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OPENSEQ.org
test
Genes: A B A+B
Length: 72 95 162
Sequences: 101 93 66
Seq/Len: 1.4 0.98 0.41
MirrorTree (Pazo et al. 2001) 0.38
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 0.38
2 0.00 0.00 0.40
5 0.00 0.00 0.40
10 0.00 0.00 0.40
20 0.00 0.00 0.40
100 0.00 0.00 0.40
∞ 0.00 0.00 0.40
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
57_L 75_F 1.52 0.52 0.00
3_Y 28_I 1.47 0.48 0.00
5_Y 55_Q 1.45 0.46 0.00
61_D 24_L 1.33 0.38 0.00
39_D 30_F 1.33 0.38 0.00
16_C 5_T 1.30 0.36 0.00
3_Y 25_N 1.23 0.31 0.00
50_K 30_F 1.21 0.30 0.00
68_N 39_S 1.17 0.28 0.00
11_K 33_K 1.17 0.28 0.00
63_P 81_E 1.17 0.28 0.00
70_K 40_K 1.16 0.27 0.00
57_L 55_Q 1.11 0.24 0.00
56_E 12_I 1.08 0.23 0.00
35_L 81_E 1.07 0.22 0.00
47_E 54_D 1.06 0.22 0.00
15_K 19_K 1.06 0.22 0.00
18_T 41_S 1.06 0.22 0.00
19_Q 29_P 1.05 0.21 0.00
45_D 64_T 1.05 0.21 0.00
52_V 11_Q 1.04 0.21 0.00
2_S 19_K 1.02 0.20 0.00
43_W 43_L 1.02 0.20 0.00
44_K 43_L 1.01 0.19 0.00
38_N 17_N 1.00 0.19 0.00
21_N 11_Q 1.00 0.19 0.00
49_L 68_S 0.99 0.19 0.00
56_E 17_N 0.99 0.18 0.00
68_N 34_F 0.98 0.18 0.00
20_Y 59_Y 0.97 0.18 0.00
27_G 37_K 0.97 0.17 0.00
55_L 46_Y 0.96 0.17 0.00
27_G 29_P 0.95 0.17 0.00
13_T 79_M 0.95 0.17 0.00
39_D 56_N 0.94 0.16 0.00
3_Y 50_V 0.93 0.16 0.00
57_L 4_D 0.93 0.16 0.00
68_N 48_N 0.93 0.16 0.00
11_K 57_R 0.93 0.16 0.00
31_R 70_A 0.92 0.15 0.00
11_K 68_S 0.90 0.15 0.00
69_A 42_T 0.90 0.15 0.00
18_T 16_R 0.89 0.15 0.00
7_S 39_S 0.89 0.15 0.00
49_L 25_N 0.87 0.14 0.00
23_A 35_G 0.87 0.14 0.00
70_K 30_F 0.87 0.14 0.00
25_A 77_V 0.87 0.14 0.00
11_K 4_D 0.86 0.14 0.00
47_E 45_Q 0.86 0.13 0.00
50_K 78_P 0.86 0.13 0.00
47_E 47_V 0.85 0.13 0.00
3_Y 55_Q 0.84 0.13 0.00
59_P 50_V 0.84 0.13 0.00
47_E 4_D 0.83 0.12 0.00
35_L 55_Q 0.83 0.12 0.00
45_D 48_N 0.83 0.12 0.00
25_A 69_E 0.82 0.12 0.00
47_E 63_K 0.82 0.12 0.00
20_Y 57_R 0.81 0.12 0.00
51_A 23_I 0.81 0.12 0.00
51_A 13_M 0.81 0.12 0.00
63_P 68_S 0.80 0.12 0.00
9_L 79_M 0.80 0.12 0.00
62_I 22_D 0.80 0.11 0.00
6_S 23_I 0.80 0.11 0.00
23_A 68_S 0.80 0.11 0.00
43_W 27_S 0.79 0.11 0.00
26_M 56_N 0.79 0.11 0.00
64_K 12_I 0.79 0.11 0.00
61_D 33_K 0.78 0.11 0.00
2_S 58_I 0.78 0.11 0.00
24_I 39_S 0.78 0.11 0.00
3_Y 42_T 0.78 0.11 0.00
56_E 24_L 0.78 0.11 0.00
24_I 56_N 0.78 0.11 0.00
18_T 5_T 0.78 0.11 0.00
16_C 9_L 0.78 0.11 0.00
18_T 38_L 0.78 0.11 0.00
30_E 69_E 0.77 0.11 0.00
50_K 4_D 0.77 0.11 0.00
51_A 43_L 0.77 0.11 0.00
32_T 73_M 0.77 0.11 0.00
61_D 14_A 0.76 0.10 0.00
31_R 10_K 0.76 0.10 0.00
38_N 70_A 0.76 0.10 0.00
13_T 59_Y 0.76 0.10 0.00
23_A 3_T 0.76 0.10 0.00
35_L 10_K 0.76 0.10 0.00
27_G 42_T 0.75 0.10 0.00
21_N 83_S 0.75 0.10 0.00
2_S 62_A 0.75 0.10 0.00
21_N 23_I 0.74 0.10 0.00
60_Q 36_I 0.74 0.10 0.00
61_D 47_V 0.74 0.10 0.00
26_M 58_I 0.74 0.10 0.00
16_C 48_N 0.74 0.10 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
9045 0.41 test Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
9044 0.18 test Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
8890 0.66 O48503-4 Δgene:(1, 20) A:(1E-10, 8) B:(1E-04, 8) msa: HHblits (2015_06) 0.00 Done - Shared
8882 0.06 O48503-4 Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) Killed - Shared
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