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OPENSEQ.org
cI_M_cIII_isp_Pdenitr
Genes: A B A+B
Length: 513 190 685
Sequences: 2379 1043 313
Seq/Len: 4.64 5.49 0.46
MirrorTree (Pazo et al. 2001) 0.50
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 0.01 0.01 0.00
2 0.01 0.01 0.00
5 0.01 0.01 0.00
10 0.02 0.01 0.00
20 0.02 0.01 0.00
100 0.03 0.01 0.04
∞ 0.06 0.02 0.45
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
318_V 131_V 1.66 0.66 0.00
89_V 128_M 1.48 0.52 0.00
294_I 162_S 1.39 0.46 0.00
160_I 69_V 1.31 0.39 0.00
318_V 78_I 1.30 0.39 0.00
483_T 78_I 1.27 0.37 0.00
282_G 78_I 1.26 0.36 0.00
74_G 129_I 1.21 0.32 0.00
494_V 56_V 1.19 0.32 0.00
410_M 131_V 1.16 0.29 0.00
351_G 26_A 1.15 0.29 0.00
403_V 52_A 1.15 0.28 0.00
290_W 78_I 1.12 0.27 0.00
332_N 143_G 1.11 0.27 0.00
406_F 19_L 1.10 0.26 0.00
63_F 32_G 1.09 0.26 0.00
416_D 68_T 1.09 0.25 0.00
318_V 165_I 1.09 0.25 0.00
85_S 82_T 1.07 0.24 0.00
74_G 186_T 1.06 0.24 0.00
313_I 78_I 1.06 0.24 0.00
171_F 55_Q 1.06 0.24 0.00
210_G 184_D 1.06 0.24 0.00
123_L 127_V 1.06 0.23 0.00
468_L 189_L 1.06 0.23 0.00
90_L 29_V 1.04 0.23 0.00
94_F 182_L 1.04 0.23 0.00
296_I 28_T 1.03 0.22 0.00
477_V 68_T 1.01 0.21 0.00
445_Q 23_T 1.01 0.21 0.00
119_V 78_I 1.01 0.21 0.00
120_L 107_K 1.01 0.21 0.00
79_M 51_L 0.99 0.20 0.00
323_Y 68_T 0.99 0.20 0.00
415_V 183_D 0.98 0.20 0.00
120_L 163_G 0.98 0.19 0.00
336_V 84_D 0.97 0.19 0.00
344_L 123_G 0.97 0.19 0.00
93_T 114_D 0.97 0.19 0.00
288_V 129_I 0.97 0.19 0.00
38_A 188_K 0.96 0.19 0.00
99_T 116_N 0.95 0.18 0.00
332_N 187_I 0.95 0.18 0.00
464_V 24_A 0.95 0.18 0.00
66_V 61_V 0.94 0.18 0.00
342_Q 81_R 0.94 0.18 0.00
7_I 122_A 0.94 0.18 0.00
71_W 81_R 0.94 0.17 0.00
49_S 176_I 0.94 0.17 0.00
454_I 165_I 0.93 0.17 0.00
14_V 95_G 0.93 0.17 0.00
465_F 34_A 0.93 0.17 0.00
255_V 126_L 0.92 0.17 0.00
370_D 22_A 0.92 0.17 0.00
163_S 27_G 0.91 0.17 0.00
489_A 97_L 0.91 0.17 0.00
171_F 122_A 0.91 0.17 0.00
473_L 26_A 0.91 0.16 0.00
411_G 74_K 0.91 0.16 0.00
424_T 122_A 0.91 0.16 0.00
182_I 12_G 0.91 0.16 0.00
50_L 34_A 0.91 0.16 0.00
140_F 150_W 0.90 0.16 0.00
148_F 19_L 0.90 0.16 0.00
75_V 40_N 0.90 0.16 0.00
46_F 182_L 0.90 0.16 0.00
14_V 78_I 0.90 0.16 0.00
284_A 93_D 0.90 0.16 0.00
34_A 66_Q 0.89 0.16 0.00
289_F 189_L 0.89 0.16 0.00
313_I 32_G 0.89 0.16 0.00
