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OPENSEQ.org
fliFfliP
Genes: A B A+B
Length: 560 247 777
Sequences: 1496 1484 994
Seq/Len: 2.67 6.01 1.28
MirrorTree (Pazo et al. 2001) 0.71
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 0.00 0.00
2 0.00 0.00 0.03
5 0.00 0.01 0.22
10 0.00 0.01 0.64
20 0.00 0.02 1.23
100 0.01 0.03 1.34
∞ 0.03 0.07 1.54
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
203_I 197_V 1.51 0.83 0.09
264_V 82_T 1.48 0.82 0.08
197_N 220_S 1.42 0.78 0.07
386_V 237_L 1.27 0.66 0.05
123_G 186_E 1.27 0.66 0.04
90_P 80_M 1.26 0.65 0.04
368_D 237_L 1.22 0.61 0.04
61_D 80_M 1.16 0.55 0.03
205_K 242_V 1.14 0.54 0.03
152_R 132_G 1.14 0.53 0.03
397_E 203_S 1.13 0.52 0.03
117_F 161_P 1.12 0.52 0.03
22_R 123_I 1.11 0.51 0.03
26_A 127_E 1.11 0.50 0.03
407_S 104_E 1.10 0.50 0.03
21_Q 85_M 1.10 0.50 0.03
475_V 80_M 1.10 0.50 0.03
101_I 74_S 1.10 0.50 0.03
345_S 193_L 1.10 0.50 0.03
378_N 95_A 1.09 0.48 0.03
242_Q 71_V 1.07 0.47 0.02
125_T 61_F 1.06 0.46 0.02
368_D 111_Y 1.06 0.46 0.02
387_P 197_V 1.06 0.46 0.02
345_S 71_V 1.05 0.44 0.02
330_I 142_K 1.04 0.44 0.02
57_V 169_L 1.02 0.42 0.02
262_D 130_T 1.00 0.40 0.02
314_A 55_L 0.99 0.39 0.02
348_I 107_A 0.99 0.39 0.02
416_V 187_I 0.99 0.39 0.02
169_R 133_V 0.98 0.39 0.02
438_R 110_S 0.98 0.38 0.02
128_E 75_F 0.98 0.38 0.02
546_Q 56_A 0.98 0.38 0.02
338_V 203_S 0.97 0.37 0.02
409_N 113_E 0.97 0.37 0.02
89_V 203_S 0.97 0.37 0.02
419_L 84_S 0.96 0.36 0.02
81_L 95_A 0.96 0.36 0.02
126_N 75_F 0.96 0.36 0.02
365_V 54_A 0.96 0.36 0.02
69_V 106_V 0.96 0.36 0.02
483_Q 124_G 0.96 0.36 0.02
398_S 127_E 0.95 0.35 0.02
301_T 38_N 0.95 0.35 0.02
319_G 45_N 0.94 0.35 0.01
291_R 45_N 0.94 0.35 0.01
243_E 229_V 0.94 0.34 0.01
274_F 193_L 0.94 0.34 0.01
350_N 226_L 0.94 0.34 0.01
28_S 229_V 0.93 0.34 0.01
23_I 197_V 0.93 0.34 0.01
389_S 100_F 0.93 0.34 0.01
476_A 122_Q 0.93 0.33 0.01
243_E 69_L 0.93 0.33 0.01
549_I 157_N 0.93 0.33 0.01
256_P 81_G 0.93 0.33 0.01
84_E 110_S 0.92 0.33 0.01
35_F 102_I 0.92 0.33 0.01
327_K 98_L 0.92 0.33 0.01
435_F 215_P 0.92 0.33 0.01
248_D 200_M 0.92 0.33 0.01
15_Q 36_T 0.92 0.32 0.01
286_P 145_R 0.92 0.32 0.01
357_T 203_S 0.91 0.32 0.01
41_L 106_V 0.91 0.32 0.01
469_Q 181_L 0.91 0.32 0.01
535_S 191_I 0.91 0.31 0.01
172_P 54_A 0.90 0.31 0.01
82_E 84_S 0.90 0.31 0.01
394_A 109_K 0.90 0.31 0.01
213_I 107_A 0.90 0.30 0.01
141_L 72_V 0.90 0.30 0.01
533_L 83_Q 0.89 0.30 0.01
476_A 102_I 0.89 0.30 0.01
148_L 43_T 0.89 0.30 0.01
303_R 102_I 0.89 0.30 0.01
64_S 151_L 0.89 0.30 0.01
351_T 187_I 0.89 0.30 0.01
