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OPENSEQ.org
Gazunga1
Genes: A B A+B
Length: 382 85 399
Sequences: 1313 742 332
Seq/Len: 3.44 8.73 0.83
MirrorTree (Pazo et al. 2001) 0.65
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 0.00 0.00 0.00
2 0.00 0.00 0.00
5 0.00 0.00 0.01
10 0.00 0.00 0.01
20 0.00 0.00 0.01
100 0.01 0.00 0.10
∞ 0.03 0.01 0.71
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
311_I 58_L 1.91 0.92 0.45
311_I 22_G 1.48 0.70 0.17
123_D 45_E 1.25 0.51 0.09
188_N 64_V 1.25 0.51 0.08
2_L 22_G 1.23 0.49 0.08
59_M 57_V 1.23 0.49 0.08
266_G 64_V 1.19 0.46 0.07
245_I 15_G 1.18 0.44 0.06
282_V 63_V 1.17 0.44 0.06
97_D 33_A 1.15 0.42 0.06
181_E 70_L 1.14 0.41 0.06
187_D 65_H 1.14 0.41 0.06
61_I 24_E 1.09 0.37 0.05
245_I 10_T 1.07 0.35 0.04
299_N 16_Q 1.06 0.35 0.04
292_M 64_V 1.05 0.34 0.04
56_E 20_I 1.05 0.34 0.04
33_N 32_V 1.03 0.32 0.04
311_I 19_T 1.02 0.31 0.04
308_V 54_K 1.00 0.30 0.03
269_N 40_M 0.96 0.27 0.03
270_L 15_G 0.95 0.27 0.03
241_A 37_D 0.95 0.26 0.03
133_T 62_N 0.94 0.26 0.03
294_F 36_V 0.94 0.26 0.03
27_V 37_D 0.94 0.26 0.03
175_K 11_V 0.94 0.26 0.03
193_G 47_N 0.93 0.25 0.03
289_D 37_D 0.93 0.25 0.03
67_R 61_V 0.93 0.25 0.03
251_E 42_E 0.93 0.25 0.03
259_G 59_T 0.93 0.25 0.03
200_L 9_T 0.93 0.25 0.03
309_T 52_I 0.93 0.25 0.03
254_I 32_V 0.93 0.25 0.02
289_D 41_R 0.93 0.25 0.02
29_R 22_G 0.92 0.25 0.02
299_N 58_L 0.92 0.24 0.02
13_S 65_H 0.92 0.24 0.02
202_A 13_I 0.91 0.24 0.02
28_N 77_L 0.91 0.24 0.02
215_K 38_D 0.90 0.23 0.02
116_V 31_Y 0.89 0.23 0.02
308_V 65_H 0.89 0.23 0.02
229_G 33_A 0.89 0.23 0.02
284_S 47_N 0.89 0.23 0.02
101_V 76_K 0.89 0.23 0.02
36_Q 54_K 0.89 0.22 0.02
61_I 18_F 0.88 0.22 0.02
61_I 31_Y 0.88 0.22 0.02
254_I 75_E 0.88 0.22 0.02
246_S 72_E 0.88 0.22 0.02
7_N 67_Y 0.88 0.22 0.02
81_A 20_I 0.87 0.21 0.02
188_N 53_N 0.87 0.21 0.02
304_D 7_T 0.87 0.21 0.02
280_D 70_L 0.87 0.21 0.02
93_L 39_K 0.87 0.21 0.02
288_Q 44_N 0.86 0.21 0.02
270_L 29_M 0.86 0.21 0.02
177_T 32_V 0.86 0.21 0.02
193_G 53_N 0.86 0.21 0.02
311_I 51_D 0.86 0.21 0.02
291_N 22_G 0.86 0.21 0.02
277_E 77_L 0.86 0.21 0.02
15_K 60_A 0.86 0.21 0.02
170_L 62_N 0.85 0.20 0.02
85_S 8_K 0.85 0.20 0.02
99_V 77_L 0.85 0.20 0.02
91_E 51_D 0.85 0.20 0.02
246_S 29_M 0.85 0.20 0.02
167_D 9_T 0.84 0.20 0.02
56_E 64_V 0.84 0.20 0.02
81_A 51_D 0.84 0.20 0.02
22_G 9_T 0.84 0.20 0.02
87_E 77_L 0.84 0.19 0.02
292_M 44_N 0.84 0.19 0.02
315_F 53_N 0.83 0.19 0.02
2_L 20_I 0.83 0.19 0.02
201_I 56_A 0.83 0.19 0.02
284_S 73_K 0.82 0.19 0.01
113_A 38_D 0.82 0.19 0.01
146_Q 59_T 0.82 0.19 0.01
315_F 40_M 0.81 0.18 0.01
282_V 6_K 0.81 0.18 0.01
178_P 26_R 0.81 0.18 0.01
275_V 32_V 0.81 0.18 0.01
116_V 15_G 0.81 0.18 0.01
160_T 32_V 0.81 0.18 0.01
276_Q 61_V 0.81 0.18 0.01
260_V 33_A 0.80 0.18 0.01
141_R 72_E 0.80 0.17 0.01
142_K 59_T 0.80 0.17 0.01
67_R 16_Q 0.79 0.17 0.01
130_G 35_I 0.79 0.17 0.01
129_V 57_V 0.79 0.17 0.01
31_I 75_E 0.79 0.17 0.01
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
0535 1.2 Gazunga2 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-06, 8) msa: Jackhmmer (2014_03) 0.27 Done - Shared
0531 0.83 Gazunga1 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: HHblits (2013_03) 0.45 Done - Shared
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