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OPENSEQ.org
cIV_B_20_cI_J_40_Pdenitr
Genes: A B A+B
Length: 252 200 441
Sequences: 4606 733 485
Seq/Len: 18.28 3.67 1.1
MirrorTree (Pazo et al. 2001) 0.10
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 0.04
2 0.00 0.00 0.08
5 0.00 0.00 0.17
10 0.01 0.00 0.31
20 0.01 0.00 0.38
100 0.02 0.00 0.46
∞ 0.04 0.00 1.07
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
176_A 41_A 1.56 0.83 0.07
97_L 32_W 1.39 0.72 0.04
44_A 41_A 1.32 0.66 0.04
34_L 76_D 1.26 0.60 0.03
170_V 159_I 1.26 0.60 0.03
153_E 57_V 1.25 0.59 0.03
114_I 29_S 1.18 0.53 0.02
237_E 40_A 1.18 0.53 0.02
54_L 21_V 1.16 0.51 0.02
112_L 173_K 1.12 0.48 0.02
94_A 198_Q 1.07 0.42 0.02
57_I 147_F 1.06 0.41 0.02
233_A 166_M 1.05 0.41 0.02
170_V 77_V 1.01 0.37 0.01
180_I 145_L 1.01 0.37 0.01
83_L 41_A 1.00 0.36 0.01
172_V 77_V 0.99 0.36 0.01
180_I 56_L 0.99 0.35 0.01
185_I 139_L 0.99 0.35 0.01
194_A 138_V 0.98 0.35 0.01
243_L 92_L 0.98 0.34 0.01
128_P 64_V 0.98 0.34 0.01
192_Q 34_I 0.96 0.33 0.01
97_L 44_F 0.96 0.33 0.01
163_V 148_Q 0.96 0.33 0.01
92_I 27_V 0.96 0.33 0.01
212_Y 159_I 0.96 0.33 0.01
72_T 7_Y 0.95 0.32 0.01
114_I 170_K 0.95 0.32 0.01
132_V 77_V 0.95 0.32 0.01
88_I 90_L 0.93 0.30 0.01
41_I 36_A 0.92 0.29 0.01
164_V 34_I 0.92 0.29 0.01
138_M 74_M 0.91 0.29 0.01
92_I 17_G 0.91 0.29 0.01
112_L 105_G 0.90 0.28 0.01
249_E 95_V 0.90 0.28 0.01
75_T 40_A 0.90 0.28 0.01
112_L 125_V 0.89 0.27 0.01
153_E 59_V 0.89 0.27 0.01
185_I 108_F 0.88 0.27 0.01
84_V 142_R 0.88 0.26 0.01
162_V 138_V 0.88 0.26 0.01
188_F 151_G 0.88 0.26 0.01
211_V 93_A 0.88 0.26 0.01
206_V 27_V 0.88 0.26 0.01
55_I 64_V 0.87 0.26 0.01
116_A 143_Y 0.87 0.26 0.01
114_I 149_L 0.87 0.26 0.01
212_Y 94_L 0.86 0.25 0.01
162_V 189_M 0.85 0.24 0.01
56_C 47_Q 0.85 0.24 0.01
64_A 28_H 0.85 0.24 0.01
176_A 153_V 0.84 0.24 0.01
83_L 54_M 0.84 0.24 0.01
190_V 97_G 0.84 0.24 0.01
203_W 24_R 0.84 0.24 0.01
39_L 135_L 0.84 0.24 0.01
19_N 93_A 0.84 0.24 0.01
195_V 97_G 0.83 0.23 0.01
243_L 42_G 0.83 0.23 0.01
204_F 143_Y 0.82 0.23 0.01
119_H 55_L 0.82 0.23 0.01
80_I 135_L 0.82 0.22 0.01
176_A 141_D 0.82 0.22 0.01
225_A 44_F 0.81 0.22 0.01
19_N 27_V 0.81 0.22 0.01
39_L 89_Y 0.81 0.22 0.01
84_V 149_L 0.81 0.22 0.01
76_P 17_G 0.81 0.22 0.01
117_I 128_A 0.81 0.21 0.01
243_L 150_A 0.81 0.21 0.01
108_N 49_A 0.81 0.21 0.01
114_I 96_I 0.81 0.21 0.01
219_L 84_G 0.80 0.21 0.01
54_L 95_V 0.80 0.21 0.01
170_V 4_F 0.80 0.21 0.01
182_A 132_T 0.80 0.21 0.01
130_D 77_V 0.80 0.21 0.01
87_L 24_R 0.80 0.21 0.01
173_Q 172_V 0.80 0.21 0.01
111_D 156_V 0.80 0.21 0.01
161_P 191_L 0.79 0.20 0.01
68_P 41_A 0.79 0.20 0.01
17_G 24_R 0.79 0.20 0.01
112_L 123_A 0.79 0.20 0.01
164_V 166_M 0.79 0.20 0.01
164_V 44_F 0.79 0.20 0.01
98_P 56_L 0.79 0.20 0.01
239_Y 20_V 0.79 0.20 0.01
109_D 45_V 0.78 0.20 0.01
34_L 81_E 0.78 0.20 0.01
244_A 122_A 0.78 0.20 0.01
180_I 66_V 0.78 0.20 0.01
207_D 183_R 0.78 0.20 0.01
87_L 55_L 0.78 0.20 0.01
49_V 69_L 0.78 0.20 0.01
98_P 57_V 0.78 0.19 0.01
170_V 12_S 0.77 0.19 0.01
239_Y 166_M 0.77 0.19 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
3238 0.58 cIV_B_40_cI_J_60_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3237 0.92 cIV_B_40_cI_J_40_Pdenitr Δgene:(1, ∞) A:(1E-60, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.04 Done - Shared
3236 0.99 cIV_B_40_cI_J_40_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.31 Done - Shared
3235 2.02 cIV_B_40_cI_J_10_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.13 Done - Shared
3234 2 cIV_B_40_cI_J_20_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.14 Done - Shared
3233 1.1 cIV_B_20_cI_J_40_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
3232 2.3 cIV_B_20_cI_J_20_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.12 Done - Shared
3231 2.3 cIV_B_4_cI_J_20_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.05 Done - Shared
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