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OPENSEQ.org
1jiw_A_B
Genes: A B A+B
Length: 470 99 560
Sequences: 159 105 53
Seq/Len: 0.34 1.06 0.09
MirrorTree (Pazo et al. 2001) 0.68
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 0.07 0.03 0.09
2 0.07 0.03 0.09
5 0.07 0.03 0.09
10 0.07 0.03 0.09
20 0.07 0.03 0.09
100 0.09 0.06 0.10
∞ 0.17 0.08 0.10
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
316_L 61_I 1.44 0.17 0.00
8_Q 46_W 1.43 0.17 0.00
228_G 43_L 1.41 0.17 0.00
283_V 47_L 1.33 0.14 0.00
292_L 53_A 1.33 0.14 0.00
120_G 72_M 1.31 0.14 0.00
383_E 25_D 1.31 0.14 0.00
266_E 67_G 1.30 0.14 0.00
340_L 57_T 1.29 0.14 0.00
254_T 73_L 1.28 0.13 0.00
375_T 5_A 1.26 0.13 0.00
236_L 65_E 1.26 0.13 0.00
51_G 46_W 1.25 0.13 0.00
271_S 5_A 1.24 0.12 0.00
435_D 63_L 1.21 0.12 0.00
307_E 1_A 1.20 0.12 0.00
397_S 93_V 1.20 0.12 0.00
378_Y 25_D 1.19 0.11 0.00
104_S 69_L 1.19 0.11 0.00
388_A 47_L 1.19 0.11 0.00
373_A 43_L 1.16 0.11 0.00
421_D 67_G 1.15 0.11 0.00
378_Y 39_D 1.14 0.10 0.00
139_L 92_L 1.14 0.10 0.00
292_L 46_W 1.12 0.10 0.00
346_A 21_L 1.12 0.10 0.00
225_D 55_R 1.10 0.10 0.00
18_R 82_Y 1.10 0.10 0.00
164_P 82_Y 1.10 0.10 0.00
212_S 82_Y 1.10 0.10 0.00
237_D 82_Y 1.10 0.10 0.00
364_A 47_L 1.09 0.10 0.00
254_T 55_R 1.09 0.10 0.00
379_G 10_L 1.08 0.09 0.00
266_E 52_R 1.08 0.09 0.00
258_V 67_G 1.08 0.09 0.00
228_G 55_R 1.07 0.09 0.00
46_W 74_L 1.07 0.09 0.00
85_F 38_G 1.07 0.09 0.00
107_T 59_A 1.07 0.09 0.00
392_L 59_A 1.07 0.09 0.00
378_Y 66_R 1.06 0.09 0.00
265_T 61_I 1.06 0.09 0.00
233_A 67_G 1.06 0.09 0.00
87_A 65_E 1.05 0.09 0.00
441_G 73_L 1.05 0.09 0.00
250_L 5_A 1.04 0.09 0.00
104_S 44_T 1.03 0.09 0.00
327_T 79_E 1.02 0.09 0.00
115_G 96_R 1.02 0.08 0.00
429_Q 71_L 1.01 0.08 0.00
38_Q 80_G 1.01 0.08 0.00
27_H 25_D 1.01 0.08 0.00
217_W 5_A 1.00 0.08 0.00
364_A 43_L 1.00 0.08 0.00
108_N 60_G 0.99 0.08 0.00
282_S 32_S 0.98 0.08 0.00
286_A 73_L 0.98 0.08 0.00
457_I 74_L 0.98 0.08 0.00
62_L 64_L 0.98 0.08 0.00
255_G 89_G 0.97 0.08 0.00
254_T 40_T 0.97 0.08 0.00
310_L 59_A 0.97 0.08 0.00
443_L 94_L 0.97 0.08 0.00
459_L 55_R 0.96 0.08 0.00
128_S 71_L 0.96 0.08 0.00
