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OPENSEQ.org
cIV_B_40_cIII_cyt1_40_Pdenitr
Genes: A B A+B
Length: 252 263 491
Sequences: 4089 570 156
Seq/Len: 16.23 2.17 0.32
MirrorTree (Pazo et al. 2001) 0.15
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 0.02 0.00
2 0.00 0.02 0.00
5 0.00 0.02 0.01
10 0.00 0.02 0.01
20 0.01 0.02 0.01
100 0.01 0.02 0.05
∞ 0.03 0.02 0.30
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
185_I 141_L 1.77 0.62 0.00
25_S 161_Y 1.54 0.46 0.00
70_R 208_M 1.41 0.37 0.00
172_V 185_Q 1.31 0.32 0.00
84_V 42_F 1.25 0.28 0.00
167_G 204_T 1.24 0.27 0.00
245_G 90_A 1.22 0.26 0.00
28_A 256_I 1.22 0.26 0.00
238_K 59_S 1.20 0.25 0.00
143_A 205_V 1.18 0.24 0.00
113_V 224_M 1.17 0.24 0.00
48_F 209_A 1.12 0.21 0.00
237_E 17_Q 1.10 0.20 0.00
116_A 187_A 1.09 0.20 0.00
53_L 246_Y 1.09 0.20 0.00
170_V 56_E 1.08 0.19 0.00
77_I 116_G 1.07 0.19 0.00
233_A 175_H 1.06 0.19 0.00
72_T 219_T 1.04 0.18 0.00
97_L 219_T 1.04 0.18 0.00
57_I 108_T 1.04 0.18 0.00
241_A 18_E 1.03 0.17 0.00
233_A 165_E 1.02 0.17 0.00
189_A 135_G 1.02 0.17 0.00
209_E 242_A 1.02 0.17 0.00
61_N 212_V 1.02 0.17 0.00
200_A 178_A 1.01 0.17 0.00
185_I 179_F 1.01 0.17 0.00
176_A 90_A 0.99 0.16 0.00
77_I 99_T 0.99 0.16 0.00
248_E 187_A 0.98 0.16 0.00
208_Q 60_A 0.98 0.15 0.00
47_I 209_A 0.97 0.15 0.00
58_V 212_V 0.97 0.15 0.00
130_D 240_V 0.97 0.15 0.00
195_V 59_S 0.96 0.15 0.00
51_L 94_I 0.96 0.15 0.00
84_V 213_A 0.96 0.15 0.00
180_I 179_F 0.95 0.15 0.00
200_A 147_G 0.95 0.14 0.00
223_N 69_L 0.95 0.14 0.00
117_I 38_P 0.95 0.14 0.00
189_A 96_D 0.94 0.14 0.00
117_I 77_G 0.94 0.14 0.00
231_V 157_V 0.94 0.14 0.00
185_I 255_P 0.94 0.14 0.00
170_V 110_H 0.94 0.14 0.00
172_V 100_E 0.94 0.14 0.00
208_Q 110_H 0.94 0.14 0.00
109_D 39_F 0.93 0.14 0.00
239_Y 85_V 0.93 0.14 0.00
177_T 16_A 0.92 0.14 0.00
182_A 187_A 0.92 0.14 0.00
114_I 41_K 0.92 0.13 0.00
176_A 210_T 0.92 0.13 0.00
93_G 86_R 0.91 0.13 0.00
41_I 134_H 0.91 0.13 0.00
138_M 68_P 0.90 0.13 0.00
83_L 59_S 0.90 0.13 0.00
225_A 161_Y 0.90 0.13 0.00
61_N 44_Q 0.90 0.13 0.00
109_D 8_G 0.89 0.13 0.00
94_A 63_G 0.89 0.13 0.00
238_K 74_D 0.89 0.12 0.00
15_N 17_Q 0.89 0.12 0.00
83_L 45_H 0.88 0.12 0.00
108_N 42_F 0.88 0.12 0.00
176_A 246_Y 0.88 0.12 0.00
86_V 15_A 0.88 0.12 0.00
182_A 100_E 0.88 0.12 0.00
241_A 240_V 0.88 0.12 0.00
80_I 187_A 0.88 0.12 0.00
17_G 33_F 0.88 0.12 0.00
94_A 55_T 0.87 0.12 0.00
18_M 41_K 0.87 0.12 0.00
83_L 81_P 0.87 0.12 0.00
161_P 208_M 0.87 0.12 0.00
