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OPENSEQ.org
cIV_B_40_cI_J_40_Pdenitr
Genes: A B A+B
Length: 252 200 442
Sequences: 4089 733 439
Seq/Len: 16.23 3.67 0.99
MirrorTree (Pazo et al. 2001) 0.16
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 0.09
5 0.00 0.00 0.17
10 0.00 0.00 0.31
20 0.01 0.00 0.37
100 0.01 0.00 0.44
∞ 0.03 0.00 0.97
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
237_E 40_A 1.76 0.90 0.31
176_A 41_A 1.62 0.83 0.22
97_L 32_W 1.45 0.73 0.14
44_A 41_A 1.43 0.71 0.13
80_I 82_L 1.35 0.65 0.11
34_L 76_D 1.34 0.64 0.10
112_L 173_K 1.33 0.64 0.10
162_V 138_V 1.30 0.61 0.09
233_A 166_M 1.29 0.60 0.09
170_V 4_F 1.24 0.56 0.07
153_E 57_V 1.24 0.55 0.07
180_I 145_L 1.23 0.55 0.07
164_V 166_M 1.21 0.53 0.07
116_A 143_Y 1.21 0.52 0.07
57_I 147_F 1.20 0.52 0.07
185_I 108_F 1.16 0.48 0.06
170_V 159_I 1.16 0.48 0.06
243_L 92_L 1.15 0.47 0.05
20_F 12_S 1.12 0.45 0.05
83_L 41_A 1.11 0.43 0.05
170_V 77_V 1.09 0.41 0.04
180_I 56_L 1.08 0.41 0.04
114_I 107_A 1.07 0.40 0.04
53_L 159_I 1.07 0.40 0.04
97_L 44_F 1.06 0.39 0.04
172_V 77_V 1.06 0.39 0.04
143_A 12_S 1.06 0.39 0.04
92_I 27_V 1.05 0.38 0.04
128_P 64_V 1.05 0.38 0.04
72_T 7_Y 1.04 0.37 0.04
188_F 151_G 1.03 0.36 0.04
185_I 107_A 1.03 0.36 0.03
92_I 17_G 1.02 0.35 0.03
114_I 147_F 1.01 0.35 0.03
15_N 173_K 1.01 0.35 0.03
41_I 36_A 1.01 0.35 0.03
190_V 97_G 1.00 0.34 0.03
243_L 150_A 0.99 0.33 0.03
212_Y 142_R 0.96 0.31 0.03
20_F 47_Q 0.96 0.31 0.03
31_Q 142_R 0.96 0.30 0.03
111_D 21_V 0.96 0.30 0.03
138_M 74_M 0.95 0.30 0.03
119_H 55_L 0.94 0.29 0.03
180_I 45_V 0.94 0.29 0.03
153_E 59_V 0.93 0.28 0.02
170_V 145_L 0.93 0.28 0.02
56_C 135_L 0.93 0.28 0.02
19_N 93_A 0.92 0.27 0.02
55_I 64_V 0.92 0.27 0.02
68_P 72_V 0.91 0.27 0.02
60_F 13_A 0.91 0.27 0.02
110_P 32_W 0.91 0.27 0.02
45_V 139_L 0.91 0.27 0.02
114_I 157_A 0.90 0.26 0.02
134_F 135_L 0.90 0.26 0.02
172_V 15_V 0.90 0.26 0.02
19_N 27_V 0.89 0.25 0.02
205_S 29_S 0.89 0.25 0.02
237_E 174_R 0.88 0.25 0.02
239_Y 172_V 0.88 0.25 0.02
50_C 157_A 0.88 0.25 0.02
230_V 42_G 0.88 0.25 0.02
180_I 66_V 0.88 0.25 0.02
44_A 47_Q 0.88 0.25 0.02
225_A 44_F 0.88 0.24 0.02
239_Y 166_M 0.87 0.24 0.02
243_L 156_V 0.87 0.24 0.02
246_A 92_L 0.87 0.24 0.02
42_I 100_L 0.87 0.24 0.02
133_A 72_V 0.87 0.24 0.02
163_V 150_A 0.86 0.24 0.02
176_A 153_V 0.86 0.23 0.02
183_W 110_G 0.86 0.23 0.02
241_A 92_L 0.86 0.23 0.02
176_A 129_V 0.86 0.23 0.02
239_Y 20_V 0.85 0.23 0.02
11_G 21_V 0.85 0.23 0.02
43_T 140_Y 0.85 0.23 0.02
243_L 167_R 0.85 0.23 0.02
56_C 38_L 0.85 0.22 0.02
190_V 9_F 0.84 0.22 0.02
203_W 24_R 0.84 0.22 0.02
231_V 74_M 0.84 0.22 0.02
114_I 149_L 0.84 0.22 0.02
206_V 27_V 0.84 0.22 0.02
130_D 77_V 0.83 0.21 0.01
77_I 135_L 0.83 0.21 0.01
207_D 122_A 0.83 0.21 0.01
112_L 123_A 0.82 0.21 0.01
22_P 96_I 0.82 0.21 0.01
226_Y 162_I 0.82 0.21 0.01
98_P 56_L 0.82 0.21 0.01
141_K 39_S 0.82 0.20 0.01
108_N 49_A 0.81 0.20 0.01
112_L 88_R 0.81 0.20 0.01
208_Q 191_L 0.81 0.20 0.01
173_Q 147_F 0.81 0.20 0.01
49_V 69_L 0.81 0.20 0.01
173_Q 61_V 0.81 0.20 0.01
245_G 150_A 0.81 0.20 0.01
235_S 21_V 0.81 0.20 0.01
211_V 10_A 0.81 0.20 0.01
88_I 90_L 0.81 0.20 0.01
114_I 17_G 0.81 0.20 0.01
240_E 148_Q 0.81 0.20 0.01
83_L 25_N 0.80 0.20 0.01
54_L 77_V 0.80 0.20 0.01
207_D 64_V 0.80 0.20 0.01
237_E 18_F 0.80 0.20 0.01
27_L 17_G 0.80 0.20 0.01
212_Y 92_L 0.80 0.19 0.01
103_S 17_G 0.80 0.19 0.01
161_P 132_T 0.80 0.19 0.01
243_L 42_G 0.79 0.19 0.01
173_Q 172_V 0.79 0.19 0.01
212_Y 148_Q 0.79 0.19 0.01
170_V 157_A 0.79 0.19 0.01
202_L 27_V 0.79 0.19 0.01
207_D 183_R 0.79 0.19 0.01
72_T 49_A 0.79 0.19 0.01
212_Y 170_K 0.79 0.19 0.01
170_V 16_A 0.78 0.19 0.01
192_Q 34_I 0.78 0.18 0.01
48_F 75_L 0.78 0.18 0.01
238_K 46_L 0.78 0.18 0.01
163_V 148_Q 0.78 0.18 0.01
188_F 61_V 0.78 0.18 0.01
29_H 181_M 0.78 0.18 0.01
231_V 57_V 0.78 0.18 0.01
27_L 21_V 0.78 0.18 0.01
116_A 125_V 0.78 0.18 0.01
237_E 126_D 0.78 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
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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