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OPENSEQ.org
1FQ1_reduced
Genes: A B A+B
Length: 183 295 449
Sequences: 1972 61333 424
Seq/Len: 10.78 207.91 0.94
MirrorTree (Pazo et al. 2001) 0.16
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.02 0.10 0.05
2 0.03 0.13 0.12
5 0.03 0.16 0.26
10 0.03 0.20 0.48
20 0.04 0.24 0.89
100 0.04 0.31 1.80
∞ 0.06 0.34 2.23
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_G 35_I 1.24 0.54 0.00
147_A 60_H 1.05 0.37 0.00
79_C 195_M 1.02 0.35 0.00
51_G 54_L 0.94 0.28 0.00
146_Q 114_G 0.93 0.27 0.00
81_I 187_S 0.90 0.25 0.00
119_H 51_E 0.88 0.24 0.00
53_Q 60_H 0.88 0.24 0.00
129_L 80_F 0.87 0.23 0.00
75_L 190_C 0.87 0.23 0.00
52_I 135_I 0.85 0.22 0.00
79_C 76_L 0.84 0.21 0.00
176_L 133_L 0.83 0.21 0.00
107_T 22_R 0.82 0.20 0.00
142_I 120_S 0.82 0.20 0.00
97_A 63_I 0.81 0.20 0.00
159_A 183_V 0.80 0.19 0.00
23_L 200_A 0.80 0.19 0.00
172_F 203_P 0.80 0.19 0.00
118_I 104_I 0.79 0.18 0.00
114_R 82_F 0.77 0.17 0.00
55_I 168_R 0.77 0.17 0.00
75_L 164_T 0.76 0.17 0.00
84_H 278_A 0.76 0.17 0.00
53_Q 16_G 0.75 0.17 0.00
48_K 265_M 0.74 0.16 0.00
81_I 24_K 0.74 0.16 0.00
104_E 67_L 0.74 0.16 0.00
154_L 187_S 0.74 0.16 0.00
52_I 164_T 0.74 0.16 0.00
111_K 187_S 0.74 0.16 0.00
169_L 17_V 0.73 0.15 0.00
123_G 273_R 0.73 0.15 0.00
55_I 48_A 0.73 0.15 0.00
106_L 63_I 0.73 0.15 0.00
110_L 81_E 0.73 0.15 0.00
151_L 10_I 0.73 0.15 0.00
55_I 135_I 0.72 0.15 0.00
99_C 27_G 0.72 0.15 0.00
130_V 211_L 0.72 0.15 0.00
12_L 81_E 0.72 0.15 0.00
51_G 190_C 0.72 0.15 0.00
135_L 59_N 0.71 0.15 0.00
55_I 41_T 0.71 0.14 0.00
171_E 49_I 0.71 0.14 0.00
89_A 4_F 0.71 0.14 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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