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RB_mod

Genes: A B A+B
Length: 350 430 711
Sequences: 887 24768 65
Seq/Len: 2.53 57.6 0.09
MirrorTree (Pazo et al. 2001) 0.13
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.

Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.04 0.02 0.00
2 0.04 0.03 0.01
5 0.04 0.04 0.03
10 0.04 0.05 0.04
20 0.05 0.07 0.08
100 0.10 0.16 0.37
0.13 0.24 0.74
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
214_L 180_I 1.64 0.24 0.00
169_W 367_I 1.38 0.16 0.00
70_L 168_L 1.35 0.15 0.00
275_I 168_L 1.24 0.12 0.00
230_I 153_Y 1.16 0.11 0.00
251_R 80_G 1.15 0.11 0.00
230_I 92_L 1.13 0.10 0.00
146_L 52_L 1.12 0.10 0.00
126_G 82_G 1.11 0.10 0.00
126_G 83_K 1.11 0.10 0.00
126_G 183_D 1.11 0.10 0.00
126_G 184_E 1.11 0.10 0.00
126_G 220_T 1.11 0.10 0.00
126_G 404_R 1.11 0.10 0.00
126_G 407_R 1.11 0.10 0.00
134_E 82_G 1.11 0.10 0.00
134_E 83_K 1.11 0.10 0.00
134_E 183_D 1.11 0.10 0.00
134_E 184_E 1.11 0.10 0.00
134_E 220_T 1.11 0.10 0.00
134_E 404_R 1.11 0.10 0.00
134_E 407_R 1.11 0.10 0.00
143_K 82_G 1.11 0.10 0.00
143_K 83_K 1.11 0.10 0.00
143_K 183_D 1.11 0.10 0.00
143_K 184_E 1.11 0.10 0.00
143_K 220_T 1.11 0.10 0.00
143_K 404_R 1.11 0.10 0.00
143_K 407_R 1.11 0.10 0.00
299_G 82_G 1.11 0.10 0.00
299_G 83_K 1.11 0.10 0.00
299_G 183_D 1.11 0.10 0.00
299_G 184_E 1.11 0.10 0.00
299_G 220_T 1.11 0.10 0.00
299_G 404_R 1.11 0.10 0.00
299_G 407_R 1.11 0.10 0.00
84_L 405_C 1.11 0.10 0.00
199_I 182_I 1.10 0.10 0.00
157_P 370_A 1.10 0.10 0.00
235_T 100_V 1.09 0.10 0.00
272_A 101_I 1.07 0.09 0.00
135_L 120_I 1.06 0.09 0.00
127_I 74_L 1.06 0.09 0.00
228_L 334_L 1.06 0.09 0.00
242_Y 389_Y 1.04 0.09 0.00
137_G 82_G 1.04 0.09 0.00
137_G 83_K 1.04 0.09 0.00
137_G 183_D 1.04 0.09 0.00
137_G 184_E 1.04 0.09 0.00
137_G 220_T 1.04 0.09 0.00
137_G 404_R 1.04 0.09 0.00
137_G 407_R 1.04 0.09 0.00
211_T 306_I 1.03 0.09 0.00
306_S 387_I 1.03 0.09 0.00
54_G 99_I 1.02 0.09 0.00
249_A 421_E 1.02 0.08 0.00
84_L 418_Y 1.02 0.08 0.00
322_C 317_G 1.01 0.08 0.00
151_A 417_F 1.00 0.08 0.00
51_L 241_D 0.99 0.08 0.00
199_I 189_S 0.99 0.08 0.00
266_A 409_G 0.99 0.08 0.00
50_L 180_I 0.98 0.08 0.00
123_L 82_G 0.98 0.08 0.00
123_L 83_K 0.98 0.08 0.00
123_L 183_D 0.98 0.08 0.00
123_L 184_E 0.98 0.08 0.00
123_L 220_T 0.98 0.08 0.00
123_L 404_R 0.98 0.08 0.00
123_L 407_R 0.98 0.08 0.00
236_A 116_R 0.97 0.08 0.00
327_S 389_Y 0.96 0.08 0.00
126_G 377_G 0.96 0.07 0.00
134_E 377_G 0.96 0.07 0.00
143_K 377_G 0.96 0.07 0.00
299_G 377_G 0.96 0.07 0.00
126_G 80_G 0.95 0.07 0.00
134_E 80_G 0.95 0.07 0.00
143_K 80_G 0.95 0.07 0.00
299_G 80_G 0.95 0.07 0.00
292_H 153_Y 0.95 0.07 0.00
169_W 84_S 0.94 0.07 0.00
232_D 82_G 0.94 0.07 0.00
232_D 83_K 0.94 0.07 0.00
