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OPENSEQ.org
cI_1_40_cI_4_40_tt
Genes: A B A+B
Length: 438 409 815
Sequences: 2218 1636 881
Seq/Len: 5.06 4 1.08
MirrorTree (Pazo et al. 2001) 0.69
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 0.01 0.00 0.03
2 0.01 0.00 0.72
5 0.01 0.00 0.81
10 0.02 0.01 0.83
20 0.02 0.01 0.83
100 0.04 0.01 0.86
∞ 0.12 0.05 1.04
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
90_I 109_V 1.27 0.61 0.00
401_P 293_A 0.99 0.34 0.00
238_F 205_E 0.97 0.33 0.00
417_F 399_S 0.96 0.33 0.00
177_A 221_V 0.95 0.31 0.00
74_L 372_A 0.95 0.31 0.00
154_A 268_E 0.94 0.31 0.00
107_L 380_S 0.94 0.30 0.00
25_G 101_V 0.92 0.29 0.00
149_I 301_P 0.91 0.29 0.00
260_R 295_E 0.89 0.27 0.00
22_G 285_E 0.89 0.27 0.00
122_G 136_G 0.89 0.27 0.00
235_A 225_P 0.89 0.27 0.00
227_V 156_I 0.88 0.26 0.00
394_I 235_T 0.86 0.25 0.00
54_I 378_L 0.85 0.24 0.00
374_I 112_R 0.85 0.24 0.00
161_N 52_V 0.84 0.23 0.00
336_S 52_V 0.84 0.23 0.00
53_V 223_V 0.83 0.23 0.00
223_T 385_C 0.83 0.23 0.00
14_E 264_V 0.83 0.23 0.00
375_G 294_L 0.83 0.22 0.00
118_M 158_D 0.82 0.22 0.00
260_R 350_R 0.82 0.22 0.00
53_V 260_Y 0.81 0.22 0.00
134_V 357_I 0.81 0.21 0.00
156_G 220_G 0.80 0.21 0.00
301_P 47_L 0.80 0.21 0.00
417_F 395_A 0.80 0.21 0.00
123_Y 241_A 0.80 0.20 0.00
138_Y 397_I 0.79 0.20 0.00
49_T 397_I 0.79 0.20 0.00
28_T 241_A 0.79 0.20 0.00
258_V 100_A 0.78 0.20 0.00
374_I 287_V 0.78 0.19 0.00
321_S 295_E 0.78 0.19 0.00
420_Q 164_T 0.78 0.19 0.00
107_L 106_G 0.77 0.19 0.00
414_L 264_V 0.77 0.19 0.00
40_T 152_E 0.77 0.19 0.00
269_G 28_L 0.76 0.18 0.00
90_I 374_S 0.76 0.18 0.00
142_A 226_P 0.76 0.18 0.00
272_F 396_I 0.76 0.18 0.00
165_T 258_E 0.76 0.18 0.00
212_W 41_L 0.75 0.18 0.00
227_V 261_T 0.75 0.18 0.00
323_L 94_D 0.75 0.18 0.00
57_V 133_L 0.75 0.18 0.00
235_A 55_V 0.75 0.18 0.00
58_K 262_F 0.75 0.18 0.00
121_A 285_E 0.75 0.18 0.00
260_R 201_I 0.75 0.18 0.00
196_R 374_S 0.75 0.18 0.00
120_L 222_G 0.74 0.17 0.00
304_E 96_A 0.74 0.17 0.00
186_T 287_V 0.74 0.17 0.00
384_V 362_G 0.74 0.17 0.00
189_M 118_V 0.74 0.17 0.00
51_D 357_I 0.74 0.17 0.00
414_L 294_L 0.74 0.17 0.00
134_V 250_K 0.74 0.17 0.00
233_R 85_M 0.73 0.17 0.00
29_L 208_F 0.73 0.17 0.00
285_E 215_Y 0.73 0.17 0.00
52_E 206_A 0.73 0.17 0.00
149_I 52_V 0.73 0.17 0.00
45_L 258_E 0.73 0.17 0.00
251_L 168_F 0.73 0.17 0.00
42_K 225_P 0.73 0.17 0.00
107_L 234_L 0.73 0.17 0.00
325_T 93_H 0.73 0.17 0.00
384_V 109_V 0.73 0.17 0.00
118_M 237_G 0.72 0.16 0.00
154_A 223_V 0.72 0.16 0.00
157_Y 221_V 0.72 0.16 0.00
336_S 148_Y 0.72 0.16 0.00
192_L 368_V 0.72 0.16 0.00
357_T 81_Y 0.72 0.16 0.00
138_Y 166_Q 0.72 0.16 0.00
217_T 290_I 0.72 0.16 0.00
321_S 403_V 0.71 0.16 0.00
87_H 233_G 0.71 0.15 0.00
55_E 225_P 0.71 0.15 0.00
167_F 156_I 0.70 0.15 0.00
72_T 178_V 0.70 0.15 0.00
30_D 55_V 0.70 0.15 0.00
247_K 123_L 0.70 0.15 0.00
36_G 339_K 0.70 0.15 0.00
115_I 52_V 0.70 0.15 0.00
328_V 41_L 0.70 0.15 0.00
168_S 248_V 0.70 0.15 0.00
192_L 97_Y 0.70 0.15 0.00
192_L 80_T 0.69 0.15 0.00
325_T 109_V 0.69 0.15 0.00
179_A 62_L 0.69 0.15 0.00
355_K 36_S 0.69 0.15 0.00
387_L 311_P 0.69 0.15 0.00
16_T 184_E 0.69 0.14 0.00
207_A 405_G 0.68 0.14 0.00
209_S 390_V 0.68 0.14 0.00
157_Y 250_K 0.68 0.14 0.00
24_E 381_L 0.68 0.14 0.00
391_L 203_E 0.68 0.14 0.00
144_R 228_V 0.68 0.14 0.00
162_L 349_A 0.68 0.14 0.00
150_K 294_L 0.68 0.14 0.00
195_L 148_Y 0.68 0.14 0.00
68_A 198_P 0.68 0.14 0.00
144_R 369_K 0.68 0.14 0.00
51_D 133_L 0.68 0.14 0.00
348_Y 36_S 0.68 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)
ID Seq/Len Name Options I_Prob Status
4826 1.08 cI_1_40_cI_4_40_tt Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4825 1.44 cI_1_4_cI_4_4_tt Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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