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OPENSEQ.org
cIV_A_20_cI_A_10_human
Genes: A B A+B
Length: 513 115 623
Sequences: 4396 4670 2086
Seq/Len: 8.57 40.61 3.35
MirrorTree (Pazo et al. 2001) 0.27
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 0.08
2 0.01 0.00 0.21
5 0.02 0.00 1.49
10 0.02 0.00 1.81
20 0.03 0.00 1.96
100 0.04 0.01 2.19
∞ 0.08 0.02 3.32
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
215_L 108_Q 1.18 0.84 0.11
274_V 67_L 1.10 0.78 0.09
87_I 72_L 1.03 0.71 0.07
270_Y 77_W 0.99 0.67 0.06
294_T 106_W 0.97 0.64 0.06
339_L 60_I 0.95 0.62 0.05
263_G 58_V 0.92 0.58 0.05
359_A 30_Y 0.89 0.55 0.04
318_V 63_L 0.86 0.51 0.04
363_L 110_G 0.86 0.51 0.04
500_P 58_V 0.86 0.51 0.04
29_L 70_A 0.85 0.50 0.04
504_T 59_A 0.85 0.49 0.04
220_F 69_I 0.84 0.49 0.04
254_I 16_L 0.83 0.47 0.04
472_I 8_M 0.83 0.47 0.04
504_T 104_Y 0.83 0.47 0.04
412_I 69_I 0.82 0.46 0.04
12_H 113_W 0.82 0.46 0.04
501_P 72_L 0.82 0.46 0.03
447_Y 8_M 0.82 0.45 0.03
85_L 72_L 0.82 0.45 0.03
274_V 37_Y 0.81 0.45 0.03
53_I 102_L 0.81 0.44 0.03
441_S 56_F 0.81 0.44 0.03
334_W 11_T 0.81 0.44 0.03
113_L 81_T 0.80 0.43 0.03
87_I 108_Q 0.79 0.42 0.03
117_M 75_L 0.79 0.42 0.03
413_H 54_K 0.78 0.41 0.03
393_F 98_L 0.77 0.40 0.03
24_A 11_T 0.77 0.40 0.03
166_T 12_L 0.77 0.40 0.03
342_L 37_Y 0.77 0.39 0.03
328_H 56_F 0.76 0.39 0.03
17_T 56_F 0.76 0.38 0.03
346_F 80_Q 0.75 0.38 0.03
461_S 73_L 0.75 0.37 0.03
289_A 113_W 0.75 0.37 0.03
117_M 64_L 0.74 0.36 0.03
83_V 75_L 0.74 0.36 0.03
311_I 32_E 0.74 0.35 0.03
50_N 56_F 0.73 0.35 0.02
261_Y 67_L 0.72 0.34 0.02
363_L 70_A 0.72 0.33 0.02
28_V 69_I 0.72 0.33 0.02
155_V 25_P 0.72 0.33 0.02
353_L 63_L 0.72 0.33 0.02
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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