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OPENSEQ.org
Complexe NarX-NarL
Genes: A B A+B
Length: 598 216 799
Sequences: 712 37243 344
Seq/Len: 1.19 172.42 0.43
MirrorTree (Pazo et al. 2001) 0.77
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 0.00 0.01 0.35
2 0.00 0.02 0.36
5 0.00 0.04 0.37
10 0.00 0.07 0.39
20 0.00 0.11 0.42
100 0.01 0.21 0.61
∞ 0.08 0.26 0.80
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
246_Q 11_L 1.70 0.66 0.00
462_R 32_I 1.45 0.48 0.00
360_Q 114_E 1.36 0.41 0.00
464_A 39_S 1.32 0.39 0.00
456_L 68_L 1.29 0.37 0.00
384_Q 185_S 1.25 0.34 0.00
258_L 60_L 1.22 0.32 0.00
108_N 83_I 1.21 0.31 0.00
538_G 102_G 1.20 0.31 0.00
451_T 157_T 1.18 0.30 0.00
343_I 84_V 1.18 0.29 0.00
123_V 74_L 1.18 0.29 0.00
223_L 177_A 1.17 0.29 0.00
161_V 11_L 1.17 0.28 0.00
156_H 191_V 1.15 0.28 0.00
539_C 9_I 1.15 0.28 0.00
385_L 11_L 1.15 0.28 0.00
429_E 9_I 1.15 0.27 0.00
534_V 76_E 1.13 0.26 0.00
495_Q 141_S 1.13 0.26 0.00
408_C 120_L 1.12 0.26 0.00
112_P 36_G 1.12 0.26 0.00
540_G 109_K 1.11 0.25 0.00
552_G 109_K 1.11 0.25 0.00
461_L 185_S 1.11 0.25 0.00
459_P 11_L 1.09 0.24 0.00
195_R 132_E 1.09 0.24 0.00
567_C 22_V 1.09 0.24 0.00
536_D 109_K 1.09 0.24 0.00
509_N 109_K 1.09 0.24 0.00
445_L 113_P 1.08 0.24 0.00
220_S 161_R 1.06 0.23 0.00
15_V 22_V 1.06 0.23 0.00
14_Q 210_V 1.05 0.22 0.00
577_T 172_P 1.04 0.22 0.00
230_L 184_E 1.04 0.21 0.00
514_S 10_L 1.04 0.21 0.00
241_L 71_L 1.04 0.21 0.00
534_V 8_T 1.03 0.21 0.00
431_L 132_E 1.03 0.21 0.00
534_V 33_T 1.03 0.21 0.00
143_R 74_L 1.03 0.21 0.00
272_L 60_L 1.03 0.21 0.00
299_E 83_I 1.03 0.21 0.00
495_Q 157_T 1.02 0.21 0.00
198_T 114_E 1.02 0.20 0.00
36_L 185_S 1.02 0.20 0.00
540_G 67_G 1.01 0.20 0.00
552_G 67_G 1.01 0.20 0.00
429_E 34_V 1.01 0.20 0.00
254_A 95_V 1.01 0.20 0.00
503_A 113_P 1.01 0.20 0.00
502_I 159_R 1.00 0.20 0.00
540_G 59_D 0.99 0.19 0.00
552_G 59_D 0.99 0.19 0.00
536_D 67_G 0.99 0.19 0.00
509_N 67_G 0.99 0.19 0.00
557_R 167_I 0.99 0.19 0.00
177_R 123_A 0.99 0.19 0.00
405_S 193_H 0.99 0.19 0.00
93_D 34_V 0.99 0.19 0.00
472_Y 181_D 0.98 0.19 0.00
578_E 27_S 0.98 0.18 0.00
450_T 11_L 0.98 0.18 0.00
536_D 59_D 0.97 0.18 0.00
491_V 198_M 0.97 0.18 0.00
509_N 59_D 0.97 0.18 0.00
512_K 102_G 0.97 0.18 0.00
286_L 85_V 0.97 0.18 0.00
217_N 100_K 0.96 0.18 0.00
95_Q 185_S 0.95 0.17 0.00
445_L 192_K 0.95 0.17 0.00
152_V 162_D 0.95 0.17 0.00
276_Q 9_I 0.94 0.17 0.00
246_Q 199_K 0.94 0.17 0.00
346_A 205_E 0.94 0.17 0.00
152_V 163_I 0.94 0.17 0.00
199_Q 22_V 0.94 0.17 0.00
331_K 69_E 0.94 0.17 0.00
195_R 194_M 0.94 0.17 0.00
438_L 112_E 0.94 0.17 0.00
161_V 85_V 0.94 0.17 0.00
443_A 182_I 0.94 0.17 0.00
90_A 31_D 0.93 0.17 0.00
333_R 45_I 0.93 0.16 0.00
26_G 191_V 0.93 0.16 0.00
420_G 85_V 0.92 0.16 0.00
259_H 44_G 0.92 0.16 0.00
151_T 213_E 0.92 0.16 0.00
142_D 12_I 0.92 0.16 0.00
171_I 83_I 0.91 0.16 0.00
480_V 161_R 0.91 0.16 0.00
63_A 130_L 0.91 0.16 0.00
210_A 9_I 0.91 0.16 0.00
411_M 9_I 0.91 0.15 0.00
271_V 85_V 0.90 0.15 0.00
