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OPENSEQ.org
L3-L23
Genes: A B A+B
Length: 209 100 304
Sequences: 2524 2126 1867
Seq/Len: 12.08 21.26 6.14
MirrorTree (Pazo et al. 2001) 0.76
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 0.00 0.08
2 0.00 0.00 6.02
5 0.00 0.00 6.04
10 0.00 0.00 6.04
20 0.00 0.00 6.04
100 0.00 0.00 6.05
∞ 0.00 0.00 6.09
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
104_V 29_T 0.83 0.66 0.00
39_D 85_V 0.82 0.63 0.00
161_M 19_K 0.78 0.58 0.00
34_V 16_V 0.77 0.57 0.00
37_V 86_T 0.74 0.53 0.00
9_V 52_E 0.73 0.50 0.00
24_V 85_V 0.72 0.50 0.00
198_G 59_N 0.69 0.45 0.00
4_L 27_S 0.64 0.38 0.00
162_A 41_A 0.64 0.38 0.00
152_P 44_K 0.64 0.37 0.00
13_R 96_V 0.63 0.36 0.00
169_R 86_T 0.63 0.36 0.00
127_F 19_K 0.62 0.35 0.00
7_K 82_K 0.62 0.35 0.00
13_R 31_V 0.62 0.35 0.00
200_D 86_T 0.61 0.33 0.00
122_V 63_V 0.60 0.32 0.00
111_G 86_T 0.60 0.31 0.00
149_N 71_G 0.59 0.31 0.00
172_V 37_D 0.59 0.31 0.00
15_F 16_V 0.59 0.30 0.00
179_R 56_E 0.59 0.30 0.00
125_W 70_H 0.59 0.30 0.00
165_M 49_K 0.58 0.30 0.00
80_W 80_W 0.58 0.30 0.00
138_L 93_L 0.58 0.29 0.00
28_E 68_K 0.58 0.29 0.00
164_Q 92_N 0.58 0.29 0.00
169_R 78_S 0.58 0.29 0.00
33_R 16_V 0.57 0.28 0.00
162_A 97_G 0.57 0.28 0.00
201_L 27_S 0.57 0.28 0.00
92_V 54_E 0.57 0.28 0.00
157_K 45_A 0.56 0.28 0.00
183_E 52_E 0.56 0.27 0.00
198_G 24_M 0.56 0.27 0.00
160_K 33_K 0.56 0.26 0.00
24_V 51_F 0.56 0.26 0.00
199_S 39_T 0.55 0.26 0.00
127_F 90_G 0.55 0.26 0.00
30_E 81_K 0.55 0.26 0.00
108_D 9_K 0.55 0.25 0.00
206_A 20_A 0.55 0.25 0.00
29_V 91_Q 0.55 0.25 0.00
63_P 30_I 0.54 0.25 0.00
3_G 44_K 0.54 0.25 0.00
92_V 96_V 0.54 0.24 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)
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