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OPENSEQ.org
cIV_A_80_cI_H_80_human
Genes: A B A+B
Length: 513 318 823
Sequences: 4483 4680 2440
Seq/Len: 8.74 14.72 2.96
MirrorTree (Pazo et al. 2001) 0.47
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 0.00 0.10
2 0.01 0.00 0.56
5 0.02 0.00 0.76
10 0.02 0.01 1.12
20 0.03 0.01 1.79
100 0.05 0.02 2.00
∞ 0.08 0.05 2.94
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
413_H 165_L 0.95 0.58 0.00
87_I 222_L 0.95 0.58 0.00
115_S 27_I 0.92 0.55 0.00
395_H 129_L 0.92 0.55 0.00
397_F 237_L 0.92 0.54 0.00
505_F 287_H 0.90 0.53 0.00
335_S 106_L 0.90 0.52 0.00
340_W 205_S 0.90 0.52 0.00
161_A 146_L 0.87 0.49 0.00
18_L 128_A 0.87 0.49 0.00
419_I 96_V 0.86 0.47 0.00
473_W 116_I 0.84 0.45 0.00
336_A 165_L 0.81 0.42 0.00
85_L 82_A 0.81 0.42 0.00
89_A 132_A 0.81 0.41 0.00
362_S 205_S 0.80 0.40 0.00
199_L 22_L 0.79 0.38 0.00
234_L 242_F 0.78 0.38 0.00
279_S 102_L 0.78 0.37 0.00
193_I 110_S 0.78 0.37 0.00
27_G 97_N 0.76 0.36 0.00
193_I 226_A 0.76 0.35 0.00
29_L 102_L 0.76 0.35 0.00
7_L 177_P 0.76 0.35 0.00
464_A 201_A 0.76 0.35 0.00
114_A 133_L 0.75 0.35 0.00
7_L 159_S 0.75 0.34 0.00
391_G 74_A 0.75 0.34 0.00
413_H 105_I 0.75 0.34 0.00
253_M 87_T 0.75 0.34 0.00
297_M 231_I 0.74 0.34 0.00
301_T 270_F 0.74 0.33 0.00
336_A 168_T 0.74 0.33 0.00
363_L 31_M 0.74 0.33 0.00
482_V 42_P 0.73 0.32 0.00
453_L 102_L 0.73 0.32 0.00
505_F 49_F 0.73 0.32 0.00
113_L 277_Y 0.73 0.32 0.00
307_S 71_Y 0.73 0.32 0.00
110_L 70_L 0.72 0.32 0.00
440_Y 203_G 0.72 0.31 0.00
314_I 161_N 0.72 0.31 0.00
338_V 88_P 0.72 0.31 0.00
29_L 42_P 0.71 0.30 0.00
507_E 35_K 0.71 0.30 0.00
279_S 85_L 0.71 0.30 0.00
155_V 258_Y 0.71 0.30 0.00
196_L 49_F 0.71 0.30 0.00
177_T 277_Y 0.70 0.29 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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