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OPENSEQ.org
1HUR_A Arf1 GTPase GDP 1R8M_E Sec 7 domain
Genes: A B A+B
Length: 180 203 369
Sequences: 13559 1220 223
Seq/Len: 75.33 6.01 0.6
MirrorTree (Pazo et al. 2001) 0.18
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 0.10 0.05 0.04
2 0.11 0.05 0.07
5 0.13 0.06 0.15
10 0.14 0.06 0.32
20 0.15 0.06 0.58
100 0.20 0.07 1.51
∞ 0.22 0.10 2.28
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
30_T 76_V 1.24 0.41 0.00
33_L 31_I 1.22 0.40 0.00
81_F 186_Y 1.07 0.29 0.00
104_E 119_A 1.06 0.28 0.00
35_K 129_V 1.02 0.26 0.00
19_I 139_L 1.00 0.24 0.00
165_L 87_T 1.00 0.24 0.00
83_N 158_K 0.98 0.23 0.00
32_I 163_R 0.97 0.23 0.00
98_R 86_F 0.95 0.22 0.00
120_L 66_L 0.93 0.20 0.00
138_I 81_V 0.93 0.20 0.00
157_T 66_L 0.91 0.20 0.00
159_A 85_E 0.91 0.19 0.00
162_G 122_Y 0.90 0.19 0.00
40_E 142_S 0.88 0.18 0.00
100_N 98_F 0.88 0.18 0.00
55_V 122_Y 0.87 0.17 0.00
89_F 20_R 0.87 0.17 0.00
151_N 180_E 0.86 0.17 0.00
150_R 132_S 0.84 0.16 0.00
39_G 127_P 0.84 0.16 0.00
21_M 156_R 0.83 0.16 0.00
132_A 88_D 0.83 0.16 0.00
84_T 136_C 0.83 0.16 0.00
126_K 118_F 0.83 0.16 0.00
142_L 28_K 0.83 0.15 0.00
139_T 150_L 0.81 0.15 0.00
138_I 59_K 0.81 0.15 0.00
56_E 144_I 0.80 0.14 0.00
121_L 14_R 0.80 0.14 0.00
159_A 88_D 0.79 0.14 0.00
145_H 189_I 0.78 0.14 0.00
56_E 143_V 0.78 0.14 0.00
20_L 91_L 0.78 0.14 0.00
151_N 70_E 0.77 0.13 0.00
19_I 117_A 0.77 0.13 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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