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OPENSEQ.org
LAMA1_LAMC1 (T0925_T0927)
Genes: A B A+B
Length: 87 91 169
Sequences: 9052 9447 261
Seq/Len: 104.05 103.81 1.54
MirrorTree (Pazo et al. 2001) 0.13
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 0.03 0.03 0.06
2 0.03 0.03 0.08
5 0.04 0.04 0.13
10 0.04 0.05 0.17
20 0.05 0.05 0.21
100 0.07 0.07 0.50
∞ 0.12 0.12 1.47
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
37_M 42_D 1.33 0.76 0.03
13_V 54_I 1.32 0.76 0.03
68_L 61_I 1.31 0.75 0.03
39_M 67_D 1.28 0.72 0.02
27_T 59_R 1.26 0.71 0.02
40_Q 71_L 1.21 0.66 0.02
22_N 46_E 1.20 0.65 0.02
50_P 17_L 1.18 0.63 0.02
39_M 73_D 1.17 0.62 0.02
40_Q 62_A 1.13 0.58 0.01
25_M 26_K 1.13 0.58 0.01
16_T 44_E 1.12 0.58 0.01
49_K 37_D 1.11 0.57 0.01
39_M 61_I 1.11 0.56 0.01
67_L 67_D 1.11 0.56 0.01
17_N 27_A 1.08 0.53 0.01
32_R 16_K 1.07 0.52 0.01
55_E 6_L 1.06 0.51 0.01
47_R 14_L 1.06 0.51 0.01
49_K 47_A 1.05 0.50 0.01
12_T 43_L 1.03 0.48 0.01
48_L 24_L 1.03 0.48 0.01
23_S 11_T 1.03 0.47 0.01
36_D 26_K 1.03 0.47 0.01
75_Q 60_D 1.01 0.46 0.01
68_L 16_K 1.00 0.45 0.01
17_N 56_D 1.00 0.45 0.01
70_S 25_N 1.00 0.45 0.01
40_Q 72_E 0.99 0.44 0.01
64_E 21_E 0.99 0.43 0.01
13_V 28_K 0.98 0.43 0.01
21_H 8_Q 0.98 0.43 0.01
50_P 73_D 0.98 0.43 0.01
44_L 58_N 0.98 0.43 0.01
74_K 77_T 0.97 0.42 0.01
79_I 37_D 0.97 0.41 0.01
46_D 26_K 0.96 0.41 0.01
46_D 56_D 0.96 0.41 0.01
45_L 67_D 0.96 0.40 0.01
29_L 69_H 0.95 0.40 0.01
29_L 24_L 0.95 0.39 0.01
76_A 29_D 0.95 0.39 0.01
71_R 65_I 0.94 0.39 0.01
25_M 41_S 0.94 0.39 0.01
20_L 21_E 0.94 0.38 0.01
43_L 45_S 0.93 0.38 0.01
62_L 23_S 0.93 0.38 0.01
36_D 45_S 0.93 0.38 0.01
21_H 35_D 0.93 0.38 0.01
11_A 8_Q 0.93 0.37 0.01
33_K 60_D 0.92 0.36 0.01
21_H 48_R 0.91 0.36 0.01
72_A 72_E 0.91 0.36 0.01
26_T 67_D 0.91 0.36 0.01
16_T 59_R 0.90 0.35 0.01
26_T 25_N 0.89 0.34 0.01
76_A 26_K 0.89 0.34 0.01
34_M 55_M 0.89 0.34 0.01
52_K 6_L 0.88 0.33 0.01
75_Q 66_K 0.88 0.33 0.01
57_N 15_N 0.88 0.33 0.01
27_T 53_A 0.87 0.32 0.01
27_T 63_E 0.87 0.32 0.01
79_I 7_G 0.86 0.31 0.01
12_T 31_M 0.86 0.31 0.01
70_S 31_M 0.85 0.31 0.01
19_L 5_Q 0.85 0.31 0.01
4_E 21_E 0.85 0.31 0.01
44_L 40_V 0.85 0.30 0.01
31_G 36_L 0.85 0.30 0.01
76_A 70_N 0.85 0.30 0.01
65_I 73_D 0.84 0.30 0.01
9_V 37_D 0.84 0.30 0.01
36_D 49_K 0.84 0.29 0.01
42_N 56_D 0.84 0.29 0.01
64_E 25_N 0.83 0.29 0.01
70_S 76_K 0.83 0.29 0.01
20_L 25_N 0.83 0.29 0.01
42_N 9_L 0.83 0.29 0.01
25_M 35_D 0.83 0.28 0.01
26_T 50_Q 0.82 0.28 0.01
19_L 22_G 0.82 0.28 0.01
18_D 16_K 0.82 0.28 0.01
35_K 47_A 0.82 0.28 0.01
65_I 71_L 0.82 0.28 0.01
36_D 43_L 0.81 0.27 0.01
74_K 18_N 0.81 0.27 0.01
80_K 25_N 0.81 0.27 0.01
11_A 29_D 0.81 0.27 0.01
9_V 46_E 0.81 0.27 0.01
52_K 75_K 0.80 0.26 0.01
48_L 76_K 0.80 0.26 0.01
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)
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