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OPENSEQ.org
cI_H_40_cIII_isp_6_Pdenitr
Genes: A B A+B
Length: 345 190 515
Sequences: 4228 1587 474
Seq/Len: 12.26 8.35 0.92
MirrorTree (Pazo et al. 2001) 0.60
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 0.00
5 0.00 0.01 0.00
10 0.00 0.01 0.01
20 0.01 0.01 0.01
100 0.01 0.01 0.07
∞ 0.02 0.04 0.89
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
51_N 22_A 1.27 0.56 0.00
27_M 15_R 1.21 0.50 0.00
113_I 151_F 1.20 0.50 0.00
290_M 62_E 1.19 0.48 0.00
73_I 189_L 1.09 0.39 0.00
313_V 176_I 1.06 0.37 0.00
24_A 188_K 1.04 0.36 0.00
96_L 124_E 1.04 0.35 0.00
155_I 13_A 1.02 0.34 0.00
102_I 18_F 1.01 0.33 0.00
15_M 187_I 1.01 0.33 0.00
199_L 174_L 1.01 0.33 0.00
289_Y 168_G 1.00 0.32 0.00
144_F 185_T 0.98 0.31 0.00
165_I 162_S 0.97 0.30 0.00
203_V 84_D 0.97 0.30 0.00
28_G 28_T 0.96 0.29 0.00
56_W 18_F 0.96 0.29 0.00
17_L 159_Y 0.95 0.29 0.00
12_A 29_V 0.94 0.27 0.00
132_I 131_V 0.93 0.27 0.00
317_L 61_V 0.92 0.26 0.00
74_V 22_A 0.92 0.26 0.00
197_P 123_G 0.91 0.26 0.00
326_A 15_R 0.90 0.25 0.00
82_F 27_G 0.89 0.24 0.00
28_G 96_Q 0.89 0.24 0.00
313_V 33_A 0.89 0.24 0.00
172_T 18_F 0.88 0.24 0.00
284_M 15_R 0.88 0.23 0.00
258_L 189_L 0.88 0.23 0.00
102_I 30_A 0.87 0.23 0.00
273_I 163_G 0.87 0.23 0.00
196_L 37_T 0.86 0.23 0.00
108_W 187_I 0.86 0.22 0.00
282_I 184_D 0.86 0.22 0.00
227_L 36_W 0.86 0.22 0.00
286_F 88_A 0.85 0.22 0.00
268_S 83_E 0.84 0.21 0.00
12_A 32_G 0.84 0.21 0.00
15_M 87_Q 0.84 0.21 0.00
281_V 34_A 0.84 0.21 0.00
123_A 28_T 0.84 0.21 0.00
23_I 19_L 0.83 0.21 0.00
16_L 127_V 0.83 0.20 0.00
12_A 33_A 0.83 0.20 0.00
290_M 176_I 0.83 0.20 0.00
21_A 189_L 0.83 0.20 0.00
320_G 104_N 0.83 0.20 0.00
324_L 88_A 0.82 0.20 0.00
75_I 22_A 0.82 0.20 0.00
210_L 28_T 0.81 0.19 0.00
287_W 46_A 0.81 0.19 0.00
199_L 34_A 0.81 0.19 0.00
245_A 189_L 0.81 0.19 0.00
315_L 159_Y 0.81 0.19 0.00
104_F 63_T 0.81 0.19 0.00
15_M 129_I 0.81 0.19 0.00
115_V 145_G 0.80 0.19 0.00
144_F 50_A 0.80 0.19 0.00
233_T 116_N 0.80 0.19 0.00
93_M 127_V 0.80 0.19 0.00
144_F 68_T 0.80 0.19 0.00
80_D 187_I 0.79 0.18 0.00
221_V 62_E 0.79 0.18 0.00
259_S 84_D 0.79 0.18 0.00
65_A 49_Q 0.79 0.18 0.00
254_M 19_L 0.79 0.18 0.00
81_K 93_D 0.78 0.17 0.00
102_I 69_V 0.78 0.17 0.00
166_I 142_D 0.77 0.17 0.00
9_Y 182_L 0.77 0.17 0.00
256_A 133_T 0.77 0.17 0.00
150_S 31_A 0.77 0.17 0.00
121_F 78_I 0.77 0.17 0.00
328_L 32_G 0.77 0.17 0.00
291_F 64_G 0.77 0.17 0.00
148_L 88_A 0.77 0.17 0.00
294_V 127_V 0.77 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
3041 0.92 cI_H_40_cIII_isp_6_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3040 0.94 cI_H_40_cIII_isp_2_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3038 0.95 cI_H_40_cIII_isp_4_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
2723 1.03 cI_H_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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