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OPENSEQ.org
LAMB1_LAMC1 (T0926_T0927)
Genes: A B A+B
Length: 88 91 170
Sequences: 12354 9447 4137
Seq/Len: 140.39 103.81 24.34
MirrorTree (Pazo et al. 2001) 0.36
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 0.04 0.03 23.20
2 0.04 0.03 23.21
5 0.05 0.04 23.27
10 0.06 0.05 23.31
20 0.07 0.05 23.37
100 0.09 0.07 23.82
∞ 0.14 0.12 25.10
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
33_A 29_D 1.70 1.00 0.95
19_R 15_N 1.70 1.00 0.95
26_N 22_G 1.68 1.00 0.95
23_L 19_E 1.64 1.00 0.94
16_D 12_V 1.61 1.00 0.93
75_K 73_D 1.59 1.00 0.93
30_T 26_K 1.58 1.00 0.93
40_Q 38_R 1.58 1.00 0.93
22_E 18_N 1.58 1.00 0.93
60_A 58_N 1.57 1.00 0.93
44_D 42_D 1.55 1.00 0.92
47_R 45_S 1.52 1.00 0.91
58_D 56_D 1.52 1.00 0.91
57_E 55_M 1.52 1.00 0.91
54_K 52_A 1.51 1.00 0.91
19_R 22_G 1.50 1.00 0.91
9_Q 5_Q 1.50 1.00 0.90
64_V 62_A 1.49 1.00 0.90
8_A 4_D 1.48 1.00 0.90
12_E 8_Q 1.47 1.00 0.90
68_G 66_K 1.47 1.00 0.89
61_Q 59_R 1.46 1.00 0.89
47_R 52_A 1.45 1.00 0.89
71_R 69_H 1.45 1.00 0.89
18_R 14_L 1.44 1.00 0.88
68_G 73_D 1.44 1.00 0.88
72_S 70_N 1.43 1.00 0.88
29_K 25_N 1.42 0.99 0.88
11_T 7_G 1.42 0.99 0.88
14_S 10_D 1.42 0.99 0.87
62_E 60_D 1.42 0.99 0.87
50_E 48_R 1.42 0.99 0.87
36_N 34_S 1.41 0.99 0.87
15_A 11_T 1.41 0.99 0.87
54_K 59_R 1.41 0.99 0.87
67_E 65_I 1.41 0.99 0.87
20_K 16_K 1.40 0.99 0.87
27_E 23_S 1.40 0.99 0.86
65_R 63_E 1.40 0.99 0.86
65_R 70_N 1.40 0.99 0.86
13_E 9_L 1.39 0.99 0.86
78_S 76_K 1.38 0.99 0.86
71_R 76_K 1.38 0.99 0.85
48_K 46_E 1.38 0.99 0.85
25_Q 21_E 1.37 0.99 0.85
53_Q 51_E 1.36 0.99 0.85
61_Q 66_K 1.36 0.99 0.85
51_D 49_K 1.36 0.99 0.84
39_L 37_D 1.36 0.99 0.84
17_A 13_D 1.35 0.99 0.84
72_S 77_T 1.35 0.99 0.84
37_S 35_D 1.35 0.99 0.84
57_E 62_A 1.35 0.99 0.84
75_K 80_T 1.34 0.99 0.84
58_D 63_E 1.34 0.99 0.83
55_Y 53_A 1.33 0.99 0.83
9_Q 12_V 1.33 0.99 0.83
46_E 44_E 1.32 0.99 0.82
40_Q 45_S 1.31 0.99 0.81
44_D 49_K 1.30 0.99 0.81
30_T 35_D 1.30 0.99 0.81
32_L 28_K 1.30 0.99 0.81
26_N 29_D 1.30 0.99 0.81
43_E 48_R 1.28 0.99 0.80
33_A 38_R 1.28 0.99 0.80
69_E 67_D 1.27 0.99 0.79
74_L 72_E 1.27 0.99 0.79
21_A 17_L 1.26 0.99 0.79
51_D 56_D 1.26 0.99 0.78
43_E 41_S 1.26 0.99 0.78
