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OPENSEQ.org
cIV_A_40_cI_A_20_human
Genes: A B A+B
Length: 513 115 623
Sequences: 3286 4326 1721
Seq/Len: 6.41 37.62 2.76
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 0.00 0.05
2 0.00 0.00 0.14
5 0.01 0.00 1.33
10 0.01 0.00 1.58
20 0.01 0.00 1.70
100 0.02 0.01 1.85
∞ 0.06 0.02 2.74
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
504_T 76_P 1.19 0.81 0.07
36_L 59_A 1.16 0.78 0.07
27_G 76_P 1.15 0.77 0.06
181_T 23_W 1.09 0.72 0.05
17_T 56_F 1.01 0.64 0.04
220_F 113_W 0.98 0.60 0.04
254_I 8_M 0.97 0.58 0.04
412_I 69_I 0.96 0.58 0.04
87_I 72_L 0.95 0.56 0.03
395_H 73_L 0.93 0.54 0.03
266_E 76_P 0.91 0.52 0.03
28_V 69_I 0.90 0.50 0.03
7_L 18_M 0.88 0.47 0.03
12_H 113_W 0.86 0.46 0.03
453_L 96_I 0.84 0.43 0.02
410_A 26_Q 0.84 0.43 0.02
328_H 56_F 0.83 0.42 0.02
473_W 9_I 0.83 0.42 0.02
340_W 52_S 0.82 0.40 0.02
270_Y 75_L 0.81 0.40 0.02
388_A 97_I 0.81 0.40 0.02
183_L 3_F 0.81 0.39 0.02
155_V 25_P 0.80 0.38 0.02
504_T 37_Y 0.80 0.38 0.02
261_Y 87_M 0.79 0.37 0.02
289_A 113_W 0.79 0.37 0.02
353_L 35_T 0.78 0.36 0.02
350_V 7_L 0.78 0.36 0.02
87_I 108_Q 0.78 0.35 0.02
215_L 108_Q 0.78 0.35 0.02
337_A 109_K 0.77 0.35 0.02
363_L 70_A 0.77 0.35 0.02
328_H 36_P 0.77 0.35 0.02
260_Y 56_F 0.77 0.34 0.02
196_I 93_L 0.77 0.34 0.02
36_L 61_T 0.76 0.34 0.02
374_V 19_I 0.76 0.33 0.02
391_G 47_A 0.76 0.33 0.02
359_A 20_I 0.74 0.32 0.02
253_M 100_L 0.74 0.32 0.02
505_F 58_V 0.74 0.32 0.02
447_Y 8_M 0.74 0.31 0.02
196_I 13_L 0.73 0.31 0.02
289_A 106_W 0.73 0.30 0.02
415_T 87_M 0.73 0.30 0.01
350_V 91_S 0.72 0.30 0.01
502_Y 64_L 0.72 0.30 0.01
472_I 112_D 0.72 0.30 0.01
325_A 59_A 0.72 0.29 0.01
487_E 76_P 0.72 0.29 0.01
359_A 86_L 0.72 0.29 0.01
89_A 18_M 0.71 0.29 0.01
143_V 17_L 0.71 0.29 0.01
342_L 23_W 0.71 0.29 0.01
345_I 85_P 0.71 0.28 0.01
85_L 72_L 0.71 0.28 0.01
314_I 20_I 0.71 0.28 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
4474 0.34 cIV_A_20_cI_A_40_human Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.18 Done - Shared
4471 3.35 cIV_A_20_cI_A_10_human Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.11 Done - Shared
4470 3.05 cIV_A_10_cI_A_20_human Δgene:(1, ∞) A:(1E-10, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.23 Done - Shared
4468 2.76 cIV_A_40_cI_A_20_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
4466 0.34 cIV_A_20_cI_A_20_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.18 Done - Shared
4460 3.04 cIV_A_20_cI_A_20_human Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.27 Done - Shared
4458 3.54 cIV_A_4_cI_A_4_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.05 Done - Shared
4456 0 cIV_A_80_cI_A_80_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 8) msa: Jackhmmer (2015_06) Killed - Shared
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