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OPENSEQ.org
cI_D_cIII_cyt1
Genes: A B A+B
Length: 485 263 719
Sequences: 1691 884 278
Seq/Len: 3.49 3.36 0.39
MirrorTree (Pazo et al. 2001) 0.62
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 0.01 0.00
2 0.00 0.01 0.00
5 0.00 0.01 0.00
10 0.00 0.01 0.00
20 0.01 0.01 0.00
100 0.01 0.01 0.03
∞ 0.02 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
380_M 54_Y 1.64 0.59 0.00
347_M 240_V 1.50 0.49 0.00
186_F 124_S 1.38 0.40 0.00
327_G 63_G 1.34 0.38 0.00
139_L 96_D 1.32 0.36 0.00
362_Y 86_R 1.30 0.35 0.00
243_A 216_L 1.27 0.33 0.00
281_I 242_A 1.26 0.32 0.00
436_A 206_D 1.25 0.32 0.00
69_V 241_L 1.22 0.30 0.00
221_V 84_Q 1.20 0.29 0.00
122_A 43_D 1.18 0.28 0.00
125_L 74_D 1.18 0.27 0.00
396_F 69_L 1.17 0.27 0.00
232_Q 39_F 1.16 0.26 0.00
120_A 191_S 1.15 0.26 0.00
212_V 38_P 1.14 0.25 0.00
416_V 73_A 1.14 0.25 0.00
305_H 249_N 1.13 0.25 0.00
146_A 249_N 1.12 0.24 0.00
289_L 250_K 1.12 0.24 0.00
117_I 249_N 1.11 0.24 0.00
378_V 163_G 1.11 0.23 0.00
152_S 177_A 1.10 0.23 0.00
339_G 74_D 1.08 0.22 0.00
309_L 60_A 1.06 0.21 0.00
106_Y 215_F 1.05 0.21 0.00
336_S 249_N 1.05 0.21 0.00
366_F 221_E 1.05 0.21 0.00
107_L 240_V 1.05 0.20 0.00
389_T 224_M 1.05 0.20 0.00
404_Q 105_R 1.04 0.20 0.00
287_M 76_G 1.04 0.20 0.00
124_H 217_M 1.03 0.20 0.00
399_L 139_T 1.03 0.20 0.00
89_T 94_I 1.03 0.20 0.00
330_L 213_A 1.03 0.20 0.00
407_L 65_R 1.02 0.19 0.00
142_L 248_T 1.02 0.19 0.00
405_A 38_P 1.02 0.19 0.00
102_K 220_A 1.01 0.19 0.00
113_A 249_N 1.00 0.18 0.00
95_L 136_P 1.00 0.18 0.00
273_L 159_T 1.00 0.18 0.00
125_L 137_Y 0.99 0.18 0.00
432_L 213_A 0.99 0.18 0.00
114_L 23_H 0.99 0.18 0.00
313_L 213_A 0.99 0.18 0.00
275_I 118_G 0.98 0.18 0.00
370_P 84_Q 0.97 0.17 0.00
56_G 151_P 0.97 0.17 0.00
116_G 246_Y 0.97 0.17 0.00
238_V 100_E 0.97 0.17 0.00
47_A 101_E 0.96 0.17 0.00
215_G 72_L 0.96 0.17 0.00
421_G 237_F 0.96 0.17 0.00
303_I 212_V 0.96 0.17 0.00
72_F 200_G 0.95 0.17 0.00
71_G 69_L 0.95 0.16 0.00
278_F 96_D 0.95 0.16 0.00
470_W 136_P 0.95 0.16 0.00
362_Y 151_P 0.95 0.16 0.00
25_M 82_E 0.95 0.16 0.00
202_L 235_V 0.94 0.16 0.00
139_L 207_Q 0.94 0.16 0.00
383_L 47_L 0.94 0.16 0.00
275_I 241_L 0.93 0.16 0.00
373_A 227_R 0.93 0.16 0.00
192_N 216_L 0.93 0.16 0.00
428_V 240_V 0.93 0.15 0.00
254_V 250_K 0.92 0.15 0.00
88_C 76_G 0.92 0.15 0.00
116_G 40_G 0.92 0.15 0.00
112_A 251_K 0.92 0.15 0.00
102_K 246_Y 0.92 0.15 0.00
49_L 73_A 0.92 0.15 0.00
429_A 245_L 0.92 0.15 0.00
313_L 195_V 0.91 0.15 0.00
286_L 215_F 0.91 0.15 0.00
181_S 230_V 0.91 0.15 0.00
189_L 124_S 0.91 0.15 0.00
