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OPENSEQ.org
1UB4_Jackhmmer
Genes: A B A+B
Length: 82 111 189
Sequences: 1336 2055 471
Seq/Len: 16.29 18.51 2.49
MirrorTree (Pazo et al. 2001) 0.74
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 2.44
2 0.00 0.00 2.46
5 0.01 0.00 2.50
10 0.01 0.00 2.51
20 0.02 0.01 2.56
100 0.03 0.05 2.72
∞ 0.06 0.09 3.32
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
9_W 25_Q 1.54 0.95 0.69
59_V 60_F 1.44 0.92 0.60
58_L 105_K 1.36 0.89 0.54
59_V 58_Y 1.32 0.86 0.49
9_W 27_G 1.24 0.82 0.42
2_I 49_V 1.21 0.79 0.39
62_I 60_F 1.18 0.77 0.37
56_A 38_M 1.16 0.75 0.35
6_V 64_L 1.14 0.74 0.33
73_W 48_C 1.13 0.72 0.32
26_N 12_L 1.07 0.67 0.27
53_F 104_A 1.04 0.64 0.25
57_E 62_V 1.01 0.60 0.22
19_A 48_C 1.01 0.60 0.22
73_W 79_K 1.00 0.59 0.22
39_D 65_S 0.96 0.55 0.19
9_W 74_L 0.95 0.53 0.18
16_R 76_D 0.95 0.53 0.18
32_E 73_A 0.94 0.52 0.17
55_L 60_F 0.93 0.51 0.17
10_G 86_R 0.93 0.51 0.17
67_L 53_T 0.92 0.49 0.16
55_L 38_M 0.89 0.46 0.14
66_N 76_D 0.88 0.45 0.14
62_I 59_P 0.87 0.44 0.13
5_S 18_D 0.87 0.44 0.13
50_E 64_L 0.87 0.43 0.13
59_V 59_P 0.87 0.43 0.13
10_G 77_Q 0.86 0.42 0.13
68_H 57_G 0.85 0.42 0.12
34_K 104_A 0.84 0.41 0.12
14_A 81_I 0.84 0.41 0.12
35_I 34_L 0.84 0.41 0.12
68_H 61_E 0.84 0.40 0.12
35_I 7_P 0.84 0.40 0.12
13_P 106_I 0.84 0.40 0.12
6_V 53_T 0.83 0.39 0.11
19_A 71_G 0.82 0.38 0.11
4_S 85_A 0.82 0.38 0.11
10_G 24_E 0.82 0.38 0.11
73_W 106_I 0.80 0.36 0.10
21_L 35_S 0.80 0.36 0.10
58_L 62_V 0.80 0.36 0.10
36_D 93_T 0.80 0.36 0.10
55_L 27_G 0.80 0.35 0.10
79_K 52_T 0.80 0.35 0.10
10_G 50_P 0.80 0.35 0.10
60_N 44_G 0.80 0.35 0.10
52_V 15_V 0.79 0.35 0.10
53_F 101_L 0.79 0.34 0.09
44_I 47_L 0.79 0.34 0.09
59_V 61_E 0.79 0.34 0.09
9_W 45_M 0.78 0.33 0.09
31_D 71_G 0.78 0.33 0.09
59_V 81_I 0.78 0.33 0.09
18_P 35_S 0.77 0.33 0.09
62_I 39_Y 0.77 0.32 0.08
59_V 40_N 0.76 0.32 0.08
17_I 105_K 0.76 0.32 0.08
40_G 8_D 0.76 0.31 0.08
62_I 76_D 0.76 0.31 0.08
44_I 102_I 0.75 0.30 0.08
42_L 56_K 0.75 0.30 0.08
30_D 37_F 0.75 0.30 0.08
70_N 20_T 0.74 0.30 0.08
32_E 28_H 0.74 0.29 0.07
80_E 82_A 0.74 0.29 0.07
30_D 54_Q 0.73 0.28 0.07
66_N 58_Y 0.73 0.28 0.07
4_S 99_L 0.72 0.28 0.07
8_R 62_V 0.72 0.28 0.07
59_V 75_A 0.72 0.28 0.07
57_E 65_S 0.72 0.27 0.07
22_M 69_R 0.71 0.27 0.07
77_K 104_A 0.71 0.27 0.07
26_N 106_I 0.71 0.27 0.07
10_G 22_G 0.71 0.27 0.06
79_K 84_R 0.71 0.26 0.06
12_S 29_R 0.71 0.26 0.06
62_I 74_L 0.70 0.26 0.06
69_E 73_A 0.70 0.26 0.06
26_N 71_G 0.70 0.26 0.06
8_R 51_C 0.70 0.25 0.06
6_V 41_N 0.69 0.25 0.06
23_Q 110_I 0.69 0.25 0.06
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
4753 3.27 TA_five Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.77 Done - Shared
0721 2.49 1UB4_Jackhmmer Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) 0.69 Done - Shared
0719 1.61 1UB4 Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2013_03) 0.79 Done - Shared
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