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OPENSEQ.org
cIV_B_10_cIII_isp_10_Pdenitr
Genes: A B A+B
Length: 252 190 427
Sequences: 4618 1539 707
Seq/Len: 18.33 8.1 1.66
MirrorTree (Pazo et al. 2001) 0.52
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 0.01 0.00
2 0.00 0.01 0.01
5 0.00 0.01 0.31
10 0.01 0.01 0.59
20 0.01 0.01 0.63
100 0.02 0.01 0.76
∞ 0.04 0.04 1.60
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
91_A 28_T 1.12 0.60 0.00
114_I 187_I 1.11 0.59 0.00
217_S 185_T 1.05 0.53 0.00
121_W 157_S 1.00 0.47 0.00
24_S 34_A 0.99 0.45 0.00
121_W 170_A 0.98 0.45 0.00
162_V 163_G 0.96 0.42 0.00
225_A 22_A 0.95 0.41 0.00
44_A 187_I 0.93 0.40 0.00
77_I 10_D 0.92 0.38 0.00
239_Y 42_M 0.91 0.37 0.00
174_V 19_L 0.88 0.35 0.00
225_A 168_G 0.85 0.32 0.00
167_G 123_G 0.85 0.32 0.00
80_I 29_V 0.84 0.31 0.00
169_K 28_T 0.84 0.31 0.00
114_I 28_T 0.82 0.29 0.00
235_S 131_V 0.81 0.28 0.00
248_E 184_D 0.81 0.28 0.00
225_A 24_A 0.81 0.28 0.00
114_I 67_L 0.81 0.28 0.00
87_L 79_R 0.80 0.28 0.00
22_P 34_A 0.80 0.27 0.00
246_A 88_A 0.80 0.27 0.00
114_I 5_D 0.79 0.27 0.00
45_V 54_I 0.78 0.26 0.00
234_V 35_A 0.77 0.25 0.00
43_T 53_S 0.77 0.25 0.00
68_P 140_I 0.77 0.25 0.00
63_R 19_L 0.77 0.25 0.00
204_F 30_A 0.77 0.25 0.00
68_P 144_A 0.77 0.24 0.00
117_I 162_S 0.76 0.24 0.00
156_L 162_S 0.76 0.24 0.00
47_I 140_I 0.76 0.24 0.00
176_A 37_T 0.75 0.23 0.00
53_L 49_Q 0.75 0.23 0.00
58_V 29_V 0.75 0.23 0.00
186_P 29_V 0.75 0.23 0.00
84_V 29_V 0.74 0.23 0.00
170_V 52_A 0.74 0.23 0.00
44_A 15_R 0.74 0.23 0.00
89_L 17_D 0.74 0.23 0.00
235_S 33_A 0.73 0.22 0.00
26_P 96_Q 0.73 0.22 0.00
243_L 34_A 0.72 0.21 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
3113 0.9 cIV_B_6_cIII_isp_40_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.03 Done - Shared
3112 0.35 cIV_B_10_cIII_isp_60_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3111 0.9 cIV_B_10_cIII_isp_40_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.24 Done - Shared
3110 1.66 cIV_B_10_cIII_isp_10_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3109 0.91 cIV_B_10_cIII_isp_20_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.21 Done - Shared
3108 1.65 cIV_B_20_cIII_isp_10_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
3107 0.8 cIV_B_40_cIII_isp_40_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
3106 1.7 cIV_B_4_cIII_isp_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3099 0.9 cIV_A_20_cIII_isp_20_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.15 Done - Shared
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