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OPENSEQ.org
cIV_A_cIII_cyt1_Pdenitr
Genes: A B A+B
Length: 538 263 768
Sequences: 4187 651 240
Seq/Len: 7.78 2.48 0.31
MirrorTree (Pazo et al. 2001) 0.05
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 0.02 0.00
2 0.01 0.02 0.00
5 0.02 0.02 0.00
10 0.02 0.02 0.01
20 0.03 0.02 0.01
100 0.04 0.02 0.05
∞ 0.08 0.02 0.30
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
273_I 240_V 1.65 0.52 0.00
166_A 220_A 1.15 0.22 0.00
175_A 54_Y 1.15 0.22 0.00
492_F 195_V 1.13 0.21 0.00
425_P 59_S 1.10 0.20 0.00
184_I 240_V 1.08 0.19 0.00
270_G 179_F 1.08 0.19 0.00
182_I 201_T 1.08 0.19 0.00
337_I 198_E 1.07 0.19 0.00
506_Y 100_E 1.07 0.19 0.00
68_G 249_N 1.06 0.18 0.00
74_M 59_S 1.05 0.18 0.00
9_S 144_L 1.05 0.18 0.00
425_P 187_A 1.03 0.17 0.00
533_R 46_Q 1.03 0.17 0.00
20_L 77_G 1.02 0.17 0.00
251_Y 214_A 1.01 0.17 0.00
339_V 220_A 1.01 0.16 0.00
533_R 214_A 1.01 0.16 0.00
393_V 115_S 0.99 0.16 0.00
278_I 194_Q 0.99 0.16 0.00
491_V 242_A 0.98 0.15 0.00
35_V 32_S 0.97 0.15 0.00
123_V 111_F 0.96 0.15 0.00
414_Y 206_D 0.95 0.14 0.00
182_I 82_E 0.95 0.14 0.00
29_I 154_I 0.94 0.14 0.00
483_S 254_Q 0.94 0.14 0.00
472_I 52_Q 0.94 0.14 0.00
123_V 107_P 0.93 0.14 0.00
106_A 240_V 0.93 0.14 0.00
71_W 240_V 0.92 0.13 0.00
411_G 27_H 0.92 0.13 0.00
529_T 187_A 0.92 0.13 0.00
21_F 250_K 0.91 0.13 0.00
495_L 154_I 0.90 0.13 0.00
355_T 202_P 0.89 0.12 0.00
519_P 241_L 0.89 0.12 0.00
35_V 41_K 0.89 0.12 0.00
482_A 80_L 0.89 0.12 0.00
435_M 236_I 0.89 0.12 0.00
242_P 216_L 0.88 0.12 0.00
134_L 108_T 0.88 0.12 0.00
474_S 216_L 0.87 0.12 0.00
278_I 248_T 0.87 0.12 0.00
290_L 241_L 0.87 0.12 0.00
273_I 209_A 0.87 0.12 0.00
492_F 155_H 0.86 0.12 0.00
103_H 192_D 0.86 0.12 0.00
172_V 115_S 0.86 0.12 0.00
488_I 242_A 0.86 0.12 0.00
298_A 246_Y 0.86 0.12 0.00
316_M 213_A 0.86 0.12 0.00
411_G 213_A 0.85 0.11 0.00
427_W 74_D 0.84 0.11 0.00
7_F 154_I 0.84 0.11 0.00
185_I 52_Q 0.84 0.11 0.00
438_I 236_I 0.84 0.11 0.00
35_V 60_A 0.84 0.11 0.00
485_L 195_V 0.83 0.11 0.00
362_G 154_I 0.83 0.11 0.00
134_L 54_Y 0.83 0.11 0.00
25_I 225_M 0.82 0.11 0.00
133_L 67_V 0.82 0.10 0.00
25_I 144_L 0.82 0.10 0.00
417_G 46_Q 0.82 0.10 0.00
21_F 38_P 0.81 0.10 0.00
277_V 64_L 0.81 0.10 0.00
186_T 30_D 0.81 0.10 0.00
479_I 44_Q 0.81 0.10 0.00
7_F 155_H 0.80 0.10 0.00
491_V 143_Q 0.80 0.10 0.00
492_F 86_R 0.80 0.10 0.00
359_W 8_G 0.80 0.10 0.00
445_F 251_K 0.79 0.10 0.00
405_V 196_T 0.79 0.10 0.00
438_I 105_R 0.79 0.10 0.00
278_I 170_G 0.79 0.10 0.00
479_I 126_M 0.79 0.10 0.00
71_W 237_F 0.79 0.10 0.00
212_A 175_H 0.79 0.10 0.00
86_V 52_Q 0.79 0.10 0.00
407_G 235_V 0.79 0.10 0.00
103_H 157_V 0.79 0.10 0.00
39_M 162_D 0.79 0.10 0.00
29_I 254_Q 0.78 0.10 0.00
389_T 176_N 0.78 0.10 0.00
435_M 255_P 0.78 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)
ID Seq/Len Name Options I_Prob Status
3080 0.57 cIV_A_4_cIII_cyt1_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3079 0.43 cIV_A_40_cIII_cyt1_4_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3078 0.55 cIV_A_20_cIII_cyt1_4_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3077 0.31 cIV_A_cIII_cyt1_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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