232_D 183_D 0.94 0.07 0.00
232_D 184_E 0.94 0.07 0.00
232_D 220_T 0.94 0.07 0.00
232_D 404_R 0.94 0.07 0.00
232_D 407_R 0.94 0.07 0.00
309_R 82_G 0.94 0.07 0.00
309_R 83_K 0.94 0.07 0.00
309_R 183_D 0.94 0.07 0.00
309_R 184_E 0.94 0.07 0.00
309_R 220_T 0.94 0.07 0.00
309_R 404_R 0.94 0.07 0.00
309_R 407_R 0.94 0.07 0.00
126_G 60_Q 0.94 0.07 0.00
134_E 60_Q 0.94 0.07 0.00
143_K 60_Q 0.94 0.07 0.00
299_G 60_Q 0.94 0.07 0.00
199_I 387_I 0.94 0.07 0.00
51_L 285_L 0.94 0.07 0.00
286_M 89_V 0.94 0.07 0.00
141_T 352_T 0.93 0.07 0.00
87_A 215_Y 0.93 0.07 0.00
56_L 387_I 0.92 0.07 0.00
125_G 82_G 0.92 0.07 0.00
125_G 83_K 0.92 0.07 0.00
125_G 183_D 0.92 0.07 0.00
125_G 184_E 0.92 0.07 0.00
125_G 220_T 0.92 0.07 0.00
125_G 404_R 0.92 0.07 0.00
125_G 407_R 0.92 0.07 0.00
197_N 100_V 0.92 0.07 0.00
340_T 386_I 0.92 0.07 0.00
155_Q 319_I 0.92 0.07 0.00
321_I 100_V 0.91 0.07 0.00
62_V 378_I 0.91 0.07 0.00
231_V 226_E 0.91 0.07 0.00
135_L 228_D 0.90 0.07 0.00
172_T 392_P 0.90 0.07 0.00
157_P 371_T 0.90 0.07 0.00
214_L 147_G 0.90 0.07 0.00
199_I 118_K 0.90 0.07 0.00
313_R 62_E 0.90 0.07 0.00
199_I 181_S 0.90 0.07 0.00
154_C 115_L 0.89 0.07 0.00
64_Y 41_E 0.89 0.07 0.00
65_A 306_I 0.89 0.07 0.00
216_D 188_I 0.89 0.07 0.00
311_Y 369_V 0.89 0.07 0.00
126_G 103_P 0.89 0.07 0.00
134_E 103_P 0.89 0.07 0.00
143_K 103_P 0.89 0.07 0.00
299_G 103_P 0.89 0.07 0.00
166_K 371_T 0.89 0.07 0.00
66_P 381_K 0.88 0.07 0.00
125_G 155_T 0.88 0.07 0.00
327_S 390_N 0.88 0.07 0.00
35_I 146_L 0.88 0.07 0.00
46_R 307_I 0.88 0.07 0.00
242_Y 120_I 0.87 0.06 0.00
137_G 80_G 0.87 0.06 0.00
183_A 56_F 0.87 0.06 0.00
125_G 103_P 0.87 0.06 0.00
310_L 196_R 0.86 0.06 0.00
137_G 377_G 0.86 0.06 0.00
258_F 154_I 0.86 0.06 0.00
199_I 394_S 0.86 0.06 0.00
88_C 124_T 0.85 0.06 0.00
126_G 219_A 0.85 0.06 0.00
134_E 219_A 0.85 0.06 0.00
143_K 219_A 0.85 0.06 0.00
299_G 219_A 0.85 0.06 0.00
271_V 70_F 0.85 0.06 0.00
335_A 319_I 0.85 0.06 0.00
261_G 73_V 0.85 0.06 0.00
132_I 420_K 0.85 0.06 0.00
227_A 227_K 0.85 0.06 0.00
271_V 358_Q 0.85 0.06 0.00
112_F 101_I 0.84 0.06 0.00
69_T 358_Q 0.84 0.06 0.00
249_A 306_I 0.84 0.06 0.00
137_G 60_Q 0.84 0.06 0.00
266_A 317_G 0.84 0.06 0.00
153_T 285_L 0.84 0.06 0.00
120_D 218_T 0.84 0.06 0.00
324_I 99_I 0.84 0.06 0.00
288_M 154_I 0.84 0.06 0.00
199_I 305_D 0.83 0.06 0.00
276_T 152_L 0.83 0.06 0.00
153_T 152_L 0.83 0.06 0.00
158_I 364_K 0.83 0.06 0.00
135_L 127_S 0.83 0.06 0.00
101_D 141_L 0.83 0.06 0.00
334_E 369_V 0.83 0.06 0.00
147_C 208_I 0.83 0.06 0.00
183_A 58_E 0.83 0.06 0.00
87_A 85_L 0.82 0.06 0.00
167_C 122_A 0.82 0.06 0.00
212_E 100_V 0.82 0.06 0.00
161_S 371_T 0.82 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)

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