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OPENSEQ.org
3CPI_G Ras-related protein Sec4 1G16_A Rab GDP-dissociation inhibitor GNP
Genes: A B A+B
Length: 451 170 612
Sequences: 645 7616 58
Seq/Len: 1.43 44.8 0.09
MirrorTree (Pazo et al. 2001) 0.38
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 0.02 0.11 0.00
2 0.02 0.12 0.01
5 0.02 0.14 0.02
10 0.03 0.16 0.05
20 0.03 0.18 0.09
100 0.03 0.23 0.38
∞ 0.04 0.26 0.69
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
13_I 56_I 1.59 0.22 0.00
129_A 138_G 1.44 0.17 0.00
345_V 129_Q 1.36 0.15 0.00
223_S 119_D 1.36 0.15 0.00
23_I 152_V 1.35 0.15 0.00
429_K 17_S 1.28 0.13 0.00
314_I 152_V 1.27 0.13 0.00
214_F 45_V 1.21 0.12 0.00
233_L 79_I 1.17 0.11 0.00
210_A 83_Y 1.17 0.11 0.00
13_I 17_S 1.16 0.11 0.00
304_T 45_V 1.14 0.10 0.00
361_L 144_S 1.13 0.10 0.00
73_K 13_G 1.13 0.10 0.00
100_I 151_N 1.13 0.10 0.00
119_F 152_V 1.12 0.10 0.00
380_A 152_V 1.12 0.10 0.00
310_R 59_T 1.11 0.10 0.00
372_K 45_V 1.11 0.10 0.00
91_A 7_L 1.10 0.10 0.00
86_P 119_D 1.10 0.10 0.00
425_T 94_I 1.07 0.09 0.00
254_G 117_K 1.07 0.09 0.00
263_I 108_E 1.06 0.09 0.00
142_I 4_M 1.06 0.09 0.00
251_A 145_S 1.05 0.09 0.00
141_G 114_V 1.05 0.09 0.00
89_L 94_I 1.04 0.09 0.00
173_K 151_N 1.04 0.09 0.00
434_R 6_I 1.03 0.09 0.00
358_G 56_I 1.03 0.09 0.00
113_V 138_G 1.02 0.09 0.00
39_D 10_G 1.01 0.08 0.00
39_D 15_G 1.01 0.08 0.00
39_D 16_K 1.01 0.08 0.00
44_Y 10_G 1.01 0.08 0.00
44_Y 15_G 1.01 0.08 0.00
44_Y 16_K 1.01 0.08 0.00
238_G 10_G 1.01 0.08 0.00
238_G 15_G 1.01 0.08 0.00
238_G 16_K 1.01 0.08 0.00
259_L 10_G 1.01 0.08 0.00
259_L 15_G 1.01 0.08 0.00
259_L 16_K 1.01 0.08 0.00
242_L 163_I 1.01 0.08 0.00
145_K 145_S 0.99 0.08 0.00
236_M 120_M 0.99 0.08 0.00
98_I 161_K 0.98 0.08 0.00
345_V 152_V 0.98 0.08 0.00
292_A 8_L 0.98 0.08 0.00
288_P 66_R 0.98 0.08 0.00
352_H 152_V 0.97 0.08 0.00
54_S 99_K 0.97 0.08 0.00
78_R 145_S 0.97 0.08 0.00
38_I 152_V 0.97 0.08 0.00
237_Y 56_I 0.96 0.08 0.00
95_L 18_C 0.96 0.08 0.00
198_A 28_F 0.96 0.08 0.00
13_I 8_L 0.96 0.07 0.00
152_L 154_E 0.96 0.07 0.00
49_A 17_S 0.95 0.07 0.00
124_I 90_T 0.95 0.07 0.00
221_C 18_C 0.95 0.07 0.00
287_A 132_A 0.94 0.07 0.00
291_I 152_V 0.94 0.07 0.00
312_I 143_E 0.94 0.07 0.00
107_Y 14_V 0.94 0.07 0.00
45_G 10_G 0.94 0.07 0.00
45_G 15_G 0.94 0.07 0.00
45_G 16_K 0.94 0.07 0.00
360_Y 115_G 0.93 0.07 0.00
161_D 162_L 0.93 0.07 0.00
233_L 90_T 0.93 0.07 0.00
