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OPENSEQ.org
cI_B_cIII_cyt1
Genes: A B A+B
Length: 613 263 851
Sequences: 2476 884 180
Seq/Len: 4.04 3.36 0.21
MirrorTree (Pazo et al. 2001) 0.31
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 0.00 0.01 0.00
100 0.00 0.01 0.03
∞ 0.01 0.01 0.21
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
19_A 105_R 1.72 0.46 0.00
331_A 64_L 1.45 0.30 0.00
321_L 124_S 1.38 0.27 0.00
33_V 82_E 1.37 0.27 0.00
117_F 122_D 1.35 0.26 0.00
331_A 94_I 1.35 0.25 0.00
44_V 85_V 1.34 0.25 0.00
226_A 47_L 1.26 0.21 0.00
426_S 249_N 1.25 0.21 0.00
396_F 29_E 1.22 0.20 0.00
409_N 69_L 1.21 0.19 0.00
269_T 120_G 1.17 0.18 0.00
436_V 47_L 1.17 0.18 0.00
181_L 73_A 1.16 0.18 0.00
133_A 232_F 1.12 0.16 0.00
381_V 67_V 1.11 0.16 0.00
267_A 234_S 1.09 0.15 0.00
330_A 249_N 1.08 0.15 0.00
16_V 240_V 1.07 0.15 0.00
373_P 48_Q 1.05 0.14 0.00
370_K 224_M 1.04 0.14 0.00
135_N 56_E 1.03 0.14 0.00
396_F 250_K 1.01 0.13 0.00
387_S 46_Q 1.01 0.13 0.00
133_A 224_M 1.00 0.13 0.00
444_H 151_P 1.00 0.13 0.00
465_T 44_Q 1.00 0.13 0.00
299_L 75_E 1.00 0.13 0.00
405_G 74_D 0.99 0.13 0.00
72_D 243_A 0.99 0.12 0.00
181_L 64_L 0.99 0.12 0.00
370_K 158_L 0.98 0.12 0.00
104_S 67_V 0.98 0.12 0.00
292_L 125_L 0.98 0.12 0.00
234_P 114_V 0.98 0.12 0.00
389_L 162_D 0.97 0.12 0.00
277_P 69_L 0.97 0.12 0.00
133_A 73_A 0.97 0.12 0.00
97_F 87_A 0.96 0.12 0.00
118_A 29_E 0.96 0.12 0.00
183_F 240_V 0.96 0.12 0.00
33_V 91_N 0.95 0.11 0.00
434_F 156_A 0.94 0.11 0.00
159_T 94_I 0.94 0.11 0.00
220_L 234_S 0.94 0.11 0.00
269_T 33_F 0.94 0.11 0.00
8_I 85_V 0.93 0.11 0.00
307_V 247_L 0.93 0.11 0.00
85_S 241_L 0.93 0.11 0.00
454_S 256_I 0.93 0.11 0.00
119_Y 250_K 0.91 0.10 0.00
85_S 130_R 0.91 0.10 0.00
64_L 84_Q 0.91 0.10 0.00
180_F 246_Y 0.91 0.10 0.00
397_F 230_V 0.91 0.10 0.00
49_G 64_L 0.91 0.10 0.00
307_V 47_L 0.91 0.10 0.00
43_L 85_V 0.90 0.10 0.00
158_Y 47_L 0.90 0.10 0.00
404_A 246_Y 0.90 0.10 0.00
226_A 214_A 0.90 0.10 0.00
326_Q 223_K 0.90 0.10 0.00
79_L 187_A 0.89 0.10 0.00
117_F 233_V 0.89 0.10 0.00
285_I 157_V 0.89 0.10 0.00
64_L 236_I 0.89 0.10 0.00
470_L 66_Y 0.89 0.10 0.00
465_T 240_V 0.89 0.10 0.00
20_F 169_A 0.88 0.10 0.00
392_V 177_A 0.88 0.10 0.00
407_M 155_H 0.87 0.10 0.00
441_E 170_G 0.87 0.10 0.00
473_P 243_A 0.87 0.10 0.00
362_I 152_E 0.87 0.10 0.00
183_F 250_K 0.87 0.10 0.00
280_L 241_L 0.86 0.09 0.00
161_P 226_D 0.86 0.09 0.00
55_N 151_P 0.86 0.09 0.00
234_P 143_Q 0.86 0.09 0.00
394_A 256_I 0.86 0.09 0.00
321_L 127_A 0.86 0.09 0.00
116_F 96_D 0.85 0.09 0.00
108_R 122_D 0.85 0.09 0.00
20_F 241_L 0.85 0.09 0.00
440_K 64_L 0.85 0.09 0.00
326_Q 141_L 0.84 0.09 0.00
272_L 129_A 0.84 0.09 0.00
139_M 230_V 0.84 0.09 0.00
215_L 32_S 0.83 0.09 0.00
27_E 151_P 0.83 0.09 0.00
183_F 59_S 0.83 0.09 0.00
368_L 124_S 0.83 0.09 0.00
369_R 214_A 0.83 0.09 0.00
416_V 44_Q 0.83 0.09 0.00
135_N 145_F 0.83 0.09 0.00
187_I 177_A 0.83 0.09 0.00
36_G 85_V 0.83 0.09 0.00
370_K 132_G 0.83 0.09 0.00
93_T 92_F 0.83 0.09 0.00
320_F 125_L 0.83 0.09 0.00
299_L 77_G 0.83 0.09 0.00
379_F 244_L 0.82 0.09 0.00
374_L 94_I 0.82 0.09 0.00
370_K 240_V 0.82 0.09 0.00
46_A 69_L 0.82 0.09 0.00
461_L 203_A 0.82 0.09 0.00
441_E 151_P 0.82 0.09 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)
ID Seq/Len Name Options I_Prob Status
2450 0.21 cI_L_cIII_cyt1 Δgene:(1, ∞) A:(1E-40, 1) B:(1E-06, 8) msa: Jackhmmer (2015_03) 0.00 Done - Shared
2449 0.18 cI_L_cIII_cyt1 Δgene:(1, ∞) A:(1E-60, 1) B:(1E-06, 8) msa: Jackhmmer (2015_03) 0.00 Done - Shared
2413 0.21 cI_B_cIII_cyt1 Δgene:(1, ∞) A:(1E-40, 1) B:(1E-10, 8) msa: Jackhmmer (2015_03) 0.00 Done - Shared
2410 0.12 cI_B_cIII_cyt1 Δgene:(1, ∞) A:(1E-60, 1) B:(1E-20, 8) msa: Jackhmmer (2015_03) 0.00 Done - Shared
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