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OPENSEQ.org
cIV_A_40_cI_H_40_human
Genes: A B A+B
Length: 513 318 823
Sequences: 3245 4127 2151
Seq/Len: 6.33 12.98 2.61
MirrorTree (Pazo et al. 2001) 0.61
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 0.00 0.11
2 0.00 0.00 0.56
5 0.01 0.00 0.75
10 0.01 0.00 1.10
20 0.01 0.01 1.76
100 0.02 0.01 1.87
∞ 0.06 0.02 2.59
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
33_L 73_T 1.13 0.74 0.03
161_A 146_L 1.09 0.70 0.02
187_S 226_A 1.03 0.64 0.02
397_F 237_L 1.02 0.62 0.02
473_W 116_I 1.01 0.62 0.02
87_I 222_L 1.01 0.61 0.02
220_F 84_L 1.01 0.61 0.02
18_L 128_A 0.97 0.57 0.02
505_F 287_H 0.96 0.56 0.02
335_S 106_L 0.94 0.54 0.02
293_F 203_G 0.94 0.53 0.02
413_H 165_L 0.94 0.53 0.01
193_I 110_S 0.91 0.49 0.01
350_V 27_I 0.89 0.47 0.01
362_S 205_S 0.88 0.46 0.01
359_A 152_S 0.88 0.46 0.01
254_I 151_L 0.87 0.45 0.01
350_V 302_M 0.87 0.45 0.01
175_A 295_P 0.86 0.44 0.01
400_F 159_S 0.85 0.42 0.01
202_L 146_L 0.84 0.42 0.01
293_F 205_S 0.84 0.42 0.01
453_L 102_L 0.84 0.41 0.01
320_V 245_T 0.84 0.41 0.01
27_G 97_N 0.83 0.41 0.01
89_A 132_A 0.83 0.41 0.01
339_L 4_A 0.83 0.40 0.01
134_G 79_L 0.83 0.40 0.01
297_M 231_I 0.82 0.40 0.01
29_L 102_L 0.80 0.37 0.01
135_N 176_L 0.80 0.37 0.01
293_F 28_L 0.80 0.36 0.01
470_F 89_L 0.79 0.36 0.01
507_E 35_K 0.79 0.36 0.01
444_P 186_F 0.79 0.36 0.01
455_S 261_T 0.79 0.35 0.01
485_V 151_L 0.78 0.35 0.01
7_L 277_Y 0.78 0.35 0.01
470_F 76_T 0.78 0.34 0.01
459_F 129_L 0.78 0.34 0.01
39_A 297_T 0.78 0.34 0.01
356_I 132_A 0.78 0.34 0.01
193_I 243_L 0.77 0.34 0.01
169_I 273_I 0.77 0.34 0.01
161_A 196_T 0.77 0.34 0.01
148_F 128_A 0.77 0.34 0.01
113_L 111_L 0.77 0.34 0.01
25_W 136_V 0.77 0.33 0.01
97_M 128_A 0.77 0.33 0.01
115_S 27_I 0.76 0.33 0.01
182_P 244_G 0.76 0.33 0.01
48_L 108_T 0.76 0.32 0.01
345_I 145_T 0.76 0.32 0.01
62_A 164_T 0.75 0.32 0.01
231_Y 27_I 0.75 0.32 0.01
395_H 129_L 0.75 0.32 0.01
361_S 231_I 0.75 0.31 0.01
142_S 132_A 0.75 0.31 0.01
262_S 155_L 0.75 0.31 0.01
394_I 126_N 0.75 0.31 0.01
286_I 15_I 0.75 0.31 0.01
413_H 105_I 0.74 0.31 0.01
428_Q 23_T 0.74 0.31 0.01
508_P 108_T 0.74 0.31 0.01
409_Y 148_I 0.74 0.31 0.01
89_A 198_F 0.74 0.30 0.01
328_H 289_L 0.74 0.30 0.01
447_Y 150_L 0.74 0.30 0.01
258_V 49_F 0.73 0.30 0.01
231_Y 13_I 0.73 0.30 0.01
314_I 161_N 0.73 0.30 0.01
374_V 225_M 0.73 0.29 0.01
340_W 203_G 0.73 0.29 0.01
270_Y 223_F 0.72 0.29 0.01
395_H 118_W 0.72 0.29 0.01
375_A 211_F 0.72 0.29 0.01
505_F 49_F 0.72 0.29 0.01
73_I 213_I 0.72 0.29 0.01
204_A 16_A 0.72 0.29 0.01
21_L 110_S 0.72 0.28 0.01
274_V 187_I 0.72 0.28 0.01
79_G 228_Y 0.71 0.28 0.01
87_I 11_V 0.71 0.28 0.01
97_M 50_A 0.71 0.28 0.01
328_H 155_L 0.71 0.28 0.01
476_F 106_L 0.71 0.28 0.01
155_V 273_I 0.71 0.28 0.01
346_F 19_F 0.71 0.27 0.01
306_T 224_F 0.71 0.27 0.01
467_L 71_Y 0.71 0.27 0.01
356_I 88_P 0.71 0.27 0.01
180_Q 107_A 0.71 0.27 0.01
325_A 77_L 0.71 0.27 0.01
112_L 221_A 0.71 0.27 0.01
327_L 13_I 0.70 0.27 0.01
318_V 71_Y 0.70 0.27 0.01
81_W 150_L 0.70 0.27 0.01
399_L 136_V 0.70 0.27 0.01
66_I 42_P 0.70 0.27 0.01
33_L 13_I 0.70 0.27 0.01
169_I 187_I 0.70 0.26 0.01
114_A 133_L 0.70 0.26 0.01
440_Y 203_G 0.69 0.26 0.01
489_S 73_T 0.69 0.26 0.01
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
4535 2.96 cIV_A_80_cI_H_80_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4534 2.39 cIV_A_80_cI_H_80_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
4533 2.57 cIV_A_40_cI_H_60_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
4532 2.59 cIV_A_60_cI_H_40_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.03 Done - Shared
4529 2.61 cIV_A_40_cI_H_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.03 Done - Shared
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