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OPENSEQ.org
mxij spa24
Genes: A B A+B
Length: 241 216 427
Sequences: 3945 3130 2622
Seq/Len: 16.37 14.49 6.14
MirrorTree (Pazo et al. 2001) 0.75
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 0.01
2 0.00 0.00 0.11
5 0.00 0.00 1.04
10 0.00 0.00 3.05
20 0.00 0.00 5.74
100 0.01 0.01 6.09
∞ 0.06 0.06 6.56
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
101_A 36_M 1.14 0.92 0.16
109_A 186_S 0.98 0.82 0.10
101_A 39_N 0.97 0.81 0.10
101_A 184_T 0.95 0.79 0.09
177_V 37_V 0.91 0.75 0.08
73_M 45_Q 0.89 0.73 0.07
173_T 157_L 0.87 0.70 0.07
111_E 205_K 0.86 0.69 0.07
73_M 35_V 0.84 0.67 0.06
99_P 195_V 0.83 0.65 0.06
90_F 39_N 0.81 0.62 0.05
131_V 181_S 0.81 0.62 0.05
96_V 152_K 0.80 0.62 0.05
60_Q 187_V 0.80 0.61 0.05
49_K 56_A 0.79 0.60 0.05
102_E 17_L 0.79 0.60 0.05
174_F 163_V 0.79 0.59 0.05
130_H 152_K 0.79 0.59 0.05
103_K 11_L 0.78 0.57 0.05
36_I 159_L 0.78 0.57 0.05
94_S 153_I 0.77 0.57 0.05
98_S 60_A 0.76 0.55 0.04
34_N 34_F 0.76 0.55 0.04
36_I 164_V 0.76 0.55 0.04
144_P 52_L 0.75 0.54 0.04
131_V 167_V 0.75 0.54 0.04
81_P 52_L 0.75 0.53 0.04
37_I 159_L 0.75 0.53 0.04
17_G 34_F 0.74 0.53 0.04
14_M 93_D 0.74 0.52 0.04
150_I 17_L 0.74 0.52 0.04
148_S 40_A 0.73 0.51 0.04
79_P 20_L 0.73 0.51 0.04
150_I 39_N 0.73 0.51 0.04
194_Y 56_A 0.73 0.50 0.04
6_G 152_K 0.72 0.50 0.04
102_E 181_S 0.72 0.49 0.04
29_S 41_L 0.72 0.49 0.04
173_T 22_A 0.72 0.49 0.04
36_I 26_C 0.71 0.47 0.04
172_N 191_L 0.70 0.47 0.04
16_I 26_C 0.70 0.47 0.04
177_V 143_A 0.70 0.46 0.04
150_I 4_D 0.70 0.46 0.04
155_S 48_S 0.69 0.45 0.03
131_V 157_L 0.69 0.45 0.03
124_V 209_E 0.69 0.45 0.03
12_L 113_R 0.69 0.45 0.03
33_A 153_I 0.69 0.44 0.03
20_Q 206_A 0.69 0.44 0.03
191_E 17_L 0.68 0.44 0.03
159_S 99_Y 0.68 0.43 0.03
121_I 211_Y 0.68 0.43 0.03
81_P 136_F 0.68 0.43 0.03
132_S 205_K 0.68 0.43 0.03
90_F 185_I 0.68 0.43 0.03
199_P 56_A 0.68 0.43 0.03
211_E 79_P 0.68 0.43 0.03
50_V 72_Y 0.68 0.43 0.03
50_V 45_Q 0.68 0.42 0.03
96_V 149_D 0.67 0.42 0.03
17_G 162_V 0.67 0.41 0.03
38_S 80_Q 0.67 0.41 0.03
51_D 31_S 0.67 0.41 0.03
139_N 59_M 0.67 0.41 0.03
179_Y 174_A 0.67 0.41 0.03
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
8982 6.14 mxij spa24 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.16 Done
7087 7.04 mxij_spa24 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.46 Done
6868 0.52 jp Δgene:(1, 20) A:(1E-06, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.02 Done - Shared
6862 mxij_spa24_jackhammer Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2016_06b) Running
6829 0.63 mxij_spa24 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.02 Done
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