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OPENSEQ.org
cIV_B_40_cI_J_60_Pdenitr
Genes: A B A+B
Length: 252 200 442
Sequences: 4089 494 257
Seq/Len: 16.23 2.47 0.58
MirrorTree (Pazo et al. 2001) 0.23
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 0.01
2 0.00 0.00 0.02
5 0.00 0.00 0.02
10 0.00 0.00 0.03
20 0.01 0.00 0.04
100 0.01 0.00 0.08
∞ 0.03 0.00 0.57
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
111_D 21_V 1.44 0.56 0.00
170_V 4_F 1.35 0.49 0.00
112_L 173_K 1.24 0.40 0.00
20_F 12_S 1.21 0.38 0.00
80_I 82_L 1.19 0.36 0.00
244_A 159_I 1.13 0.32 0.00
233_A 166_M 1.12 0.32 0.00
176_A 76_D 1.12 0.31 0.00
22_P 96_I 1.11 0.31 0.00
188_F 151_G 1.08 0.29 0.00
92_I 17_G 1.06 0.27 0.00
91_A 14_C 1.04 0.26 0.00
232_K 186_A 1.04 0.26 0.00
91_A 17_G 1.03 0.26 0.00
241_A 99_V 1.02 0.25 0.00
94_A 198_Q 1.02 0.25 0.00
80_I 17_G 1.01 0.24 0.00
170_V 23_G 1.01 0.24 0.00
27_L 21_V 1.00 0.24 0.00
180_I 145_L 1.00 0.24 0.00
209_E 135_L 0.99 0.23 0.00
244_A 122_A 0.98 0.23 0.00
80_I 16_A 0.98 0.23 0.00
162_V 138_V 0.98 0.23 0.00
143_A 12_S 0.98 0.22 0.00
114_I 134_G 0.97 0.22 0.00
231_V 177_V 0.97 0.22 0.00
167_G 132_T 0.97 0.22 0.00
176_A 129_V 0.97 0.22 0.00
152_D 138_V 0.94 0.20 0.00
58_V 77_V 0.94 0.20 0.00
114_I 17_G 0.93 0.20 0.00
90_V 138_V 0.93 0.20 0.00
141_K 39_S 0.93 0.20 0.00
64_A 42_G 0.92 0.19 0.00
212_Y 186_A 0.91 0.19 0.00
17_G 24_R 0.91 0.19 0.00
52_L 153_V 0.91 0.19 0.00
167_G 114_S 0.90 0.18 0.00
41_I 130_E 0.90 0.18 0.00
31_Q 55_L 0.90 0.18 0.00
129_N 136_G 0.90 0.18 0.00
239_Y 166_M 0.89 0.18 0.00
91_A 170_K 0.89 0.18 0.00
161_P 52_V 0.89 0.18 0.00
231_V 29_S 0.88 0.18 0.00
62_R 124_P 0.88 0.17 0.00
31_Q 115_D 0.88 0.17 0.00
199_I 134_G 0.88 0.17 0.00
61_N 148_Q 0.88 0.17 0.00
139_L 146_M 0.87 0.17 0.00
79_V 15_V 0.86 0.17 0.00
38_V 130_E 0.86 0.17 0.00
53_L 153_V 0.86 0.17 0.00
112_L 123_A 0.85 0.16 0.00
20_F 156_V 0.85 0.16 0.00
184_T 83_K 0.85 0.16 0.00
237_E 16_A 0.85 0.16 0.00
27_L 17_G 0.85 0.16 0.00
176_A 149_L 0.85 0.16 0.00
202_L 97_G 0.84 0.16 0.00
11_G 36_A 0.84 0.16 0.00
124_S 58_V 0.84 0.16 0.00
21_Q 159_I 0.84 0.16 0.00
53_L 135_L 0.84 0.16 0.00
246_A 108_F 0.84 0.16 0.00
219_L 173_K 0.84 0.16 0.00
231_V 57_V 0.84 0.16 0.00
69_A 104_L 0.83 0.15 0.00
128_P 199_G 0.83 0.15 0.00
60_F 13_A 0.83 0.15 0.00
235_S 9_F 0.82 0.15 0.00
44_A 144_V 0.82 0.15 0.00
112_L 22_I 0.82 0.15 0.00
55_I 58_V 0.82 0.15 0.00
59_R 99_V 0.82 0.15 0.00
239_Y 135_L 0.81 0.15 0.00
47_I 98_V 0.81 0.15 0.00
79_V 93_A 0.81 0.15 0.00
246_A 96_I 0.81 0.14 0.00
47_I 43_L 0.81 0.14 0.00
212_Y 92_L 0.81 0.14 0.00
154_Y 87_A 0.81 0.14 0.00
40_Y 95_V 0.80 0.14 0.00
77_I 29_S 0.80 0.14 0.00
23_A 42_G 0.80 0.14 0.00
162_V 189_M 0.80 0.14 0.00
167_G 179_E 0.80 0.14 0.00
58_V 168_H 0.80 0.14 0.00
58_V 102_A 0.79 0.14 0.00
31_Q 182_W 0.79 0.14 0.00
131_G 153_V 0.79 0.14 0.00
84_V 77_V 0.79 0.14 0.00
176_A 153_V 0.79 0.14 0.00
114_I 22_I 0.79 0.14 0.00
76_P 17_G 0.78 0.13 0.00
226_Y 162_I 0.78 0.13 0.00
75_T 30_V 0.78 0.13 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
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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