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OPENSEQ.org
cI_M_cIII_cytc1_Pdenitr
Genes: A B A+B
Length: 513 263 748
Sequences: 2379 954 286
Seq/Len: 4.64 3.63 0.38
MirrorTree (Pazo et al. 2001) 0.51
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 0.01 0.37
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
297_V 256_I 1.66 0.59 0.00
227_A 214_A 1.53 0.51 0.00
297_V 216_L 1.50 0.48 0.00
287_Y 207_Q 1.37 0.39 0.00
148_F 174_Y 1.36 0.38 0.00
43_T 94_I 1.24 0.31 0.00
153_I 221_E 1.20 0.28 0.00
220_L 249_N 1.20 0.28 0.00
89_V 118_G 1.18 0.27 0.00
48_I 254_Q 1.18 0.27 0.00
15_A 257_K 1.17 0.27 0.00
37_L 163_G 1.17 0.26 0.00
143_G 249_N 1.17 0.26 0.00
164_F 218_W 1.16 0.26 0.00
366_T 37_G 1.15 0.26 0.00
89_V 250_K 1.15 0.25 0.00
351_G 235_V 1.15 0.25 0.00
301_L 82_E 1.15 0.25 0.00
467_P 43_D 1.13 0.24 0.00
406_F 134_H 1.10 0.23 0.00
182_I 100_E 1.10 0.23 0.00
464_V 129_A 1.10 0.23 0.00
297_V 132_G 1.09 0.23 0.00
58_P 241_L 1.09 0.22 0.00
442_T 206_D 1.08 0.22 0.00
19_M 130_R 1.07 0.21 0.00
450_S 140_G 1.06 0.21 0.00
120_L 249_N 1.06 0.21 0.00
366_T 85_V 1.05 0.20 0.00
248_Q 182_N 1.05 0.20 0.00
131_L 167_E 1.04 0.20 0.00
182_I 102_D 1.03 0.20 0.00
248_Q 51_L 1.03 0.19 0.00
34_A 203_A 1.03 0.19 0.00
409_L 14_G 1.02 0.19 0.00
339_A 220_A 1.00 0.18 0.00
474_I 247_L 1.00 0.18 0.00
376_V 127_A 1.00 0.18 0.00
337_D 256_I 1.00 0.18 0.00
488_P 235_V 1.00 0.18 0.00
387_M 83_D 0.99 0.18 0.00
129_T 237_F 0.99 0.18 0.00
182_I 137_Y 0.99 0.18 0.00
340_I 108_T 0.99 0.18 0.00
441_V 67_V 0.99 0.17 0.00
86_V 94_I 0.98 0.17 0.00
175_V 73_A 0.98 0.17 0.00
50_L 236_I 0.97 0.17 0.00
120_L 246_Y 0.97 0.17 0.00
318_V 240_V 0.97 0.17 0.00
259_A 185_Q 0.97 0.17 0.00
47_V 250_K 0.96 0.17 0.00
446_L 82_E 0.96 0.17 0.00
318_V 41_K 0.96 0.17 0.00
266_G 49_R 0.96 0.17 0.00
48_I 91_N 0.96 0.16 0.00
332_N 170_G 0.96 0.16 0.00
46_F 250_K 0.96 0.16 0.00
340_I 106_V 0.95 0.16 0.00
226_F 161_Y 0.95 0.16 0.00
472_T 87_A 0.94 0.16 0.00
112_E 51_L 0.94 0.16 0.00
58_P 240_V 0.94 0.16 0.00
339_A 129_A 0.94 0.16 0.00
110_V 206_D 0.94 0.16 0.00
90_L 94_I 0.94 0.15 0.00
287_Y 125_L 0.93 0.15 0.00
406_F 136_P 0.93 0.15 0.00
484_D 247_L 0.93 0.15 0.00
324_V 96_D 0.93 0.15 0.00
96_M 46_Q 0.93 0.15 0.00
101_L 43_D 0.92 0.15 0.00
24_R 220_A 0.92 0.15 0.00
420_A 175_H 0.91 0.15 0.00
140_F 169_A 0.91 0.15 0.00
120_L 218_W 0.91 0.14 0.00
15_A 215_F 0.90 0.14 0.00
464_V 44_Q 0.90 0.14 0.00
184_M 154_I 0.90 0.14 0.00
158_D 118_G 0.90 0.14 0.00
407_L 87_A 0.89 0.14 0.00
221_L 53_V 0.89 0.14 0.00
412_V 156_A 0.89 0.14 0.00
472_T 77_G 0.89 0.14 0.00
339_A 148_I 0.89 0.14 0.00
97_P 223_K 0.89 0.14 0.00
454_I 130_R 0.89 0.14 0.00
131_L 84_Q 0.88 0.14 0.00
403_V 24_A 0.88 0.14 0.00
440_R 45_H 0.88 0.14 0.00
140_F 39_F 0.88 0.14 0.00
428_I 67_V 0.88 0.14 0.00
121_E 142_S 0.88 0.14 0.00
119_V 20_G 0.88 0.13 0.00
171_F 225_M 0.87 0.13 0.00
