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OPENSEQ.org
cIm_J_2_cytb_2_human
Genes: A B A+B
Length: 174 378 547
Sequences: 8320 4500 4143
Seq/Len: 47.82 11.9 7.57
MirrorTree (Pazo et al. 2001) 0.57
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 5.30
2 0.00 0.00 5.40
5 0.00 0.00 5.87
10 0.00 0.00 6.10
20 0.00 0.00 6.21
100 0.00 0.00 6.35
∞ 0.01 0.00 7.51
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
157_G 27_I 1.04 0.90 0.05
65_V 30_W 1.00 0.88 0.05
61_G 239_L 0.91 0.81 0.04
73_M 179_F 0.91 0.80 0.03
65_V 58_D 0.88 0.78 0.03
61_G 140_F 0.88 0.78 0.03
105_W 107_F 0.87 0.77 0.03
33_I 169_S 0.86 0.75 0.03
40_C 322_Q 0.80 0.67 0.02
164_V 243_T 0.79 0.66 0.02
70_T 322_Q 0.78 0.64 0.02
59_Y 181_F 0.76 0.61 0.02
145_L 197_L 0.76 0.61 0.02
61_G 58_D 0.75 0.60 0.02
33_I 251_G 0.75 0.60 0.02
30_L 219_T 0.74 0.59 0.02
73_M 180_T 0.73 0.57 0.02
161_F 322_Q 0.73 0.57 0.02
23_P 222_P 0.73 0.57 0.02
30_L 78_I 0.72 0.55 0.02
70_T 71_R 0.71 0.54 0.02
57_L 199_F 0.71 0.54 0.02
37_V 238_S 0.71 0.54 0.02
59_Y 56_S 0.71 0.54 0.02
161_F 325_Y 0.70 0.53 0.02
154_V 195_L 0.70 0.53 0.02
47_G 328_L 0.70 0.52 0.02
16_F 164_I 0.70 0.52 0.02
32_L 114_N 0.70 0.52 0.02
164_V 343_V 0.68 0.49 0.02
130_E 333_L 0.68 0.48 0.01
14_M 185_L 0.67 0.48 0.01
8_L 197_L 0.67 0.48 0.01
33_I 29_A 0.67 0.47 0.01
80_E 236_I 0.67 0.47 0.01
70_T 216_D 0.66 0.46 0.01
70_T 340_G 0.66 0.46 0.01
61_G 47_T 0.66 0.45 0.01
61_G 169_S 0.65 0.45 0.01
164_V 180_T 0.65 0.45 0.01
57_L 233_L 0.65 0.45 0.01
50_Y 57_P 0.65 0.44 0.01
171_A 189_I 0.65 0.44 0.01
73_M 342_P 0.65 0.44 0.01
153_V 129_M 0.65 0.44 0.01
73_M 338_I 0.65 0.43 0.01
145_L 375_K 0.65 0.43 0.01
128_E 10_L 0.64 0.43 0.01
157_G 105_G 0.64 0.42 0.01
151_W 230_L 0.63 0.41 0.01
150_R 46_T 0.62 0.40 0.01
126_I 356_V 0.62 0.40 0.01
54_M 155_Y 0.62 0.40 0.01
127_Y 46_T 0.62 0.40 0.01
73_M 301_L 0.62 0.39 0.01
63_M 322_Q 0.62 0.39 0.01
130_E 46_T 0.62 0.39 0.01
104_L 236_I 0.61 0.38 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
5763 0.35 cIm_J_40_cytb_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2016_06b) 0.01 Done - Shared
5757 7.25 cIm_J_4_cytb_4_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2016_06b) 0.03 Done - Shared
5756 7.57 cIm_J_2_cytb_2_human Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.05 Done - Shared
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