446_P 102_I 0.89 0.30 0.01
258_A 95_A 0.88 0.29 0.01
400_V 208_A 0.88 0.29 0.01
216_Q 183_T 0.88 0.29 0.01
264_V 75_F 0.88 0.29 0.01
164_S 183_T 0.88 0.29 0.01
272_F 181_L 0.88 0.29 0.01
286_P 135_P 0.88 0.29 0.01
301_T 176_F 0.87 0.29 0.01
447_V 124_G 0.87 0.29 0.01
102_A 150_A 0.87 0.29 0.01
186_K 70_I 0.87 0.29 0.01
278_E 82_T 0.87 0.29 0.01
232_V 197_V 0.87 0.29 0.01
367_I 115_I 0.87 0.28 0.01
466_P 239_Q 0.87 0.28 0.01
231_L 163_T 0.87 0.28 0.01
204_P 110_S 0.87 0.28 0.01
209_E 104_E 0.87 0.28 0.01
174_T 59_I 0.87 0.28 0.01
397_E 157_N 0.86 0.28 0.01
401_K 92_V 0.86 0.28 0.01
447_V 102_I 0.86 0.28 0.01
157_H 186_E 0.86 0.28 0.01
81_L 187_I 0.86 0.28 0.01
397_E 106_V 0.86 0.28 0.01
368_D 62_V 0.86 0.27 0.01
93_Q 124_G 0.85 0.27 0.01
123_G 183_T 0.85 0.27 0.01
262_D 169_L 0.85 0.27 0.01
161_P 148_D 0.85 0.27 0.01
192_I 183_T 0.85 0.27 0.01
270_I 169_L 0.85 0.27 0.01
213_I 218_M 0.85 0.27 0.01
201_A 191_I 0.85 0.27 0.01
87_I 131_R 0.85 0.27 0.01
12_Q 112_N 0.84 0.26 0.01
341_N 97_I 0.84 0.26 0.01
88_L 221_L 0.84 0.26 0.01
224_Q 225_L 0.84 0.26 0.01
204_P 212_M 0.84 0.26 0.01
262_D 112_N 0.84 0.26 0.01
286_P 148_D 0.84 0.26 0.01
358_V 162_K 0.84 0.26 0.01
118_D 70_I 0.84 0.26 0.01
228_E 109_K 0.83 0.26 0.01
27_A 191_I 0.83 0.26 0.01
136_A 55_L 0.83 0.26 0.01
162_K 106_V 0.83 0.26 0.01
546_Q 209_M 0.83 0.25 0.01
407_S 54_A 0.83 0.25 0.01
334_K 208_A 0.83 0.25 0.01
120_Q 197_V 0.83 0.25 0.01
359_V 177_M 0.83 0.25 0.01
211_V 137_K 0.82 0.25 0.01
416_V 231_V 0.82 0.25 0.01
330_I 98_L 0.82 0.25 0.01
36_L 29_L 0.82 0.25 0.01
266_V 109_K 0.82 0.25 0.01
239_K 167_V 0.82 0.25 0.01
316_S 132_G 0.82 0.24 0.01
80_I 69_L 0.82 0.24 0.01
361_T 123_I 0.82 0.24 0.01
149_E 166_D 0.82 0.24 0.01
90_P 85_M 0.82 0.24 0.01
167_T 144_T 0.82 0.24 0.01
125_T 75_F 0.82 0.24 0.01
263_K 62_V 0.81 0.24 0.01
220_P 40_L 0.81 0.24 0.01
353_K 55_L 0.81 0.24 0.01
471_M 215_P 0.81 0.24 0.01
482_Q 47_V 0.81 0.24 0.01
450_I 132_G 0.81 0.24 0.01
74_Q 203_S 0.81 0.24 0.01
232_V 208_A 0.81 0.24 0.01
343_E 45_N 0.81 0.24 0.01
450_I 102_I 0.81 0.24 0.01
342_N 76_L 0.81 0.24 0.01
119_T 156_R 0.81 0.24 0.01
402_N 171_V 0.81 0.24 0.01
31_V 159_P 0.81 0.24 0.01
546_Q 215_P 0.81 0.24 0.01
3_F 110_S 0.81 0.24 0.01
212_R 60_I 0.81 0.23 0.01
544_L 137_K 0.81 0.23 0.01
65_S 61_F 0.81 0.23 0.01
130_R 245_F 0.81 0.23 0.01
450_I 191_I 0.81 0.23 0.01
274_F 183_T 0.80 0.23 0.01
358_V 37_P 0.80 0.23 0.01
480_E 137_K 0.80 0.23 0.01
486_N 163_T 0.80 0.23 0.01
66_A 73_F 0.80 0.23 0.01
401_K 208_A 0.80 0.23 0.01
422_H 231_V 0.80 0.23 0.01
350_N 106_V 0.80 0.23 0.01
