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OPENSEQ.org
PopN - PscB
Genes: A B A+B
Length: 288 140 383
Sequences: 121 821 116
Seq/Len: 0.42 5.86 0.3
MirrorTree (Pazo et al. 2001) 0.63
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.01 0.02 0.03
2 0.01 0.05 0.11
5 0.01 0.08 0.13
10 0.01 0.10 0.16
20 0.01 0.19 0.22
100 0.01 0.22 0.25
∞ 0.02 0.24 0.27
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
115_L 9_A 1.74 0.58 0.00
239_S 110_L 1.45 0.39 0.00
67_L 36_L 1.43 0.37 0.00
51_T 121_A 1.36 0.33 0.00
121_G 90_L 1.23 0.26 0.00
256_M 5_L 1.23 0.26 0.00
155_Q 43_L 1.21 0.25 0.00
242_S 43_L 1.20 0.24 0.00
136_A 111_A 1.19 0.24 0.00
220_T 49_L 1.18 0.23 0.00
96_K 110_L 1.17 0.23 0.00
188_D 35_L 1.17 0.23 0.00
193_R 92_L 1.16 0.22 0.00
288_F 106_L 1.12 0.20 0.00
125_E 113_Q 1.11 0.20 0.00
62_L 9_A 1.10 0.20 0.00
180_E 7_G 1.09 0.19 0.00
190_Q 90_L 1.08 0.19 0.00
93_S 52_A 1.07 0.18 0.00
31_G 71_V 1.06 0.18 0.00
260_R 87_D 1.06 0.18 0.00
126_I 9_A 1.06 0.18 0.00
62_L 52_A 1.05 0.18 0.00
114_Q 83_V 1.05 0.18 0.00
143_R 45_L 1.04 0.17 0.00
170_L 12_L 1.04 0.17 0.00
159_R 113_Q 1.03 0.17 0.00
170_L 81_A 1.03 0.17 0.00
47_A 45_L 1.02 0.16 0.00
149_M 43_L 1.02 0.16 0.00
149_M 15_G 1.01 0.16 0.00
259_L 118_E 0.99 0.15 0.00
237_L 109_A 0.98 0.15 0.00
142_G 114_V 0.98 0.15 0.00
41_Q 49_L 0.98 0.15 0.00
99_A 42_D 0.98 0.15 0.00
255_D 45_L 0.97 0.15 0.00
248_K 70_R 0.97 0.15 0.00
198_D 122_P 0.96 0.14 0.00
67_L 124_L 0.96 0.14 0.00
198_D 104_E 0.95 0.14 0.00
258_K 29_I 0.95 0.14 0.00
217_F 101_L 0.95 0.14 0.00
122_F 5_L 0.95 0.14 0.00
265_L 38_R 0.94 0.14 0.00
94_Q 110_L 0.94 0.14 0.00
252_V 94_A 0.94 0.14 0.00
26_G 27_L 0.94 0.14 0.00
126_I 2_D 0.94 0.14 0.00
98_E 49_L 0.94 0.14 0.00
64_K 55_D 0.94 0.14 0.00
229_L 23_G 0.94 0.14 0.00
123_S 12_L 0.94 0.14 0.00
39_V 59_D 0.94 0.14 0.00
140_L 29_I 0.94 0.14 0.00
206_L 66_A 0.93 0.13 0.00
92_E 67_L 0.92 0.13 0.00
56_E 8_L 0.92 0.13 0.00
65_R 64_L 0.92 0.13 0.00
51_T 45_L 0.92 0.13 0.00
259_L 124_L 0.91 0.13 0.00
192_L 43_L 0.91 0.13 0.00
200_V 36_L 0.91 0.13 0.00
227_A 5_L 0.91 0.13 0.00
116_S 102_D 0.91 0.13 0.00
143_R 97_G 0.91 0.13 0.00
128_Q 25_Y 0.91 0.13 0.00
87_R 110_L 0.91 0.13 0.00
138_D 26_H 0.90 0.12 0.00
36_Y 95_R 0.90 0.12 0.00
267_E 110_L 0.90 0.12 0.00
74_L 31_G 0.90 0.12 0.00
229_L 15_G 0.90 0.12 0.00
232_A 106_L 0.90 0.12 0.00
111_S 19_A 0.90 0.12 0.00
155_Q 45_L 0.90 0.12 0.00
68_S 110_L 0.89 0.12 0.00
158_L 100_G 0.89 0.12 0.00
235_A 90_L 0.89 0.12 0.00
238_D 32_Q 0.89 0.12 0.00
169_E 6_S 0.89 0.12 0.00
158_L 29_I 0.89 0.12 0.00
212_D 25_Y 0.89 0.12 0.00
43_L 68_L 0.89 0.12 0.00
69_D 86_A 0.88 0.12 0.00
234_S 12_L 0.88 0.12 0.00
192_L 45_L 0.88 0.12 0.00
221_P 95_R 0.88 0.12 0.00
55_S 60_Q 0.88 0.12 0.00
193_R 43_L 0.88 0.12 0.00
157_L 92_L 0.87 0.12 0.00
66_R 125_E 0.87 0.12 0.00
200_V 53_P 0.87 0.12 0.00
119_L 45_L 0.87 0.12 0.00
27_G 34_V 0.87 0.12 0.00
255_D 96_L 0.87 0.12 0.00
224_R 88_G 0.86 0.11 0.00
120_E 34_V 0.86 0.11 0.00
55_S 66_A 0.86 0.11 0.00
259_L 75_S 0.86 0.11 0.00
173_R 43_L 0.86 0.11 0.00
30_Q 41_D 0.86 0.11 0.00
134_S 110_L 0.85 0.11 0.00
237_L 69_S 0.85 0.11 0.00
252_V 24_S 0.85 0.11 0.00
234_S 122_P 0.85 0.11 0.00
267_E 25_Y 0.85 0.11 0.00
197_R 72_A 0.85 0.11 0.00
121_G 7_G 0.85 0.11 0.00
90_D 29_I 0.85 0.11 0.00
32_E 33_S 0.84 0.11 0.00
115_L 15_G 0.84 0.11 0.00
152_L 87_D 0.84 0.11 0.00
61_S 47_S 0.84 0.11 0.00
153_V 103_P 0.84 0.11 0.00
172_L 68_L 0.84 0.11 0.00
246_P 36_L 0.84 0.11 0.00
46_A 103_P 0.84 0.11 0.00
163_E 113_Q 0.84 0.11 0.00
111_S 14_Q 0.83 0.11 0.00
153_V 108_R 0.83 0.11 0.00
161_A 5_L 0.83 0.10 0.00
127_S 47_S 0.83 0.10 0.00
50_L 30_D 0.83 0.10 0.00
249_L 59_D 0.83 0.10 0.00
166_L 76_R 0.83 0.10 0.00
147_R 22_T 0.83 0.10 0.00
168_I 84_L 0.83 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
9187 0.3 PopN - PscB Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: HHblits (2015_06) 0.00 Done - Shared
9184 0.31 PopN - PscB Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) 0.00 Done - Shared
9179 0.23 PopN - PscB Δgene:(1, ∞) A:(1E-10, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.00 Done - Shared
9158 0.04 PopN - PscB Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) Killed - Shared
9154 0.02 PopN - PscB Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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