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OPENSEQ.org
cI_A_20_cIII_isp_20_Pdenitr
Genes: A B A+B
Length: 147 190 303
Sequences: 3799 1043 299
Seq/Len: 25.84 5.49 0.99
MirrorTree (Pazo et al. 2001) 0.38
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 0.01
20 0.00 0.01 0.02
100 0.01 0.01 0.09
∞ 0.02 0.02 0.89
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
33_G 176_I 1.79 0.90 0.35
20_L 58_V 1.58 0.81 0.22
16_F 131_V 1.51 0.77 0.18
24_I 58_V 1.33 0.64 0.11
98_V 38_L 1.27 0.58 0.09
124_D 19_L 1.27 0.58 0.09
24_I 124_E 1.17 0.49 0.07
23_A 125_W 1.13 0.45 0.06
94_E 22_A 1.12 0.45 0.05
29_L 31_A 1.10 0.43 0.05
124_D 33_A 1.09 0.41 0.05
33_G 36_W 1.08 0.41 0.05
108_F 32_G 1.07 0.40 0.04
108_F 48_V 1.07 0.40 0.04
117_L 156_G 1.06 0.39 0.04
25_G 31_A 1.05 0.38 0.04
18_I 42_M 1.05 0.38 0.04
47_N 55_Q 1.03 0.36 0.04
35_W 41_Q 1.01 0.35 0.04
92_I 141_G 1.00 0.34 0.03
22_V 92_V 0.99 0.33 0.03
58_G 78_I 0.99 0.33 0.03
115_V 18_F 0.98 0.33 0.03
47_N 172_Q 0.98 0.33 0.03
100_F 78_I 0.98 0.32 0.03
90_T 159_Y 0.96 0.31 0.03
112_A 86_I 0.96 0.30 0.03
23_A 159_Y 0.96 0.30 0.03
91_S 38_L 0.95 0.30 0.03
95_S 31_A 0.95 0.29 0.03
71_V 59_S 0.94 0.29 0.03
90_T 187_I 0.93 0.28 0.03
26_L 131_V 0.93 0.28 0.03
38_G 168_G 0.92 0.28 0.03
37_L 112_A 0.91 0.27 0.02
115_V 83_E 0.91 0.27 0.02
16_F 42_M 0.90 0.26 0.02
34_G 47_D 0.89 0.26 0.02
95_S 35_A 0.89 0.25 0.02
39_G 98_I 0.89 0.25 0.02
119_R 40_N 0.89 0.25 0.02
41_A 25_G 0.88 0.25 0.02
12_H 47_D 0.88 0.24 0.02
16_F 151_F 0.87 0.24 0.02
17_A 142_D 0.87 0.24 0.02
50_F 166_R 0.87 0.24 0.02
14_W 79_R 0.87 0.24 0.02
32_V 101_S 0.86 0.24 0.02
88_W 71_W 0.86 0.23 0.02
77_I 150_W 0.85 0.23 0.02
35_W 72_L 0.85 0.23 0.02
37_L 140_I 0.85 0.23 0.02
44_R 22_A 0.85 0.23 0.02
30_M 41_Q 0.85 0.23 0.02
82_A 52_A 0.85 0.23 0.02
40_R 32_G 0.84 0.22 0.02
77_I 30_A 0.84 0.22 0.02
117_L 50_A 0.84 0.22 0.02
16_F 88_A 0.84 0.22 0.02
115_V 35_A 0.83 0.22 0.02
44_R 41_Q 0.83 0.22 0.02
40_R 70_K 0.83 0.22 0.02
90_T 23_T 0.83 0.21 0.02
82_A 23_T 0.83 0.21 0.02
72_A 53_S 0.82 0.21 0.02
124_D 62_E 0.82 0.21 0.02
72_A 39_V 0.82 0.21 0.02
96_G 30_A 0.82 0.21 0.02
60_A 185_T 0.82 0.21 0.02
115_V 105_S 0.82 0.21 0.02
23_A 181_F 0.82 0.20 0.02
18_I 65_T 0.81 0.20 0.02
80_V 179_A 0.81 0.20 0.02
91_S 13_A 0.81 0.20 0.01
23_A 138_V 0.81 0.20 0.01
34_G 45_S 0.80 0.20 0.01
23_A 23_T 0.80 0.20 0.01
85_L 87_Q 0.80 0.19 0.01
100_F 114_D 0.80 0.19 0.01
95_S 34_A 0.80 0.19 0.01
17_A 48_V 0.79 0.19 0.01
112_A 140_I 0.79 0.19 0.01
21_I 112_A 0.79 0.19 0.01
118_V 77_F 0.79 0.19 0.01
101_V 80_R 0.79 0.19 0.01
103_A 19_L 0.78 0.19 0.01
40_R 96_Q 0.78 0.19 0.01
56_S 185_T 0.78 0.18 0.01
103_A 15_R 0.78 0.18 0.01
40_R 46_A 0.77 0.18 0.01
55_D 26_A 0.77 0.18 0.01
40_R 19_L 0.77 0.18 0.01
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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