359_V 106_V 0.80 0.23 0.01
165_V 43_T 0.80 0.23 0.01
222_D 61_F 0.80 0.23 0.01
110_S 215_P 0.80 0.23 0.01
138_E 229_V 0.80 0.23 0.01
125_T 50_L 0.80 0.23 0.01
377_E 123_I 0.80 0.23 0.01
458_I 121_E 0.80 0.23 0.01
546_Q 29_L 0.79 0.23 0.01
327_K 187_I 0.79 0.23 0.01
551_N 115_I 0.79 0.23 0.01
266_V 145_R 0.79 0.23 0.01
543_A 209_M 0.79 0.22 0.01
346_K 204_S 0.79 0.22 0.01
79_Y 190_L 0.79 0.22 0.01
552_D 203_S 0.79 0.22 0.01
503_R 127_E 0.79 0.22 0.01
453_A 84_S 0.79 0.22 0.01
100_F 123_I 0.79 0.22 0.01
464_I 76_L 0.78 0.22 0.01
386_V 124_G 0.78 0.22 0.01
475_V 50_L 0.78 0.22 0.01
213_I 36_T 0.78 0.22 0.01
312_P 183_T 0.78 0.22 0.01
370_K 201_V 0.78 0.22 0.01
33_V 95_A 0.78 0.22 0.01
280_Q 190_L 0.78 0.22 0.01
161_P 145_R 0.78 0.22 0.01
317_N 171_V 0.78 0.21 0.01
85_S 244_S 0.78 0.21 0.01
64_S 174_P 0.78 0.21 0.01
164_S 182_K 0.78 0.21 0.01
350_N 209_M 0.78 0.21 0.01
229_D 112_N 0.78 0.21 0.01
177_V 197_V 0.78 0.21 0.01
8_H 41_V 0.77 0.21 0.01
136_A 137_K 0.77 0.21 0.01
267_S 230_L 0.77 0.21 0.01
483_Q 110_S 0.77 0.21 0.01
137_I 143_N 0.77 0.21 0.01
319_G 178_I 0.77 0.21 0.01
345_S 93_T 0.77 0.21 0.01
394_A 122_Q 0.77 0.21 0.01
121_S 187_I 0.77 0.21 0.01
265_R 56_A 0.77 0.21 0.01
481_V 122_Q 0.77 0.21 0.01
467_F 38_N 0.77 0.21 0.01
419_L 225_L 0.77 0.21 0.01
409_N 130_T 0.77 0.21 0.01
99_M 186_E 0.77 0.21 0.01
210_N 109_K 0.77 0.21 0.01
273_D 200_M 0.77 0.21 0.01
55_V 214_L 0.76 0.21 0.01
345_S 215_P 0.76 0.21 0.01
457_F 197_V 0.76 0.21 0.01
262_D 127_E 0.76 0.21 0.01
114_F 82_T 0.76 0.20 0.01
153_S 91_L 0.76 0.20 0.01
130_R 106_V 0.76 0.20 0.01
71_K 43_T 0.76 0.20 0.01
243_E 191_I 0.76 0.20 0.01
181_V 114_G 0.76 0.20 0.01
295_T 173_V 0.76 0.20 0.01
188_T 156_R 0.76 0.20 0.01
50_N 225_L 0.76 0.20 0.01
536_D 122_Q 0.76 0.20 0.01
253_T 236_L 0.76 0.20 0.01
148_L 212_M 0.76 0.20 0.01
474_D 136_F 0.76 0.20 0.01
534_V 115_I 0.76 0.20 0.01
335_K 203_S 0.76 0.20 0.01
414_V 219_I 0.76 0.20 0.01
540_E 75_F 0.76 0.20 0.01
237_K 132_G 0.76 0.20 0.01
193_D 70_I 0.76 0.20 0.01
538_S 143_N 0.76 0.20 0.01
136_A 220_S 0.76 0.20 0.01
539_E 214_L 0.75 0.20 0.01
138_E 239_Q 0.75 0.20 0.01
546_Q 173_V 0.75 0.20 0.01
214_S 95_A 0.75 0.20 0.01
400_V 112_N 0.75 0.20 0.01
124_A 106_V 0.75 0.20 0.01
249_K 243_E 0.75 0.20 0.01
416_V 25_P 0.75 0.20 0.01
264_V 215_P 0.75 0.20 0.01
57_V 118_Y 0.75 0.20 0.01
26_A 55_L 0.75 0.20 0.01
77_V 162_K 0.75 0.20 0.01
21_Q 218_M 0.75 0.20 0.01
163_D 217_V 0.75 0.20 0.01
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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