69_E 74_I 1.25 0.99 0.78
15_A 18_N 1.25 0.99 0.78
37_S 42_D 1.25 0.98 0.78
76_D 74_I 1.24 0.98 0.77
49_Y 47_A 1.24 0.98 0.77
50_E 55_M 1.24 0.98 0.77
38_K 36_L 1.24 0.98 0.77
41_L 39_K 1.24 0.98 0.77
36_N 41_S 1.24 0.98 0.77
23_L 26_K 1.23 0.98 0.76
31_L 27_A 1.22 0.98 0.76
67_E 72_E 1.21 0.98 0.74
22_E 25_N 1.21 0.98 0.74
64_V 69_H 1.20 0.98 0.74
11_T 14_L 1.20 0.98 0.73
32_L 37_D 1.20 0.98 0.73
46_E 51_E 1.19 0.98 0.73
70_V 75_K 1.19 0.98 0.73
52_N 50_Q 1.19 0.98 0.73
13_E 16_K 1.19 0.98 0.73
60_A 65_I 1.19 0.98 0.73
8_A 11_T 1.19 0.98 0.73
16_D 19_E 1.18 0.98 0.72
34_Q 30_E 1.18 0.98 0.72
18_R 21_E 1.18 0.98 0.72
79_E 77_T 1.17 0.97 0.71
12_E 15_N 1.16 0.97 0.70
76_D 81_G 1.16 0.97 0.70
34_Q 39_K 1.15 0.97 0.69
59_K 57_Y 1.15 0.97 0.69
62_E 67_D 1.15 0.97 0.69
29_K 34_S 1.14 0.97 0.69
20_K 23_S 1.14 0.97 0.69
63_L 61_I 1.13 0.97 0.67
55_Y 60_D 1.13 0.97 0.67
74_L 79_P 1.10 0.96 0.64
48_K 53_A 1.09 0.96 0.63
24_L 20_I 1.09 0.96 0.63
5_S 8_Q 1.08 0.95 0.62
45_L 50_Q 1.07 0.95 0.61
10_K 6_L 1.07 0.95 0.61
82_A 80_T 1.07 0.95 0.61
42_L 47_A 1.06 0.95 0.60
28_A 24_L 1.06 0.95 0.60
53_Q 58_N 1.05 0.95 0.59
39_L 44_E 1.05 0.95 0.59
49_Y 54_I 1.05 0.94 0.58
41_L 46_E 1.04 0.94 0.58
35_A 31_M 1.04 0.94 0.58
56_L 54_I 1.03 0.94 0.57
10_K 13_D 1.02 0.93 0.55
77_I 82_C 1.02 0.93 0.55
79_E 84_N 1.01 0.93 0.55
6_L 9_L 1.01 0.93 0.54
63_L 68_I 1.01 0.93 0.54
56_L 61_I 1.01 0.93 0.54
52_N 57_Y 1.00 0.92 0.53
25_Q 28_K 0.99 0.92 0.53
7_I 10_D 0.99 0.92 0.52
78_S 83_F 0.98 0.92 0.51
81_V 79_P 0.98 0.91 0.51
42_L 40_V 0.97 0.91 0.50
45_L 43_L 0.97 0.91 0.49
17_A 20_I 0.96 0.90 0.48
80_K 78_L 0.95 0.90 0.48
59_K 64_I 0.95 0.90 0.48
66_L 71_L 0.95 0.90 0.47
70_V 68_I 0.95 0.89 0.47
66_L 64_I 0.93 0.88 0.45
83_V 81_G 0.91 0.87 0.43
28_A 31_M 0.91 0.86 0.42
14_S 17_L 0.91 0.86 0.42
24_L 27_A 0.89 0.85 0.40
21_A 24_L 0.88 0.84 0.39
4_E 7_G 0.88 0.84 0.39
35_A 40_V 0.87 0.83 0.38
31_L 36_L 0.87 0.83 0.38
6_L 2_G 0.87 0.83 0.37
77_I 75_K 0.86 0.82 0.37
38_K 43_L 0.85 0.82 0.36
7_I 3_F 0.85 0.81 0.35
73_L 71_L 0.84 0.80 0.34
80_K 85_T 0.83 0.79 0.33
27_E 30_E 0.81 0.77 0.31
43_E 55_M 0.80 0.75 0.29
51_D 42_D 0.79 0.73 0.28
50_E 41_S 0.78 0.72 0.27
64_V 55_M 0.77 0.71 0.26
47_R 38_R 0.76 0.70 0.25