155_A 202_P 0.91 0.15 0.00
304_S 125_L 0.91 0.15 0.00
311_V 98_E 0.91 0.15 0.00
95_L 141_L 0.91 0.15 0.00
418_S 206_D 0.91 0.15 0.00
89_T 114_V 0.90 0.14 0.00
324_E 84_Q 0.90 0.14 0.00
177_V 94_I 0.90 0.14 0.00
336_S 246_Y 0.89 0.14 0.00
257_L 66_Y 0.89 0.14 0.00
407_L 66_Y 0.89 0.14 0.00
195_D 15_A 0.88 0.14 0.00
310_L 137_Y 0.88 0.14 0.00
221_V 205_V 0.88 0.14 0.00
188_A 167_E 0.88 0.14 0.00
152_S 187_A 0.88 0.14 0.00
386_I 185_Q 0.88 0.14 0.00
433_Y 54_Y 0.88 0.14 0.00
367_W 131_A 0.88 0.14 0.00
105_F 177_A 0.88 0.14 0.00
177_V 213_A 0.88 0.14 0.00
85_L 203_A 0.88 0.14 0.00
404_Q 64_L 0.88 0.14 0.00
111_I 242_A 0.88 0.14 0.00
195_D 85_V 0.88 0.14 0.00
273_L 256_I 0.88 0.14 0.00
238_V 130_R 0.87 0.14 0.00
241_F 85_V 0.87 0.14 0.00
431_S 60_A 0.87 0.13 0.00
238_V 94_I 0.87 0.13 0.00
464_V 245_L 0.87 0.13 0.00
112_A 141_L 0.87 0.13 0.00
340_A 43_D 0.86 0.13 0.00
418_S 218_W 0.86 0.13 0.00
252_G 187_A 0.86 0.13 0.00
353_G 166_K 0.86 0.13 0.00
252_G 84_Q 0.86 0.13 0.00
285_N 144_L 0.86 0.13 0.00
110_L 230_V 0.86 0.13 0.00
421_G 147_G 0.86 0.13 0.00
65_P 108_T 0.86 0.13 0.00
354_P 54_Y 0.86 0.13 0.00
292_T 81_P 0.86 0.13 0.00
338_L 125_L 0.86 0.13 0.00
404_Q 83_D 0.86 0.13 0.00
177_V 182_N 0.85 0.13 0.00
376_M 151_P 0.85 0.13 0.00
157_I 69_L 0.85 0.13 0.00
338_L 142_S 0.85 0.13 0.00
242_L 96_D 0.85 0.13 0.00
205_A 248_T 0.85 0.13 0.00
118_L 201_T 0.85 0.13 0.00
100_D 192_D 0.85 0.13 0.00
397_Y 229_Q 0.85 0.13 0.00
169_F 194_Q 0.84 0.13 0.00
346_L 213_A 0.84 0.13 0.00
12_L 82_E 0.84 0.12 0.00
310_L 228_K 0.84 0.12 0.00
308_Y 257_K 0.84 0.12 0.00
152_S 51_L 0.84 0.12 0.00
254_V 104_P 0.84 0.12 0.00
360_F 74_D 0.84 0.12 0.00
457_V 44_Q 0.84 0.12 0.00
433_Y 66_Y 0.84 0.12 0.00
378_V 66_Y 0.84 0.12 0.00
297_L 150_G 0.83 0.12 0.00
409_W 136_P 0.83 0.12 0.00
43_I 108_T 0.83 0.12 0.00
378_V 164_E 0.83 0.12 0.00
237_P 212_V 0.83 0.12 0.00
459_I 195_V 0.83 0.12 0.00
318_T 45_H 0.83 0.12 0.00
116_G 130_R 0.83 0.12 0.00
393_I 64_L 0.82 0.12 0.00
423_Y 71_T 0.82 0.12 0.00
197_M 127_A 0.82 0.12 0.00
374_A 124_S 0.82 0.12 0.00
418_S 163_G 0.82 0.12 0.00
86_A 254_Q 0.82 0.12 0.00
277_A 87_A 0.82 0.12 0.00
265_D 239_I 0.81 0.12 0.00
131_G 253_W 0.81 0.12 0.00
287_M 218_W 0.81 0.12 0.00
339_G 103_R 0.81 0.12 0.00
91_A 256_I 0.81 0.11 0.00
297_L 67_V 0.81 0.11 0.00
268_A 74_D 0.81 0.11 0.00
50_V 81_P 0.81 0.11 0.00
433_Y 221_E 0.81 0.11 0.00
252_G 196_T 0.80 0.11 0.00
166_A 137_Y 0.80 0.11 0.00
372_L 216_L 0.80 0.11 0.00
419_A 59_S 0.80 0.11 0.00
334_L 229_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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