86_V 111_P 0.89 0.16 0.00
475_L 41_Q 0.89 0.15 0.00
478_Y 43_N 0.88 0.15 0.00
468_L 167_R 0.88 0.15 0.00
462_R 46_A 0.88 0.15 0.00
411_G 32_G 0.88 0.15 0.00
330_A 58_V 0.88 0.15 0.00
266_G 72_L 0.87 0.15 0.00
143_G 168_G 0.87 0.15 0.00
403_V 129_I 0.87 0.15 0.00
164_F 182_L 0.87 0.15 0.00
160_I 52_A 0.86 0.15 0.00
342_Q 76_V 0.86 0.15 0.00
351_G 168_G 0.86 0.14 0.00
398_G 37_T 0.86 0.14 0.00
135_L 174_L 0.86 0.14 0.00
85_S 124_E 0.86 0.14 0.00
231_V 33_A 0.85 0.14 0.00
25_G 124_E 0.85 0.14 0.00
290_W 76_V 0.85 0.14 0.00
222_F 89_G 0.85 0.14 0.00
419_V 168_G 0.85 0.14 0.00
160_I 115_E 0.85 0.14 0.00
360_I 24_A 0.85 0.14 0.00
481_L 72_L 0.84 0.14 0.00
14_V 26_A 0.84 0.14 0.00
175_V 33_A 0.84 0.14 0.00
339_A 91_E 0.84 0.14 0.00
47_V 38_L 0.84 0.14 0.00
127_V 52_A 0.84 0.14 0.00
101_L 141_G 0.84 0.14 0.00
88_F 51_L 0.84 0.14 0.00
339_A 131_V 0.83 0.14 0.00
182_I 47_D 0.83 0.13 0.00
51_F 187_I 0.83 0.13 0.00
222_F 150_W 0.83 0.13 0.00
4_L 17_D 0.83 0.13 0.00
182_I 98_I 0.83 0.13 0.00
490_V 74_K 0.83 0.13 0.00
484_D 129_I 0.83 0.13 0.00
217_M 80_R 0.83 0.13 0.00
456_D 57_D 0.83 0.13 0.00
245_A 19_L 0.83 0.13 0.00
449_E 27_G 0.83 0.13 0.00
270_L 83_E 0.83 0.13 0.00
414_R 141_G 0.83 0.13 0.00
184_M 70_K 0.83 0.13 0.00
307_S 10_D 0.83 0.13 0.00
54_F 15_R 0.83 0.13 0.00
52_V 51_L 0.82 0.13 0.00
153_I 98_I 0.82 0.13 0.00
70_A 80_R 0.82 0.13 0.00
131_L 109_D 0.82 0.13 0.00
223_L 22_A 0.82 0.13 0.00
448_K 23_T 0.82 0.13 0.00
225_F 23_T 0.82 0.13 0.00
11_L 23_T 0.82 0.13 0.00
386_F 159_Y 0.82 0.13 0.00
351_G 185_T 0.82 0.13 0.00
470_A 105_S 0.81 0.13 0.00
42_T 179_A 0.81 0.13 0.00
23_L 186_T 0.81 0.13 0.00
131_L 42_M 0.81 0.13 0.00
72_I 176_I 0.81 0.13 0.00
140_F 181_F 0.81 0.12 0.00
370_D 131_V 0.81 0.12 0.00
490_V 68_T 0.80 0.12 0.00
222_F 67_L 0.80 0.12 0.00
297_V 11_H 0.80 0.12 0.00
335_G 78_I 0.80 0.12 0.00
384_A 22_A 0.80 0.12 0.00
184_M 86_I 0.80 0.12 0.00
294_I 40_N 0.80 0.12 0.00
480_R 19_L 0.80 0.12 0.00
130_A 176_I 0.80 0.12 0.00
454_I 179_A 0.80 0.12 0.00
318_V 129_I 0.80 0.12 0.00
259_A 38_L 0.80 0.12 0.00
439_R 165_I 0.79 0.12 0.00
281_S 181_F 0.79 0.12 0.00
11_L 97_L 0.79 0.12 0.00
413_F 46_A 0.79 0.12 0.00
46_F 78_I 0.79 0.12 0.00
100_I 125_W 0.79 0.12 0.00
427_V 27_G 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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