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OPENSEQ.org
cIV_A_4_cI_A_4_human
Genes: A B A+B
Length: 513 115 624
Sequences: 4454 4876 2206
Seq/Len: 8.68 42.4 3.54
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 0.15
2 0.01 0.00 0.30
5 0.02 0.00 1.61
10 0.03 0.00 1.96
20 0.03 0.00 2.14
100 0.05 0.01 2.37
∞ 0.08 0.02 3.51
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 1.10 0.79 0.05
155_V 25_P 1.03 0.73 0.04
29_L 70_A 0.98 0.68 0.03
274_V 67_L 0.94 0.62 0.03
294_T 106_W 0.93 0.61 0.03
447_Y 8_M 0.92 0.60 0.03
374_V 93_L 0.90 0.58 0.03
87_I 72_L 0.89 0.57 0.03
501_P 72_L 0.88 0.56 0.02
500_P 58_V 0.88 0.55 0.02
254_I 16_L 0.88 0.55 0.02
263_G 58_V 0.88 0.54 0.02
342_L 37_Y 0.87 0.54 0.02
28_V 69_I 0.86 0.53 0.02
464_A 71_L 0.86 0.53 0.02
89_A 18_M 0.85 0.51 0.02
363_L 110_G 0.84 0.51 0.02
270_Y 77_W 0.84 0.51 0.02
504_T 59_A 0.84 0.51 0.02
274_V 37_Y 0.84 0.50 0.02
114_A 18_M 0.84 0.50 0.02
504_T 104_Y 0.84 0.49 0.02
53_I 102_L 0.82 0.47 0.02
419_I 53_M 0.81 0.46 0.02
453_L 5_L 0.81 0.45 0.02
339_L 60_I 0.80 0.45 0.02
318_V 63_L 0.80 0.44 0.02
359_A 30_Y 0.79 0.43 0.02
412_I 69_I 0.78 0.42 0.02
220_F 69_I 0.78 0.42 0.02
335_S 89_M 0.77 0.41 0.02
12_H 113_W 0.77 0.41 0.02
333_K 16_L 0.76 0.40 0.02
413_H 54_K 0.76 0.40 0.02
461_S 73_L 0.76 0.39 0.02
196_I 64_L 0.75 0.39 0.02
36_L 61_T 0.74 0.38 0.01
334_W 11_T 0.74 0.37 0.01
328_H 56_F 0.73 0.37 0.01
353_L 56_F 0.73 0.36 0.01
261_Y 67_L 0.73 0.36 0.01
181_T 28_N 0.73 0.36 0.01
440_Y 102_L 0.73 0.36 0.01
220_F 113_W 0.73 0.35 0.01
328_H 36_P 0.71 0.34 0.01
442_D 95_I 0.71 0.34 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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