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OPENSEQ.org
cIV_C_6_cI_A_20_Pdenitr
Genes: A B A+B
Length: 273 121 371
Sequences: 2876 4481 2399
Seq/Len: 10.53 37.03 6.47
MirrorTree (Pazo et al. 2001) 0.63
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 4.29
2 0.00 0.00 4.46
5 0.00 0.00 4.82
10 0.00 0.00 5.09
20 0.00 0.00 5.29
100 0.00 0.01 5.39
∞ 0.01 0.02 6.09
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 1.66 1.00 0.94
22_I 80_L 1.45 0.99 0.87
196_A 32_I 1.19 0.95 0.70
80_P 87_F 1.10 0.92 0.62
6_H 66_V 1.09 0.91 0.61
13_P 84_A 1.07 0.90 0.59
26_V 117_A 1.07 0.90 0.59
13_P 78_A 1.05 0.89 0.57
18_F 78_A 1.01 0.86 0.52
177_V 16_G 0.99 0.84 0.50
107_A 62_R 0.96 0.81 0.46
21_A 79_F 0.95 0.81 0.45
138_W 62_R 0.95 0.81 0.45
22_I 89_S 0.94 0.80 0.44
54_G 78_A 0.93 0.79 0.43
183_V 11_I 0.91 0.77 0.40
55_L 19_S 0.91 0.76 0.40
54_G 68_I 0.91 0.76 0.40
99_M 66_V 0.90 0.76 0.39
121_P 99_M 0.89 0.74 0.37
160_H 64_Y 0.88 0.74 0.37
56_V 23_I 0.86 0.71 0.34
49_W 15_L 0.86 0.70 0.34
87_Q 113_W 0.85 0.70 0.34
121_P 84_A 0.85 0.70 0.33
146_L 62_R 0.85 0.70 0.33
143_I 104_V 0.85 0.70 0.33
139_H 61_V 0.83 0.67 0.31
39_T 27_L 0.83 0.67 0.31
84_I 17_M 0.83 0.67 0.31
228_F 103_A 0.83 0.66 0.30
180_I 20_A 0.82 0.66 0.30
54_G 28_A 0.82 0.65 0.30
109_I 72_I 0.82 0.65 0.30
18_F 95_F 0.82 0.65 0.29
10_I 45_Y 0.81 0.64 0.29
158_A 111_Y 0.81 0.64 0.29
153_V 62_R 0.81 0.63 0.28
169_K 100_V 0.80 0.63 0.28
190_A 67_S 0.80 0.62 0.27
99_M 79_F 0.80 0.62 0.27
13_P 101_F 0.78 0.60 0.26
125_G 62_R 0.78 0.60 0.26
240_T 106_T 0.77 0.58 0.25
21_A 45_Y 0.76 0.57 0.24
33_A 69_L 0.76 0.57 0.24
240_T 75_L 0.76 0.56 0.23
32_V 19_S 0.76 0.56 0.23
33_A 119_E 0.76 0.56 0.23
28_L 80_L 0.75 0.56 0.23
205_Y 105_L 0.75 0.56 0.23
20_G 68_I 0.75 0.55 0.23
172_I 23_I 0.75 0.55 0.22
221_I 30_A 0.74 0.54 0.22
138_W 78_A 0.73 0.52 0.21
203_T 92_D 0.73 0.52 0.21
182_G 64_Y 0.73 0.52 0.21
203_T 72_I 0.73 0.52 0.21
8_Y 22_A 0.72 0.51 0.20
150_L 81_F 0.72 0.51 0.20
146_L 69_L 0.71 0.50 0.19
172_I 16_G 0.71 0.50 0.19
242_K 55_A 0.71 0.50 0.19
87_Q 55_A 0.71 0.49 0.19
98_V 65_L 0.71 0.49 0.19
52_L 21_L 0.71 0.48 0.19
182_G 60_D 0.70 0.48 0.18
54_G 83_W 0.70 0.48 0.18
140_L 43_S 0.70 0.47 0.18
183_V 100_V 0.70 0.47 0.18
31_A 37_P 0.69 0.47 0.18
183_V 15_L 0.69 0.46 0.17
265_F 28_A 0.69 0.46 0.17
23_G 42_V 0.69 0.46 0.17
64_G 61_V 0.69 0.46 0.17
21_A 29_A 0.69 0.46 0.17
191_Y 66_V 0.69 0.46 0.17
155_V 43_S 0.69 0.45 0.17
102_V 86_S 0.68 0.45 0.17
208_A 92_D 0.68 0.45 0.17
194_S 78_A 0.68 0.44 0.16
75_T 64_Y 0.67 0.43 0.16
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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