 0.35 0.07
5_Y 46_A 0.74 0.35 0.07
34_G 5_K 0.74 0.35 0.07
10_V 206_Y 0.74 0.35 0.07
48_P 30_S 0.74 0.35 0.07
80_L 188_L 0.74 0.34 0.07
84_A 52_V 0.73 0.34 0.07
104_E 232_V 0.73 0.34 0.07
66_S 272_S 0.73 0.34 0.07
72_V 170_I 0.73 0.34 0.07
12_A 30_S 0.73 0.33 0.07
81_A 165_L 0.73 0.33 0.07
72_V 69_E 0.71 0.32 0.06
81_A 52_V 0.71 0.32 0.06
48_P 160_Y 0.70 0.30 0.06
132_I 177_N 0.70 0.30 0.06
67_G 206_Y 0.70 0.30 0.06
74_P 204_W 0.69 0.30 0.06
35_I 68_L 0.69 0.29 0.06
10_V 231_G 0.69 0.29 0.06
23_K 242_A 0.68 0.29 0.05
10_V 233_V 0.68 0.28 0.05
51_I 67_Y 0.68 0.28 0.05
79_V 56_L 0.68 0.28 0.05
136_K 115_L 0.68 0.28 0.05
70_L 39_M 0.68 0.28 0.05
43_L 83_T 0.68 0.28 0.05
27_T 275_Q 0.67 0.28 0.05
67_G 222_R 0.67 0.27 0.05
79_V 220_L 0.67 0.27 0.05
97_E 66_P 0.67 0.27 0.05
114_D 123_V 0.67 0.27 0.05
101_K 207_L 0.67 0.27 0.05
47_K 26_M 0.66 0.26 0.05
52_R 62_E 0.66 0.26 0.05
124_K 172_S 0.66 0.26 0.05
79_V 160_Y 0.66 0.26 0.05
30_E 251_T 0.66 0.26 0.05
71_E 26_M 0.66 0.26 0.05
34_G 263_L 0.66 0.26 0.05
129_L 93_I 0.66 0.26 0.05
44_T 278_T 0.66 0.26 0.05
56_Q 132_N 0.66 0.26 0.05
73_Q 52_V 0.65 0.26 0.05
39_H 237_A 0.65 0.25 0.05
19_G 124_S 0.65 0.25 0.05
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
1209 3.2 test Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.51 Done - Shared
1208 2.42 test Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) 0.86 Done - Shared
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