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OPENSEQ.org
cIV_B_40_cIII_cyt1_20_Pdenitr
Genes: A B A+B
Length: 252 263 492
Sequences: 4089 651 204
Seq/Len: 16.23 2.48 0.41
MirrorTree (Pazo et al. 2001) 0.24
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 0.40
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 1.94 0.79 0.06
183_W 194_Q 1.34 0.39 0.01
25_S 161_Y 1.28 0.35 0.01
245_G 236_I 1.26 0.34 0.01
167_G 204_T 1.26 0.34 0.01
28_A 256_I 1.26 0.33 0.01
190_V 240_V 1.23 0.31 0.01
70_R 208_M 1.22 0.31 0.01
185_I 144_L 1.18 0.29 0.01
84_V 42_F 1.13 0.25 0.01
182_A 187_A 1.10 0.24 0.01
233_A 175_H 1.10 0.24 0.01
72_T 219_T 1.10 0.24 0.01
189_A 135_G 1.09 0.23 0.01
245_G 90_A 1.08 0.23 0.01
17_G 33_F 1.07 0.22 0.01
117_I 38_P 1.06 0.22 0.01
200_A 178_A 1.06 0.22 0.01
23_A 76_G 1.06 0.22 0.01
213_F 153_Y 1.06 0.22 0.01
51_L 243_A 1.06 0.22 0.01
104_Q 147_G 1.03 0.20 0.00
238_K 59_S 1.02 0.20 0.00
143_A 205_V 1.02 0.20 0.00
116_A 187_A 1.00 0.19 0.00
117_I 80_L 0.99 0.19 0.00
77_I 99_T 0.99 0.18 0.00
233_A 152_E 0.98 0.18 0.00
59_R 94_I 0.97 0.18 0.00
209_E 242_A 0.96 0.17 0.00
185_I 93_D 0.96 0.17 0.00
170_V 56_E 0.96 0.17 0.00
171_L 52_Q 0.95 0.17 0.00
193_D 43_D 0.95 0.17 0.00
109_D 8_G 0.95 0.17 0.00
79_V 232_F 0.94 0.16 0.00
195_V 84_Q 0.93 0.16 0.00
130_D 240_V 0.93 0.16 0.00
172_V 100_E 0.93 0.16 0.00
129_N 230_V 0.93 0.16 0.00
170_V 131_A 0.92 0.16 0.00
87_L 240_V 0.92 0.16 0.00
188_F 143_Q 0.92 0.16 0.00
177_T 16_A 0.92 0.15 0.00
113_V 224_M 0.91 0.15 0.00
97_L 219_T 0.90 0.15 0.00
25_S 250_K 0.90 0.15 0.00
166_V 161_Y 0.90 0.15 0.00
26_P 94_I 0.90 0.15 0.00
233_A 212_V 0.90 0.15 0.00
18_M 41_K 0.89 0.15 0.00
212_Y 157_V 0.89 0.14 0.00
112_L 194_Q 0.89 0.14 0.00
94_A 63_G 0.88 0.14 0.00
235_S 154_I 0.88 0.14 0.00
47_I 209_A 0.87 0.14 0.00
57_I 84_Q 0.87 0.14 0.00
54_L 235_V 0.87 0.14 0.00
61_N 44_Q 0.86 0.14 0.00
236_Q 84_Q 0.86 0.14 0.00
118_G 20_G 0.86 0.14 0.00
162_V 154_I 0.86 0.13 0.00
93_G 86_R 0.85 0.13 0.00
114_I 130_R 0.85 0.13 0.00
54_L 81_P 0.85 0.13 0.00
187_A 74_D 0.85 0.13 0.00
180_I 179_F 0.85 0.13 0.00
117_I 229_Q 0.85 0.13 0.00
109_D 42_F 0.85 0.13 0.00
189_A 96_D 0.85 0.13 0.00
225_A 161_Y 0.85 0.13 0.00
176_A 256_I 0.84 0.13 0.00
76_P 52_Q 0.84 0.13 0.00
58_V 200_G 0.84 0.13 0.00
208_Q 144_L 0.84 0.13 0.00
84_V 256_I 0.84 0.13 0.00
89_L 246_Y 0.84 0.13 0.00
53_L 41_K 0.84 0.13 0.00
92_I 130_R 0.84 0.13 0.00
188_F 251_K 0.84 0.13 0.00
89_L 144_L 0.83 0.13 0.00
172_V 185_Q 0.83 0.13 0.00
168_K 177_A 0.83 0.12 0.00
48_F 56_E 0.83 0.12 0.00
176_A 210_T 0.83 0.12 0.00
237_E 245_L 0.83 0.12 0.00
148_G 86_R 0.83 0.12 0.00
106_M 54_Y 0.82 0.12 0.00
138_M 68_P 0.82 0.12 0.00
195_V 59_S 0.82 0.12 0.00
114_I 137_Y 0.82 0.12 0.00
48_F 209_A 0.81 0.12 0.00
53_L 246_Y 0.81 0.12 0.00
80_I 177_A 0.81 0.12 0.00
183_W 166_K 0.81 0.12 0.00
170_V 110_H 0.81 0.12 0.00
208_Q 110_H 0.80 0.12 0.00
26_P 142_S 0.80 0.12 0.00
245_G 67_V 0.80 0.12 0.00
40_Y 249_N 0.80 0.12 0.00
86_V 206_D 0.80 0.12 0.00
87_L 134_H 0.80 0.12 0.00
239_Y 144_L 0.80 0.12 0.00
161_P 208_M 0.80 0.12 0.00
86_V 15_A 0.80 0.11 0.00
211_V 59_S 0.79 0.11 0.00
99_I 136_P 0.79 0.11 0.00
44_A 25_A 0.79 0.11 0.00
208_Q 99_T 0.79 0.11 0.00
238_K 226_D 0.79 0.11 0.00
185_I 255_P 0.79 0.11 0.00
83_L 45_H 0.79 0.11 0.00
248_E 187_A 0.79 0.11 0.00
223_N 224_M 0.79 0.11 0.00
185_I 179_F 0.79 0.11 0.00
16_G 209_A 0.79 0.11 0.00
170_V 154_I 0.78 0.11 0.00
38_V 232_F 0.78 0.11 0.00
89_L 230_V 0.78 0.11 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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