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OPENSEQ.org
cI_I_40_cIII_isp_4_Pdenitr
Genes: A B A+B
Length: 163 190 346
Sequences: 644 1692 383
Seq/Len: 3.95 8.91 1.11
MirrorTree (Pazo et al. 2001) 0.67
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 0.01
100 0.00 0.01 0.07
∞ 0.01 0.05 1.08
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
150_A 144_A 1.32 0.66 0.00
12_F 131_V 1.29 0.63 0.00
18_I 28_T 1.29 0.63 0.00
48_F 22_A 1.22 0.57 0.00
156_L 47_D 1.21 0.56 0.00
117_A 176_I 1.13 0.48 0.00
108_F 188_K 1.09 0.44 0.00
155_N 72_L 1.07 0.42 0.00
12_F 66_Q 1.06 0.42 0.00
9_T 60_G 1.05 0.41 0.00
27_Y 34_A 1.05 0.41 0.00
88_D 164_R 1.04 0.40 0.00
90_S 87_Q 1.04 0.40 0.00
13_L 59_S 1.03 0.39 0.00
20_G 41_Q 1.00 0.36 0.00
160_A 29_V 0.99 0.35 0.00
4_D 31_A 0.98 0.35 0.00
29_V 10_D 0.98 0.35 0.00
12_F 25_G 0.98 0.35 0.00
156_L 45_S 0.95 0.32 0.00
136_Y 49_Q 0.94 0.31 0.00
5_F 31_A 0.93 0.30 0.00
23_L 9_G 0.93 0.30 0.00
39_H 150_W 0.92 0.30 0.00
18_I 18_F 0.92 0.30 0.00
6_A 35_A 0.91 0.29 0.00
158_L 27_G 0.91 0.29 0.00
40_E 39_V 0.90 0.28 0.00
147_R 175_H 0.90 0.28 0.00
157_Q 19_L 0.90 0.28 0.00
15_W 39_V 0.89 0.27 0.00
134_L 42_M 0.88 0.27 0.00
21_F 131_V 0.88 0.27 0.00
16_D 146_D 0.88 0.27 0.00
131_R 23_T 0.88 0.27 0.00
35_L 57_D 0.88 0.27 0.00
11_Y 178_V 0.88 0.27 0.00
84_E 178_V 0.88 0.26 0.00
22_G 189_L 0.87 0.26 0.00
37_Y 147_F 0.87 0.26 0.00
135_F 13_A 0.87 0.26 0.00
156_L 144_A 0.87 0.26 0.00
108_F 52_A 0.86 0.26 0.00
5_F 32_G 0.86 0.25 0.00
11_Y 131_V 0.86 0.25 0.00
160_A 22_A 0.86 0.25 0.00
90_S 47_D 0.86 0.25 0.00
151_E 61_V 0.86 0.25 0.00
11_Y 184_D 0.86 0.25 0.00
84_E 143_G 0.85 0.25 0.00
48_F 178_V 0.85 0.24 0.00
161_P 61_V 0.85 0.24 0.00
33_P 41_Q 0.84 0.24 0.00
41_K 91_E 0.84 0.24 0.00
8_A 28_T 0.84 0.23 0.00
15_W 10_D 0.84 0.23 0.00
89_G 124_E 0.83 0.23 0.00
13_L 13_A 0.83 0.23 0.00
44_L 80_R 0.83 0.23 0.00
157_Q 33_A 0.83 0.23 0.00
23_L 88_A 0.82 0.22 0.00
155_N 175_H 0.82 0.22 0.00
29_V 176_I 0.81 0.22 0.00
28_F 115_E 0.81 0.22 0.00
73_V 67_L 0.81 0.22 0.00
154_R 27_G 0.81 0.22 0.00
10_K 131_V 0.81 0.21 0.00
101_T 141_G 0.80 0.21 0.00
22_G 175_H 0.80 0.21 0.00
101_T 42_M 0.80 0.21 0.00
105_Y 43_N 0.80 0.21 0.00
134_L 33_A 0.80 0.21 0.00
127_A 40_N 0.79 0.20 0.00
121_G 36_W 0.78 0.20 0.00
10_K 90_R 0.78 0.20 0.00
160_A 128_M 0.78 0.20 0.00
161_P 10_D 0.78 0.20 0.00
82_D 158_H 0.78 0.20 0.00
13_L 28_T 0.78 0.20 0.00
88_D 99_D 0.78 0.20 0.00
26_R 19_L 0.77 0.20 0.00
54_L 163_G 0.77 0.19 0.00
5_F 62_E 0.77 0.19 0.00
112_A 167_R 0.77 0.19 0.00
124_F 183_D 0.77 0.19 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
3050 1.29 cI_I_20_cIII_isp_10_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3049 0.71 cI_I_60_cIII_isp_10_Pdenitr Δgene:(1, ∞) A:(1E-60, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
3048 0.78 cI_I_40_cIII_isp_20_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3047 1.09 cI_I_40_cIII_isp_10_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.19 Done - Shared
3046 1.11 cI_I_40_cIII_isp_6_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.03 Done - Shared
3044 1.11 cI_I_40_cIII_isp_4_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3043 1.84 cI_I_4_cIII_isp_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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