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OPENSEQ.org
1MH1_ Rac GTPase GNP 1NTY_A DHPH domain of TRIO
Genes: A B A+B
Length: 186 311 485
Sequences: 7585 2826 453
Seq/Len: 40.78 9.09 0.93
MirrorTree (Pazo et al. 2001) 0.29
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 0.11 0.08 0.05
2 0.12 0.09 0.18
5 0.14 0.10 0.37
10 0.16 0.10 0.63
20 0.17 0.11 0.91
100 0.22 0.13 2.07
∞ 0.26 0.16 2.81
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
50_G 24_Y 1.16 0.46 0.00
114_L 234_V 1.02 0.34 0.00
66_Y 31_C 0.97 0.30 0.00
86_L 156_L 0.96 0.29 0.00
149_K 117_H 0.94 0.28 0.00
95_V 292_S 0.91 0.26 0.00
50_G 13_I 0.90 0.25 0.00
108_P 263_E 0.88 0.23 0.00
149_K 20_T 0.86 0.23 0.00
150_E 92_T 0.86 0.22 0.00
91_S 246_S 0.86 0.22 0.00
169_T 233_L 0.85 0.22 0.00
163_T 35_Y 0.84 0.21 0.00
46_V 167_I 0.84 0.21 0.00
110_T 52_N 0.84 0.21 0.00
90_A 204_I 0.82 0.20 0.00
91_S 14_M 0.82 0.20 0.00
20_C 239_V 0.81 0.20 0.00
167_L 67_F 0.81 0.19 0.00
115_V 32_M 0.81 0.19 0.00
13_D 173_V 0.80 0.19 0.00
66_Y 234_V 0.79 0.18 0.00
139_I 297_Q 0.79 0.18 0.00
176_R 76_L 0.78 0.18 0.00
66_Y 233_L 0.78 0.17 0.00
57_L 286_I 0.77 0.17 0.00
139_I 191_E 0.77 0.17 0.00
79_V 143_V 0.77 0.17 0.00
46_V 243_S 0.76 0.17 0.00
80_S 162_E 0.75 0.16 0.00
66_Y 70_N 0.75 0.16 0.00
51_K 234_V 0.74 0.16 0.00
152_G 261_V 0.74 0.16 0.00
109_N 72_F 0.74 0.16 0.00
121_L 158_T 0.73 0.15 0.00
28_N 18_I 0.73 0.15 0.00
95_V 171_L 0.72 0.15 0.00
82_I 37_W 0.72 0.15 0.00
159_C 146_I 0.72 0.15 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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