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OPENSEQ.org
cI_L_cIII_cyt1
Genes: A B A+B
Length: 613 263 852
Sequences: 2092 904 154
Seq/Len: 3.41 3.44 0.18
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 0.00 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 0.02
∞ 0.01 0.01 0.18
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
117_F 122_D 1.57 0.33 0.00
19_A 105_R 1.54 0.32 0.00
436_V 47_L 1.51 0.30 0.00
226_A 47_L 1.50 0.30 0.00
321_L 124_S 1.41 0.26 0.00
33_V 82_E 1.35 0.23 0.00
396_F 250_K 1.35 0.23 0.00
307_V 47_L 1.31 0.21 0.00
326_Q 141_L 1.26 0.20 0.00
44_V 125_L 1.26 0.19 0.00
330_A 249_N 1.25 0.19 0.00
454_S 256_I 1.24 0.19 0.00
373_P 48_Q 1.23 0.18 0.00
326_Q 223_K 1.22 0.18 0.00
392_V 177_A 1.20 0.17 0.00
292_L 125_L 1.20 0.17 0.00
44_V 85_V 1.19 0.17 0.00
325_V 230_V 1.18 0.17 0.00
396_F 29_E 1.17 0.16 0.00
321_L 127_A 1.15 0.16 0.00
220_L 170_G 1.14 0.16 0.00
389_L 257_K 1.12 0.15 0.00
158_Y 47_L 1.10 0.14 0.00
97_F 87_A 1.07 0.14 0.00
299_L 75_E 1.06 0.13 0.00
413_N 256_I 1.06 0.13 0.00
16_V 240_V 1.06 0.13 0.00
133_A 73_A 1.05 0.13 0.00
397_F 230_V 1.05 0.13 0.00
370_K 132_G 1.04 0.13 0.00
409_N 69_L 1.04 0.13 0.00
64_L 232_F 1.04 0.13 0.00
133_A 224_M 1.02 0.12 0.00
33_V 91_N 1.02 0.12 0.00
111_E 120_G 1.01 0.12 0.00
226_A 217_M 0.99 0.12 0.00
25_W 91_N 0.99 0.12 0.00
139_M 254_Q 0.99 0.11 0.00
426_S 249_N 0.99 0.11 0.00
387_S 46_Q 0.99 0.11 0.00
121_N 158_L 0.98 0.11 0.00
283_V 30_D 0.98 0.11 0.00
181_L 73_A 0.97 0.11 0.00
267_A 234_S 0.97 0.11 0.00
133_A 232_F 0.97 0.11 0.00
183_F 250_K 0.97 0.11 0.00
226_A 245_L 0.97 0.11 0.00
41_A 141_L 0.97 0.11 0.00
265_L 142_S 0.96 0.11 0.00
383_G 223_K 0.96 0.11 0.00
15_F 251_K 0.96 0.11 0.00
85_S 130_R 0.96 0.11 0.00
234_P 143_Q 0.96 0.11 0.00
463_L 71_T 0.96 0.11 0.00
71_G 124_S 0.95 0.10 0.00
417_A 164_E 0.95 0.10 0.00
237_T 137_Y 0.95 0.10 0.00
84_L 222_P 0.94 0.10 0.00
379_F 244_L 0.94 0.10 0.00
64_L 84_Q 0.94 0.10 0.00
90_S 68_P 0.94 0.10 0.00
17_L 66_Y 0.94 0.10 0.00
79_L 196_T 0.94 0.10 0.00
233_L 124_S 0.93 0.10 0.00
87_T 63_G 0.93 0.10 0.00
362_I 152_E 0.93 0.10 0.00
321_L 122_D 0.92 0.10 0.00
20_F 241_L 0.92 0.10 0.00
33_V 108_T 0.92 0.10 0.00
43_L 85_V 0.92 0.10 0.00
464_S 244_L 0.92 0.10 0.00
240_A 211_D 0.91 0.10 0.00
