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OPENSEQ.org
cIV_D_2_cI_J_4_Pdenitr
Genes: A B A+B
Length: 43 200 237
Sequences: 221 6534 97
Seq/Len: 5.14 32.67 0.41
MirrorTree (Pazo et al. 2001) 0.05
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 0.00
2 0.00 0.00 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 0.03 0.06
∞ 0.01 0.06 0.40
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
24_A 117_A 1.21 0.30 0.00
13_Q 39_S 1.18 0.28 0.00
30_L 192_K 1.18 0.28 0.00
26_W 192_K 1.17 0.28 0.00
29_I 116_Q 1.11 0.25 0.00
40_L 124_P 1.08 0.23 0.00
21_I 102_A 1.06 0.22 0.00
13_Q 5_A 1.06 0.22 0.00
26_W 145_L 1.04 0.21 0.00
35_L 20_V 1.04 0.21 0.00
9_D 104_L 1.03 0.20 0.00
18_A 83_K 1.00 0.19 0.00
16_T 69_L 1.00 0.19 0.00
17_F 39_S 1.00 0.19 0.00
18_A 148_Q 0.98 0.18 0.00
14_Q 188_T 0.98 0.18 0.00
8_M 69_L 0.95 0.17 0.00
39_A 23_G 0.95 0.17 0.00
12_H 17_G 0.95 0.17 0.00
38_L 44_F 0.94 0.16 0.00
13_Q 152_L 0.94 0.16 0.00
30_L 100_L 0.93 0.16 0.00
22_K 149_L 0.93 0.16 0.00
29_I 40_A 0.91 0.15 0.00
34_V 11_I 0.90 0.15 0.00
31_S 14_C 0.89 0.15 0.00
35_L 188_T 0.89 0.15 0.00
23_G 90_L 0.89 0.14 0.00
13_Q 193_D 0.87 0.14 0.00
26_W 106_I 0.86 0.14 0.00
34_V 139_L 0.86 0.14 0.00
41_A 150_A 0.85 0.13 0.00
21_I 178_L 0.85 0.13 0.00
2_D 109_S 0.85 0.13 0.00
40_L 153_V 0.85 0.13 0.00
3_H 97_G 0.84 0.13 0.00
32_I 198_Q 0.83 0.12 0.00
10_I 39_S 0.83 0.12 0.00
6_G 58_V 0.83 0.12 0.00
29_I 55_L 0.82 0.12 0.00
12_H 190_E 0.82 0.12 0.00
27_V 17_G 0.81 0.12 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
3214 0.42 cIV_D_2_cI_J_2_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3213 0.41 cIV_D_2_cI_J_4_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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