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OPENSEQ.org
cI_E_cIII_isp_6
Genes: A B A+B
Length: 147 190 305
Sequences: 3696 1489 452
Seq/Len: 25.14 7.84 1.48
MirrorTree (Pazo et al. 2001) 0.60
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 0.00 0.02
10 0.00 0.00 0.02
20 0.00 0.00 0.04
100 0.01 0.01 0.11
∞ 0.01 0.02 1.34
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
16_F 131_V 2.25 0.99 0.97
108_F 32_G 1.46 0.84 0.68
94_E 22_A 1.23 0.67 0.46
36_F 22_A 1.20 0.64 0.42
20_L 10_D 1.19 0.63 0.41
41_A 174_L 1.15 0.59 0.37
18_I 42_M 1.15 0.59 0.37
24_I 23_T 1.14 0.57 0.35
33_G 36_W 1.10 0.54 0.32
33_G 176_I 1.07 0.51 0.29
119_R 140_I 1.07 0.51 0.29
33_G 67_L 1.05 0.49 0.27
68_F 178_V 1.04 0.48 0.27
29_L 31_A 1.03 0.47 0.25
77_I 126_L 1.02 0.46 0.24
23_A 18_F 1.01 0.44 0.23
90_T 159_Y 1.00 0.43 0.23
92_I 10_D 0.98 0.42 0.21
56_S 185_T 0.97 0.41 0.20
40_R 19_L 0.97 0.40 0.20
119_R 40_N 0.96 0.40 0.20
38_G 168_G 0.96 0.40 0.20
80_V 179_A 0.96 0.40 0.19
39_G 98_I 0.93 0.37 0.17
86_F 32_G 0.93 0.37 0.17
77_I 66_Q 0.93 0.36 0.17
40_R 32_G 0.92 0.36 0.17
44_R 22_A 0.92 0.35 0.16
112_A 142_D 0.90 0.34 0.15
82_A 142_D 0.89 0.33 0.15
37_L 140_I 0.89 0.33 0.14
37_L 83_E 0.89 0.33 0.14
23_A 125_W 0.87 0.31 0.13
29_L 184_D 0.85 0.30 0.12
108_F 12_G 0.85 0.30 0.12
90_T 13_A 0.85 0.29 0.12
16_F 151_F 0.85 0.29 0.12
10_I 33_A 0.85 0.29 0.12
22_V 187_I 0.84 0.29 0.12
34_G 119_M 0.84 0.29 0.12
38_G 28_T 0.84 0.28 0.12
18_I 65_T 0.84 0.28 0.12
21_I 14_T 0.83 0.28 0.11
47_N 144_A 0.83 0.28 0.11
104_A 63_T 0.83 0.28 0.11
37_L 175_H 0.83 0.28 0.11
47_N 55_Q 0.83 0.28 0.11
115_V 35_A 0.82 0.27 0.11
111_L 140_I 0.82 0.27 0.11
23_A 43_N 0.82 0.27 0.10
34_G 47_D 0.80 0.26 0.10
34_G 87_Q 0.80 0.25 0.10
13_H 76_V 0.80 0.25 0.10
36_F 95_G 0.80 0.25 0.10
33_G 21_Y 0.80 0.25 0.10
108_F 35_A 0.79 0.25 0.09
24_I 124_E 0.79 0.25 0.09
52_S 139_P 0.79 0.24 0.09
20_L 24_A 0.78 0.24 0.09
108_F 131_V 0.78 0.24 0.09
16_F 42_M 0.78 0.24 0.09
49_P 73_G 0.78 0.24 0.09
29_L 39_V 0.78 0.24 0.09
36_F 33_A 0.78 0.23 0.09
40_R 183_D 0.77 0.23 0.09
24_I 183_D 0.77 0.23 0.08
98_V 38_L 0.77 0.23 0.08
25_G 74_K 0.77 0.23 0.08
117_L 156_G 0.76 0.23 0.08
36_F 9_G 0.76 0.23 0.08
88_W 71_W 0.76 0.23 0.08
12_H 28_T 0.76 0.23 0.08
112_A 140_I 0.76 0.23 0.08
98_V 159_Y 0.76 0.23 0.08
100_F 156_G 0.76 0.22 0.08
86_F 63_T 0.76 0.22 0.08
96_G 60_G 0.76 0.22 0.08
29_L 24_A 0.75 0.22 0.08
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
2955 1.6 cI_A_10_cIII_isp_6_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.94 Done - Shared
2954 1.55 cI_A_6_cIII_isp_10_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.97 Done - Shared
2953 1.53 cI_A_10_cIII_isp_10_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.98 Done - Shared
2952 0.99 cI_A_10_cIII_isp_20_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.54 Done - Shared
2951 0.1 cI_A_40_cIII_isp_20_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) Killed - Shared
2950 0.99 cI_A_20_cIII_isp_20_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.35 Done - Shared
2434 1.48 cI_E_cIII_isp_6 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-06, 8) msa: Jackhmmer (2015_03) 0.97 Done - Shared
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