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OPENSEQ.org
cI_C_cIII_cyt1
Genes: A B A+B
Length: 509 263 736
Sequences: 1997 884 268
Seq/Len: 3.92 3.36 0.36
MirrorTree (Pazo et al. 2001) 0.54
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 0.01 0.01 0.00
10 0.01 0.01 0.00
20 0.01 0.01 0.00
100 0.01 0.01 0.04
∞ 0.03 0.01 0.35
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
299_F 256_I 1.74 0.63 0.00
299_F 216_L 1.50 0.46 0.00
289_I 207_Q 1.36 0.37 0.00
229_I 214_A 1.27 0.32 0.00
31_I 163_G 1.22 0.28 0.00
473_V 201_T 1.20 0.27 0.00
475_L 87_A 1.15 0.25 0.00
389_L 83_D 1.13 0.23 0.00
156_L 221_E 1.13 0.23 0.00
261_G 185_Q 1.12 0.23 0.00
37_G 94_I 1.11 0.23 0.00
222_L 249_N 1.11 0.22 0.00
143_W 169_A 1.10 0.22 0.00
368_T 37_G 1.08 0.21 0.00
368_T 85_V 1.08 0.21 0.00
190_L 137_Y 1.08 0.21 0.00
341_A 129_A 1.08 0.21 0.00
353_A 235_V 1.06 0.20 0.00
92_V 94_I 1.05 0.20 0.00
172_T 218_W 1.05 0.20 0.00
28_P 203_A 1.02 0.18 0.00
457_L 130_R 1.02 0.18 0.00
417_V 177_A 1.01 0.18 0.00
19_Q 220_A 1.00 0.17 0.00
179_Q 75_E 0.99 0.17 0.00
42_L 91_N 0.97 0.16 0.00
227_F 255_P 0.97 0.16 0.00
91_V 118_G 0.96 0.16 0.00
353_A 240_V 0.96 0.16 0.00
206_N 216_L 0.95 0.16 0.00
368_T 228_K 0.95 0.16 0.00
179_Q 86_R 0.95 0.16 0.00
151_Y 174_Y 0.94 0.15 0.00
40_L 240_V 0.94 0.15 0.00
320_V 41_K 0.94 0.15 0.00
413_G 43_D 0.93 0.15 0.00
487_D 247_L 0.93 0.15 0.00
250_Q 51_L 0.93 0.15 0.00
146_M 249_N 0.93 0.15 0.00
378_W 127_A 0.92 0.14 0.00
99_V 223_K 0.91 0.14 0.00
228_F 161_Y 0.91 0.14 0.00
268_A 49_R 0.91 0.14 0.00
98_G 46_Q 0.91 0.14 0.00
444_Y 206_D 0.90 0.14 0.00
484_P 202_P 0.90 0.14 0.00
335_Q 52_Q 0.90 0.14 0.00
347_A 230_V 0.90 0.14 0.00
183_L 73_A 0.90 0.14 0.00
53_S 220_A 0.90 0.14 0.00
408_F 134_H 0.89 0.14 0.00
341_A 229_Q 0.88 0.13 0.00
411_L 169_A 0.88 0.13 0.00
250_Q 182_N 0.88 0.13 0.00
337_A 194_Q 0.88 0.13 0.00
59_G 52_Q 0.87 0.13 0.00
102_V 55_T 0.87 0.13 0.00
235_M 52_Q 0.87 0.13 0.00
132_L 237_F 0.87 0.13 0.00
299_F 132_G 0.87 0.13 0.00
342_V 106_V 0.87 0.13 0.00
91_V 72_L 0.86 0.13 0.00
44_L 48_Q 0.86 0.12 0.00
416_Q 74_D 0.86 0.12 0.00
103_L 43_D 0.86 0.12 0.00
210_L 243_A 0.86 0.12 0.00
390_F 81_P 0.86 0.12 0.00
342_V 108_T 0.86 0.12 0.00
92_V 135_G 0.86 0.12 0.00
273_R 216_L 0.85 0.12 0.00
303_W 82_E 0.85 0.12 0.00
101_A 212_V 0.85 0.12 0.00
353_A 36_E 0.85 0.12 0.00
263_L 40_G 0.85 0.12 0.00
174_F 130_R 0.85 0.12 0.00
