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OPENSEQ.org
cIV_D_2_cI_M_40_1_Pdenitr
Genes: A B A+B
Length: 43 513 546
Sequences: 221 3566 75
Seq/Len: 5.14 6.95 0.14
MirrorTree (Pazo et al. 2001) 0.16
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 0.00
100 0.00 0.02 0.01
∞ 0.01 0.03 0.13
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
13_Q 481_L 1.73 0.36 0.00
6_G 248_Q 1.31 0.18 0.00
13_Q 202_P 1.28 0.17 0.00
13_Q 475_L 1.27 0.17 0.00
32_I 142_A 1.24 0.16 0.00
21_I 89_V 1.22 0.15 0.00
10_I 90_L 1.21 0.15 0.00
35_L 101_L 1.19 0.15 0.00
31_S 248_Q 1.16 0.14 0.00
7_E 454_I 1.15 0.14 0.00
23_G 330_A 1.12 0.13 0.00
35_L 65_F 1.09 0.12 0.00
25_T 326_M 1.08 0.12 0.00
10_I 471_M 1.05 0.11 0.00
10_I 163_S 1.05 0.11 0.00
6_G 260_V 1.05 0.11 0.00
10_I 475_L 1.04 0.11 0.00
8_M 127_V 1.04 0.11 0.00
24_A 309_M 1.03 0.11 0.00
37_F 61_T 1.01 0.10 0.00
26_W 17_I 1.01 0.10 0.00
29_I 38_A 1.01 0.10 0.00
33_A 160_I 1.01 0.10 0.00
41_A 40_L 1.01 0.10 0.00
32_I 403_V 1.00 0.10 0.00
39_A 164_F 1.00 0.10 0.00
19_G 450_S 0.97 0.10 0.00
10_I 220_L 0.97 0.10 0.00
38_L 474_I 0.97 0.10 0.00
35_L 54_F 0.97 0.10 0.00
23_G 28_E 0.96 0.10 0.00
38_L 328_V 0.96 0.10 0.00
13_Q 35_K 0.96 0.09 0.00
10_I 481_L 0.96 0.09 0.00
13_Q 90_L 0.95 0.09 0.00
5_H 222_F 0.95 0.09 0.00
30_L 492_A 0.93 0.09 0.00
28_S 419_V 0.92 0.09 0.00
38_L 90_L 0.92 0.09 0.00
38_L 478_Y 0.91 0.09 0.00
19_G 360_I 0.91 0.09 0.00
8_M 87_L 0.91 0.08 0.00
13_Q 220_L 0.90 0.08 0.00
26_W 330_A 0.89 0.08 0.00
28_S 53_L 0.89 0.08 0.00
28_S 305_A 0.88 0.08 0.00
37_F 15_A 0.88 0.08 0.00
34_V 409_L 0.88 0.08 0.00
33_A 47_V 0.88 0.08 0.00
25_T 103_T 0.88 0.08 0.00
34_V 256_L 0.88 0.08 0.00
34_V 424_T 0.87 0.08 0.00
23_G 473_L 0.87 0.08 0.00
37_F 86_V 0.86 0.08 0.00
23_G 466_I 0.86 0.08 0.00
18_A 37_L 0.86 0.08 0.00
25_T 288_V 0.85 0.08 0.00
14_Q 448_K 0.85 0.08 0.00
22_K 138_L 0.85 0.07 0.00
17_F 220_L 0.85 0.07 0.00
34_V 188_A 0.84 0.07 0.00
33_A 58_P 0.84 0.07 0.00
21_I 88_F 0.84 0.07 0.00
31_S 264_M 0.84 0.07 0.00
32_I 65_F 0.83 0.07 0.00
41_A 307_S 0.83 0.07 0.00
25_T 153_I 0.83 0.07 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
3209 0.16 cIV_D_2_cI_M_20_1_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-20, 1) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3208 0.14 cIV_D_2_cI_M_40_1_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-40, 1) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3207 0.18 cIV_D_2_cI_M_10_1_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-10, 1) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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