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OPENSEQ.org
cIV_A_4_cI_M_40_1_Pdenitr
Genes: A B A+B
Length: 538 513 1007
Sequences: 4477 3566 1671
Seq/Len: 8.32 6.95 1.66
MirrorTree (Pazo et al. 2001) 0.28
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 0.02
2 0.01 0.01 0.04
5 0.02 0.01 0.12
10 0.03 0.01 0.61
20 0.03 0.01 0.68
100 0.05 0.02 0.82
∞ 0.08 0.03 1.59
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
378_S 94_F 1.27 0.73 0.02
378_S 50_L 0.93 0.40 0.01
181_A 348_F 0.92 0.39 0.01
277_V 48_I 0.91 0.38 0.01
127_A 327_G 0.90 0.37 0.01
67_N 375_L 0.90 0.36 0.01
491_V 408_T 0.87 0.34 0.01
343_I 252_A 0.87 0.34 0.01
438_I 318_V 0.86 0.33 0.01
213_W 231_V 0.86 0.32 0.01
312_Y 95_M 0.85 0.31 0.01
359_W 436_W 0.83 0.30 0.01
485_L 46_F 0.83 0.30 0.01
267_I 403_V 0.82 0.29 0.01
83_M 256_L 0.82 0.29 0.01
410_A 130_A 0.82 0.29 0.01
472_I 81_V 0.81 0.28 0.01
71_W 318_V 0.81 0.28 0.01
500_R 44_A 0.81 0.28 0.01
420_S 395_G 0.81 0.28 0.01
135_A 422_V 0.80 0.27 0.01
12_H 265_G 0.79 0.27 0.01
102_L 89_V 0.79 0.26 0.00
49_M 92_T 0.79 0.26 0.00
376_V 366_T 0.78 0.26 0.00
527_F 394_V 0.78 0.26 0.00
378_S 224_A 0.78 0.25 0.00
410_A 172_L 0.77 0.25 0.00
102_L 406_F 0.77 0.25 0.00
90_A 126_G 0.77 0.25 0.00
100_M 340_I 0.77 0.25 0.00
37_M 22_F 0.77 0.25 0.00
445_F 247_V 0.76 0.24 0.00
416_I 422_V 0.75 0.24 0.00
23_A 469_I 0.75 0.24 0.00
273_I 238_V 0.75 0.23 0.00
364_L 153_I 0.75 0.23 0.00
7_F 117_F 0.75 0.23 0.00
282_A 61_T 0.75 0.23 0.00
361_F 373_G 0.74 0.23 0.00
36_Y 62_G 0.74 0.23 0.00
179_L 50_L 0.74 0.22 0.00
79_G 18_I 0.74 0.22 0.00
347_W 401_G 0.73 0.22 0.00
378_S 339_A 0.73 0.22 0.00
48_Y 420_A 0.72 0.21 0.00
207_S 151_I 0.72 0.21 0.00
35_V 138_L 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
3340 1.98 cIV_A_6_cI_M_20_1_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-20, 1) msa: Jackhmmer (2015_06) 0.06 Done - Shared
3339 1.66 cIV_A_4_cI_M_40_1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-40, 1) msa: Jackhmmer (2015_06) 0.02 Done - Shared
3328 1.98 cIV_A_4_cI_M_20_1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-20, 1) msa: Jackhmmer (2015_06) 0.09 Done - Shared
3327 2.23 cIV_A_4_cI_M_4_1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 1) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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