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OPENSEQ.org
1QG4_A Ran GTPase GDP 1F59_A Importin beta
Genes: A B A+B
Length: 216 442 623
Sequences: 7049 4978 420
Seq/Len: 32.63 11.26 0.67
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 0.11 0.08 0.06
2 0.12 0.09 0.11
5 0.14 0.11 0.18
10 0.16 0.12 0.33
20 0.17 0.13 0.64
100 0.22 0.16 1.99
∞ 0.26 0.22 3.22
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
134_K 282_F 1.28 0.47 0.00
141_K 173_I 1.07 0.31 0.00
131_V 194_A 1.04 0.29 0.00
97_T 91_V 1.04 0.29 0.00
55_N 266_E 1.03 0.28 0.00
92_V 109_A 1.02 0.28 0.00
120_C 83_I 1.02 0.27 0.00
90_F 8_E 1.01 0.27 0.00
15_L 145_H 1.00 0.26 0.00
143_N 174_L 0.95 0.23 0.00
115_I 98_T 0.94 0.23 0.00
118_V 416_L 0.94 0.22 0.00
34_E 91_V 0.94 0.22 0.00
87_I 59_L 0.92 0.21 0.00
26_F 222_V 0.92 0.21 0.00
137_V 390_F 0.92 0.21 0.00
162_L 393_I 0.91 0.21 0.00
132_K 181_M 0.91 0.21 0.00
30_H 43_V 0.90 0.20 0.00
16_V 135_A 0.89 0.20 0.00
97_T 138_T 0.89 0.20 0.00
131_V 195_T 0.88 0.19 0.00
24_T 329_T 0.86 0.18 0.00
56_R 88_R 0.84 0.17 0.00
156_N 125_Q 0.83 0.17 0.00
120_C 432_V 0.82 0.16 0.00
85_C 93_N 0.82 0.16 0.00
35_F 176_A 0.82 0.16 0.00
93_T 377_N 0.82 0.16 0.00
119_L 8_E 0.82 0.16 0.00
166_R 113_V 0.81 0.16 0.00
97_T 158_C 0.81 0.16 0.00
139_H 61_I 0.81 0.16 0.00
135_S 5_T 0.81 0.16 0.00
156_N 344_P 0.81 0.16 0.00
87_I 281_E 0.80 0.15 0.00
91_D 326_L 0.79 0.15 0.00
90_F 345_C 0.79 0.15 0.00
158_E 326_L 0.79 0.15 0.00
157_F 157_I 0.79 0.15 0.00
63_V 177_I 0.78 0.14 0.00
137_V 202_L 0.78 0.14 0.00
101_V 386_A 0.78 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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