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OPENSEQ.org
cI_2_4_cI_6_4_tt
Genes: A B A+B
Length: 181 181 328
Sequences: 2539 1709 950
Seq/Len: 14.03 9.44 2.9
MirrorTree (Pazo et al. 2001) 0.51
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 0.06
2 0.00 0.01 0.43
5 0.01 0.02 1.97
10 0.01 0.02 1.99
20 0.02 0.03 2.03
100 0.04 0.04 2.12
∞ 0.10 0.10 2.62
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
131_A 108_M 0.94 0.56 0.00
77_K 56_A 0.93 0.56 0.00
12_E 36_L 0.90 0.51 0.00
29_P 120_N 0.86 0.46 0.00
153_L 158_V 0.84 0.44 0.00
131_A 147_L 0.83 0.43 0.00
159_A 20_L 0.82 0.42 0.00
69_Y 137_V 0.81 0.41 0.00
119_V 37_W 0.78 0.36 0.00
48_E 84_L 0.77 0.36 0.00
149_R 153_Q 0.75 0.34 0.00
95_E 77_V 0.74 0.32 0.00
53_V 78_M 0.73 0.32 0.00
126_G 17_E 0.71 0.30 0.00
163_L 22_T 0.71 0.29 0.00
49_I 78_M 0.71 0.29 0.00
89_K 48_I 0.70 0.29 0.00
29_P 44_A 0.70 0.28 0.00
157_L 97_E 0.69 0.28 0.00
137_N 92_M 0.69 0.28 0.00
24_R 78_M 0.69 0.28 0.00
42_R 81_A 0.69 0.28 0.00
99_Y 28_V 0.69 0.28 0.00
40_W 127_V 0.69 0.27 0.00
62_G 118_F 0.69 0.27 0.00
6_D 150_A 0.69 0.27 0.00
141_Y 24_L 0.68 0.27 0.00
80_L 104_W 0.68 0.27 0.00
130_T 125_Q 0.68 0.26 0.00
59_E 63_F 0.68 0.26 0.00
69_Y 95_V 0.67 0.26 0.00
145_V 155_Q 0.67 0.25 0.00
27_I 28_V 0.66 0.25 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
4936 2.84 cI_2_10_cI_6_20_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
4934 2.73 cI_2_10_cI_6_20_tt Δgene:(1, ∞) A:(1E-10, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
4933 2.82 cI_2_10_cI_6_10_tt Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
4932 2.56 cI_2_40_cI_6_40_tt Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
4931 2.74 cI_2_20_cI_6_20_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.09 Done - Shared
4930 2.9 cI_2_4_cI_6_4_tt Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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