34_L 220_A 0.87 0.12 0.00
109_D 42_F 0.87 0.12 0.00
55_I 42_F 0.86 0.12 0.00
223_N 224_M 0.86 0.12 0.00
211_V 59_S 0.86 0.12 0.00
48_F 56_E 0.85 0.12 0.00
116_A 213_A 0.85 0.11 0.00
162_V 154_I 0.85 0.11 0.00
173_Q 241_L 0.85 0.11 0.00
173_Q 149_G 0.84 0.11 0.00
53_L 41_K 0.84 0.11 0.00
208_Q 180_A 0.84 0.11 0.00
72_T 177_A 0.84 0.11 0.00
226_Y 132_G 0.84 0.11 0.00
166_V 187_A 0.84 0.11 0.00
237_E 134_H 0.84 0.11 0.00
31_Q 97_P 0.84 0.11 0.00
185_I 57_V 0.84 0.11 0.00
129_N 223_K 0.84 0.11 0.00
216_C 176_N 0.84 0.11 0.00
220_C 176_N 0.84 0.11 0.00
224_H 176_N 0.84 0.11 0.00
212_Y 66_Y 0.84 0.11 0.00
72_T 184_I 0.83 0.11 0.00
188_F 251_K 0.83 0.11 0.00
183_W 194_Q 0.83 0.11 0.00
80_I 177_A 0.83 0.11 0.00
146_D 59_S 0.83 0.11 0.00
40_Y 192_D 0.83 0.11 0.00
141_K 44_Q 0.83 0.11 0.00
87_L 134_H 0.82 0.11 0.00
212_Y 161_Y 0.82 0.11 0.00
63_R 130_R 0.82 0.11 0.00
245_G 236_I 0.82 0.11 0.00
39_L 88_Y 0.82 0.11 0.00
92_I 230_V 0.82 0.11 0.00
86_V 206_D 0.82 0.11 0.00
235_S 154_I 0.81 0.10 0.00
57_I 69_L 0.81 0.10 0.00
86_V 235_V 0.81 0.10 0.00
239_Y 144_L 0.81 0.10 0.00
118_G 20_G 0.81 0.10 0.00
59_R 204_T 0.81 0.10 0.00
167_G 42_F 0.81 0.10 0.00
38_V 232_F 0.80 0.10 0.00
75_T 204_T 0.80 0.10 0.00
41_I 42_F 0.80 0.10 0.00
176_A 191_S 0.80 0.10 0.00
58_V 161_Y 0.80 0.10 0.00
142_E 94_I 0.80 0.10 0.00
29_H 59_S 0.80 0.10 0.00
101_F 174_Y 0.80 0.10 0.00
240_E 74_D 0.80 0.10 0.00
206_V 77_G 0.80 0.10 0.00
230_V 147_G 0.80 0.10 0.00
26_P 94_I 0.80 0.10 0.00
137_L 81_P 0.79 0.10 0.00
59_R 94_I 0.79 0.10 0.00
54_L 235_V 0.79 0.10 0.00
22_P 27_H 0.79 0.10 0.00
112_L 194_Q 0.79 0.10 0.00
114_I 175_H 0.79 0.10 0.00
114_I 240_V 0.79 0.10 0.00
61_N 192_D 0.79 0.10 0.00
114_I 63_G 0.79 0.10 0.00
168_K 198_E 0.79 0.10 0.00
207_D 47_L 0.79 0.10 0.00
58_V 156_A 0.79 0.10 0.00
76_P 52_Q 0.79 0.10 0.00
245_G 235_V 0.79 0.10 0.00
172_V 162_D 0.78 0.10 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
3119 0.35 cIV_B_60_cIII_cyt1_20_Pdenitr Δgene:(1, ∞) A:(1E-60, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3118 0.46 cIV_B_20_cIII_cyt1_20_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3116 0.41 cIV_B_40_cIII_cyt1_20_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.06 Done - Shared
3115 0.67 cIV_B_40_cIII_cyt1_10_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3114 0.32 cIV_B_40_cIII_cyt1_40_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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