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OPENSEQ.org
cI_N_cIII_isp_Pdenitr
Genes: A B A+B
Length: 499 190 652
Sequences: 1133 1539 314
Seq/Len: 2.27 8.1 0.48
MirrorTree (Pazo et al. 2001) 0.68
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 0.00 0.01 0.00
2 0.00 0.01 0.00
5 0.00 0.01 0.00
10 0.00 0.01 0.00
20 0.02 0.01 0.01
100 0.03 0.01 0.04
∞ 0.03 0.04 0.46
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
308_F 39_V 1.49 0.54 0.00
128_T 28_T 1.44 0.50 0.00
51_A 27_G 1.39 0.47 0.00
113_A 95_G 1.27 0.38 0.00
425_V 129_I 1.22 0.34 0.00
414_S 184_D 1.20 0.33 0.00
342_I 56_V 1.20 0.33 0.00
423_R 73_G 1.09 0.26 0.00
166_L 42_M 1.05 0.24 0.00
408_V 87_Q 1.05 0.24 0.00
83_V 122_A 1.05 0.23 0.00
243_A 39_V 1.05 0.23 0.00
370_L 61_V 1.05 0.23 0.00
408_V 35_A 1.02 0.22 0.00
282_F 34_A 1.02 0.22 0.00
113_A 131_V 1.01 0.22 0.00
243_A 76_V 1.00 0.21 0.00
277_A 91_E 1.00 0.21 0.00
140_L 81_R 1.00 0.21 0.00
278_V 34_A 1.00 0.21 0.00
140_L 30_A 0.99 0.21 0.00
353_T 72_L 0.99 0.21 0.00
289_I 42_M 0.99 0.20 0.00
309_A 35_A 0.99 0.20 0.00
278_V 93_D 0.99 0.20 0.00
238_V 185_T 0.98 0.20 0.00
186_G 61_V 0.98 0.20 0.00
167_S 12_G 0.98 0.20 0.00
28_Y 8_A 0.98 0.20 0.00
66_G 18_F 0.97 0.20 0.00
167_S 150_W 0.96 0.19 0.00
275_A 55_Q 0.96 0.19 0.00
458_V 78_I 0.96 0.19 0.00
306_M 127_V 0.96 0.19 0.00
74_S 61_V 0.95 0.19 0.00
124_G 28_T 0.95 0.18 0.00
123_A 17_D 0.95 0.18 0.00
15_L 65_T 0.94 0.18 0.00
263_G 158_H 0.94 0.18 0.00
124_G 167_R 0.94 0.18 0.00
232_E 184_D 0.93 0.18 0.00
263_G 189_L 0.93 0.18 0.00
406_L 29_V 0.93 0.18 0.00
424_I 62_E 0.93 0.18 0.00
139_A 88_A 0.93 0.18 0.00
285_S 70_K 0.93 0.17 0.00
314_A 161_T 0.93 0.17 0.00
126_L 15_R 0.93 0.17 0.00
211_L 78_I 0.92 0.17 0.00
221_V 103_Q 0.92 0.17 0.00
468_S 76_V 0.92 0.17 0.00
73_F 168_G 0.92 0.17 0.00
279_M 183_D 0.91 0.17 0.00
232_E 42_M 0.90 0.17 0.00
221_V 101_S 0.90 0.16 0.00
297_L 145_G 0.90 0.16 0.00
165_S 78_I 0.90 0.16 0.00
306_M 86_I 0.89 0.16 0.00
63_A 53_S 0.89 0.16 0.00
401_A 80_R 0.89 0.16 0.00
91_M 27_G 0.89 0.16 0.00
194_I 52_A 0.88 0.16 0.00
316_G 174_L 0.88 0.16 0.00
118_M 123_G 0.88 0.15 0.00
280_S 127_V 0.87 0.15 0.00
336_I 90_R 0.87 0.15 0.00
323_N 42_M 0.87 0.15 0.00
336_I 38_L 0.87 0.15 0.00
