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OPENSEQ.org
cIV_D_2_cI_K_40_Pdenitr
Genes: A B A+B
Length: 43 101 141
Sequences: 221 222 63
Seq/Len: 5.14 2.2 0.45
MirrorTree (Pazo et al. 2001) 0.53
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 0.01
2 0.00 0.00 0.01
5 0.00 0.00 0.01
10 0.00 0.00 0.01
20 0.00 0.00 0.01
100 0.00 0.00 0.01
∞ 0.01 0.00 0.44
Paired alignment generation
None of the genomes have hits within 20 Δgene.
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
29_I 36_I 1.42 0.47 0.00
40_L 2_I 1.31 0.39 0.00
25_T 63_T 1.24 0.34 0.00
36_V 56_D 1.22 0.33 0.00
29_I 57_L 1.20 0.31 0.00
19_G 16_V 1.19 0.31 0.00
38_L 17_T 1.16 0.29 0.00
34_V 84_F 1.14 0.28 0.00
34_V 42_A 1.14 0.28 0.00
17_F 13_I 1.10 0.26 0.00
26_W 74_A 1.06 0.23 0.00
38_L 87_N 1.03 0.22 0.00
10_I 90_T 1.03 0.22 0.00
33_A 36_I 1.03 0.21 0.00
6_G 36_I 1.02 0.21 0.00
35_L 84_F 1.02 0.21 0.00
13_Q 29_V 1.02 0.21 0.00
29_I 76_I 1.02 0.21 0.00
38_L 35_S 0.99 0.20 0.00
38_L 83_V 0.98 0.19 0.00
25_T 32_I 0.97 0.19 0.00
21_I 97_N 0.97 0.19 0.00
35_L 42_A 0.97 0.19 0.00
11_R 57_L 0.95 0.18 0.00
13_Q 32_I 0.94 0.17 0.00
14_Q 96_V 0.93 0.17 0.00
25_T 11_G 0.93 0.17 0.00
39_A 76_I 0.92 0.17 0.00
12_H 84_F 0.91 0.16 0.00
31_S 45_I 0.90 0.16 0.00
13_Q 17_T 0.90 0.16 0.00
9_D 31_V 0.90 0.16 0.00
39_A 64_M 0.89 0.15 0.00
3_H 90_T 0.88 0.15 0.00
26_W 7_Y 0.86 0.14 0.00
18_A 65_F 0.85 0.14 0.00
17_F 98_V 0.84 0.13 0.00
39_A 94_E 0.83 0.13 0.00
36_V 94_E 0.82 0.13 0.00
30_L 23_F 0.82 0.13 0.00
40_L 47_F 0.82 0.13 0.00
21_I 52_T 0.82 0.13 0.00
36_V 19_I 0.81 0.12 0.00
26_W 90_T 0.81 0.12 0.00
8_M 20_F 0.80 0.12 0.00
27_V 31_V 0.80 0.12 0.00
12_H 20_F 0.80 0.12 0.00
30_L 36_I 0.79 0.12 0.00
18_A 29_V 0.79 0.12 0.00
4_K 36_I 0.78 0.12 0.00
14_Q 99_M 0.78 0.12 0.00
25_T 12_A 0.78 0.12 0.00
19_G 96_V 0.77 0.11 0.00
6_G 20_F 0.77 0.11 0.00
9_D 64_M 0.77 0.11 0.00
22_K 74_A 0.76 0.11 0.00
9_D 61_V 0.76 0.11 0.00
17_F 19_I 0.76 0.11 0.00
3_H 96_V 0.76 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
3218 0.61 cIV_D_2_cI_K_2_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3216 0.45 cIV_D_2_cI_K_40_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3215 0.61 cIV_D_2_cI_K_4_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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