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OPENSEQ.org
1QG4_A Ran GTPase GNP 1A12_A RCC1
Genes: A B A+B
Length: 216 413 589
Sequences: 22911 340 60
Seq/Len: 106.07 0.82 0.1
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 0.12 0.01 0.00
2 0.13 0.01 0.00
5 0.14 0.01 0.01
10 0.15 0.01 0.04
20 0.18 0.01 0.10
100 0.24 0.01 0.27
∞ 0.28 0.01 0.38
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
22_G 311_G 1.35 0.16 0.00
23_K 311_G 1.35 0.16 0.00
65_D 311_G 1.35 0.16 0.00
68_G 311_G 1.35 0.16 0.00
125_D 311_G 1.35 0.16 0.00
158_E 166_V 1.34 0.16 0.00
22_G 319_G 1.22 0.13 0.00
23_K 319_G 1.22 0.13 0.00
65_D 319_G 1.22 0.13 0.00
68_G 319_G 1.22 0.13 0.00
125_D 319_G 1.22 0.13 0.00
131_V 167_V 1.20 0.12 0.00
86_A 221_V 1.20 0.12 0.00
92_V 237_A 1.19 0.12 0.00
123_K 311_G 1.17 0.12 0.00
72_Y 275_P 1.17 0.12 0.00
20_G 237_A 1.15 0.11 0.00
24_T 170_A 1.14 0.11 0.00
129_R 349_G 1.12 0.11 0.00
66_T 361_W 1.11 0.10 0.00
42_T 218_P 1.11 0.10 0.00
13_L 91_L 1.09 0.10 0.00
116_P 254_Y 1.07 0.10 0.00
159_K 234_F 1.05 0.10 0.00
123_K 318_L 1.04 0.09 0.00
123_K 319_G 1.03 0.09 0.00
149_I 339_V 1.03 0.09 0.00
55_N 234_F 1.01 0.09 0.00
98_Y 130_G 1.00 0.09 0.00
150_S 361_W 0.99 0.08 0.00
39_Y 33_G 0.99 0.08 0.00
7_P 342_V 0.98 0.08 0.00
27_V 221_V 0.98 0.08 0.00
164_L 78_G 0.98 0.08 0.00
157_F 341_S 0.98 0.08 0.00
17_G 311_G 0.97 0.08 0.00
157_F 231_H 0.95 0.08 0.00
118_V 288_W 0.94 0.08 0.00
63_V 309_S 0.94 0.08 0.00
17_G 218_P 0.94 0.08 0.00
30_H 163_D 0.94 0.08 0.00
139_H 197_G 0.93 0.07 0.00
42_T 311_G 0.93 0.07 0.00
139_H 345_G 0.93 0.07 0.00
161_F 132_V 0.92 0.07 0.00
44_G 218_P 0.91 0.07 0.00
140_R 333_I 0.91 0.07 0.00
24_T 113_V 0.91 0.07 0.00
48_H 291_F 0.91 0.07 0.00
41_A 129_D 0.90 0.07 0.00
146_Y 377_A 0.90 0.07 0.00
64_W 218_P 0.90 0.07 0.00
11_F 264_L 0.90 0.07 0.00
115_I 257_G 0.90 0.07 0.00
92_V 220_C 0.89 0.07 0.00
22_G 362_G 0.89 0.07 0.00
23_K 362_G 0.89 0.07 0.00
65_D 362_G 0.89 0.07 0.00
68_G 362_G 0.89 0.07 0.00
125_D 362_G 0.89 0.07 0.00
42_T 345_G 0.88 0.07 0.00
63_V 115_Q 0.88 0.07 0.00
16_V 342_V 0.88 0.07 0.00
119_L 137_S 0.87 0.07 0.00
140_R 342_V 0.87 0.07 0.00
14_V 72_V 0.87 0.07 0.00
157_F 367_Y 0.87 0.07 0.00
54_T 124_A 0.86 0.07 0.00
55_N 333_I 0.86 0.07 0.00
54_T 198_R 0.86 0.07 0.00
88_I 369_L 0.86 0.07 0.00
136_I 272_C 0.85 0.07 0.00
22_G 294_G 0.85 0.07 0.00
23_K 294_G 0.85 0.07 0.00
65_D 294_G 0.85 0.07 0.00
68_G 294_G 0.85 0.07 0.00
125_D 294_G 0.85 0.07 0.00
126_I 185_L 0.85 0.07 0.00
87_I 221_V 0.85 0.07 0.00
149_I 291_F 0.84 0.06 0.00
126_I 30_L 0.84 0.06 0.00
118_V 166_V 0.84 0.06 0.00
59_I 164_V 0.84 0.06 0.00
138_F 73_C 0.84 0.06 0.00
150_S 380_P 0.84 0.06 0.00
115_I 197_G 0.84 0.06 0.00
150_S 311_G 0.84 0.06 0.00
153_S 61_V 0.84 0.06 0.00
129_R 336_L 0.84 0.06 0.00
72_Y 63_Q 0.83 0.06 0.00
17_G 294_G 0.83 0.06 0.00
24_T 311_G 0.83 0.06 0.00
17_G 319_G 0.83 0.06 0.00
6_E 316_G 0.82 0.06 0.00
146_Y 384_M 0.82 0.06 0.00
22_G 172_G 0.82 0.06 0.00
23_K 172_G 0.82 0.06 0.00
65_D 172_G 0.82 0.06 0.00
68_G 172_G 0.82 0.06 0.00
125_D 172_G 0.82 0.06 0.00
8_Q 166_V 0.81 0.06 0.00
164_L 81_Y 0.81 0.06 0.00
101_V 192_E 0.81 0.06 0.00
113_E 128_D 0.81 0.06 0.00
13_L 267_P 0.81 0.06 0.00
42_T 294_G 0.81 0.06 0.00
123_K 316_G 0.81 0.06 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)
ID Seq/Len Name Options I_Prob Status
4115 0.07 1QG4_A Ran GTPase GNP 1A12_A RCC1 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) Killed - Shared
4078 0.1 1QG4_A Ran GTPase GNP 1A12_A RCC1 Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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