429_Y 48_V 0.87 0.15 0.00
99_R 45_S 0.87 0.15 0.00
306_M 187_I 0.87 0.15 0.00
117_M 107_K 0.87 0.15 0.00
204_L 39_V 0.87 0.15 0.00
170_L 24_A 0.87 0.15 0.00
124_G 189_L 0.87 0.15 0.00
96_M 159_Y 0.87 0.15 0.00
343_L 26_A 0.86 0.15 0.00
147_R 159_Y 0.86 0.15 0.00
325_L 65_T 0.86 0.15 0.00
129_L 22_A 0.86 0.15 0.00
290_G 188_K 0.86 0.15 0.00
324_M 47_D 0.86 0.15 0.00
292_T 24_A 0.85 0.15 0.00
385_T 184_D 0.85 0.15 0.00
48_V 93_D 0.85 0.15 0.00
386_L 116_N 0.85 0.15 0.00
305_H 27_G 0.85 0.14 0.00
45_A 12_G 0.85 0.14 0.00
24_M 138_V 0.85 0.14 0.00
87_G 35_A 0.85 0.14 0.00
405_W 15_R 0.85 0.14 0.00
77_A 47_D 0.85 0.14 0.00
166_L 173_N 0.85 0.14 0.00
66_G 151_F 0.84 0.14 0.00
10_L 35_A 0.84 0.14 0.00
334_M 168_G 0.84 0.14 0.00
200_S 185_T 0.84 0.14 0.00
402_G 145_G 0.84 0.14 0.00
95_Y 52_A 0.84 0.14 0.00
143_V 92_V 0.84 0.14 0.00
370_L 105_S 0.84 0.14 0.00
227_T 126_L 0.83 0.14 0.00
393_G 28_T 0.83 0.14 0.00
96_M 66_Q 0.83 0.14 0.00
385_T 65_T 0.83 0.14 0.00
210_M 59_S 0.83 0.14 0.00
308_F 94_L 0.83 0.14 0.00
24_M 185_T 0.83 0.14 0.00
50_A 83_E 0.83 0.14 0.00
430_F 173_N 0.83 0.14 0.00
65_H 32_G 0.83 0.14 0.00
140_L 114_D 0.83 0.14 0.00
218_V 165_I 0.83 0.14 0.00
92_S 62_E 0.82 0.14 0.00
250_A 68_T 0.82 0.13 0.00
31_K 35_A 0.82 0.13 0.00
25_A 35_A 0.82 0.13 0.00
10_L 19_L 0.82 0.13 0.00
53_V 69_V 0.82 0.13 0.00
185_T 144_A 0.82 0.13 0.00
181_F 166_R 0.82 0.13 0.00
111_A 84_D 0.81 0.13 0.00
10_L 140_I 0.81 0.13 0.00
373_L 25_G 0.81 0.13 0.00
211_L 122_A 0.81 0.13 0.00
150_S 62_E 0.81 0.13 0.00
185_T 142_D 0.81 0.13 0.00
66_G 78_I 0.81 0.13 0.00
281_M 90_R 0.81 0.13 0.00
305_H 23_T 0.81 0.13 0.00
82_L 125_W 0.81 0.13 0.00
390_A 58_V 0.80 0.13 0.00
412_I 183_D 0.80 0.13 0.00
286_I 14_T 0.80 0.13 0.00
74_S 67_L 0.80 0.13 0.00
65_H 91_E 0.80 0.13 0.00
403_M 151_F 0.80 0.13 0.00
294_I 106_N 0.80 0.13 0.00
162_V 44_P 0.80 0.13 0.00
283_L 19_L 0.80 0.13 0.00
274_A 175_H 0.80 0.12 0.00
385_T 84_D 0.80 0.12 0.00
49_V 80_R 0.79 0.12 0.00
205_F 40_N 0.79 0.12 0.00
305_H 81_R 0.79 0.12 0.00
237_P 15_R 0.79 0.12 0.00
424_I 42_M 0.79 0.12 0.00
241_F 168_G 0.79 0.12 0.00
107_P 150_W 0.79 0.12 0.00
136_Q 150_W 0.79 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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