May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
LAMA1_LAMB1 (T0925_T0926)
Genes: A B A+B
Length: 87 88 166
Sequences: 9052 12354 251
Seq/Len: 104.05 140.39 1.51
MirrorTree (Pazo et al. 2001) 0.10
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 0.04 0.11
2 0.03 0.04 0.13
5 0.04 0.05 0.15
10 0.04 0.06 0.21
20 0.05 0.07 0.28
100 0.07 0.09 0.53
∞ 0.12 0.14 1.43
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
8_R 21_A 1.35 0.77 0.03
20_L 25_Q 1.31 0.74 0.03
76_A 18_R 1.27 0.71 0.02
14_Q 71_R 1.20 0.65 0.02
46_D 6_L 1.20 0.64 0.02
17_N 27_E 1.17 0.62 0.02
49_K 25_Q 1.15 0.59 0.02
33_K 67_E 1.14 0.58 0.02
6_L 83_V 1.13 0.58 0.02
53_T 15_A 1.12 0.57 0.02
61_N 50_E 1.09 0.53 0.01
21_H 15_A 1.07 0.52 0.01
39_M 32_L 1.03 0.47 0.01
57_N 21_A 1.02 0.47 0.01
23_S 42_L 1.02 0.46 0.01
13_V 70_V 1.02 0.46 0.01
12_T 54_K 1.01 0.45 0.01
21_H 65_R 1.01 0.45 0.01
44_L 26_N 1.00 0.44 0.01
29_L 23_L 0.99 0.44 0.01
42_N 84_Y 0.99 0.44 0.01
60_R 51_D 0.99 0.43 0.01
78_S 14_S 0.97 0.41 0.01
27_T 39_L 0.96 0.41 0.01
38_E 37_S 0.96 0.40 0.01
16_T 42_L 0.96 0.40 0.01
65_I 22_E 0.96 0.40 0.01
48_L 80_K 0.96 0.40 0.01
56_E 23_L 0.95 0.39 0.01
37_M 82_A 0.95 0.39 0.01
67_L 69_E 0.94 0.39 0.01
28_L 7_I 0.94 0.38 0.01
44_L 60_A 0.93 0.37 0.01
36_D 49_Y 0.93 0.37 0.01
53_T 50_E 0.92 0.36 0.01
64_E 16_D 0.92 0.36 0.01
59_S 67_E 0.91 0.36 0.01
22_N 53_Q 0.91 0.35 0.01
76_A 23_L 0.90 0.34 0.01
48_L 69_E 0.90 0.34 0.01
51_L 42_L 0.90 0.34 0.01
24_T 63_L 0.90 0.34 0.01
79_I 67_E 0.90 0.34 0.01
20_L 67_E 0.89 0.34 0.01
77_A 8_A 0.89 0.34 0.01
78_S 55_Y 0.89 0.33 0.01
17_N 64_V 0.89 0.33 0.01
82_A 29_K 0.88 0.33 0.01
10_N 74_L 0.88 0.32 0.01
13_V 62_E 0.87 0.32 0.01
74_K 37_S 0.87 0.32 0.01
22_N 68_G 0.87 0.32 0.01
24_T 48_K 0.86 0.31 0.01
47_R 45_L 0.86 0.31 0.01
25_M 70_V 0.86 0.31 0.01
4_E 38_K 0.85 0.30 0.01
15_E 8_A 0.85 0.30 0.01
40_Q 8_A 0.85 0.30 0.01
71_R 80_K 0.85 0.30 0.01
68_L 14_S 0.85 0.30 0.01
58_L 58_D 0.85 0.30 0.01
24_T 78_S 0.85 0.30 0.01
9_V 28_A 0.84 0.29 0.01
30_A 18_R 0.83 0.28 0.01
62_L 51_D 0.83 0.28 0.01
28_L 27_E 0.83 0.28 0.01
41_A 77_I 0.83 0.28 0.01
31_G 61_Q 0.83 0.28 0.01
55_E 34_Q 0.82 0.28 0.01
34_M 27_E 0.81 0.27 0.01
49_K 16_D 0.81 0.27 0.01
35_K 69_E 0.81 0.27 0.01
65_I 6_L 0.81 0.27 0.01
4_E 67_E 0.81 0.26 0.01
32_R 69_E 0.81 0.26 0.01
15_E 9_Q 0.81 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)
ID Seq/Len Name Options I_Prob Status
4633 0.01 ab Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) Killed - Shared
4575 1.51 LAMA1_LAMB1 (T0925_T0926) Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.03 Done - Shared
Page generated in 1.2243 seconds.