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OPENSEQ.org
cIV_D_2_cIII_isp_4_Pdenitr
Genes: A B A+B
Length: 43 190 225
Sequences: 221 1692 96
Seq/Len: 5.14 8.91 0.43
MirrorTree (Pazo et al. 2001) 0.20
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 0.01 0.00
10 0.00 0.01 0.00
20 0.00 0.01 0.01
100 0.00 0.01 0.04
∞ 0.01 0.05 0.41
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
13_Q 47_D 1.56 0.56 0.00
13_Q 45_S 1.39 0.43 0.00
13_Q 72_L 1.25 0.34 0.00
21_I 138_V 1.25 0.34 0.00
18_A 118_T 1.23 0.32 0.00
35_L 51_L 1.21 0.31 0.00
10_I 47_D 1.20 0.31 0.00
14_Q 175_H 1.17 0.28 0.00
13_Q 39_V 1.12 0.26 0.00
24_A 89_G 1.11 0.25 0.00
36_V 67_L 1.10 0.24 0.00
13_Q 19_L 1.07 0.23 0.00
32_I 147_F 1.04 0.22 0.00
5_H 40_N 1.03 0.21 0.00
34_V 127_V 1.03 0.21 0.00
22_K 91_E 1.03 0.21 0.00
41_A 131_V 1.02 0.20 0.00
35_L 178_V 1.01 0.20 0.00
25_T 123_G 1.01 0.20 0.00
13_Q 66_Q 1.01 0.20 0.00
33_A 41_Q 0.99 0.19 0.00
38_L 128_M 0.99 0.19 0.00
34_V 67_L 0.98 0.18 0.00
36_V 188_K 0.95 0.17 0.00
34_V 70_K 0.94 0.17 0.00
41_A 35_A 0.94 0.17 0.00
37_F 143_G 0.93 0.17 0.00
37_F 26_A 0.93 0.16 0.00
29_I 48_V 0.92 0.16 0.00
33_A 115_E 0.92 0.16 0.00
17_F 25_G 0.92 0.16 0.00
6_G 25_G 0.92 0.16 0.00
6_G 65_T 0.92 0.16 0.00
34_V 100_R 0.92 0.16 0.00
22_K 88_A 0.91 0.15 0.00
13_Q 30_A 0.90 0.15 0.00
4_K 39_V 0.90 0.15 0.00
11_R 59_S 0.89 0.15 0.00
39_A 19_L 0.88 0.14 0.00
32_I 61_V 0.88 0.14 0.00
36_V 70_K 0.87 0.14 0.00
36_V 63_T 0.86 0.14 0.00
33_A 20_Y 0.86 0.14 0.00
3_H 23_T 0.85 0.14 0.00
11_R 109_D 0.85 0.13 0.00
2_D 143_G 0.85 0.13 0.00
27_V 91_E 0.84 0.13 0.00
28_S 35_A 0.84 0.13 0.00
16_T 73_G 0.83 0.13 0.00
7_E 95_G 0.83 0.13 0.00
41_A 55_Q 0.83 0.13 0.00
32_I 84_D 0.82 0.13 0.00
16_T 145_G 0.82 0.13 0.00
37_F 66_Q 0.82 0.13 0.00
21_I 54_I 0.82 0.12 0.00
18_A 146_D 0.82 0.12 0.00
34_V 68_T 0.82 0.12 0.00
39_A 63_T 0.82 0.12 0.00
10_I 66_Q 0.81 0.12 0.00
22_K 31_A 0.81 0.12 0.00
32_I 162_S 0.80 0.12 0.00
38_L 138_V 0.80 0.12 0.00
38_L 30_A 0.80 0.12 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
3151 0.4 cIV_D_2_cIII_isp_20_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3150 0.43 cIV_D_2_cIII_isp_4_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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