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OPENSEQ.org
PopN - PscB
Genes: A B A+B
Length: 288 140 381
Sequences: 120 402 88
Seq/Len: 0.42 2.87 0.23
MirrorTree (Pazo et al. 2001) 0.52
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 0.03 0.00
2 0.01 0.06 0.00
5 0.01 0.12 0.01
10 0.01 0.13 0.07
20 0.01 0.15 0.14
100 0.01 0.22 0.18
∞ 0.02 0.26 0.21
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
157_L 106_L 1.44 0.32 0.00
136_A 111_A 1.34 0.27 0.00
79_A 82_I 1.27 0.23 0.00
164_Q 49_L 1.22 0.21 0.00
217_F 101_L 1.21 0.20 0.00
217_F 23_G 1.18 0.20 0.00
98_E 49_L 1.12 0.17 0.00
224_R 8_L 1.11 0.17 0.00
196_Y 68_L 1.11 0.17 0.00
96_K 8_L 1.10 0.17 0.00
147_R 22_T 1.08 0.16 0.00
90_D 88_G 1.07 0.15 0.00
59_E 114_V 1.06 0.15 0.00
171_G 92_L 1.06 0.15 0.00
207_S 110_L 1.05 0.15 0.00
256_M 92_L 1.05 0.15 0.00
64_K 90_L 1.04 0.15 0.00
232_A 23_G 1.04 0.14 0.00
127_S 47_S 1.03 0.14 0.00
216_R 90_L 1.03 0.14 0.00
125_E 116_L 1.01 0.14 0.00
200_V 76_R 1.01 0.14 0.00
157_L 92_L 1.01 0.14 0.00
104_L 88_G 1.01 0.14 0.00
127_S 45_L 1.01 0.14 0.00
114_Q 98_L 1.00 0.13 0.00
225_V 112_A 1.00 0.13 0.00
163_E 43_L 1.00 0.13 0.00
145_E 8_L 0.99 0.13 0.00
239_S 113_Q 0.99 0.13 0.00
213_I 37_L 0.99 0.13 0.00
263_G 101_L 0.98 0.13 0.00
134_S 43_L 0.98 0.13 0.00
106_S 9_A 0.98 0.13 0.00
253_M 15_G 0.98 0.13 0.00
172_L 68_L 0.97 0.13 0.00
232_A 85_D 0.97 0.13 0.00
145_E 83_V 0.97 0.12 0.00
226_V 68_L 0.96 0.12 0.00
269_V 5_L 0.96 0.12 0.00
150_L 51_H 0.96 0.12 0.00
43_L 22_T 0.96 0.12 0.00
277_V 61_Q 0.96 0.12 0.00
26_G 15_G 0.95 0.12 0.00
205_G 77_R 0.95 0.12 0.00
168_I 114_V 0.94 0.12 0.00
46_A 4_L 0.94 0.12 0.00
264_G 8_L 0.93 0.12 0.00
239_S 110_L 0.93 0.12 0.00
268_Q 83_V 0.93 0.11 0.00
134_S 5_L 0.93 0.11 0.00
62_L 9_A 0.92 0.11 0.00
220_T 21_R 0.92 0.11 0.00
115_L 9_A 0.92 0.11 0.00
49_E 82_I 0.92 0.11 0.00
168_I 84_L 0.92 0.11 0.00
252_V 120_L 0.91 0.11 0.00
199_A 13_G 0.91 0.11 0.00
99_A 114_V 0.91 0.11 0.00
107_G 7_G 0.91 0.11 0.00
81_L 47_S 0.91 0.11 0.00
205_G 70_R 0.91 0.11 0.00
141_A 41_D 0.90 0.11 0.00
184_A 116_L 0.90 0.11 0.00
70_A 21_R 0.90 0.11 0.00
245_D 9_A 0.90 0.11 0.00
85_W 34_V 0.90 0.11 0.00
68_S 9_A 0.89 0.11 0.00
96_K 30_D 0.89 0.10 0.00
213_I 68_L 0.89 0.10 0.00
193_R 68_L 0.89 0.10 0.00
274_Q 16_P 0.89 0.10 0.00
174_I 27_L 0.89 0.10 0.00
202_D 5_L 0.89 0.10 0.00
145_E 77_R 0.89 0.10 0.00
239_S 85_D 0.88 0.10 0.00
170_L 113_Q 0.88 0.10 0.00
80_M 38_R 0.88 0.10 0.00
264_G 2_D 0.88 0.10 0.00
262_L 82_I 0.87 0.10 0.00
121_G 106_L 0.87 0.10 0.00
209_A 76_R 0.87 0.10 0.00
132_A 30_D 0.87 0.10 0.00
140_L 29_I 0.86 0.10 0.00
87_R 16_P 0.86 0.10 0.00
213_I 25_Y 0.86 0.10 0.00
253_M 36_L 0.86 0.10 0.00
157_L 44_L 0.85 0.10 0.00
120_E 117_L 0.85 0.10 0.00
64_K 110_L 0.85 0.10 0.00
247_V 41_D 0.85 0.10 0.00
213_I 1_M 0.85 0.10 0.00
234_S 122_P 0.85 0.10 0.00
179_A 67_L 0.85 0.10 0.00
264_G 120_L 0.84 0.10 0.00
269_V 44_L 0.84 0.09 0.00
167_E 43_L 0.84 0.09 0.00
71_H 10_T 0.84 0.09 0.00
235_A 86_A 0.84 0.09 0.00
197_R 81_A 0.84 0.09 0.00
177_L 64_L 0.84 0.09 0.00
222_L 64_L 0.83 0.09 0.00
131_L 14_Q 0.83 0.09 0.00
125_E 92_L 0.83 0.09 0.00
43_L 68_L 0.83 0.09 0.00
90_D 17_F 0.83 0.09 0.00
49_E 85_D 0.83 0.09 0.00
46_A 39_Q 0.83 0.09 0.00
49_E 30_D 0.83 0.09 0.00
252_V 24_S 0.83 0.09 0.00
246_P 110_L 0.82 0.09 0.00
272_L 103_P 0.82 0.09 0.00
222_L 34_V 0.82 0.09 0.00
260_R 49_L 0.82 0.09 0.00
52_F 68_L 0.82 0.09 0.00
175_E 113_Q 0.82 0.09 0.00
219_A 43_L 0.82 0.09 0.00
212_D 68_L 0.81 0.09 0.00
164_Q 64_L 0.81 0.09 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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