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OPENSEQ.org
MSX_D12_Ths
Genes: A B A+B
Length: 474 192 625
Sequences: 115 121 58
Seq/Len: 0.24 0.63 0.09
MirrorTree (Pazo et al. 2001) 0.21
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 0.04 0.09
2 0.00 0.04 0.09
5 0.00 0.07 0.09
10 0.00 0.07 0.09
20 0.00 0.07 0.09
100 0.00 0.07 0.09
∞ 0.00 0.07 0.09
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
448_F 22_V 1.49 0.19 0.00
176_Y 3_K 1.41 0.17 0.00
78_N 106_D 1.35 0.15 0.00
285_L 114_K 1.34 0.15 0.00
204_I 100_H 1.34 0.15 0.00
52_D 62_L 1.31 0.14 0.00
405_S 117_N 1.27 0.13 0.00
318_I 179_V 1.27 0.13 0.00
259_I 45_D 1.25 0.13 0.00
469_V 164_G 1.25 0.12 0.00
35_Y 88_K 1.22 0.12 0.00
326_V 95_K 1.22 0.12 0.00
285_L 55_K 1.21 0.12 0.00
274_I 176_Y 1.19 0.11 0.00
465_I 182_D 1.17 0.11 0.00
351_I 74_S 1.16 0.11 0.00
353_R 105_K 1.15 0.11 0.00
128_V 177_D 1.15 0.10 0.00
125_I 69_C 1.14 0.10 0.00
380_I 119_F 1.12 0.10 0.00
421_I 69_C 1.12 0.10 0.00
263_N 11_Y 1.11 0.10 0.00
126_A 19_V 1.11 0.10 0.00
469_V 59_N 1.11 0.10 0.00
169_Y 62_L 1.09 0.10 0.00
402_F 62_L 1.09 0.10 0.00
469_V 177_D 1.08 0.09 0.00
12_F 48_K 1.08 0.09 0.00
465_I 90_I 1.08 0.09 0.00
224_K 40_A 1.06 0.09 0.00
370_R 91_E 1.06 0.09 0.00
228_R 102_N 1.05 0.09 0.00
376_T 188_S 1.05 0.09 0.00
201_L 61_G 1.05 0.09 0.00
316_F 84_Y 1.05 0.09 0.00
465_I 72_I 1.04 0.09 0.00
374_T 100_H 1.04 0.09 0.00
309_K 106_D 1.04 0.09 0.00
261_L 75_Q 1.03 0.09 0.00
50_G 25_H 1.03 0.09 0.00
65_Y 105_K 1.02 0.09 0.00
398_V 191_V 1.02 0.08 0.00
201_L 51_D 1.02 0.08 0.00
422_A 82_V 1.01 0.08 0.00
197_T 185_N 1.00 0.08 0.00
208_V 13_D 1.00 0.08 0.00
283_V 27_V 0.99 0.08 0.00
53_V 48_K 0.99 0.08 0.00
29_L 179_V 0.98 0.08 0.00
234_E 74_S 0.98 0.08 0.00
84_E 81_W 0.98 0.08 0.00
12_F 96_I 0.98 0.08 0.00
50_G 56_R 0.98 0.08 0.00
61_S 62_L 0.98 0.08 0.00
393_V 22_V 0.97 0.08 0.00
217_R 39_D 0.97 0.08 0.00
91_L 192_N 0.97 0.08 0.00
186_S 96_I 0.97 0.08 0.00
32_S 121_Y 0.96 0.08 0.00
469_V 7_F 0.96 0.08 0.00
292_Y 59_N 0.96 0.08 0.00
157_S 192_N 0.96 0.08 0.00
283_V 175_V 0.96 0.08 0.00
212_Y 7_F 0.96 0.08 0.00
217_R 25_H 0.95 0.07 0.00
430_N 74_S 0.95 0.07 0.00
39_A 19_V 0.95 0.07 0.00
299_H 124_Y 0.95 0.07 0.00
409_N 101_I 0.94 0.07 0.00
55_K 22_V 0.94 0.07 0.00
285_L 59_N 0.94 0.07 0.00
133_K 110_N 0.94 0.07 0.00
39_A 109_G 0.93 0.07 0.00
283_V 15_I 0.93 0.07 0.00
243_K 35_A 0.93 0.07 0.00
