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OPENSEQ.org
cIV_C_4_cI_A_4_Pdenitr
Genes: A B A+B
Length: 273 121 371
Sequences: 2888 4975 2658
Seq/Len: 10.58 41.12 7.16
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 0.00 4.41
2 0.00 0.00 4.67
5 0.00 0.00 5.23
10 0.00 0.00 5.74
20 0.00 0.00 5.92
100 0.00 0.01 6.10
∞ 0.01 0.02 6.75
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
87_Q 115_K 1.52 0.99 0.88
22_I 80_L 1.07 0.91 0.53
80_P 87_F 1.05 0.90 0.51
107_A 62_R 1.04 0.90 0.50
87_Q 113_W 1.02 0.88 0.47
121_P 84_A 0.94 0.82 0.38
83_R 72_I 0.93 0.81 0.37
13_P 78_A 0.92 0.80 0.36
6_H 66_V 0.91 0.80 0.35
84_I 17_M 0.89 0.78 0.33
13_P 84_A 0.88 0.76 0.32
18_F 78_A 0.88 0.76 0.32
138_W 78_A 0.88 0.76 0.32
240_T 75_L 0.88 0.76 0.32
138_W 62_R 0.86 0.74 0.30
121_P 99_M 0.85 0.73 0.29
228_F 19_S 0.85 0.73 0.29
160_H 64_Y 0.83 0.70 0.27
196_A 32_I 0.81 0.67 0.25
177_V 16_G 0.80 0.66 0.24
181_L 45_Y 0.80 0.66 0.24
125_G 62_R 0.80 0.65 0.23
52_L 21_L 0.77 0.62 0.21
146_L 62_R 0.77 0.62 0.21
54_G 78_A 0.77 0.61 0.21
33_A 75_L 0.77 0.61 0.21
205_Y 105_L 0.76 0.60 0.20
190_A 67_S 0.75 0.59 0.20
26_V 117_A 0.75 0.59 0.20
99_M 79_F 0.75 0.58 0.20
228_F 103_A 0.74 0.57 0.19
239_M 105_L 0.74 0.57 0.19
56_V 23_I 0.74 0.57 0.19
172_I 21_L 0.74 0.57 0.19
31_A 37_P 0.73 0.56 0.18
111_N 64_Y 0.73 0.56 0.18
180_I 20_A 0.73 0.55 0.18
106_W 49_F 0.73 0.55 0.18
56_V 20_A 0.73 0.55 0.18
20_G 68_I 0.72 0.54 0.17
210_Y 33_A 0.72 0.54 0.17
140_L 43_S 0.72 0.53 0.17
58_V 52_F 0.71 0.53 0.17
191_Y 66_V 0.71 0.53 0.17
221_I 30_A 0.71 0.53 0.17
228_F 13_V 0.71 0.53 0.17
18_F 95_F 0.71 0.52 0.17
108_F 64_Y 0.71 0.52 0.16
99_M 66_V 0.71 0.52 0.16
240_T 106_T 0.71 0.52 0.16
31_A 12_L 0.71 0.52 0.16
21_A 45_Y 0.70 0.51 0.16
37_G 107_V 0.70 0.51 0.16
228_F 114_K 0.70 0.51 0.16
240_T 37_P 0.70 0.51 0.16
13_P 101_F 0.70 0.51 0.16
24_A 68_I 0.70 0.50 0.15
172_I 16_G 0.70 0.50 0.15
143_I 104_V 0.70 0.50 0.15
272_G 101_F 0.69 0.49 0.15
18_F 27_L 0.69 0.49 0.15
265_F 58_K 0.68 0.48 0.14
242_K 55_A 0.68 0.47 0.14
228_F 100_V 0.68 0.47 0.14
169_K 16_G 0.67 0.46 0.14
35_M 89_S 0.67 0.46 0.14
151_S 74_D 0.67 0.45 0.13
215_F 74_D 0.67 0.45 0.13
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
3161 6.49 cIV_C_2_cI_A_20_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.95 Done - Shared
3160 6.88 cIV_C_4_cI_A_10_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.91 Done - Shared
3159 6.47 cIV_C_6_cI_A_20_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.94 Done - Shared
3158 0.87 cIV_C_4_cI_A_40_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3157 6.47 cIV_C_4_cI_A_20_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.95 Done - Shared
3156 7.13 cIV_C_4_cI_A_6_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.88 Done - Shared
3155 7.16 cIV_C_4_cI_A_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.88 Done - Shared
3154 0.82 cIV_C_40_cI_A_40_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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