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OPENSEQ.org
Gazunga2
Genes: A B A+B
Length: 382 85 459
Sequences: 2192 1212 549
Seq/Len: 5.74 14.26 1.2
MirrorTree (Pazo et al. 2001) 0.59
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 0.00 0.00 0.00
2 0.00 0.00 0.00
5 0.00 0.00 0.01
10 0.00 0.00 0.02
20 0.00 0.00 0.03
100 0.01 0.00 0.16
∞ 0.02 0.00 1.18
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
2_L 22_G 1.66 0.89 0.27
187_D 65_H 1.33 0.70 0.12
311_I 22_G 1.22 0.59 0.08
76_E 13_I 1.20 0.57 0.07
29_R 32_V 1.13 0.51 0.06
299_N 16_Q 1.10 0.47 0.05
292_M 44_N 1.07 0.45 0.05
311_I 58_L 1.06 0.44 0.05
29_R 28_H 1.05 0.43 0.04
96_A 11_V 1.05 0.43 0.04
122_K 27_A 1.01 0.40 0.04
93_L 39_K 1.00 0.38 0.04
264_I 58_L 0.99 0.37 0.04
294_F 36_V 0.98 0.37 0.04
254_I 22_G 0.98 0.37 0.04
153_A 20_I 0.96 0.35 0.03
254_I 32_V 0.95 0.34 0.03
251_E 57_V 0.95 0.34 0.03
152_S 36_V 0.95 0.34 0.03
95_G 66_D 0.94 0.33 0.03
102_T 18_F 0.94 0.33 0.03
315_F 53_N 0.93 0.32 0.03
29_R 65_H 0.92 0.32 0.03
29_R 22_G 0.92 0.31 0.03
163_V 71_Q 0.91 0.31 0.03
225_L 22_G 0.91 0.31 0.03
13_S 65_H 0.91 0.31 0.03
177_T 22_G 0.89 0.29 0.02
178_P 26_R 0.89 0.29 0.02
1_M 42_E 0.88 0.28 0.02
266_G 14_Y 0.88 0.28 0.02
12_A 62_N 0.86 0.27 0.02
123_D 61_V 0.86 0.27 0.02
22_G 74_C 0.86 0.26 0.02
165_P 63_V 0.85 0.26 0.02
260_V 10_T 0.84 0.25 0.02
9_D 67_Y 0.84 0.25 0.02
309_T 62_N 0.84 0.25 0.02
182_A 20_I 0.84 0.25 0.02
306_I 53_N 0.83 0.25 0.02
93_L 38_D 0.83 0.25 0.02
292_M 59_T 0.83 0.24 0.02
373_T 29_M 0.83 0.24 0.02
196_G 56_A 0.83 0.24 0.02
308_V 65_H 0.82 0.24 0.02
272_L 50_L 0.82 0.24 0.02
277_E 37_D 0.82 0.23 0.02
173_V 65_H 0.82 0.23 0.02
300_E 68_V 0.81 0.23 0.02
229_G 20_I 0.81 0.23 0.02
126_A 33_A 0.81 0.23 0.02
278_A 58_L 0.81 0.23 0.02
177_T 32_V 0.81 0.23 0.02
165_P 65_H 0.81 0.23 0.02
67_R 21_V 0.80 0.22 0.02
61_I 31_Y 0.80 0.22 0.02
27_V 55_L 0.79 0.22 0.02
299_N 58_L 0.79 0.22 0.02
255_D 9_T 0.79 0.22 0.02
81_A 51_D 0.79 0.22 0.02
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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