72_D 243_A 0.91 0.10 0.00
158_Y 69_L 0.91 0.10 0.00
381_V 235_V 0.91 0.10 0.00
234_P 122_D 0.91 0.10 0.00
70_V 196_T 0.91 0.10 0.00
159_T 94_I 0.91 0.10 0.00
606_L 237_F 0.90 0.09 0.00
323_L 234_S 0.90 0.09 0.00
137_L 254_Q 0.90 0.09 0.00
20_F 169_A 0.90 0.09 0.00
168_M 224_M 0.90 0.09 0.00
118_A 29_E 0.90 0.09 0.00
272_L 187_A 0.89 0.09 0.00
181_L 64_L 0.89 0.09 0.00
467_V 206_D 0.89 0.09 0.00
64_L 236_I 0.89 0.09 0.00
407_M 155_H 0.89 0.09 0.00
465_T 44_Q 0.89 0.09 0.00
136_L 75_E 0.88 0.09 0.00
64_L 184_I 0.88 0.09 0.00
267_A 141_L 0.88 0.09 0.00
470_L 83_D 0.88 0.09 0.00
128_V 241_L 0.88 0.09 0.00
24_R 154_I 0.88 0.09 0.00
93_T 237_F 0.88 0.09 0.00
90_S 36_E 0.87 0.09 0.00
394_A 256_I 0.87 0.09 0.00
137_L 104_P 0.87 0.09 0.00
139_M 214_A 0.87 0.09 0.00
15_F 28_I 0.87 0.09 0.00
215_L 81_P 0.87 0.09 0.00
426_S 220_A 0.87 0.09 0.00
400_D 82_E 0.87 0.09 0.00
20_F 48_Q 0.87 0.09 0.00
426_S 232_F 0.86 0.09 0.00
441_E 170_G 0.86 0.09 0.00
441_E 151_P 0.86 0.09 0.00
160_D 235_V 0.86 0.09 0.00
368_L 124_S 0.86 0.09 0.00
117_F 127_A 0.86 0.09 0.00
108_R 122_D 0.85 0.09 0.00
114_S 224_M 0.85 0.09 0.00
405_G 74_D 0.85 0.09 0.00
397_F 146_N 0.85 0.09 0.00
382_G 215_F 0.85 0.08 0.00
36_G 168_E 0.85 0.08 0.00
320_F 125_L 0.84 0.08 0.00
586_S 105_R 0.84 0.08 0.00
201_V 59_S 0.84 0.08 0.00
436_V 181_G 0.84 0.08 0.00
373_P 222_P 0.84 0.08 0.00
234_P 116_G 0.84 0.08 0.00
117_F 204_T 0.84 0.08 0.00
348_A 105_R 0.84 0.08 0.00
419_L 247_L 0.84 0.08 0.00
187_I 59_S 0.83 0.08 0.00
285_I 148_I 0.83 0.08 0.00
416_V 44_Q 0.83 0.08 0.00
440_K 64_L 0.83 0.08 0.00
374_L 94_I 0.83 0.08 0.00
85_S 177_A 0.83 0.08 0.00
510_W 243_A 0.83 0.08 0.00
326_Q 47_L 0.83 0.08 0.00
139_M 230_V 0.83 0.08 0.00
390_P 47_L 0.83 0.08 0.00
370_K 240_V 0.82 0.08 0.00
436_V 39_F 0.82 0.08 0.00
93_T 92_F 0.82 0.08 0.00
234_P 140_G 0.82 0.08 0.00
208_F 151_P 0.82 0.08 0.00
379_F 69_L 0.82 0.08 0.00
300_V 67_V 0.82 0.08 0.00
405_G 106_V 0.82 0.08 0.00
97_F 235_V 0.82 0.08 0.00
161_P 254_Q 0.82 0.08 0.00
77_F 40_G 0.82 0.08 0.00
368_L 147_G 0.81 0.08 0.00
269_T 42_F 0.81 0.08 0.00
85_S 241_L 0.81 0.08 0.00
548_V 182_N 0.81 0.08 0.00
15_F 178_A 0.81 0.08 0.00
117_F 147_G 0.81 0.08 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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