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OPENSEQ.org
ompa-ompw
Genes: A B A+B
Length: 353 206 536
Sequences: 2440 993 243
Seq/Len: 6.91 4.82 0.45
MirrorTree (Pazo et al. 2001) 0.58
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 0.05 0.02 0.00
2 0.06 0.03 0.01
5 0.06 0.04 0.01
10 0.07 0.04 0.01
20 0.08 0.04 0.01
100 0.09 0.06 0.04
∞ 0.12 0.09 0.43
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
301_R 91_D 1.29 0.37 0.00
284_A 107_P 1.28 0.37 0.00
57_D 136_D 1.20 0.31 0.00
292_V 154_V 1.16 0.29 0.00
268_D 201_G 1.14 0.28 0.00
119_I 201_G 1.10 0.25 0.00
271_G 131_A 1.05 0.23 0.00
267_T 160_P 1.04 0.22 0.00
54_E 145_K 1.04 0.22 0.00
310_D 178_S 1.04 0.22 0.00
236_S 37_V 1.02 0.21 0.00
161_A 168_V 1.02 0.21 0.00
129_H 167_G 1.01 0.21 0.00
98_K 61_H 1.00 0.20 0.00
158_L 125_I 1.00 0.20 0.00
264_E 160_P 0.97 0.19 0.00
154_A 108_T 0.96 0.18 0.00
146_T 154_V 0.95 0.18 0.00
233_T 201_G 0.95 0.18 0.00
191_L 197_V 0.95 0.18 0.00
164_L 109_I 0.94 0.17 0.00
233_T 82_L 0.94 0.17 0.00
136_D 160_P 0.94 0.17 0.00
323_A 103_K 0.93 0.17 0.00
317_K 154_V 0.93 0.17 0.00
18_A 111_A 0.92 0.17 0.00
84_G 146_E 0.92 0.17 0.00
187_L 133_I 0.92 0.17 0.00
236_S 16_K 0.92 0.16 0.00
299_A 18_A 0.91 0.16 0.00
67_I 100_A 0.91 0.16 0.00
194_H 125_I 0.91 0.16 0.00
235_K 144_V 0.91 0.16 0.00
36_Q 44_I 0.90 0.16 0.00
151_G 198_Y 0.90 0.16 0.00
205_A 148_F 0.90 0.16 0.00
160_D 92_V 0.89 0.15 0.00
209_P 193_I 0.89 0.15 0.00
292_V 166_W 0.89 0.15 0.00
154_A 168_V 0.88 0.15 0.00
212_V 154_V 0.88 0.15 0.00
299_A 42_S 0.87 0.15 0.00
297_V 136_D 0.87 0.15 0.00
2_K 202_Y 0.87 0.14 0.00
69_L 160_P 0.87 0.14 0.00
302_L 73_F 0.86 0.14 0.00
232_D 122_T 0.86 0.14 0.00
77_A 182_T 0.86 0.14 0.00
117_S 168_V 0.85 0.14 0.00
292_V 201_G 0.85 0.14 0.00
192_G 81_E 0.85 0.14 0.00
121_P 125_I 0.84 0.14 0.00
69_L 193_I 0.84 0.14 0.00
276_N 126_G 0.84 0.14 0.00
276_N 155_G 0.84 0.14 0.00
283_R 126_G 0.84 0.14 0.00
283_R 155_G 0.84 0.14 0.00
303_S 19_L 0.84 0.13 0.00
195_L 168_V 0.83 0.13 0.00
187_L 96_G 0.83 0.13 0.00
258_N 18_A 0.83 0.13 0.00
65_L 197_V 0.83 0.13 0.00
192_G 174_Y 0.83 0.13 0.00
281_L 15_F 0.82 0.13 0.00
20_A 27_S 0.82 0.13 0.00
332_I 65_F 0.82 0.13 0.00
332_I 27_S 0.82 0.13 0.00
57_D 13_K 0.82 0.13 0.00
7_A 190_D 0.82 0.13 0.00
150_A 15_F 0.82 0.13 0.00
285_N 15_F 0.82 0.13 0.00
266_H 104_Q 0.82 0.13 0.00
8_L 196_F 0.82 0.13 0.00
297_V 99_V 0.82 0.13 0.00
62_G 87_P 0.82 0.13 0.00
262_R 180_E 0.81 0.13 0.00
152_V 16_K 0.81 0.13 0.00
62_G 204_Y 0.81 0.13 0.00
57_D 202_Y 0.81 0.13 0.00
284_A 134_P 0.81 0.12 0.00
169_R 183_L 0.81 0.12 0.00
169_R 33_G 0.80 0.12 0.00
286_S 143_K 0.80 0.12 0.00
266_H 198_Y 0.80 0.12 0.00
137_L 197_V 0.80 0.12 0.00
231_F 126_G 0.80 0.12 0.00
231_F 155_G 0.80 0.12 0.00
246_I 162_D 0.80 0.12 0.00
79_Y 32_A 0.80 0.12 0.00
256_Y 121_F 0.80 0.12 0.00
175_D 67_P 0.80 0.12 0.00
249_V 171_D 0.79 0.12 0.00
317_K 39_F 0.79 0.12 0.00
219_L 69_V 0.79 0.12 0.00
134_I 145_K 0.79 0.12 0.00
159_N 47_S 0.79 0.12 0.00
263_I 91_D 0.79 0.12 0.00
152_V 20_V 0.79 0.12 0.00
159_N 141_A 0.78 0.12 0.00
222_D 59_A 0.78 0.12 0.00
280_S 96_G 0.78 0.12 0.00
115_Y 194_N 0.78 0.12 0.00
92_G 136_D 0.78 0.12 0.00
63_A 37_V 0.78 0.12 0.00
302_L 79_S 0.77 0.11 0.00
72_W 39_F 0.77 0.11 0.00
241_Q 148_F 0.77 0.11 0.00
62_G 40_G 0.77 0.11 0.00
274_K 18_A 0.76 0.11 0.00
14_A 200_L 0.76 0.11 0.00
267_T 168_V 0.76 0.11 0.00
70_T 170_V 0.76 0.11 0.00
272_P 156_F 0.76 0.11 0.00
186_G 191_L 0.76 0.11 0.00
89_L 154_V 0.76 0.11 0.00
312_P 79_S 0.76 0.11 0.00
262_R 181_V 0.76 0.11 0.00
78_E 109_I 0.75 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
3087 0.01 ompa-ompw Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) Killed - Shared
3085 0.45 ompa-ompw Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3083 0.47 ompa-ompw Δgene:(1, ∞) A:(1E-10, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3082 0.01 ompa-ompw Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) Killed - Shared
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