397_E 157_T 0.90 0.15 0.00
338_H 62_M 0.90 0.15 0.00
217_N 45_I 0.90 0.15 0.00
534_V 167_I 0.90 0.15 0.00
573_E 8_T 0.90 0.15 0.00
334_L 93_E 0.90 0.15 0.00
194_H 55_L 0.90 0.15 0.00
341_Y 26_I 0.90 0.15 0.00
471_E 98_A 0.90 0.15 0.00
365_L 193_H 0.89 0.15 0.00
413_V 154_N 0.89 0.15 0.00
504_R 16_P 0.89 0.15 0.00
431_L 91_H 0.89 0.15 0.00
502_I 11_L 0.89 0.15 0.00
250_F 142_L 0.88 0.15 0.00
583_F 16_P 0.88 0.15 0.00
64_V 84_V 0.88 0.15 0.00
563_L 22_V 0.88 0.15 0.00
501_Q 157_T 0.88 0.15 0.00
10_T 179_R 0.88 0.15 0.00
580_V 83_I 0.88 0.14 0.00
569_V 55_L 0.88 0.14 0.00
373_L 75_R 0.88 0.14 0.00
107_R 83_I 0.88 0.14 0.00
512_K 103_A 0.87 0.14 0.00
503_A 27_S 0.87 0.14 0.00
58_Y 94_D 0.87 0.14 0.00
502_I 41_G 0.87 0.14 0.00
445_L 24_Q 0.87 0.14 0.00
271_V 194_M 0.87 0.14 0.00
472_Y 86_F 0.87 0.14 0.00
165_L 136_P 0.87 0.14 0.00
273_N 198_M 0.87 0.14 0.00
147_M 117_L 0.87 0.14 0.00
414_S 192_K 0.87 0.14 0.00
193_S 34_V 0.86 0.14 0.00
275_L 9_I 0.86 0.14 0.00
540_G 102_G 0.86 0.14 0.00
552_G 102_G 0.86 0.14 0.00
397_E 75_R 0.86 0.14 0.00
310_D 213_E 0.86 0.14 0.00
444_Q 110_D 0.86 0.14 0.00
540_G 14_D 0.86 0.14 0.00
552_G 14_D 0.86 0.14 0.00
372_T 23_K 0.86 0.14 0.00
217_N 185_S 0.85 0.14 0.00
445_L 110_D 0.85 0.14 0.00
534_V 99_L 0.85 0.14 0.00
407_S 131_S 0.85 0.14 0.00
178_L 46_E 0.85 0.14 0.00
235_Q 120_L 0.85 0.14 0.00
272_L 103_A 0.85 0.14 0.00
70_D 35_V 0.85 0.14 0.00
62_A 32_I 0.85 0.14 0.00
370_T 36_G 0.85 0.14 0.00
411_M 157_T 0.85 0.13 0.00
563_L 10_L 0.85 0.13 0.00
221_A 35_V 0.85 0.13 0.00
420_G 87_S 0.85 0.13 0.00
512_K 13_D 0.84 0.13 0.00
236_E 35_V 0.84 0.13 0.00
536_D 102_G 0.84 0.13 0.00
27_L 35_V 0.84 0.13 0.00
420_G 162_D 0.84 0.13 0.00
365_L 95_V 0.84 0.13 0.00
509_N 102_G 0.84 0.13 0.00
541_V 7_A 0.84 0.13 0.00
378_H 11_L 0.84 0.13 0.00
47_I 99_L 0.83 0.13 0.00
536_D 14_D 0.83 0.13 0.00
509_N 14_D 0.83 0.13 0.00
165_L 84_V 0.83 0.13 0.00
538_G 109_K 0.83 0.13 0.00
255_N 72_D 0.83 0.13 0.00
366_V 87_S 0.83 0.13 0.00
272_L 178_R 0.83 0.13 0.00
114_L 69_E 0.83 0.13 0.00
113_A 22_V 0.83 0.13 0.00
465_L 9_I 0.83 0.13 0.00
496_A 185_S 0.83 0.13 0.00
388_M 206_A 0.83 0.13 0.00
503_A 209_W 0.83 0.13 0.00
410_K 192_K 0.83 0.13 0.00
116_R 72_D 0.83 0.13 0.00
507_L 44_G 0.82 0.13 0.00
242_E 79_L 0.82 0.13 0.00
215_A 57_L 0.82 0.12 0.00
175_R 9_I 0.82 0.12 0.00
435_R 44_G 0.82 0.12 0.00
431_L 84_V 0.82 0.12 0.00
149_I 205_E 0.82 0.12 0.00
242_E 181_D 0.82 0.12 0.00
512_K 114_E 0.82 0.12 0.00
403_A 188_K 0.82 0.12 0.00
20_L 56_I 0.82 0.12 0.00
11_L 9_I 0.82 0.12 0.00
465_L 65_M 0.81 0.12 0.00
537_N 99_L 0.81 0.12 0.00
439_N 205_E 0.81 0.12 0.00
491_V 159_R 0.81 0.12 0.00
475_K 86_F 0.81 0.12 0.00
217_N 41_G 0.81 0.12 0.00
453_R 25_L 0.81 0.12 0.00
471_E 209_W 0.81 0.12 0.00
346_A 95_V 0.81 0.12 0.00
143_R 55_L 0.81 0.12 0.00
450_T 135_T 0.81 0.12 0.00
187_A 98_A 0.81 0.12 0.00
129_Q 74_L 0.81 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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