223_I 103_A 0.93 0.07 0.00
81_I 11_Y 0.93 0.07 0.00
261_L 45_D 0.92 0.07 0.00
144_A 93_G 0.92 0.07 0.00
225_K 89_S 0.92 0.07 0.00
273_R 4_R 0.92 0.07 0.00
419_G 117_N 0.91 0.07 0.00
49_I 112_K 0.91 0.07 0.00
262_N 62_L 0.91 0.07 0.00
351_I 189_S 0.91 0.07 0.00
55_K 181_D 0.91 0.07 0.00
281_K 179_V 0.91 0.07 0.00
338_L 111_I 0.91 0.07 0.00
470_E 84_Y 0.90 0.07 0.00
261_L 66_S 0.90 0.07 0.00
96_K 74_S 0.90 0.07 0.00
351_I 61_G 0.89 0.07 0.00
217_R 97_I 0.89 0.07 0.00
376_T 5_V 0.89 0.07 0.00
404_I 51_D 0.89 0.07 0.00
169_Y 177_D 0.89 0.07 0.00
141_K 186_K 0.89 0.07 0.00
156_P 124_Y 0.89 0.07 0.00
84_E 110_N 0.89 0.07 0.00
365_W 23_R 0.88 0.07 0.00
429_V 91_E 0.88 0.07 0.00
135_L 72_I 0.88 0.07 0.00
158_E 113_S 0.88 0.07 0.00
60_V 60_G 0.88 0.07 0.00
348_D 5_V 0.88 0.07 0.00
449_G 11_Y 0.88 0.07 0.00
283_V 106_D 0.88 0.07 0.00
419_G 118_P 0.88 0.07 0.00
258_T 116_P 0.87 0.07 0.00
43_E 107_K 0.87 0.07 0.00
222_L 62_L 0.87 0.07 0.00
415_V 93_G 0.87 0.07 0.00
383_Y 80_R 0.87 0.07 0.00
378_V 45_D 0.87 0.07 0.00
106_Y 55_K 0.87 0.07 0.00
23_I 99_I 0.87 0.06 0.00
465_I 190_W 0.87 0.06 0.00
367_K 99_I 0.87 0.06 0.00
449_G 179_V 0.87 0.06 0.00
215_D 100_H 0.87 0.06 0.00
283_V 112_K 0.86 0.06 0.00
106_Y 39_D 0.86 0.06 0.00
313_R 51_D 0.86 0.06 0.00
328_S 26_W 0.86 0.06 0.00
204_I 84_Y 0.85 0.06 0.00
258_T 191_V 0.85 0.06 0.00
156_P 66_S 0.85 0.06 0.00
33_V 1_M 0.85 0.06 0.00
317_N 83_R 0.85 0.06 0.00
8_F 191_V 0.85 0.06 0.00
400_S 186_K 0.85 0.06 0.00
117_K 64_N 0.84 0.06 0.00
262_N 186_K 0.84 0.06 0.00
95_H 23_R 0.84 0.06 0.00
160_V 66_S 0.84 0.06 0.00
274_I 190_W 0.84 0.06 0.00
147_Y 101_I 0.84 0.06 0.00
398_V 87_M 0.84 0.06 0.00
419_G 115_G 0.84 0.06 0.00
171_I 108_Y 0.83 0.06 0.00
425_L 102_N 0.83 0.06 0.00
94_N 105_K 0.83 0.06 0.00
178_K 63_N 0.83 0.06 0.00
120_E 83_R 0.83 0.06 0.00
79_Q 191_V 0.83 0.06 0.00
217_R 96_I 0.83 0.06 0.00
357_Q 81_W 0.82 0.06 0.00
462_I 17_F 0.82 0.06 0.00
320_S 3_K 0.82 0.06 0.00
217_R 36_G 0.82 0.06 0.00
465_I 50_S 0.82 0.06 0.00
66_Y 84_Y 0.82 0.06 0.00
382_L 59_N 0.82 0.06 0.00
62_L 69_C 0.81 0.06 0.00
428_K 47_K 0.81 0.06 0.00
379_S 80_R 0.81 0.06 0.00
52_D 75_Q 0.81 0.06 0.00
268_T 59_N 0.81 0.06 0.00
382_L 19_V 0.81 0.06 0.00
186_S 111_I 0.81 0.06 0.00
21_A 80_R 0.81 0.06 0.00
313_R 102_N 0.81 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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