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OPENSEQ.org
cIV_D_2_cI_A_40_Pdenitr
Genes: A B A+B
Length: 43 121 159
Sequences: 221 493 63
Seq/Len: 5.14 4.07 0.4
MirrorTree (Pazo et al. 2001) 0.56
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 0.38
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 29_A 1.51 0.51 0.00
10_I 29_A 1.46 0.47 0.00
37_F 67_S 1.29 0.35 0.00
13_Q 26_I 1.23 0.31 0.00
7_E 32_I 1.22 0.30 0.00
40_L 7_E 1.18 0.28 0.00
6_G 13_V 1.17 0.27 0.00
25_T 16_G 1.12 0.24 0.00
6_G 85_V 1.10 0.23 0.00
14_Q 25_L 1.09 0.23 0.00
33_A 110_A 1.08 0.22 0.00
3_H 19_S 1.08 0.22 0.00
14_Q 50_N 1.07 0.22 0.00
29_I 12_L 1.07 0.22 0.00
33_A 100_V 1.06 0.21 0.00
10_I 21_L 1.03 0.20 0.00
36_V 90_L 1.03 0.20 0.00
26_W 17_M 1.02 0.20 0.00
4_K 26_I 1.02 0.20 0.00
28_S 17_M 1.01 0.19 0.00
17_F 29_A 1.01 0.19 0.00
23_G 2_E 1.01 0.19 0.00
14_Q 92_D 1.01 0.19 0.00
37_F 89_S 1.01 0.19 0.00
23_G 94_A 0.99 0.18 0.00
14_Q 87_F 0.98 0.18 0.00
4_K 24_V 0.96 0.17 0.00
19_G 39_P 0.96 0.17 0.00
39_A 106_T 0.95 0.16 0.00
36_V 11_I 0.94 0.16 0.00
37_F 21_L 0.93 0.16 0.00
14_Q 23_I 0.92 0.15 0.00
28_S 20_A 0.92 0.15 0.00
16_T 78_A 0.92 0.15 0.00
25_T 42_V 0.91 0.15 0.00
27_V 13_V 0.91 0.15 0.00
12_H 16_G 0.90 0.15 0.00
39_A 28_A 0.90 0.15 0.00
31_S 90_L 0.89 0.14 0.00
34_V 110_A 0.89 0.14 0.00
30_L 32_I 0.87 0.14 0.00
34_V 114_K 0.87 0.14 0.00
22_K 26_I 0.86 0.13 0.00
28_S 94_A 0.86 0.13 0.00
19_G 11_I 0.85 0.13 0.00
37_F 91_S 0.84 0.13 0.00
10_I 94_A 0.83 0.12 0.00
41_A 7_E 0.83 0.12 0.00
38_L 50_N 0.81 0.12 0.00
25_T 20_A 0.80 0.12 0.00
36_V 31_V 0.80 0.12 0.00
41_A 77_V 0.80 0.12 0.00
11_R 31_V 0.80 0.11 0.00
4_K 36_N 0.80 0.11 0.00
25_T 110_A 0.80 0.11 0.00
28_S 42_V 0.79 0.11 0.00
38_L 107_V 0.79 0.11 0.00
14_Q 93_V 0.78 0.11 0.00
23_G 42_V 0.78 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
3223 0.4 cIV_D_2_cI_A_40_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3222 0.43 cIV_D_2_cI_A_2_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3221 0.43 cIV_D_2_cI_A_4_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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