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OPENSEQ.org
cIV_A_10_cIII_isp_4_Pdenitr
Genes: A B A+B
Length: 538 190 699
Sequences: 4448 1692 784
Seq/Len: 8.27 8.91 1.12
MirrorTree (Pazo et al. 2001) 0.09
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 0.00 0.00
2 0.01 0.00 0.02
5 0.02 0.01 0.13
10 0.02 0.01 0.18
20 0.03 0.01 0.20
100 0.04 0.01 0.35
∞ 0.08 0.05 1.08
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
414_Y 187_I 1.28 0.62 0.00
438_I 129_I 1.20 0.55 0.00
409_F 78_I 1.06 0.42 0.00
472_I 56_V 1.04 0.40 0.00
368_T 131_V 1.02 0.38 0.00
488_I 19_L 0.97 0.34 0.00
236_G 31_A 0.95 0.33 0.00
482_A 159_Y 0.95 0.32 0.00
20_L 159_Y 0.94 0.32 0.00
494_T 31_A 0.92 0.29 0.00
426_E 184_D 0.92 0.29 0.00
361_F 167_R 0.89 0.27 0.00
225_A 131_V 0.88 0.26 0.00
21_F 90_R 0.86 0.26 0.00
32_C 51_L 0.85 0.25 0.00
382_L 28_T 0.84 0.24 0.00
83_M 128_M 0.84 0.24 0.00
500_R 125_W 0.84 0.24 0.00
37_M 131_V 0.83 0.23 0.00
99_F 61_V 0.83 0.23 0.00
438_I 54_I 0.83 0.23 0.00
208_V 78_I 0.82 0.23 0.00
442_L 87_Q 0.81 0.22 0.00
193_A 32_G 0.80 0.21 0.00
42_Q 34_A 0.78 0.20 0.00
152_P 163_G 0.78 0.20 0.00
98_Y 184_D 0.78 0.20 0.00
116_N 158_H 0.78 0.20 0.00
21_F 29_V 0.78 0.20 0.00
485_L 39_V 0.77 0.19 0.00
496_F 115_E 0.77 0.19 0.00
179_L 159_Y 0.77 0.19 0.00
71_W 10_D 0.77 0.19 0.00
32_C 35_A 0.77 0.19 0.00
382_L 31_A 0.77 0.19 0.00
351_I 90_R 0.75 0.18 0.00
471_N 113_T 0.75 0.18 0.00
482_A 180_E 0.74 0.18 0.00
29_I 131_V 0.74 0.18 0.00
411_G 26_A 0.74 0.18 0.00
425_P 129_I 0.74 0.18 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
3095 0.66 cIV_A_20_cIII_isp_20_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3094 1.12 cIV_A_10_cIII_isp_4_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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