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OPENSEQ.org
iscu-frxn
Genes: A B A+B
Length: 106 167 235
Sequences: 356 822 92
Seq/Len: 3.36 4.92 0.39
MirrorTree (Pazo et al. 2001) 0.09
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 0.00
2 0.00 0.00 0.00
5 0.00 0.00 0.00
10 0.00 0.00 0.01
20 0.00 0.00 0.01
100 0.00 0.00 0.02
∞ 0.00 0.01 0.34
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
64_T 150_L 2.08 0.84 0.19
48_K 123_T 1.72 0.65 0.08
81_D 150_L 1.59 0.56 0.06
59_Q 150_L 1.56 0.53 0.05
5_E 41_D 1.55 0.53 0.05
80_C 61_T 1.43 0.44 0.03
65_K 82_K 1.36 0.39 0.03
55_E 116_E 1.23 0.31 0.02
67_G 126_A 1.21 0.29 0.02
89_D 37_K 1.19 0.28 0.01
35_N 55_T 1.19 0.28 0.01
71_F 116_E 1.18 0.28 0.01
87_F 113_T 1.15 0.26 0.01
80_C 130_C 1.15 0.26 0.01
22_D 89_R 1.11 0.24 0.01
80_C 109_V 1.11 0.23 0.01
90_L 79_V 1.10 0.23 0.01
47_S 121_K 1.06 0.21 0.01
81_D 157_Q 1.03 0.20 0.01
86_T 113_T 1.02 0.19 0.01
30_I 37_K 1.02 0.19 0.01
98_Q 121_K 1.01 0.19 0.01
37_G 52_L 1.01 0.19 0.01
42_T 124_D 0.99 0.18 0.01
8_R 40_V 0.99 0.18 0.01
90_L 34_L 0.99 0.18 0.01
93_Q 84_K 0.98 0.18 0.01
41_I 109_V 0.98 0.17 0.01
64_T 77_I 0.97 0.17 0.01
89_D 80_D 0.94 0.16 0.01
11_D 109_V 0.93 0.16 0.01
2_N 118_L 0.93 0.15 0.01
51_I 140_M 0.91 0.15 0.01
10_A 80_D 0.91 0.15 0.01
14_W 74_K 0.90 0.15 0.01
42_T 113_T 0.90 0.14 0.01
91_L 109_V 0.90 0.14 0.01
83_S 60_G 0.89 0.14 0.01
72_D 150_L 0.89 0.14 0.01
90_L 40_V 0.89 0.14 0.01
62_L 34_L 0.88 0.14 0.01
27_D 154_K 0.88 0.14 0.01
87_F 84_K 0.88 0.14 0.01
90_L 77_I 0.87 0.14 0.00
97_Q 40_V 0.87 0.13 0.00
40_T 89_R 0.87 0.13 0.00
67_G 127_K 0.86 0.13 0.00
66_Q 150_L 0.86 0.13 0.00
19_E 37_K 0.86 0.13 0.00
81_D 52_L 0.86 0.13 0.00
91_L 152_D 0.85 0.13 0.00
77_E 116_E 0.85 0.13 0.00
33_E 154_K 0.85 0.13 0.00
34_I 150_L 0.85 0.13 0.00
65_K 80_D 0.85 0.13 0.00
80_C 74_K 0.84 0.12 0.00
48_K 80_D 0.84 0.12 0.00
48_K 89_R 0.83 0.12 0.00
103_V 151_A 0.83 0.12 0.00
69_Y 61_T 0.83 0.12 0.00
74_K 154_K 0.83 0.12 0.00
60_V 45_N 0.82 0.12 0.00
15_L 37_K 0.82 0.12 0.00
37_G 140_M 0.82 0.12 0.00
48_K 154_K 0.81 0.12 0.00
23_D 155_L 0.81 0.12 0.00
41_I 157_Q 0.80 0.11 0.00
99_A 157_Q 0.80 0.11 0.00
88_W 115_E 0.80 0.11 0.00
81_D 114_V 0.80 0.11 0.00
74_K 58_N 0.80 0.11 0.00
10_A 40_V 0.80 0.11 0.00
87_F 119_T 0.80 0.11 0.00
40_T 60_G 0.80 0.11 0.00
48_K 52_L 0.80 0.11 0.00
91_L 61_T 0.79 0.11 0.00
42_T 116_E 0.78 0.11 0.00
42_T 89_R 0.78 0.11 0.00
72_D 55_T 0.78 0.11 0.00
39_L 123_T 0.78 0.11 0.00
49_I 34_L 0.78 0.11 0.00
41_I 127_K 0.78 0.11 0.00
19_E 136_L 0.77 0.10 0.00
12_Q 124_D 0.77 0.10 0.00
29_D 45_N 0.77 0.10 0.00
85_E 82_K 0.77 0.10 0.00
45_N 40_V 0.77 0.10 0.00
64_T 79_V 0.77 0.10 0.00
55_E 119_T 0.77 0.10 0.00
72_D 57_K 0.76 0.10 0.00
21_L 89_R 0.76 0.10 0.00
7_H 40_V 0.76 0.10 0.00
34_I 52_L 0.76 0.10 0.00
9_L 119_T 0.76 0.10 0.00
96_T 55_T 0.76 0.10 0.00
83_S 121_K 0.75 0.10 0.00
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
4336 0.39 iscu-frxn Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.19 Done - Shared
4335 0.03 fra iscu Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
4334 0.01 fra-isc Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) Killed - Shared
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