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OPENSEQ.org
cI_D_2_cIII_isp_2_Pdenitr
Genes: A B A+B
Length: 412 190 583
Sequences: 3478 1785 581
Seq/Len: 8.44 9.39 1
MirrorTree (Pazo et al. 2001) 0.22
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 0.01 0.00
2 0.01 0.01 0.00
5 0.03 0.01 0.01
10 0.03 0.01 0.02
20 0.05 0.01 0.03
100 0.06 0.02 0.14
∞ 0.13 0.05 0.97
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
205_L 19_L 1.22 0.54 0.00
53_V 143_G 1.22 0.54 0.00
134_V 34_A 1.18 0.50 0.00
74_R 179_A 1.10 0.43 0.00
221_D 28_T 1.06 0.39 0.00
262_D 15_R 1.04 0.38 0.00
98_W 45_S 1.04 0.37 0.00
402_T 15_R 0.97 0.31 0.00
127_I 27_G 0.95 0.30 0.00
108_T 124_E 0.91 0.27 0.00
66_G 170_A 0.90 0.26 0.00
362_A 31_A 0.89 0.25 0.00
345_V 40_N 0.88 0.25 0.00
360_L 175_H 0.87 0.24 0.00
295_V 90_R 0.87 0.24 0.00
205_L 183_D 0.86 0.23 0.00
236_T 32_G 0.86 0.23 0.00
264_Q 131_V 0.84 0.22 0.00
195_C 165_I 0.84 0.22 0.00
120_L 35_A 0.83 0.22 0.00
97_A 78_I 0.83 0.21 0.00
196_E 187_I 0.82 0.21 0.00
354_G 152_C 0.82 0.21 0.00
161_Y 27_G 0.82 0.21 0.00
354_G 134_H 0.81 0.20 0.00
53_V 66_Q 0.80 0.20 0.00
109_V 63_T 0.80 0.20 0.00
229_D 63_T 0.80 0.20 0.00
109_V 118_T 0.80 0.20 0.00
354_G 155_H 0.80 0.20 0.00
108_T 107_K 0.80 0.19 0.00
56_A 9_G 0.79 0.19 0.00
354_G 132_C 0.79 0.19 0.00
99_C 174_L 0.78 0.19 0.00
296_Q 87_Q 0.78 0.19 0.00
195_C 167_R 0.78 0.18 0.00
165_C 182_L 0.78 0.18 0.00
296_Q 178_V 0.77 0.18 0.00
221_D 88_A 0.77 0.18 0.00
261_F 21_Y 0.76 0.17 0.00
347_A 163_G 0.76 0.17 0.00
221_D 35_A 0.76 0.17 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
3013 1 cI_D_2_cIII_isp_2_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
2807 1.02 cI_D_cIII_isp_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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