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OPENSEQ.org
cIV_D_2_cIII_isp_20_Pdenitr
Genes: A B A+B
Length: 43 190 224
Sequences: 221 1043 89
Seq/Len: 5.14 5.49 0.4
MirrorTree (Pazo et al. 2001) 0.56
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 0.01 0.00
2 0.00 0.01 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 0.02 0.38
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 1.33 0.38 0.00
13_Q 45_S 1.28 0.34 0.00
21_I 138_V 1.23 0.31 0.00
35_L 51_L 1.21 0.30 0.00
18_A 118_T 1.15 0.26 0.00
13_Q 72_L 1.13 0.25 0.00
10_I 47_D 1.13 0.25 0.00
41_A 35_A 1.08 0.23 0.00
12_H 95_G 1.08 0.23 0.00
36_V 67_L 1.07 0.22 0.00
5_H 40_N 1.07 0.22 0.00
36_V 188_K 1.04 0.21 0.00
14_Q 175_H 1.04 0.20 0.00
13_Q 19_L 1.04 0.20 0.00
32_I 147_F 1.02 0.20 0.00
24_A 89_G 1.02 0.20 0.00
33_A 41_Q 1.01 0.19 0.00
35_L 178_V 1.00 0.18 0.00
38_L 128_M 0.98 0.18 0.00
21_I 31_A 0.98 0.18 0.00
13_Q 39_V 0.96 0.17 0.00
38_L 124_E 0.95 0.17 0.00
17_F 25_G 0.95 0.17 0.00
39_A 63_T 0.95 0.17 0.00
34_V 70_K 0.95 0.16 0.00
38_L 30_A 0.94 0.16 0.00
37_F 26_A 0.93 0.16 0.00
17_F 184_D 0.93 0.16 0.00
34_V 127_V 0.93 0.16 0.00
6_G 25_G 0.93 0.16 0.00
41_A 131_V 0.92 0.15 0.00
23_G 142_D 0.89 0.14 0.00
33_A 20_Y 0.89 0.14 0.00
41_A 55_Q 0.88 0.14 0.00
25_T 121_E 0.88 0.14 0.00
4_K 39_V 0.88 0.14 0.00
33_A 115_E 0.87 0.14 0.00
21_I 54_I 0.87 0.14 0.00
36_V 63_T 0.87 0.14 0.00
7_E 95_G 0.87 0.14 0.00
3_H 23_T 0.87 0.14 0.00
22_K 31_A 0.87 0.14 0.00
29_I 48_V 0.86 0.13 0.00
4_K 7_H 0.86 0.13 0.00
34_V 67_L 0.85 0.13 0.00
25_T 123_G 0.85 0.13 0.00
24_A 12_G 0.84 0.13 0.00
27_V 162_S 0.83 0.12 0.00
38_L 41_Q 0.83 0.12 0.00
18_A 146_D 0.83 0.12 0.00
39_A 19_L 0.83 0.12 0.00
13_Q 66_Q 0.82 0.12 0.00
22_K 88_A 0.82 0.12 0.00
16_T 73_G 0.82 0.12 0.00
33_A 148_G 0.82 0.12 0.00
6_G 65_T 0.82 0.12 0.00
27_V 107_K 0.81 0.12 0.00
32_I 84_D 0.80 0.12 0.00
37_F 66_Q 0.80 0.12 0.00
34_V 88_A 0.80 0.11 0.00
36_V 26_A 0.80 0.11 0.00
13_Q 30_A 0.79 0.11 0.00
36_V 12_G 0.79 0.11 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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