42_D 17_S 0.92 0.07 0.00
37_H 28_F 0.92 0.07 0.00
29_S 147_K 0.92 0.07 0.00
84_L 117_K 0.92 0.07 0.00
251_A 28_F 0.92 0.07 0.00
290_V 97_W 0.92 0.07 0.00
332_I 114_V 0.92 0.07 0.00
136_S 6_I 0.92 0.07 0.00
233_L 151_N 0.91 0.07 0.00
160_E 151_N 0.91 0.07 0.00
193_I 56_I 0.91 0.07 0.00
151_F 145_S 0.91 0.07 0.00
310_R 145_S 0.91 0.07 0.00
154_W 148_N 0.91 0.07 0.00
197_M 14_V 0.90 0.07 0.00
86_P 57_W 0.90 0.07 0.00
254_G 156_F 0.90 0.07 0.00
319_V 52_V 0.90 0.07 0.00
136_S 26_D 0.90 0.07 0.00
154_W 161_K 0.89 0.07 0.00
39_D 58_D 0.89 0.07 0.00
44_Y 58_D 0.89 0.07 0.00
238_G 58_D 0.89 0.07 0.00
259_L 58_D 0.89 0.07 0.00
435_V 45_V 0.89 0.07 0.00
371_D 26_D 0.89 0.07 0.00
157_S 151_N 0.89 0.07 0.00
312_I 5_K 0.89 0.07 0.00
197_M 83_Y 0.89 0.07 0.00
423_S 17_S 0.88 0.07 0.00
242_L 64_R 0.88 0.07 0.00
316_N 17_S 0.88 0.07 0.00
181_Y 56_I 0.88 0.07 0.00
186_G 135_K 0.88 0.07 0.00
223_S 10_G 0.88 0.07 0.00
223_S 15_G 0.88 0.07 0.00
223_S 16_K 0.88 0.07 0.00
78_R 28_F 0.87 0.07 0.00
361_L 24_V 0.87 0.07 0.00
244_Q 10_G 0.87 0.07 0.00
244_Q 15_G 0.87 0.07 0.00
244_Q 16_K 0.87 0.07 0.00
248_R 10_G 0.87 0.07 0.00
248_R 15_G 0.87 0.07 0.00
248_R 16_K 0.87 0.07 0.00
41_Q 81_L 0.87 0.07 0.00
254_G 145_S 0.87 0.07 0.00
16_G 10_G 0.87 0.07 0.00
16_G 15_G 0.87 0.07 0.00
16_G 16_K 0.87 0.07 0.00
17_T 10_G 0.87 0.07 0.00
17_T 15_G 0.87 0.07 0.00
17_T 16_K 0.87 0.07 0.00
167_Q 20_L 0.87 0.06 0.00
251_A 97_W 0.86 0.06 0.00
409_I 94_I 0.86 0.06 0.00
110_F 145_S 0.86 0.06 0.00
173_K 90_T 0.86 0.06 0.00
154_W 80_I 0.86 0.06 0.00
210_A 36_I 0.86 0.06 0.00
381_F 78_G 0.85 0.06 0.00
319_V 134_A 0.85 0.06 0.00
276_E 18_C 0.85 0.06 0.00
361_L 92_T 0.85 0.06 0.00
98_I 141_F 0.85 0.06 0.00
173_K 92_T 0.85 0.06 0.00
145_K 28_F 0.85 0.06 0.00
160_E 163_I 0.85 0.06 0.00
88_F 98_F 0.85 0.06 0.00
29_S 28_F 0.85 0.06 0.00
16_G 19_L 0.85 0.06 0.00
17_T 19_L 0.85 0.06 0.00
358_G 85_I 0.85 0.06 0.00
147_R 62_Q 0.84 0.06 0.00
39_D 119_D 0.84 0.06 0.00
44_Y 119_D 0.84 0.06 0.00
238_G 119_D 0.84 0.06 0.00
259_L 119_D 0.84 0.06 0.00
130_N 128_D 0.84 0.06 0.00
23_I 22_R 0.84 0.06 0.00
251_A 10_G 0.84 0.06 0.00
251_A 15_G 0.84 0.06 0.00
251_A 16_K 0.84 0.06 0.00
154_W 19_L 0.84 0.06 0.00
150_K 99_K 0.84 0.06 0.00
416_D 37_G 0.84 0.06 0.00
245_G 79_I 0.83 0.06 0.00
361_L 50_K 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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