84_Y 82_C 0.76 0.69 0.25
54_K 45_S 0.76 0.69 0.25
73_L 78_L 0.75 0.69 0.24
57_E 48_R 0.74 0.67 0.23
61_Q 52_A 0.73 0.66 0.22
33_A 45_S 0.71 0.63 0.21
29_K 41_S 0.71 0.63 0.20
71_R 62_A 0.71 0.62 0.20
75_K 66_K 0.70 0.61 0.20
37_S 26_K 0.70 0.61 0.20
33_A 22_G 0.70 0.61 0.20
48_K 39_K 0.70 0.60 0.19
26_N 38_R 0.70 0.60 0.19
47_R 59_R 0.69 0.59 0.19
51_D 63_E 0.69 0.59 0.18
36_N 48_R 0.69 0.59 0.18
85_S 83_F 0.67 0.56 0.17
43_E 34_S 0.67 0.55 0.17
68_G 59_R 0.67 0.55 0.17
39_L 51_E 0.67 0.55 0.17
3_F 6_L 0.66 0.54 0.16
53_Q 65_I 0.66 0.54 0.16
30_T 42_D 0.66 0.54 0.16
44_D 56_D 0.66 0.54 0.16
58_D 49_K 0.66 0.53 0.16
16_D 26_K 0.65 0.53 0.16
11_T 21_E 0.65 0.52 0.15
9_Q 19_E 0.65 0.52 0.15
44_D 35_D 0.64 0.51 0.15
59_K 50_Q 0.64 0.51 0.15
72_S 63_E 0.64 0.51 0.15
8_A 18_N 0.64 0.51 0.15
40_Q 52_A 0.64 0.50 0.14
17_A 27_A 0.64 0.50 0.14
57_E 69_H 0.63 0.49 0.14
46_E 58_N 0.63 0.48 0.14
25_Q 37_D 0.63 0.48 0.14
53_Q 44_E 0.63 0.48 0.14
60_A 51_E 0.61 0.45 0.12
34_Q 23_S 0.60 0.44 0.12
37_S 49_K 0.60 0.44 0.12
54_K 66_K 0.60 0.43 0.12
65_R 56_D 0.59 0.42 0.11
40_Q 29_D 0.58 0.41 0.11
38_K 50_Q 0.58 0.40 0.11
6_L 16_K 0.58 0.40 0.10
15_A 25_N 0.58 0.40 0.10
68_G 80_T 0.58 0.40 0.10
55_Y 46_E 0.57 0.39 0.10
50_E 62_A 0.57 0.39 0.10
5_S 15_N 0.57 0.39 0.10
12_E 22_G 0.57 0.39 0.10
26_N 15_N 0.56 0.38 0.10
78_S 69_H 0.56 0.37 0.10
30_T 19_E 0.56 0.37 0.09
81_V 86_P 0.56 0.37 0.09
55_Y 67_D 0.55 0.36 0.09
10_K 20_I 0.55 0.36 0.09
46_E 37_D 0.55 0.35 0.09
70_V 61_I 0.55 0.35 0.09
59_K 71_L 0.55 0.35 0.09
41_L 30_E 0.55 0.35 0.09
74_L 65_I 0.54 0.34 0.09
25_Q 14_L 0.54 0.34 0.09
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
4588 0.02 LAMB1_LAMC1 (T0926_T0927) Δgene:(1, ∞) A:(1E-04, 4) B:(1E-04, 4) msa: Jackhmmer (2015_06) Killed
4587 0.01 LAMB1_LAMC1 (T0926_T0927) Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) Killed
4583 0.01 LAMB1_LAMC1 (T0926_T0927) Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) Killed
4580 24.34 LAMB1_LAMC1 (T0926_T0927) Δgene:(0, 0) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.95 Done
4577 2.1 LAMB1_LAMC1 (T0926_T0927) Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
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