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OPENSEQ.org
cIV_D_2_cIII_cyt1_4_Pdenitr
Genes: A B A+B
Length: 43 263 295
Sequences: 221 973 88
Seq/Len: 5.14 3.7 0.3
MirrorTree (Pazo et al. 2001) 0.71
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 0.01
100 0.00 0.01 0.03
∞ 0.01 0.01 0.29
Paired alignment generation
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
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
9_D 130_R 1.29 0.29 0.00
25_T 69_L 1.27 0.28 0.00
41_A 59_S 1.26 0.27 0.00
32_I 187_A 1.16 0.22 0.00
41_A 185_Q 1.16 0.22 0.00
22_K 144_L 1.14 0.21 0.00
17_F 202_P 1.11 0.20 0.00
40_L 236_I 1.07 0.18 0.00
19_G 209_A 1.06 0.18 0.00
36_V 232_F 1.06 0.18 0.00
9_D 209_A 1.06 0.18 0.00
15_A 108_T 1.05 0.18 0.00
21_I 118_G 1.04 0.17 0.00
22_K 41_K 1.04 0.17 0.00
10_I 118_G 1.03 0.17 0.00
13_Q 187_A 1.02 0.16 0.00
36_V 250_K 1.01 0.16 0.00
34_V 105_R 1.00 0.16 0.00
38_L 125_L 0.99 0.15 0.00
13_Q 97_P 0.99 0.15 0.00
28_S 64_L 0.97 0.15 0.00
29_I 242_A 0.97 0.15 0.00
14_Q 145_F 0.97 0.15 0.00
38_L 213_A 0.96 0.14 0.00
36_V 73_A 0.95 0.14 0.00
26_W 193_D 0.95 0.14 0.00
3_H 81_P 0.94 0.14 0.00
11_R 187_A 0.94 0.14 0.00
29_I 204_T 0.94 0.14 0.00
35_L 226_D 0.94 0.14 0.00
12_H 226_D 0.94 0.14 0.00
20_F 246_Y 0.94 0.14 0.00
25_T 199_D 0.93 0.13 0.00
33_A 205_V 0.93 0.13 0.00
24_A 166_K 0.92 0.13 0.00
29_I 141_L 0.92 0.13 0.00
13_Q 98_E 0.92 0.13 0.00
6_G 247_L 0.92 0.13 0.00
37_F 68_P 0.91 0.13 0.00
38_L 151_P 0.91 0.13 0.00
18_A 88_Y 0.90 0.12 0.00
13_Q 120_G 0.90 0.12 0.00
10_I 144_L 0.88 0.12 0.00
10_I 208_M 0.88 0.12 0.00
40_L 59_S 0.88 0.12 0.00
17_F 152_E 0.87 0.12 0.00
12_H 156_A 0.86 0.11 0.00
31_S 202_P 0.86 0.11 0.00
11_R 156_A 0.86 0.11 0.00
37_F 23_H 0.85 0.11 0.00
18_A 205_V 0.85 0.11 0.00
26_W 80_L 0.84 0.11 0.00
32_I 11_A 0.84 0.11 0.00
13_Q 197_Y 0.83 0.11 0.00
17_F 208_M 0.83 0.11 0.00
19_G 167_E 0.83 0.10 0.00
28_S 123_L 0.82 0.10 0.00
9_D 245_L 0.82 0.10 0.00
21_I 42_F 0.82 0.10 0.00
22_K 42_F 0.81 0.10 0.00
9_D 104_P 0.81 0.10 0.00
41_A 44_Q 0.81 0.10 0.00
34_V 52_Q 0.81 0.10 0.00
2_D 113_T 0.81 0.10 0.00
19_G 224_M 0.81 0.10 0.00
24_A 188_A 0.81 0.10 0.00
40_L 177_A 0.80 0.10 0.00
10_I 115_S 0.80 0.10 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
3146 0.3 cIV_D_2_cIII_cyt1_4_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3145 0.29 cIV_D_2_cIII_cyt1_40_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3144 0 cIV_D_40_cIII_cyt1_40_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) Killed - Shared
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