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OPENSEQ.org
cIV_D_2_cI_M_10_1_Pdenitr
Genes: A B A+B
Length: 43 513 539
Sequences: 221 7887 99
Seq/Len: 5.14 15.37 0.18
MirrorTree (Pazo et al. 2001) 0.07
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 0.30 0.00
2 0.00 0.32 0.00
5 0.00 0.35 0.00
10 0.00 0.36 0.00
20 0.00 0.37 0.00
100 0.00 0.37 0.02
∞ 0.01 0.38 0.18
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
34_V 24_R 1.50 0.30 0.00
33_A 388_F 1.30 0.21 0.00
21_I 360_I 1.29 0.21 0.00
33_A 221_L 1.11 0.15 0.00
33_A 224_A 1.11 0.15 0.00
41_A 412_V 1.08 0.14 0.00
35_L 46_F 1.08 0.14 0.00
4_K 53_L 1.05 0.13 0.00
9_D 34_A 1.05 0.13 0.00
29_I 432_A 1.03 0.12 0.00
13_Q 390_T 1.03 0.12 0.00
29_I 17_I 1.01 0.12 0.00
40_L 298_Y 1.01 0.12 0.00
13_Q 181_M 1.00 0.12 0.00
21_I 101_L 1.00 0.12 0.00
24_A 432_A 0.99 0.12 0.00
13_Q 34_A 0.98 0.11 0.00
6_G 339_A 0.95 0.10 0.00
32_I 450_S 0.94 0.10 0.00
28_S 335_G 0.94 0.10 0.00
15_A 46_F 0.94 0.10 0.00
28_S 473_L 0.93 0.10 0.00
33_A 410_M 0.92 0.10 0.00
19_G 490_V 0.92 0.10 0.00
27_V 107_Q 0.91 0.10 0.00
26_W 153_I 0.91 0.10 0.00
30_L 45_T 0.91 0.10 0.00
11_R 171_F 0.91 0.10 0.00
15_A 14_V 0.91 0.10 0.00
38_L 364_M 0.91 0.10 0.00
22_K 340_I 0.89 0.09 0.00
29_I 477_V 0.89 0.09 0.00
2_D 81_V 0.89 0.09 0.00
22_K 387_M 0.89 0.09 0.00
33_A 339_A 0.89 0.09 0.00
13_Q 445_Q 0.88 0.09 0.00
29_I 446_L 0.88 0.09 0.00
13_Q 285_Q 0.86 0.09 0.00
40_L 377_N 0.86 0.09 0.00
26_W 98_L 0.86 0.09 0.00
35_L 287_Y 0.85 0.09 0.00
2_D 446_L 0.85 0.09 0.00
24_A 270_L 0.85 0.09 0.00
33_A 288_V 0.84 0.08 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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