488_P 226_D 0.87 0.13 0.00
121_E 76_G 0.87 0.13 0.00
403_V 116_G 0.87 0.13 0.00
225_F 255_P 0.87 0.13 0.00
48_I 237_F 0.87 0.13 0.00
148_F 201_T 0.87 0.13 0.00
233_M 69_L 0.87 0.13 0.00
328_V 125_L 0.87 0.13 0.00
422_V 209_A 0.87 0.13 0.00
259_A 144_L 0.87 0.13 0.00
434_A 143_Q 0.86 0.13 0.00
466_I 180_A 0.86 0.13 0.00
473_L 66_Y 0.86 0.13 0.00
470_A 129_A 0.86 0.13 0.00
288_V 196_T 0.86 0.13 0.00
61_T 85_V 0.86 0.13 0.00
44_A 201_T 0.86 0.13 0.00
287_Y 85_V 0.86 0.13 0.00
282_G 240_V 0.86 0.13 0.00
260_V 216_L 0.85 0.13 0.00
66_V 44_Q 0.85 0.13 0.00
319_A 224_M 0.85 0.13 0.00
388_F 101_E 0.85 0.13 0.00
492_A 240_V 0.85 0.13 0.00
75_V 241_L 0.85 0.13 0.00
261_L 160_G 0.85 0.12 0.00
333_Q 52_Q 0.85 0.12 0.00
140_F 224_M 0.85 0.12 0.00
121_E 59_S 0.85 0.12 0.00
88_F 250_K 0.85 0.12 0.00
226_F 233_V 0.84 0.12 0.00
136_F 218_W 0.84 0.12 0.00
90_L 90_A 0.84 0.12 0.00
81_V 240_V 0.84 0.12 0.00
166_F 130_R 0.84 0.12 0.00
236_W 55_T 0.84 0.12 0.00
348_F 154_I 0.84 0.12 0.00
459_P 180_A 0.84 0.12 0.00
86_V 154_I 0.84 0.12 0.00
140_F 218_W 0.84 0.12 0.00
90_L 135_G 0.84 0.12 0.00
284_A 129_A 0.83 0.12 0.00
294_I 51_L 0.83 0.12 0.00
25_G 21_D 0.83 0.12 0.00
407_L 197_Y 0.83 0.12 0.00
442_T 190_L 0.83 0.12 0.00
420_A 241_L 0.83 0.12 0.00
87_L 106_V 0.83 0.12 0.00
226_F 69_L 0.83 0.12 0.00
50_L 240_V 0.83 0.12 0.00
74_G 65_R 0.83 0.12 0.00
15_A 105_R 0.83 0.12 0.00
210_G 105_R 0.82 0.12 0.00
236_W 76_G 0.82 0.12 0.00
175_V 60_A 0.82 0.12 0.00
39_L 139_T 0.82 0.12 0.00
179_V 219_T 0.82 0.12 0.00
93_T 218_W 0.82 0.12 0.00
449_E 65_R 0.82 0.12 0.00
114_M 193_D 0.82 0.12 0.00
70_A 44_Q 0.82 0.12 0.00
468_L 96_D 0.82 0.12 0.00
57_D 104_P 0.82 0.12 0.00
268_G 218_W 0.82 0.12 0.00
119_V 229_Q 0.82 0.12 0.00
478_Y 256_I 0.82 0.12 0.00
150_I 179_F 0.82 0.12 0.00
211_M 224_M 0.82 0.12 0.00
198_T 166_K 0.82 0.12 0.00
351_G 240_V 0.82 0.12 0.00
222_F 71_T 0.82 0.12 0.00
351_G 36_E 0.82 0.12 0.00
375_L 46_Q 0.82 0.12 0.00
171_F 60_A 0.82 0.12 0.00
351_G 194_Q 0.81 0.12 0.00
159_R 214_A 0.81 0.12 0.00
177_M 214_A 0.81 0.12 0.00
285_Q 230_V 0.81 0.12 0.00
429_L 103_R 0.81 0.12 0.00
336_V 63_G 0.81 0.11 0.00
335_G 189_P 0.81 0.11 0.00
486_T 255_P 0.81 0.11 0.00
334_I 87_A 0.81 0.11 0.00
301_L 146_N 0.81 0.11 0.00
163_S 218_W 0.81 0.11 0.00
171_F 75_E 0.81 0.11 0.00
326_M 173_L 0.81 0.11 0.00
121_E 85_V 0.81 0.11 0.00
172_L 104_P 0.81 0.11 0.00
37_L 90_A 0.81 0.11 0.00
305_A 169_A 0.80 0.11 0.00
436_W 139_T 0.80 0.11 0.00
403_V 156_A 0.80 0.11 0.00
469_I 23_H 0.80 0.11 0.00
101_L 250_K 0.80 0.11 0.00
403_V 202_P 0.80 0.11 0.00
281_S 80_L 0.80 0.11 0.00
388_F 252_L 0.80 0.11 0.00
464_V 214_A 0.80 0.11 0.00
4_L 55_T 0.80 0.11 0.00
366_T 228_K 0.80 0.11 0.00
148_F 196_T 0.80 0.11 0.00
190_T 210_T 0.80 0.11 0.00
42_T 46_Q 0.80 0.11 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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