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OPENSEQ.org
cIV_A_80_cI_H_80_human
Genes: A B A+B
Length: 513 318 825
Sequences: 3020 3641 1970
Seq/Len: 5.89 11.45 2.39
MirrorTree (Pazo et al. 2001) 0.66
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 0.09
2 0.00 0.00 0.50
5 0.01 0.00 0.65
10 0.01 0.00 0.94
20 0.01 0.00 1.58
100 0.02 0.01 1.66
∞ 0.05 0.02 2.37
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
188_V 61_L 1.11 0.69 0.01
187_S 226_A 1.09 0.68 0.01
397_F 237_L 1.08 0.67 0.01
473_W 116_I 1.06 0.65 0.01
340_W 203_G 1.05 0.64 0.01
356_I 132_A 1.04 0.62 0.01
413_H 165_L 0.99 0.56 0.01
87_I 222_L 0.98 0.56 0.01
327_L 13_I 0.98 0.56 0.01
362_S 205_S 0.97 0.55 0.01
97_M 50_A 0.96 0.53 0.01
320_V 245_T 0.96 0.53 0.01
254_I 151_L 0.95 0.52 0.01
25_W 136_V 0.93 0.49 0.01
27_G 97_N 0.92 0.49 0.01
175_A 295_P 0.92 0.49 0.01
393_F 106_L 0.92 0.48 0.01
394_I 126_N 0.91 0.47 0.01
293_F 203_G 0.91 0.47 0.01
335_S 106_L 0.90 0.46 0.01
374_V 225_M 0.89 0.45 0.01
270_Y 223_F 0.89 0.45 0.01
108_S 136_V 0.89 0.44 0.01
409_Y 148_I 0.88 0.44 0.01
395_H 129_L 0.87 0.43 0.01
357_V 140_I 0.87 0.43 0.01
465_V 135_A 0.87 0.43 0.01
220_F 84_L 0.87 0.42 0.01
332_M 76_T 0.87 0.42 0.01
508_P 108_T 0.86 0.42 0.01
336_A 165_L 0.86 0.41 0.01
172_K 245_T 0.86 0.41 0.01
89_A 198_F 0.85 0.40 0.01
359_A 41_G 0.85 0.40 0.01
263_G 49_F 0.84 0.40 0.01
258_V 111_L 0.84 0.40 0.01
18_L 263_T 0.83 0.38 0.01
399_L 136_V 0.83 0.38 0.01
337_A 262_K 0.83 0.38 0.01
328_H 289_L 0.82 0.37 0.01
293_F 205_S 0.81 0.36 0.01
357_V 148_I 0.81 0.36 0.01
507_E 35_K 0.81 0.35 0.01
257_I 173_W 0.81 0.35 0.01
184_F 127_Y 0.80 0.35 0.01
330_S 148_I 0.80 0.35 0.01
412_I 20_L 0.80 0.34 0.01
337_A 245_T 0.79 0.34 0.01
338_V 88_P 0.79 0.34 0.01
141_A 276_A 0.79 0.34 0.01
97_M 128_A 0.79 0.34 0.01
161_A 196_T 0.79 0.34 0.01
426_F 140_I 0.79 0.33 0.01
505_F 287_H 0.78 0.33 0.01
215_L 232_I 0.78 0.33 0.01
314_I 79_L 0.78 0.33 0.01
345_I 81_I 0.78 0.33 0.01
359_A 152_S 0.78 0.32 0.01
149_S 48_P 0.78 0.32 0.01
206_I 211_F 0.78 0.32 0.01
386_V 237_L 0.77 0.32 0.01
332_M 49_F 0.77 0.32 0.01
112_L 221_A 0.77 0.32 0.01
181_T 147_A 0.77 0.32 0.01
33_L 73_T 0.77 0.32 0.01
85_L 82_A 0.77 0.31 0.01
169_I 261_T 0.77 0.31 0.01
488_P 182_A 0.77 0.31 0.01
161_A 146_L 0.76 0.31 0.01
267_P 260_V 0.76 0.30 0.01
32_A 217_A 0.76 0.30 0.01
443_Y 106_L 0.76 0.30 0.01
346_F 19_F 0.75 0.30 0.01
89_A 129_L 0.75 0.30 0.01
87_I 11_V 0.75 0.30 0.01
134_G 79_L 0.75 0.30 0.01
50_N 128_A 0.75 0.30 0.01
413_H 105_I 0.75 0.30 0.01
180_Q 107_A 0.75 0.29 0.01
279_S 299_A 0.75 0.29 0.01
100_M 129_L 0.74 0.29 0.01
12_H 215_Y 0.74 0.29 0.01
67_F 285_L 0.74 0.29 0.01
262_S 155_L 0.74 0.28 0.01
397_F 240_T 0.74 0.28 0.01
265_K 232_I 0.74 0.28 0.01
343_G 190_L 0.73 0.28 0.00
314_I 261_T 0.73 0.28 0.00
182_P 244_G 0.73 0.28 0.00
57_I 106_L 0.73 0.27 0.00
231_Y 13_I 0.73 0.27 0.00
29_L 102_L 0.72 0.27 0.00
485_V 115_S 0.72 0.27 0.00
392_G 236_T 0.72 0.27 0.00
400_F 159_S 0.72 0.27 0.00
488_P 101_G 0.72 0.27 0.00
390_M 211_F 0.72 0.27 0.00
440_Y 71_Y 0.72 0.27 0.00
391_G 107_A 0.72 0.27 0.00
345_I 145_T 0.72 0.27 0.00
400_F 185_W 0.72 0.27 0.00
64_V 7_L 0.72 0.27 0.00
314_I 117_L 0.72 0.27 0.00
210_L 29_G 0.71 0.26 0.00
453_L 66_S 0.71 0.26 0.00
253_M 87_T 0.71 0.26 0.00
39_A 148_I 0.71 0.26 0.00
303_A 18_A 0.71 0.26 0.00
455_S 261_T 0.71 0.26 0.00
73_I 284_Q 0.71 0.26 0.00
187_S 292_N 0.71 0.26 0.00
340_W 33_L 0.71 0.26 0.00
314_I 71_Y 0.71 0.26 0.00
350_V 27_I 0.71 0.26 0.00
314_I 161_N 0.71 0.26 0.00
58_V 209_S 0.71 0.26 0.00
87_I 276_A 0.71 0.26 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
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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