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OPENSEQ.org
cIV_B_20_cIII_cyt1_20_Pdenitr
Genes: A B A+B
Length: 252 263 492
Sequences: 4606 651 226
Seq/Len: 18.28 2.48 0.46
MirrorTree (Pazo et al. 2001) 0.18
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 0.01 0.02 0.01
20 0.01 0.02 0.02
100 0.02 0.02 0.07
∞ 0.04 0.02 0.44
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
59_R 94_I 1.45 0.50 0.00
185_I 141_L 1.36 0.43 0.00
245_G 236_I 1.28 0.37 0.00
176_A 210_T 1.27 0.37 0.00
51_L 243_A 1.21 0.33 0.00
238_K 74_D 1.15 0.29 0.00
113_V 224_M 1.12 0.27 0.00
77_I 99_T 1.10 0.26 0.00
60_F 59_S 1.07 0.24 0.00
114_I 130_R 1.03 0.22 0.00
189_A 135_G 1.03 0.22 0.00
185_I 254_Q 1.01 0.21 0.00
185_I 144_L 0.99 0.20 0.00
183_W 194_Q 0.98 0.20 0.00
17_G 33_F 0.97 0.19 0.00
24_S 161_Y 0.96 0.18 0.00
70_R 208_M 0.95 0.18 0.00
200_A 178_A 0.94 0.18 0.00
40_Y 249_N 0.94 0.17 0.00
114_I 137_Y 0.92 0.17 0.00
94_A 63_G 0.91 0.16 0.00
39_L 38_P 0.90 0.16 0.00
162_V 244_L 0.89 0.16 0.00
211_V 59_S 0.89 0.15 0.00
54_L 81_P 0.89 0.15 0.00
72_T 84_Q 0.89 0.15 0.00
245_G 90_A 0.88 0.15 0.00
208_Q 99_T 0.88 0.15 0.00
89_L 230_V 0.88 0.15 0.00
212_Y 161_Y 0.88 0.15 0.00
86_V 15_A 0.88 0.15 0.00
121_W 216_L 0.87 0.15 0.00
48_F 209_A 0.87 0.15 0.00
167_G 204_T 0.86 0.14 0.00
114_I 41_K 0.86 0.14 0.00
112_L 241_L 0.85 0.14 0.00
190_V 240_V 0.85 0.14 0.00
40_Y 85_V 0.85 0.14 0.00
185_I 32_S 0.84 0.14 0.00
23_A 76_G 0.84 0.14 0.00
25_S 250_K 0.84 0.14 0.00
199_I 115_S 0.84 0.14 0.00
195_V 59_S 0.84 0.14 0.00
188_F 251_K 0.83 0.13 0.00
47_I 235_V 0.83 0.13 0.00
61_N 44_Q 0.82 0.13 0.00
89_L 144_L 0.82 0.13 0.00
89_L 246_Y 0.82 0.13 0.00
176_A 60_A 0.82 0.13 0.00
236_Q 250_K 0.82 0.13 0.00
79_V 232_F 0.82 0.13 0.00
217_S 143_Q 0.82 0.13 0.00
166_V 38_P 0.81 0.13 0.00
167_G 59_S 0.81 0.13 0.00
167_G 47_L 0.81 0.13 0.00
180_I 179_F 0.81 0.13 0.00
87_L 240_V 0.81 0.13 0.00
90_V 81_P 0.81 0.13 0.00
116_A 187_A 0.80 0.12 0.00
237_E 245_L 0.79 0.12 0.00
233_A 175_H 0.78 0.12 0.00
116_A 209_A 0.78 0.12 0.00
235_S 154_I 0.78 0.12 0.00
246_A 243_A 0.78 0.12 0.00
200_A 63_G 0.77 0.11 0.00
114_I 63_G 0.77 0.11 0.00
67_V 102_D 0.77 0.11 0.00
99_I 136_P 0.77 0.11 0.00
161_P 217_M 0.77 0.11 0.00
72_T 155_H 0.77 0.11 0.00
185_I 93_D 0.77 0.11 0.00
72_T 219_T 0.76 0.11 0.00
44_A 240_V 0.76 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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