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OPENSEQ.org
1YZU_A Rab21 GTPase GNP 1TXU_A Rabex-5 VPS9 domain
Genes: A B A+B
Length: 170 273 429
Sequences: 7602 655 86
Seq/Len: 44.72 2.4 0.2
MirrorTree (Pazo et al. 2001) 0.26
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 0.03 0.02
2 0.12 0.04 0.03
5 0.15 0.04 0.07
10 0.17 0.04 0.12
20 0.18 0.04 0.19
100 0.23 0.05 0.53
∞ 0.27 0.07 0.94
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
132_Q 200_Y 1.49 0.32 0.00
151_K 249_D 1.47 0.30 0.00
117_V 233_Y 1.22 0.19 0.00
94_F 240_C 1.20 0.19 0.00
156_I 216_Y 1.18 0.18 0.00
155_G 68_V 1.18 0.18 0.00
165_K 181_I 1.16 0.17 0.00
83_I 165_D 1.14 0.16 0.00
149_S 192_D 1.08 0.15 0.00
23_V 133_C 1.07 0.14 0.00
64_G 163_P 1.07 0.14 0.00
14_E 133_C 1.05 0.14 0.00
53_K 206_N 1.05 0.14 0.00
132_Q 120_R 1.04 0.14 0.00
165_K 60_C 1.04 0.13 0.00
68_F 170_I 1.03 0.13 0.00
20_T 145_D 1.02 0.13 0.00
118_G 150_A 1.01 0.13 0.00
119_N 236_T 1.01 0.13 0.00
123_L 245_I 1.01 0.13 0.00
23_V 127_V 1.00 0.12 0.00
21_S 240_C 1.00 0.12 0.00
123_L 210_L 0.99 0.12 0.00
55_V 135_P 0.98 0.12 0.00
131_I 195_L 0.98 0.12 0.00
118_G 216_Y 0.97 0.12 0.00
8_K 99_Y 0.95 0.11 0.00
99_N 121_I 0.95 0.11 0.00
120_K 192_D 0.94 0.11 0.00
17_V 191_A 0.94 0.11 0.00
8_K 236_T 0.94 0.11 0.00
132_Q 237_N 0.93 0.11 0.00
64_G 166_K 0.93 0.11 0.00
112_I 147_V 0.93 0.11 0.00
94_F 241_A 0.92 0.10 0.00
39_L 157_M 0.92 0.10 0.00
68_F 204_K 0.91 0.10 0.00
149_S 166_K 0.91 0.10 0.00
164_C 241_A 0.90 0.10 0.00
123_L 56_E 0.89 0.10 0.00
148_T 153_D 0.89 0.10 0.00
130_S 117_I 0.89 0.10 0.00
94_F 212_S 0.89 0.10 0.00
61_D 192_D 0.89 0.10 0.00
61_D 163_P 0.89 0.10 0.00
115_C 261_D 0.88 0.10 0.00
167_M 200_Y 0.88 0.10 0.00
108_L 202_V 0.88 0.10 0.00
48_L 203_L 0.88 0.10 0.00
87_D 182_K 0.88 0.10 0.00
59_I 208_P 0.88 0.10 0.00
129_V 91_E 0.87 0.09 0.00
4_A 210_L 0.87 0.09 0.00
150_A 170_I 0.87 0.09 0.00
104_L 58_S 0.87 0.09 0.00
48_L 137_N 0.86 0.09 0.00
57_L 249_D 0.86 0.09 0.00
80_N 129_P 0.86 0.09 0.00
114_L 237_N 0.85 0.09 0.00
83_I 233_Y 0.85 0.09 0.00
29_N 237_N 0.85 0.09 0.00
95_Q 221_C 0.85 0.09 0.00
32_N 258_E 0.84 0.09 0.00
13_G 117_I 0.84 0.09 0.00
18_G 117_I 0.84 0.09 0.00
19_K 117_I 0.84 0.09 0.00
87_D 195_L 0.84 0.09 0.00
153_N 28_F 0.84 0.09 0.00
10_V 65_Y 0.84 0.09 0.00
21_S 200_Y 0.84 0.09 0.00
54_R 194_F 0.83 0.09 0.00
94_F 203_L 0.83 0.09 0.00
135_E 216_Y 0.83 0.09 0.00
168_I 157_M 0.83 0.09 0.00
13_G 192_D 0.83 0.09 0.00
18_G 192_D 0.83 0.09 0.00
19_K 192_D 0.83 0.09 0.00
22_L 256_S 0.81 0.08 0.00
117_V 39_T 0.81 0.08 0.00
117_V 170_I 0.81 0.08 0.00
165_K 59_E 0.81 0.08 0.00
122_D 220_F 0.81 0.08 0.00
129_V 114_D 0.81 0.08 0.00
116_I 208_P 0.81 0.08 0.00
12_L 153_D 0.81 0.08 0.00
105_R 87_M 0.80 0.08 0.00
94_F 167_L 0.80 0.08 0.00
34_K 226_L 0.80 0.08 0.00
78_D 97_R 0.80 0.08 0.00
51_G 131_M 0.79 0.08 0.00
121_I 194_F 0.79 0.08 0.00
118_G 114_D 0.79 0.08 0.00
66_E 199_I 0.79 0.08 0.00
122_D 192_D 0.79 0.08 0.00
5_Y 194_F 0.79 0.08 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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