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OPENSEQ.org
RAC1-GAPDH
Genes: A B A+B
Length: 211 335 506
Sequences: 7055 3911 66
Seq/Len: 33.44 11.67 0.13
MirrorTree (Pazo et al. 2001) 0.24
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 0.02 0.01
2 0.12 0.02 0.01
5 0.14 0.03 0.04
10 0.15 0.04 0.08
20 0.17 0.04 0.12
100 0.22 0.05 0.35
∞ 0.26 0.12 0.72
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
23_Y 63_E 1.34 0.18 0.00
157_T 23_F 1.27 0.16 0.00
120_V 33_I 1.23 0.15 0.00
17_T 106_E 1.22 0.15 0.00
9_V 41_N 1.20 0.14 0.00
131_L 256_D 1.14 0.13 0.00
133_G 274_L 1.12 0.12 0.00
64_Y 17_L 1.10 0.12 0.00
38_D 17_L 1.08 0.11 0.00
127_T 266_S 1.07 0.11 0.00
179_L 254_K 1.04 0.11 0.00
192_I 180_A 1.04 0.10 0.00
46_V 262_V 1.02 0.10 0.00
72_Y 266_S 1.02 0.10 0.00
120_V 324_V 0.98 0.10 0.00
109_F 232_A 0.98 0.10 0.00
9_V 106_E 0.98 0.09 0.00
129_I 6_V 0.97 0.09 0.00
9_V 164_I 0.97 0.09 0.00
13_A 25_S 0.96 0.09 0.00
157_T 29_D 0.96 0.09 0.00
38_D 325_V 0.96 0.09 0.00
32_Y 266_S 0.95 0.09 0.00
14_V 328_M 0.95 0.09 0.00
26_N 101_V 0.95 0.09 0.00
48_G 28_V 0.93 0.09 0.00
192_I 69_I 0.93 0.09 0.00
55_L 165_H 0.93 0.09 0.00
131_L 166_D 0.92 0.08 0.00
60_G 119_V 0.92 0.08 0.00
9_V 57_H 0.90 0.08 0.00
8_V 233_F 0.90 0.08 0.00
6_C 93_E 0.90 0.08 0.00
44_V 138_E 0.90 0.08 0.00
25_T 256_D 0.89 0.08 0.00
186_T 232_A 0.89 0.08 0.00
108_S 253_A 0.87 0.08 0.00
95_D 74_I 0.87 0.07 0.00
155_P 143_S 0.86 0.07 0.00
108_S 281_V 0.86 0.07 0.00
181_Q 93_E 0.86 0.07 0.00
28_F 76_I 0.86 0.07 0.00
51_V 288_S 0.86 0.07 0.00
17_T 194_K 0.85 0.07 0.00
139_R 165_H 0.85 0.07 0.00
35_T 119_V 0.85 0.07 0.00
129_I 41_N 0.85 0.07 0.00
30_G 120_I 0.85 0.07 0.00
157_T 325_V 0.84 0.07 0.00
108_S 232_A 0.84 0.07 0.00
180_T 113_Q 0.84 0.07 0.00
178_A 238_A 0.84 0.07 0.00
62_E 81_D 0.83 0.07 0.00
69_P 106_E 0.82 0.07 0.00
26_N 31_V 0.82 0.07 0.00
38_D 201_G 0.82 0.07 0.00
172_K 27_K 0.82 0.07 0.00
164_M 6_V 0.82 0.07 0.00
69_P 256_D 0.82 0.07 0.00
175_E 232_A 0.81 0.07 0.00
176_C 131_F 0.81 0.07 0.00
108_S 40_L 0.81 0.07 0.00
9_V 141_D 0.81 0.07 0.00
125_P 110_A 0.80 0.07 0.00
48_G 44_V 0.80 0.07 0.00
34_P 94_Y 0.80 0.07 0.00
180_T 41_N 0.80 0.07 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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