181_T 93_V 0.96 0.07 0.00
19_G 51_P 0.96 0.07 0.00
293_D 19_C 0.96 0.07 0.00
296_G 19_C 0.96 0.07 0.00
193_G 5_A 0.95 0.07 0.00
152_Y 92_L 0.95 0.07 0.00
62_L 57_T 0.94 0.07 0.00
434_Y 92_L 0.94 0.07 0.00
320_V 43_L 0.94 0.07 0.00
275_S 47_L 0.93 0.07 0.00
245_L 63_L 0.93 0.07 0.00
328_V 21_L 0.93 0.07 0.00
407_L 95_R 0.93 0.07 0.00
97_K 67_G 0.93 0.07 0.00
167_G 53_A 0.93 0.07 0.00
109_I 1_A 0.92 0.07 0.00
89_S 5_A 0.92 0.07 0.00
389_P 46_W 0.92 0.07 0.00
194_E 78_G 0.92 0.07 0.00
128_S 92_L 0.92 0.07 0.00
101_Q 56_P 0.92 0.07 0.00
138_F 7_Q 0.92 0.07 0.00
340_L 71_L 0.91 0.07 0.00
188_G 34_Y 0.91 0.07 0.00
210_A 92_L 0.91 0.07 0.00
34_Q 21_L 0.91 0.07 0.00
33_D 2_S 0.90 0.07 0.00
95_Q 82_Y 0.90 0.07 0.00
357_I 5_A 0.90 0.07 0.00
213_V 83_R 0.90 0.07 0.00
147_K 18_I 0.90 0.07 0.00
236_L 61_I 0.89 0.07 0.00
362_L 75_G 0.89 0.07 0.00
388_A 82_Y 0.89 0.07 0.00
217_W 25_D 0.89 0.07 0.00
401_K 19_C 0.89 0.07 0.00
109_I 2_S 0.89 0.07 0.00
341_I 40_T 0.89 0.07 0.00
383_E 75_G 0.89 0.07 0.00
385_S 69_L 0.89 0.07 0.00
31_T 1_A 0.89 0.07 0.00
226_F 89_G 0.88 0.07 0.00
127_F 25_D 0.88 0.07 0.00
53_S 95_R 0.88 0.07 0.00
203_T 20_H 0.88 0.07 0.00
468_I 74_L 0.88 0.07 0.00
297_F 92_L 0.88 0.07 0.00
108_N 56_P 0.88 0.07 0.00
362_L 25_D 0.88 0.07 0.00
235_L 74_L 0.88 0.07 0.00
327_T 7_Q 0.87 0.07 0.00
95_Q 94_L 0.87 0.07 0.00
226_F 3_D 0.87 0.06 0.00
383_E 5_A 0.87 0.06 0.00
235_L 36_L 0.87 0.06 0.00
427_A 49_S 0.86 0.06 0.00
282_S 39_D 0.86 0.06 0.00
325_G 28_V 0.86 0.06 0.00
327_T 14_E 0.86 0.06 0.00
364_A 82_Y 0.85 0.06 0.00
14_H 5_A 0.85 0.06 0.00
120_G 9_T 0.85 0.06 0.00
277_S 80_G 0.85 0.06 0.00
33_D 89_G 0.85 0.06 0.00
14_H 71_L 0.85 0.06 0.00
442_S 72_M 0.85 0.06 0.00
408_D 73_L 0.85 0.06 0.00
36_A 91_Q 0.85 0.06 0.00
433_S 9_T 0.85 0.06 0.00
137_A 14_E 0.85 0.06 0.00
195_G 5_A 0.85 0.06 0.00
232_S 80_G 0.85 0.06 0.00
113_D 67_G 0.85 0.06 0.00
265_T 12_Q 0.84 0.06 0.00
126_N 76_R 0.84 0.06 0.00
57_L 57_T 0.84 0.06 0.00
393_R 48_P 0.84 0.06 0.00
453_A 47_L 0.84 0.06 0.00
404_L 88_D 0.83 0.06 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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