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OPENSEQ.org
cIV_D_2_cI_M_20_1_Pdenitr
Genes: A B A+B
Length: 43 513 542
Sequences: 221 5240 89
Seq/Len: 5.14 10.21 0.16
MirrorTree (Pazo et al. 2001) 0.12
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 0.06 0.00
2 0.00 0.06 0.00
5 0.00 0.07 0.00
10 0.00 0.08 0.00
20 0.00 0.08 0.00
100 0.00 0.09 0.02
∞ 0.01 0.12 0.16
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
33_A 388_F 1.53 0.29 0.00
32_I 403_V 1.50 0.28 0.00
32_I 142_A 1.45 0.25 0.00
33_A 224_A 1.33 0.21 0.00
35_L 53_L 1.24 0.17 0.00
23_G 330_A 1.24 0.17 0.00
29_I 38_A 1.22 0.17 0.00
13_Q 475_L 1.20 0.16 0.00
41_A 412_V 1.18 0.15 0.00
29_I 17_I 1.12 0.14 0.00
10_I 138_L 1.09 0.13 0.00
41_A 281_S 1.09 0.13 0.00
18_A 424_T 1.07 0.12 0.00
34_V 424_T 1.05 0.12 0.00
27_V 177_M 1.05 0.12 0.00
29_I 446_L 1.01 0.11 0.00
13_Q 445_Q 1.01 0.11 0.00
26_W 17_I 1.00 0.11 0.00
17_F 481_L 1.00 0.11 0.00
13_Q 481_L 1.00 0.11 0.00
15_A 14_V 1.00 0.11 0.00
38_L 37_L 0.99 0.11 0.00
31_S 47_V 0.99 0.11 0.00
13_Q 202_P 0.97 0.10 0.00
4_K 53_L 0.96 0.10 0.00
40_L 17_I 0.96 0.10 0.00
25_T 318_V 0.95 0.10 0.00
11_R 391_M 0.94 0.10 0.00
28_S 385_V 0.94 0.10 0.00
35_L 46_F 0.93 0.10 0.00
12_H 490_V 0.93 0.10 0.00
22_K 172_L 0.93 0.10 0.00
28_S 330_A 0.92 0.09 0.00
2_D 388_F 0.92 0.09 0.00
26_W 330_A 0.92 0.09 0.00
35_L 41_T 0.91 0.09 0.00
17_F 475_L 0.91 0.09 0.00
3_H 99_T 0.90 0.09 0.00
35_L 449_E 0.90 0.09 0.00
21_I 348_F 0.89 0.09 0.00
34_V 14_V 0.89 0.09 0.00
39_A 436_W 0.88 0.08 0.00
22_K 62_G 0.87 0.08 0.00
19_G 229_F 0.87 0.08 0.00
35_L 133_L 0.87 0.08 0.00
38_L 186_R 0.87 0.08 0.00
26_W 489_A 0.87 0.08 0.00
26_W 58_P 0.86 0.08 0.00
13_Q 158_D 0.86 0.08 0.00
6_G 260_V 0.85 0.08 0.00
13_Q 349_I 0.84 0.08 0.00
23_G 86_V 0.84 0.08 0.00
24_A 432_A 0.84 0.08 0.00
32_I 41_T 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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