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OPENSEQ.org
LAMB1_LAMC1 (T0926_T0927)
Genes: A B A+B
Length: 88 91 171
Sequences: 12354 9447 359
Seq/Len: 140.39 103.81 2.1
MirrorTree (Pazo et al. 2001) 0.08
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 0.09
2 0.04 0.03 0.11
5 0.05 0.04 0.15
10 0.06 0.05 0.21
20 0.07 0.05 0.28
100 0.09 0.07 0.71
∞ 0.14 0.12 2.01
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
17_A 17_L 1.17 0.71 0.02
72_S 12_V 1.17 0.71 0.02
77_I 11_T 1.10 0.65 0.01
26_N 27_A 1.09 0.64 0.01
67_E 25_N 1.04 0.59 0.01
68_G 36_L 1.04 0.58 0.01
80_K 27_A 1.02 0.56 0.01
76_D 79_P 1.02 0.56 0.01
71_R 62_A 1.02 0.56 0.01
14_S 41_S 1.00 0.54 0.01
78_S 45_S 1.00 0.54 0.01
10_K 62_A 1.00 0.54 0.01
41_L 19_E 0.99 0.53 0.01
22_E 43_L 0.98 0.52 0.01
38_K 15_N 0.97 0.51 0.01
49_Y 23_S 0.96 0.50 0.01
25_Q 28_K 0.96 0.50 0.01
46_E 43_L 0.96 0.49 0.01
19_R 17_L 0.96 0.49 0.01
34_Q 77_T 0.95 0.49 0.01
74_L 27_A 0.94 0.46 0.01
21_A 71_L 0.93 0.46 0.01
70_V 39_K 0.93 0.46 0.01
35_A 76_K 0.93 0.45 0.01
27_E 24_L 0.92 0.45 0.01
34_Q 74_I 0.92 0.45 0.01
20_K 38_R 0.91 0.44 0.01
36_N 57_Y 0.91 0.43 0.01
8_A 46_E 0.91 0.43 0.01
74_L 79_P 0.89 0.41 0.01
43_E 49_K 0.88 0.41 0.01
13_E 72_E 0.88 0.40 0.01
71_R 63_E 0.87 0.39 0.01
37_S 11_T 0.87 0.39 0.01
28_A 54_I 0.87 0.39 0.01
28_A 77_T 0.87 0.39 0.01
55_Y 58_N 0.86 0.38 0.01
8_A 57_Y 0.86 0.38 0.01
9_Q 69_H 0.85 0.38 0.01
26_N 66_K 0.85 0.37 0.01
63_L 35_D 0.85 0.37 0.01
52_N 73_D 0.84 0.37 0.01
15_A 9_L 0.84 0.36 0.01
35_A 16_K 0.84 0.36 0.01
49_Y 50_Q 0.84 0.36 0.01
51_D 68_I 0.83 0.35 0.01
75_K 40_V 0.83 0.35 0.01
73_L 57_Y 0.83 0.35 0.01
20_K 74_I 0.83 0.35 0.01
16_D 54_I 0.83 0.35 0.01
64_V 9_L 0.83 0.35 0.01
70_V 25_N 0.83 0.35 0.01
39_L 81_G 0.83 0.35 0.01
67_E 7_G 0.82 0.34 0.01
17_A 61_I 0.82 0.34 0.01
55_Y 72_E 0.82 0.34 0.01
64_V 40_V 0.81 0.34 0.01
86_T 20_I 0.81 0.33 0.01
69_E 13_D 0.81 0.33 0.01
46_E 80_T 0.81 0.33 0.01
14_S 55_M 0.81 0.33 0.01
78_S 59_R 0.80 0.32 0.01
63_L 20_I 0.80 0.32 0.01
30_T 69_H 0.80 0.32 0.01
59_K 49_K 0.80 0.32 0.01
75_K 73_D 0.80 0.32 0.01
54_K 24_L 0.79 0.31 0.01
48_K 39_K 0.79 0.31 0.01
47_R 59_R 0.79 0.31 0.01
34_Q 83_F 0.79 0.31 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)
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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