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OPENSEQ.org
3lvk_B_C
Genes: A B A+B
Length: 394 81 446
Sequences: 18417 2108 238
Seq/Len: 46.74 26.02 0.53
MirrorTree (Pazo et al. 2001) 0.51
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 0.03 0.03 0.10
2 0.03 0.03 0.25
5 0.05 0.04 0.31
10 0.05 0.04 0.37
20 0.07 0.05 0.50
100 0.12 0.06 1.05
∞ 0.21 0.13 2.96
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
177_R 79_K 1.29 0.42 0.00
175_M 24_M 1.29 0.41 0.00
47_H 44_D 1.19 0.34 0.00
224_V 11_T 1.16 0.32 0.00
24_R 77_I 1.15 0.32 0.00
141_K 77_I 1.14 0.31 0.00
366_E 42_I 1.12 0.29 0.00
69_G 12_L 1.10 0.28 0.00
371_I 40_L 1.07 0.26 0.00
175_M 26_V 1.05 0.26 0.00
364_E 30_V 1.05 0.25 0.00
154_V 28_K 1.03 0.24 0.00
361_F 60_E 1.03 0.24 0.00
186_D 19_C 1.02 0.24 0.00
112_A 23_V 1.02 0.23 0.00
118_R 79_K 1.02 0.23 0.00
357_S 68_T 1.01 0.23 0.00
76_V 26_V 1.00 0.22 0.00
183_Y 12_L 0.99 0.22 0.00
67_L 30_V 0.99 0.22 0.00
104_I 52_I 0.98 0.21 0.00
272_E 52_I 0.98 0.21 0.00
46_S 56_C 0.97 0.21 0.00
103_I 79_K 0.96 0.21 0.00
65_A 55_F 0.95 0.20 0.00
56_A 64_V 0.95 0.20 0.00
265_A 39_L 0.94 0.20 0.00
50_G 37_E 0.94 0.19 0.00
187_A 36_G 0.92 0.18 0.00
222_L 47_A 0.92 0.18 0.00
218_G 13_D 0.91 0.18 0.00
13_L 39_L 0.91 0.18 0.00
198_L 63_L 0.90 0.17 0.00
195_P 11_T 0.89 0.17 0.00
186_D 20_P 0.89 0.17 0.00
168_D 41_I 0.88 0.17 0.00
137_I 30_V 0.88 0.17 0.00
204_D 77_I 0.88 0.16 0.00
80_G 55_F 0.87 0.16 0.00
68_V 57_T 0.87 0.16 0.00
189_Q 51_D 0.87 0.16 0.00
58_D 25_M 0.86 0.16 0.00
277_R 30_V 0.86 0.16 0.00
62_N 53_P 0.86 0.16 0.00
252_V 77_I 0.86 0.16 0.00
32_F 79_K 0.86 0.16 0.00
278_G 30_V 0.86 0.16 0.00
377_S 12_L 0.86 0.15 0.00
65_A 41_I 0.85 0.15 0.00
274_E 32_N 0.85 0.15 0.00
60_A 53_P 0.85 0.15 0.00
154_V 78_R 0.85 0.15 0.00
366_E 70_G 0.85 0.15 0.00
203_V 50_R 0.84 0.15 0.00
140_L 30_V 0.84 0.15 0.00
66_D 44_D 0.84 0.15 0.00
245_M 25_M 0.84 0.15 0.00
244_G 56_C 0.83 0.15 0.00
167_Q 48_T 0.83 0.14 0.00
27_E 62_E 0.83 0.14 0.00
89_I 68_T 0.83 0.14 0.00
319_L 24_M 0.83 0.14 0.00
40_G 26_V 0.82 0.14 0.00
41_N 52_I 0.82 0.14 0.00
203_V 53_P 0.82 0.14 0.00
21_V 10_H 0.81 0.14 0.00
24_R 52_I 0.81 0.14 0.00
23_P 31_R 0.81 0.14 0.00
270_A 21_E 0.81 0.14 0.00
131_A 37_E 0.81 0.14 0.00
147_M 11_T 0.80 0.13 0.00
31_Q 30_V 0.80 0.13 0.00
288_K 41_I 0.80 0.13 0.00
306_I 63_L 0.80 0.13 0.00
119_Q 39_L 0.80 0.13 0.00
351_H 48_T 0.79 0.13 0.00
87_L 17_L 0.79 0.13 0.00
52_Q 11_T 0.79 0.13 0.00
27_E 76_L 0.79 0.13 0.00
288_K 72_P 0.79 0.13 0.00
232_I 56_C 0.79 0.13 0.00
171_A 71_L 0.78 0.13 0.00
62_N 52_I 0.78 0.13 0.00
106_S 31_R 0.78 0.13 0.00
37_G 12_L 0.78 0.13 0.00
355_R 19_C 0.78 0.13 0.00
265_A 75_Y 0.78 0.13 0.00
262_Y 51_D 0.78 0.13 0.00
140_L 65_A 0.77 0.12 0.00
225_R 34_Q 0.77 0.12 0.00
364_E 12_L 0.77 0.12 0.00
261_A 36_G 0.77 0.12 0.00
112_A 52_I 0.77 0.12 0.00
140_L 63_L 0.77 0.12 0.00
105_T 12_L 0.77 0.12 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)
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