431_F 103_R 0.85 0.12 0.00
262_I 203_A 0.85 0.12 0.00
475_L 77_G 0.85 0.12 0.00
66_E 158_L 0.85 0.12 0.00
103_L 250_K 0.84 0.12 0.00
6_L 256_I 0.84 0.12 0.00
325_F 246_Y 0.84 0.12 0.00
152_F 44_Q 0.84 0.12 0.00
143_W 224_M 0.84 0.12 0.00
328_I 173_L 0.84 0.12 0.00
467_M 129_A 0.84 0.12 0.00
110_E 249_N 0.84 0.12 0.00
315_I 246_Y 0.84 0.12 0.00
477_L 247_L 0.83 0.12 0.00
199_A 203_A 0.83 0.12 0.00
34_I 119_M 0.83 0.12 0.00
268_A 81_P 0.83 0.12 0.00
307_A 169_A 0.83 0.12 0.00
167_R 214_A 0.83 0.12 0.00
330_I 125_L 0.83 0.12 0.00
228_F 69_L 0.83 0.12 0.00
166_T 118_G 0.83 0.12 0.00
438_A 139_T 0.82 0.12 0.00
134_I 84_Q 0.82 0.12 0.00
248_H 111_F 0.82 0.11 0.00
24_G 140_G 0.82 0.11 0.00
438_A 173_L 0.82 0.11 0.00
261_G 144_L 0.82 0.11 0.00
171_A 218_W 0.82 0.11 0.00
134_I 167_E 0.82 0.11 0.00
320_V 205_V 0.82 0.11 0.00
346_I 96_D 0.82 0.11 0.00
424_I 96_D 0.82 0.11 0.00
266_T 247_L 0.82 0.11 0.00
408_F 136_P 0.82 0.11 0.00
29_R 250_K 0.82 0.11 0.00
469_L 73_A 0.81 0.11 0.00
337_A 197_Y 0.81 0.11 0.00
390_F 101_E 0.81 0.11 0.00
223_L 53_V 0.81 0.11 0.00
98_G 112_P 0.81 0.11 0.00
99_V 213_A 0.81 0.11 0.00
77_I 241_L 0.81 0.11 0.00
189_I 33_F 0.81 0.11 0.00
107_K 237_F 0.81 0.11 0.00
213_T 180_A 0.81 0.11 0.00
266_T 170_G 0.80 0.11 0.00
462_L 180_A 0.80 0.11 0.00
40_L 158_L 0.80 0.11 0.00
430_V 67_V 0.80 0.11 0.00
325_F 101_E 0.80 0.11 0.00
476_V 81_P 0.79 0.11 0.00
296_I 51_L 0.79 0.11 0.00
284_A 240_V 0.79 0.11 0.00
497_Q 230_V 0.79 0.10 0.00
426_T 27_H 0.79 0.10 0.00
95_G 210_T 0.79 0.10 0.00
156_L 192_D 0.79 0.10 0.00
41_A 69_L 0.79 0.10 0.00
436_S 143_Q 0.79 0.10 0.00
448_A 82_E 0.79 0.10 0.00
143_W 218_W 0.79 0.10 0.00
228_F 65_R 0.79 0.10 0.00
321_S 224_M 0.78 0.10 0.00
405_V 24_A 0.78 0.10 0.00
263_L 160_G 0.78 0.10 0.00
91_V 250_K 0.78 0.10 0.00
183_L 75_E 0.78 0.10 0.00
130_V 180_A 0.78 0.10 0.00
320_V 240_V 0.78 0.10 0.00
156_L 163_G 0.78 0.10 0.00
338_Y 42_F 0.78 0.10 0.00
167_R 217_M 0.78 0.10 0.00
290_A 37_G 0.78 0.10 0.00
16_L 52_Q 0.78 0.10 0.00
201_G 64_L 0.78 0.10 0.00
19_Q 129_A 0.78 0.10 0.00
183_L 230_V 0.78 0.10 0.00
183_L 64_L 0.77 0.10 0.00
83_I 240_V 0.77 0.10 0.00
30_W 93_D 0.77 0.10 0.00
478_L 77_G 0.77 0.10 0.00
185_M 214_A 0.77 0.10 0.00
473_V 129_A 0.77 0.10 0.00
156_L 179_F 0.77 0.10 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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